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Updated helixer annotation workflow #767

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Hello, I open this PR to correct the one made by the bot : #748
Thank you! Have a nice day!
Romane

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Test Results (powered by Planemo)

Test Summary

Test State Count
Total 1
Passed 0
Error 1
Failure 0
Skipped 0
Errored Tests
  • ❌ Galaxy-Workflow-annotation_helixer.ga_0

    Execution Problem:

    • Failed to run workflow, at least one job is in [error] state.

    Workflow invocation details

    • Invocation Messages

    • Steps

      • Step 1: Genome sequence:

        • step_state: scheduled

      • Step 2: Helixer:

        • step_state: scheduled

        • Jobs

          • Job 1:

            • Job state is ok

            Command Line:

            • /usr/local/bin/fetch_helixer_models.py && Helixer.py --fasta-path '/tmp/tmpa1bygd39/files/b/e/5/dataset_be564f83-1c8c-4a6d-a41b-1823a6ce43a0.dat' --species '' --gff-output-path '/tmp/tmpa1bygd39/job_working_directory/000/2/outputs/dataset_451c1a70-6e42-4251-ae59-45ce8ff10e58.dat' --temporary-dir ./   --lineage 'land_plant' --subsequence-length '106920'  --overlap-offset '53460'  --overlap-core-length '80190'  --batch-size 8 --window-size 100 --min-coding-length 100 --edge-threshold 0.1 --peak-threshold 0.8

            Exit Code:

            • 0

            Standard Error:

            • 2025-03-25 09:13:49.275719: I tensorflow/core/platform/cpu_feature_guard.cc:182] This TensorFlow binary is optimized to use available CPU instructions in performance-critical operations.
To enable the following instructions: AVX2 FMA, in other operations, rebuild TensorFlow with the appropriate compiler flags.
2025-03-25 09:13:50.048279: W tensorflow/compiler/tf2tensorrt/utils/py_utils.cc:38] TF-TRT Warning: Could not find TensorRT
2025-03-25 09:13:55.765283: W tensorflow/tsl/framework/cpu_allocator_impl.cc:83] Allocation of 205286400 exceeds 10% of free system memory.
2025-03-25 09:13:56.038076: W tensorflow/tsl/framework/cpu_allocator_impl.cc:83] Allocation of 205286400 exceeds 10% of free system memory.
2025-03-25 09:13:58.339464: W tensorflow/tsl/framework/cpu_allocator_impl.cc:83] Allocation of 205286400 exceeds 10% of free system memory.
2025-03-25 09:14:00.636890: W tensorflow/tsl/framework/cpu_allocator_impl.cc:83] Allocation of 205286400 exceeds 10% of free system memory.
2025-03-25 09:14:02.876166: W tensorflow/tsl/framework/cpu_allocator_impl.cc:83] Allocation of 205286400 exceeds 10% of free system memory.
/usr/local/lib/python3.8/dist-packages/tensorflow_addons/utils/tfa_eol_msg.py:23: UserWarning: 

TensorFlow Addons (TFA) has ended development and introduction of new features.
TFA has entered a minimal maintenance and release mode until a planned end of life in May 2024.
Please modify downstream libraries to take dependencies from other repositories in our TensorFlow community (e.g. Keras, Keras-CV, and Keras-NLP). 

For more information see: https://github.com/tensorflow/addons/issues/2807 

  warnings.warn(
Ignoring the following unexpected models in /tmp/tmpa1bygd39/job_working_directory/000/2/home/.local/share/Helixer/models:[].
You can set --model-filepath in Helixer.py if you wish to use these.

            Standard Output:

            • ==========
== CUDA ==
==========

CUDA Version 11.8.0

Container image Copyright (c) 2016-2023, NVIDIA CORPORATION & AFFILIATES. All rights reserved.

This container image and its contents are governed by the NVIDIA Deep Learning Container License.
By pulling and using the container, you accept the terms and conditions of this license:
https://developer.nvidia.com/ngc/nvidia-deep-learning-container-license

A copy of this license is made available in this container at /NGC-DL-CONTAINER-LICENSE for your convenience.

WARNING: The NVIDIA Driver was not detected.  GPU functionality will not be available.
   Use the NVIDIA Container Toolkit to start this container with GPU support; see
   https://docs.nvidia.com/datacenter/cloud-native/ .

retrived list of available models from https://raw.githubusercontent.com/weberlab-hhu/Helixer/main/resources/model_list.csv
saved model land_plant_v0.3_a_0080.h5 to /tmp/tmpa1bygd39/job_working_directory/000/2/home/.local/share/Helixer/models
saved model vertebrate_v0.3_m_0080.h5 to /tmp/tmpa1bygd39/job_working_directory/000/2/home/.local/share/Helixer/models
saved model fungi_v0.3_a_0100.h5 to /tmp/tmpa1bygd39/job_working_directory/000/2/home/.local/share/Helixer/models
saved model invertebrate_v0.3_m_0100.h5 to /tmp/tmpa1bygd39/job_working_directory/000/2/home/.local/share/Helixer/models
HelixerPost <genome.h5> <predictions.h5> <windowSize> <edgeThresh> <peakThresh> <minCodingLength> <gff>
No config file found

retrived list of available models from https://raw.githubusercontent.com/weberlab-hhu/Helixer/main/resources/model_list.csv
Helixer.py config: 
{'batch_size': 8,
 'compression': 'gzip',
 'config_path': 'config/helixer_config.yaml',
 'debug': False,
 'edge_threshold': 0.1,
 'fasta_path': '/tmp/tmpa1bygd39/files/b/e/5/dataset_be564f83-1c8c-4a6d-a41b-1823a6ce43a0.dat',
 'gff_output_path': '/tmp/tmpa1bygd39/job_working_directory/000/2/outputs/dataset_451c1a70-6e42-4251-ae59-45ce8ff10e58.dat',
 'lineage': 'land_plant',
 'min_coding_length': 100,
 'model_filepath': '/tmp/tmpa1bygd39/job_working_directory/000/2/home/.local/share/Helixer/models/land_plant/land_plant_v0.3_a_0080.h5',
 'no_multiprocess': False,
 'no_overlap': False,
 'overlap_core_length': 80190,
 'overlap_offset': 53460,
 'peak_threshold': 0.8,
 'species': '',
 'subsequence_length': 106920,
 'temporary_dir': './',
 'window_size': 100}

Testing whether helixer_post_bin is correctly installed
Helixer.py config loaded. Starting FASTA to H5 conversion.
storing temporary files under ./tmp_nbjns97
1 expected num of chunks to write in 19994040 bases to hdf5
Numerification of 0-720580 of the sequence of sample took 0.26 secs
1 Numerified Fasta only Coordinate (seqid: sample, len: 720580) in 0.42 secs

1 expected num of chunks to write in 19994040 bases to hdf5
Numerification of 0-2030 of the sequence of sample2 took 0.00 secs
2 Numerified Fasta only Coordinate (seqid: sample2, len: 2030) in 0.01 secs

1 expected num of chunks to write in 19994040 bases to hdf5
Numerification of 0-2100 of the sequence of sample3 took 0.00 secs
3 Numerified Fasta only Coordinate (seqid: sample3, len: 2100) in 0.01 secs

1 expected num of chunks to write in 19994040 bases to hdf5
Numerification of 0-7560 of the sequence of sample4 took 0.00 secs
4 Numerified Fasta only Coordinate (seqid: sample4, len: 7560) in 0.02 secs

logged installed version in place of git commit for geenuff
logged installed version in place of git commit for helixer
FASTA to H5 conversion done. Starting neural network prediction with overlapping.
HelixerModel config: 
{'batch_size': 8,
 'calculate_uncertainty': False,
 'check_every_nth_batch': 1000000,
 'class_weights': 'None',
 'clip_norm': 3.0,
 'cnn_layers': 1,
 'compression': 'gzip',
 'core_length': 80190,
 'coverage_norm': None,
 'coverage_offset': 0.0,
 'coverage_weights': False,
 'cpus': 8,
 'data_dir': None,
 'debug': False,
 'dropout1': 0.0,
 'dropout2': 0.0,
 'epochs': 10000,
 'eval': False,
 'filter_depth': 32,
 'fine_tune': False,
 'float_precision': 'float32',
 'gpu_id': -1,
 'input_coverage': False,
 'kernel_size': 26,
 'large_eval_folder': '',
 'learning_rate': 0.0003,
 'load_model_path': '/tmp/tmpa1bygd39/job_working_directory/000/2/home/.local/share/Helixer/models/land_plant/land_plant_v0.3_a_0080.h5',
 'load_predictions': False,
 'loss': '',
 'lstm_layers': 1,
 'nni': False,
 'no_utrs': False,
 'optimizer': 'adamw',
 'overlap': True,
 'overlap_offset': 53460,
 'patience': 3,
 'pool_size': 9,
 'post_coverage_hidden_layer': False,
 'predict_phase': False,
 'prediction_output_path': './tmp_nbjns97/tmp_predictions_.h5',
 'pretrained_model_path': None,
 'resume_training': False,
 'save_every_check': False,
 'save_model_path': './best_model.h5',
 'stretch_transition_weights': 0,
 'test_data': './tmp_nbjns97/tmp_species_.h5',
 'transition_weights': 'None',
 'units': 32,
 'val_test_batch_size': 8,
 'verbose': True,
 'weight_decay': 3.5e-05,
 'workers': 1}
No err_samples dataset found, correct samples will be set to 0
No fully_intergenic_samples dataset found, fully intergenic samples will be set to 0

Data config: 
[{'geenuff_commit': 'commit not found, version: 0.3.2', 'helixer_commit': 'commit not found, version: 0.3.3', 'input_path': '/tmp/tmpa1bygd39/files/b/e/5/dataset_be564f83-1c8c-4a6d-a41b-1823a6ce43a0.dat', 'timestamp': '2025-03-25 09:13:52.886373'}]

Test data shape: (20, 106920)

Intergenic test seqs: 0.00%
Fully correct test seqs: 0.00%

Number of devices: 1
Current Helixer version: 0.3.3
Md5sum of the loaded model: f0e00efcbea83c66b69258d11119a691  /tmp/tmpa1bygd39/job_working_directory/000/2/home/.local/share/Helixer/models/land_plant/land_plant_v0.3_a_0080.h5

Model: "model"
__________________________________________________________________________________________________
 Layer (type)                Output Shape                 Param #   Connected to                  
==================================================================================================
 main_input (InputLayer)     [(None, None, 4)]            0         []                            
                                                                                                  
 conv1d (Conv1D)             (None, None, 96)             4704      ['main_input[0][0]']          
                                                                                                  
 batch_normalization (Batch  (None, None, 96)             384       ['conv1d[0][0]']              
 Normalization)                                                                                   
                                                                                                  
 conv1d_1 (Conv1D)           (None, None, 96)             110688    ['batch_normalization[0][0]'] 
                                                                                                  
 batch_normalization_1 (Bat  (None, None, 96)             384       ['conv1d_1[0][0]']            
 chNormalization)                                                                                 
                                                                                                  
 conv1d_2 (Conv1D)           (None, None, 96)             110688    ['batch_normalization_1[0][0]'
                                                                    ]                             
                                                                                                  
 batch_normalization_2 (Bat  (None, None, 96)             384       ['conv1d_2[0][0]']            
 chNormalization)                                                                                 
                                                                                                  
 conv1d_3 (Conv1D)           (None, None, 96)             110688    ['batch_normalization_2[0][0]'
                                                                    ]                             
                                                                                                  
 reshape (Reshape)           (None, None, 864)            0         ['conv1d_3[0][0]']            
                                                                                                  
 bidirectional (Bidirection  (None, None, 256)            1016832   ['reshape[0][0]']             
 al)                                                                                              
                                                                                                  
 bidirectional_1 (Bidirecti  (None, None, 256)            394240    ['bidirectional[0][0]']       
 onal)                                                                                            
                                                                                                  
 bidirectional_2 (Bidirecti  (None, None, 256)            394240    ['bidirectional_1[0][0]']     
 onal)                                                                                            
                                                                                                  
 dense (Dense)               (None, None, 72)             18504     ['bidirectional_2[0][0]']     
                                                                                                  
 tf.split (TFOpLambda)       [(None, None, 36),           0         ['dense[0][0]']               
                              (None, None, 36)]                                                   
                                                                                                  
 reshape_1 (Reshape)         (None, None, 9, 4)           0         ['tf.split[0][0]']            
                                                                                                  
 reshape_2 (Reshape)         (None, None, 9, 4)           0         ['tf.split[0][1]']            
                                                                                                  
 genic (Activation)          (None, None, 9, 4)           0         ['reshape_1[0][0]']           
                                                                                                  
 phase (Activation)          (None, None, 9, 4)           0         ['reshape_2[0][0]']           
                                                                                                  
==================================================================================================
Total params: 2161736 (8.25 MB)
Trainable params: 2161160 (8.24 MB)
Non-trainable params: 576 (2.25 KB)
__________________________________________________________________________________________________
HMM Config
  Splicing Flags: U:true US:true S:true SC:true C:true CS:true S:true SU:true U:true
  Splicing - Weights: Donor 1, Acceptor 1
  Splicing - Fixed Penalties: U2-GT-AG 0, U2-GT-AC 0 U12-GT-AG 0 U12-AT-AC 0
  Coding - Weights: Start 1000, Stop 1000
  Phase Mode: Implementation 1, Dilute to Total, Retention: 0.2

Sequences for Species  - 0
  BP_Extractor for Sequence sample - ID 0
Forward for Sequence sample - ID 0
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	      613530	         131	         479	         418		      Non Coding	      689510	        1069	        1104	        1091	
             UTR	         238	        5141	          87	         120		         Phase 0	         230	        9046	           2	           6	
          Coding	        1243	          82	       29647	         264		         Phase 1	         226	           8	        9014	           2	
          Intron	        1459	         120	         162	       67459		         Phase 2	         239	           2	           5	        9026	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     0.99523	     0.99833	     0.99678	            		      Non Coding	     0.99899	     0.99529	     0.99714	            	
             UTR	     0.93917	     0.92034	     0.92966	            		         Phase 0	     0.89343	     0.97436	     0.93214	            	
          Coding	     0.97603	     0.94913	     0.96239	            		         Phase 1	     0.89027	     0.97449	     0.93048	            	
          Intron	     0.98825	     0.97484	     0.98150	            		         Phase 2	     0.89146	     0.97347	     0.93066	            	

        Subgenic	     0.98449	     0.96684	     0.97559	            		          Coding	     0.89172	     0.97411	     0.93109	            	
           Genic	     0.98211	     0.96439	     0.97317	


Reverse for Sequence sample - ID 0
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	      555814	         209	         108	         776		      Non Coding	      659468	         985	         971	         987	
             UTR	         454	        9649	         137	         214		         Phase 0	         670	       18679	           9	          31	
          Coding	        2123	          49	       58497	         691		         Phase 1	         689	          33	       18702	          12	
          Intron	        8256	         265	         391	       82947		         Phase 2	         620	          14	          29	       18681	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     0.98088	     0.99804	     0.98939	            		      Non Coding	     0.99701	     0.99556	     0.99628	            	
             UTR	     0.94858	     0.92300	     0.93562	            		         Phase 0	     0.94764	     0.96338	     0.95545	            	
          Coding	     0.98924	     0.95334	     0.97096	            		         Phase 1	     0.94881	     0.96224	     0.95548	            	
          Intron	     0.98014	     0.90298	     0.93998	            		         Phase 2	     0.94774	     0.96573	     0.95665	            	

        Subgenic	     0.98388	     0.92315	     0.95255	            		          Coding	     0.94807	     0.96378	     0.95586	            	
           Genic	     0.98155	     0.92314	     0.95145	


  BP_Extractor for Sequence sample2 - ID 1
Forward for Sequence sample2 - ID 1
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	        2026	           0	           0	           0		      Non Coding	        2029	           0	           0	           0	
             UTR	           0	           0	           0	           0		         Phase 0	           1	           0	           0	           0	
          Coding	           4	           0	           0	           0		         Phase 1	           0	           0	           0	           0	
          Intron	           0	           0	           0	           0		         Phase 2	           0	           0	           0	           0	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     0.99803	     1.00000	     0.99901	            		      Non Coding	     0.99951	     1.00000	     0.99975	            	
             UTR	         NaN	         NaN	         NaN	            		         Phase 0	         NaN	     0.00000	     0.00000	            	
          Coding	         NaN	     0.00000	     0.00000	            		         Phase 1	         NaN	         NaN	         NaN	            	
          Intron	         NaN	         NaN	         NaN	            		         Phase 2	         NaN	         NaN	         NaN	            	

        Subgenic	         NaN	     0.00000	     0.00000	            		          Coding	         NaN	     0.00000	     0.00000	            	
           Genic	         NaN	     0.00000	     0.00000	


Reverse for Sequence sample2 - ID 1
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	        2030	           0	           0	           0		      Non Coding	        2030	           0	           0	           0	
             UTR	           0	           0	           0	           0		         Phase 0	           0	           0	           0	           0	
          Coding	           0	           0	           0	           0		         Phase 1	           0	           0	           0	           0	
          Intron	           0	           0	           0	           0		         Phase 2	           0	           0	           0	           0	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     1.00000	     1.00000	     1.00000	            		      Non Coding	     1.00000	     1.00000	     1.00000	            	
             UTR	         NaN	         NaN	         NaN	            		         Phase 0	         NaN	         NaN	         NaN	            	
          Coding	         NaN	         NaN	         NaN	            		         Phase 1	         NaN	         NaN	         NaN	            	
          Intron	         NaN	         NaN	         NaN	            		         Phase 2	         NaN	         NaN	         NaN	            	

        Subgenic	         NaN	         NaN	         NaN	            		          Coding	         NaN	         NaN	         NaN	            	
           Genic	         NaN	         NaN	         NaN	


  BP_Extractor for Sequence sample3 - ID 2
Forward for Sequence sample3 - ID 2
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	        2098	           0	           0	           0		      Non Coding	        2099	           0	           0	           0	
             UTR	           0	           0	           0	           0		         Phase 0	           1	           0	           0	           0	
          Coding	           2	           0	           0	           0		         Phase 1	           0	           0	           0	           0	
          Intron	           0	           0	           0	           0		         Phase 2	           0	           0	           0	           0	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     0.99905	     1.00000	     0.99952	            		      Non Coding	     0.99952	     1.00000	     0.99976	            	
             UTR	         NaN	         NaN	         NaN	            		         Phase 0	         NaN	     0.00000	     0.00000	            	
          Coding	         NaN	     0.00000	     0.00000	            		         Phase 1	         NaN	         NaN	         NaN	            	
          Intron	         NaN	         NaN	         NaN	            		         Phase 2	         NaN	         NaN	         NaN	            	

        Subgenic	         NaN	     0.00000	     0.00000	            		          Coding	         NaN	     0.00000	     0.00000	            	
           Genic	         NaN	     0.00000	     0.00000	


Reverse for Sequence sample3 - ID 2
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	        2100	           0	           0	           0		      Non Coding	        2100	           0	           0	           0	
             UTR	           0	           0	           0	           0		         Phase 0	           0	           0	           0	           0	
          Coding	           0	           0	           0	           0		         Phase 1	           0	           0	           0	           0	
          Intron	           0	           0	           0	           0		         Phase 2	           0	           0	           0	           0	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     1.00000	     1.00000	     1.00000	            		      Non Coding	     1.00000	     1.00000	     1.00000	            	
             UTR	         NaN	         NaN	         NaN	            		         Phase 0	         NaN	         NaN	         NaN	            	
          Coding	         NaN	         NaN	         NaN	            		         Phase 1	         NaN	         NaN	         NaN	            	
          Intron	         NaN	         NaN	         NaN	            		         Phase 2	         NaN	         NaN	         NaN	            	

        Subgenic	         NaN	         NaN	         NaN	            		          Coding	         NaN	         NaN	         NaN	            	
           Genic	         NaN	         NaN	         NaN	


  BP_Extractor for Sequence sample4 - ID 3
Forward for Sequence sample4 - ID 3
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	        7535	           0	           0	           0		      Non Coding	        7553	           0	           0	           0	
             UTR	           3	           0	           0	           0		         Phase 0	           2	           0	           0	           0	
          Coding	           8	           0	           0	           0		         Phase 1	           2	           0	           0	           0	
          Intron	          14	           0	           0	           0		         Phase 2	           3	           0	           0	           0	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     0.99669	     1.00000	     0.99834	            		      Non Coding	     0.99907	     1.00000	     0.99954	            	
             UTR	         NaN	     0.00000	     0.00000	            		         Phase 0	         NaN	     0.00000	     0.00000	            	
          Coding	         NaN	     0.00000	     0.00000	            		         Phase 1	         NaN	     0.00000	     0.00000	            	
          Intron	         NaN	     0.00000	     0.00000	            		         Phase 2	         NaN	     0.00000	     0.00000	            	

        Subgenic	         NaN	     0.00000	     0.00000	            		          Coding	         NaN	     0.00000	     0.00000	            	
           Genic	         NaN	     0.00000	     0.00000	


Reverse for Sequence sample4 - ID 3
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	        4480	          19	           0	           0		      Non Coding	        5923	           2	           6	           4	
             UTR	          40	         453	           5	           0		         Phase 0	          17	         524	           0	           0	
          Coding	         321	           0	        1573	           1		         Phase 1	          17	           0	         520	           0	
          Intron	           0	           0	           0	         668		         Phase 2	          25	           0	           0	         522	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     0.92543	     0.99578	     0.95931	            		      Non Coding	     0.99014	     0.99798	     0.99404	            	
             UTR	     0.95975	     0.90964	     0.93402	            		         Phase 0	     0.99620	     0.96858	     0.98219	            	
          Coding	     0.99683	     0.83008	     0.90585	            		         Phase 1	     0.98859	     0.96834	     0.97836	            	
          Intron	     0.99851	     1.00000	     0.99925	            		         Phase 2	     0.99240	     0.95430	     0.97297	            	

        Subgenic	     0.99733	     0.87437	     0.93181	            		          Coding	     0.99240	     0.96369	     0.97783	            	
           Genic	     0.99081	     0.88010	     0.93218	


Forward for Species  - 0
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	      625189	         131	         479	         418		      Non Coding	      701191	        1069	        1104	        1091	
             UTR	         241	        5141	          87	         120		         Phase 0	         234	        9046	           2	           6	
          Coding	        1257	          82	       29647	         264		         Phase 1	         228	           8	        9014	           2	
          Intron	        1473	         120	         162	       67459		         Phase 2	         242	           2	           5	        9026	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     0.99527	     0.99836	     0.99681	            		      Non Coding	     0.99900	     0.99537	     0.99718	            	
             UTR	     0.93917	     0.91984	     0.92940	            		         Phase 0	     0.89343	     0.97394	     0.93195	            	
          Coding	     0.97603	     0.94870	     0.96217	            		         Phase 1	     0.89027	     0.97428	     0.93038	            	
          Intron	     0.98825	     0.97464	     0.98140	            		         Phase 2	     0.89146	     0.97315	     0.93052	            	

        Subgenic	     0.98449	     0.96658	     0.97545	            		          Coding	     0.89172	     0.97379	     0.93095	            	
           Genic	     0.98211	     0.96411	     0.97303	


Reverse for Species  - 0
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	      564424	         228	         108	         776		      Non Coding	      669521	         987	         977	         991	
             UTR	         494	       10102	         142	         214		         Phase 0	         687	       19203	           9	          31	
          Coding	        2444	          49	       60070	         692		         Phase 1	         706	          33	       19222	          12	
          Intron	        8256	         265	         391	       83615		         Phase 2	         645	          14	          29	       19203	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     0.98055	     0.99803	     0.98922	            		      Non Coding	     0.99697	     0.99561	     0.99629	            	
             UTR	     0.94908	     0.92239	     0.93554	            		         Phase 0	     0.94891	     0.96352	     0.95616	            	
          Coding	     0.98944	     0.94965	     0.96914	            		         Phase 1	     0.94984	     0.96240	     0.95608	            	
          Intron	     0.98028	     0.90368	     0.94042	            		         Phase 2	     0.94891	     0.96541	     0.95709	            	

        Subgenic	     0.98409	     0.92235	     0.95222	            		          Coding	     0.94922	     0.96378	     0.95644	            	
           Genic	     0.98171	     0.92235	     0.95110	


Total for Species  - 0
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	     1189613	         359	         587	        1194		      Non Coding	     1370712	        2056	        2081	        2082	
             UTR	         735	       15243	         229	         334		         Phase 0	         921	       28249	          11	          37	
          Coding	        3701	         131	       89717	         956		         Phase 1	         934	          41	       28236	          14	
          Intron	        9729	         385	         553	      151074		         Phase 2	         887	          16	          34	       28229	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     0.98823	     0.99820	     0.99319	            		      Non Coding	     0.99800	     0.99548	     0.99674	            	
             UTR	     0.94571	     0.92153	     0.93346	            		         Phase 0	     0.93041	     0.96684	     0.94827	            	
          Coding	     0.98497	     0.94934	     0.96682	            		         Phase 1	     0.92998	     0.96616	     0.94772	            	
          Intron	     0.98382	     0.93405	     0.95829	            		         Phase 2	     0.92975	     0.96787	     0.94843	            	

        Subgenic	     0.98425	     0.93969	     0.96145	            		          Coding	     0.93004	     0.96696	     0.94814	            	
           Genic	     0.98187	     0.93859	     0.95974	


Total: 482642bp across 25 windows
None

starting to load test data into memory..
For h5 starting with species = b'':
x shape: (20, 106920, 4)
Data loading of 20 (total so far 20) samples of data/X into memory took 0.06 secs
Compressed data size of data/X is at least 0.0008 GB

setting self.n_seqs to 20, bc that is len of data/X
0 / 8
1 / 8
2 / 8
3 / 8
4 / 8
5 / 8
6 / 8
7 / 8
Neural network prediction done. Starting post processing.

Helixer successfully finished the annotation of /tmp/tmpa1bygd39/files/b/e/5/dataset_be564f83-1c8c-4a6d-a41b-1823a6ce43a0.dat in 0.07 hours. GFF file written to /tmp/tmpa1bygd39/job_working_directory/000/2/outputs/dataset_451c1a70-6e42-4251-ae59-45ce8ff10e58.dat.

            Traceback:

            • 

              • 

            

            Job Parameters:
            

              

            • 

              


              
Job parameter
Parameter value

              
              


              
__input_ext
"input"

              

              
__workflow_invocation_uuid__
"00011a22095911f08a577c1e52052d7f"

              

              
chromInfo
"/tmp/tmpa1bygd39/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"

              

              
dbkey
"?"

              

              
input_model
None

              

              
lineages
"land_plant"

              

              
option_overlap
{"__current_case__": 0, "overlap_core_length": null, "overlap_offset": null, "use_overlap": "true"}

              

              
post_processing
{"edge_threshold": "0.1", "min_coding_length": "100", "peak_threshold": "0.8", "window_size": "100"}

              

              
size
"8"

              

              
species
None

              

              
subsequence_length
None

              
              

              

              • 

            

            • 

          

          

          • 

        

        • 

      • 

        Step 3: Busco on genome:
        

          

        • 

          step_state: scheduled
          

          • 

        • 

          Jobs

            

          • 

            Job 1:
            

              

            • Job state is ok
              • 

            

            Command Line:
            

              

            • 

              if [ -z "$AUGUSTUS_CONFIG_PATH" ] ; then BUSCO_PATH=$(dirname $(which busco)) ; export AUGUSTUS_CONFIG_PATH=$(realpath ${BUSCO_PATH}/../config) ; fi && cp -r "$AUGUSTUS_CONFIG_PATH/" augustus_dir/ && export AUGUSTUS_CONFIG_PATH=`pwd`/augustus_dir/ &&    busco --in '/tmp/tmpa1bygd39/files/b/e/5/dataset_be564f83-1c8c-4a6d-a41b-1823a6ce43a0.dat' --mode 'geno' --out busco_galaxy --cpu ${GALAXY_SLOTS:-4} --evalue 0.001 --limit 3 --contig_break 10  --offline --download_path /cvmfs/data.galaxyproject.org/byhand/busco/v5  --lineage_dataset 'mucorales_odb10'   --augustus  && mkdir BUSCO_summaries && ls -l busco_galaxy/run_*/ && cp busco_galaxy/short_summary.*.txt BUSCO_summaries/ && generate_plot.py -wd BUSCO_summaries -rt specific  && echo "##gff-version 3" > busco_output.gff && cat busco_galaxy/run_*/busco_sequences/*busco_sequences/*.gff >> busco_output.gff 2> /dev/null || true
              

              • 

            

            Exit Code:
            

              

            • 

              0
              

              • 

            

            Standard Error:
            

              

            • 

              2025-03-25 09:24:26 ERROR:	
Warning message:
The `size` argument of `element_line()` is deprecated as of ggplot2 3.4.0.
ℹ Please use the `linewidth` argument instead. 


              

              • 

            

            Standard Output:
            

              

            • 

              2025-03-25 09:12:30 INFO:	***** Start a BUSCO v5.8.0 analysis, current time: 03/25/2025 09:12:30 *****
2025-03-25 09:12:30 INFO:	Configuring BUSCO with local environment
2025-03-25 09:12:30 INFO:	Running genome mode
2025-03-25 09:12:34 INFO:	Input file is /tmp/tmpa1bygd39/files/b/e/5/dataset_be564f83-1c8c-4a6d-a41b-1823a6ce43a0.dat
2025-03-25 09:12:35 INFO:	Running BUSCO using lineage dataset mucorales_odb10 (eukaryota, 2020-08-05)
2025-03-25 09:12:35 INFO:	Running 1 job(s) on bbtools, starting at 03/25/2025 09:12:35
2025-03-25 09:12:36 INFO:	[bbtools]	1 of 1 task(s) completed
2025-03-25 09:12:36 INFO:	Running 1 job(s) on makeblastdb, starting at 03/25/2025 09:12:36
2025-03-25 09:12:36 INFO:	Creating BLAST database with input file
2025-03-25 09:12:36 INFO:	[makeblastdb]	1 of 1 task(s) completed
2025-03-25 09:12:36 INFO:	Running a BLAST search for BUSCOs against created database
2025-03-25 09:12:36 INFO:	Running 1 job(s) on tblastn, starting at 03/25/2025 09:12:36
2025-03-25 09:12:47 INFO:	[tblastn]	1 of 1 task(s) completed
2025-03-25 09:12:47 INFO:	Running Augustus gene predictor on BLAST search results.
2025-03-25 09:12:47 INFO:	Running Augustus prediction using aspergillus_nidulans as species:
2025-03-25 09:12:47 INFO:	Running 76 job(s) on augustus, starting at 03/25/2025 09:12:47
2025-03-25 09:14:45 INFO:	[augustus]	8 of 76 task(s) completed
2025-03-25 09:16:01 INFO:	[augustus]	16 of 76 task(s) completed
2025-03-25 09:16:39 INFO:	[augustus]	23 of 76 task(s) completed
2025-03-25 09:16:59 INFO:	[augustus]	31 of 76 task(s) completed
2025-03-25 09:17:17 INFO:	[augustus]	38 of 76 task(s) completed
2025-03-25 09:17:36 INFO:	[augustus]	46 of 76 task(s) completed
2025-03-25 09:17:54 INFO:	[augustus]	54 of 76 task(s) completed
2025-03-25 09:18:04 INFO:	[augustus]	61 of 76 task(s) completed
2025-03-25 09:18:15 INFO:	[augustus]	69 of 76 task(s) completed
2025-03-25 09:18:30 INFO:	[augustus]	76 of 76 task(s) completed
2025-03-25 09:18:30 INFO:	Extracting predicted proteins...
2025-03-25 09:18:31 INFO:	***** Run HMMER on gene sequences *****
2025-03-25 09:18:31 INFO:	Running 75 job(s) on hmmsearch, starting at 03/25/2025 09:18:31
2025-03-25 09:18:33 INFO:	[hmmsearch]	8 of 75 task(s) completed
2025-03-25 09:18:34 INFO:	[hmmsearch]	15 of 75 task(s) completed
2025-03-25 09:18:36 INFO:	[hmmsearch]	23 of 75 task(s) completed
2025-03-25 09:18:37 INFO:	[hmmsearch]	30 of 75 task(s) completed
2025-03-25 09:18:39 INFO:	[hmmsearch]	38 of 75 task(s) completed
2025-03-25 09:18:40 INFO:	[hmmsearch]	45 of 75 task(s) completed
2025-03-25 09:18:42 INFO:	[hmmsearch]	53 of 75 task(s) completed
2025-03-25 09:18:43 INFO:	[hmmsearch]	60 of 75 task(s) completed
2025-03-25 09:18:44 INFO:	[hmmsearch]	68 of 75 task(s) completed
2025-03-25 09:18:47 INFO:	[hmmsearch]	75 of 75 task(s) completed
2025-03-25 09:18:47 INFO:	0 exons in total
2025-03-25 09:18:47 INFO:	Starting second step of analysis. The gene predictor Augustus is retrained using the results from the initial run to yield more accurate results.
2025-03-25 09:18:47 INFO:	Extracting missing and fragmented buscos from the file ancestral_variants...
2025-03-25 09:18:55 INFO:	Running a BLAST search for BUSCOs against created database
2025-03-25 09:18:55 INFO:	Running 1 job(s) on tblastn, starting at 03/25/2025 09:18:55
2025-03-25 09:20:29 INFO:	[tblastn]	1 of 1 task(s) completed
2025-03-25 09:20:29 INFO:	Converting predicted genes to short genbank files
2025-03-25 09:20:29 INFO:	Running 1 job(s) on gff2gbSmallDNA.pl, starting at 03/25/2025 09:20:29
2025-03-25 09:20:29 INFO:	[gff2gbSmallDNA.pl]	1 of 1 task(s) completed
2025-03-25 09:20:29 INFO:	All files converted to short genbank files, now training Augustus using Single-Copy Complete BUSCOs
2025-03-25 09:20:29 INFO:	Running 1 job(s) on new_species.pl, starting at 03/25/2025 09:20:29
2025-03-25 09:20:30 INFO:	[new_species.pl]	1 of 1 task(s) completed
2025-03-25 09:20:30 INFO:	Running 1 job(s) on etraining, starting at 03/25/2025 09:20:30
2025-03-25 09:20:31 INFO:	[etraining]	1 of 1 task(s) completed
2025-03-25 09:20:31 INFO:	Re-running Augustus with the new metaparameters, number of target BUSCOs: 2448
2025-03-25 09:20:31 INFO:	Running Augustus gene predictor on BLAST search results.
2025-03-25 09:20:31 INFO:	Running Augustus prediction using BUSCO_busco_galaxy as species:
2025-03-25 09:20:31 INFO:	Running 100 job(s) on augustus, starting at 03/25/2025 09:20:31
2025-03-25 09:21:34 INFO:	[augustus]	10 of 100 task(s) completed
2025-03-25 09:22:36 INFO:	[augustus]	20 of 100 task(s) completed
2025-03-25 09:23:04 INFO:	[augustus]	30 of 100 task(s) completed
2025-03-25 09:23:17 INFO:	[augustus]	40 of 100 task(s) completed
2025-03-25 09:23:30 INFO:	[augustus]	50 of 100 task(s) completed
2025-03-25 09:23:42 INFO:	[augustus]	60 of 100 task(s) completed
2025-03-25 09:23:52 INFO:	[augustus]	70 of 100 task(s) completed
2025-03-25 09:24:02 INFO:	[augustus]	80 of 100 task(s) completed
2025-03-25 09:24:13 INFO:	[augustus]	90 of 100 task(s) completed
2025-03-25 09:24:23 INFO:	[augustus]	100 of 100 task(s) completed
2025-03-25 09:24:23 INFO:	Extracting predicted proteins...
2025-03-25 09:24:23 INFO:	***** Run HMMER on gene sequences *****
2025-03-25 09:24:23 WARNING:	No jobs to run on hmmsearch
2025-03-25 09:24:23 INFO:	0 exons in total
2025-03-25 09:24:23 INFO:	Results:	C:0.0%[S:0.0%,D:0.0%],F:0.0%,M:100.0%,n:2449	   

2025-03-25 09:24:23 INFO:	

    ---------------------------------------------------
    |Results from dataset mucorales_odb10              |
    ---------------------------------------------------
    |C:0.0%[S:0.0%,D:0.0%],F:0.0%,M:100.0%,n:2449      |
    |1    Complete BUSCOs (C)                          |
    |1    Complete and single-copy BUSCOs (S)          |
    |0    Complete and duplicated BUSCOs (D)           |
    |0    Fragmented BUSCOs (F)                        |
    |2448    Missing BUSCOs (M)                        |
    |2449    Total BUSCO groups searched               |
    ---------------------------------------------------
2025-03-25 09:24:23 INFO:	BUSCO analysis done with WARNING(s). Total running time: 709 seconds

***** Summary of warnings: *****
2025-03-25 09:24:23 WARNING:busco.busco_tools.Toolset	No jobs to run on hmmsearch

2025-03-25 09:24:23 INFO:	Results written in /tmp/tmpa1bygd39/job_working_directory/000/3/working/busco_galaxy
2025-03-25 09:24:23 INFO:	For assistance with interpreting the results, please consult the userguide: https://busco.ezlab.org/busco_userguide.html

2025-03-25 09:24:23 INFO:	Visit this page https://gitlab.com/ezlab/busco#how-to-cite-busco to see how to cite BUSCO
total 100
drwxr-xr-x 8 1001 118  4096 Mar 25 09:24 augustus_output
drwxr-xr-x 3 1001 118  4096 Mar 25 09:20 blast_output
drwxr-xr-x 5 1001 118  4096 Mar 25 09:12 busco_sequences
-rw-r--r-- 1 1001 118 47630 Mar 25 09:24 full_table.tsv
drwxr-xr-x 4 1001 118  4096 Mar 25 09:18 hmmer_output
-rw-r--r-- 1 1001 118 27820 Mar 25 09:24 missing_busco_list.tsv
-rw-r--r-- 1 1001 118  3176 Mar 25 09:24 short_summary.json
-rw-r--r-- 1 1001 118  1067 Mar 25 09:24 short_summary.txt
2025-03-25 09:24:24 INFO:	****************** Start plot generation at 03/25/2025 09:24:24 ******************
2025-03-25 09:24:24 INFO:	Load data ...
2025-03-25 09:24:24 INFO:	Loaded BUSCO_summaries/short_summary.specific.mucorales_odb10.busco_galaxy.txt successfully
2025-03-25 09:24:24 INFO:	Generate the R code ...
2025-03-25 09:24:24 INFO:	Run the R code ...
2025-03-25 09:24:26 INFO:	
[1] "Plotting the figure ..."
[1] "Done"

2025-03-25 09:24:26 INFO:	Plot generation done. Total running time: 2.324524164199829 seconds
2025-03-25 09:24:26 INFO:	Results written in BUSCO_summaries/


              

              • 

            

            Traceback:
            

              

            • 

              

              • 

            

            Job Parameters:
            

              

            • 

              


              
Job parameter
Parameter value

              
              


              
__input_ext
"input"

              

              
__workflow_invocation_uuid__
"00011a22095911f08a577c1e52052d7f"

              

              
adv
{"contig_break": "10", "evalue": "0.001", "limit": "3"}

              

              
busco_mode
{"__current_case__": 0, "mode": "geno", "use_augustus": {"__current_case__": 2, "aug_prediction": {"__current_case__": 0, "augustus_mode": "no"}, "long": false, "use_augustus_selector": "augustus"}}

              

              
chromInfo
"/tmp/tmpa1bygd39/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"

              

              
dbkey
"?"

              

              
lineage
{"__current_case__": 1, "lineage_dataset": "mucorales_odb10", "lineage_mode": "select_lineage"}

              

              
lineage_conditional
{"__current_case__": 0, "cached_db": "v5", "selector": "cached"}

              

              
outputs
["short_summary", "image", "gff", "missing"]

              
              

              

              • 

            

            • 

          

          

          • 

        

        • 

      • 

        Step 4: Gffread:
        

          

        • 

          step_state: scheduled
          

          • 

        • 

          Jobs

            

          • 

            Job 1:
            

              

            • Job state is ok
              • 

            

            Command Line:
            

              

            • 

              ln -s '/tmp/tmpa1bygd39/files/b/e/5/dataset_be564f83-1c8c-4a6d-a41b-1823a6ce43a0.dat' genomeref.fa &&  gffread '/tmp/tmpa1bygd39/files/4/5/1/dataset_451c1a70-6e42-4251-ae59-45ce8ff10e58.dat' -g genomeref.fa      -y pep.fa
              

              • 

            

            Exit Code:
            

              

            • 

              0
              

              • 

            

            Standard Error:
            

              

            • 

              FASTA index file genomeref.fa.fai created.

              

              • 

            

            Traceback:
            

              

            • 

              

              • 

            

            Job Parameters:
            

              

            • 

              


              
Job parameter
Parameter value

              
              


              
__input_ext
"input"

              

              
__workflow_invocation_uuid__
"00011a22095911f08a577c1e52052d7f"

              

              
chr_replace
None

              

              
chromInfo
"/tmp/tmpa1bygd39/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"

              

              
dbkey
"?"

              

              
decode_url
false

              

              
expose
false

              

              
filtering
None

              

              
full_gff_attribute_preservation
false

              

              
gffs
{"__current_case__": 0, "gff_fmt": "none"}

              

              
maxintron
None

              

              
merging
{"__current_case__": 0, "merge_sel": "none"}

              

              
reference_genome
{"__current_case__": 2, "fa_outputs": ["-y pep.fa"], "genome_fasta": {"values": [{"id": 1, "src": "hda"}]}, "ref_filtering": null, "source": "history"}

              

              
region
{"__current_case__": 0, "region_filter": "none"}

              
              

              

              • 

            

            • 

          

          

          • 

        

        • 

      • 

        Step 5: Genome annotation statistics:
        

          

        • 

          step_state: scheduled
          

          • 

        • 

          Jobs

            

          • 

            Job 1:
            

              

            • Job state is ok
              • 

            

            Command Line:
            

              

            • 

              ln -s '/tmp/tmpa1bygd39/files/4/5/1/dataset_451c1a70-6e42-4251-ae59-45ce8ff10e58.dat' 'input.gff'  &&  python -m jcvi.annotation.stats genestats 'input.gff' > '/tmp/tmpa1bygd39/job_working_directory/000/5/outputs/dataset_5bcb5645-7f5f-476b-9ac5-6c18873cad35.dat'  &&  python -m jcvi.annotation.stats summary 'input.gff' '/tmp/tmpa1bygd39/files/b/e/5/dataset_be564f83-1c8c-4a6d-a41b-1823a6ce43a0.dat' 2>&1 | tail -n +3 >> '/tmp/tmpa1bygd39/job_working_directory/000/5/outputs/dataset_5bcb5645-7f5f-476b-9ac5-6c18873cad35.dat'  &&  python -m jcvi.annotation.stats stats 'input.gff' 2>&1 | grep Mean >> '/tmp/tmpa1bygd39/job_working_directory/000/5/outputs/dataset_5bcb5645-7f5f-476b-9ac5-6c18873cad35.dat'  &&  python -m jcvi.annotation.stats histogram 'input.gff'  &&  pdfunite *.input.pdf '/tmp/tmpa1bygd39/job_working_directory/000/5/outputs/dataset_916e4355-d849-496b-94ac-3d25c9865261.dat'
              

              • 

            

            Exit Code:
            

              

            • 

              0
              

              • 

            

            Standard Error:
            

              

            • 

              �[0;33m09:18:48 [gff]�[0m�[0;35m Indexing `input.gff`�[0m
�[0;33m09:18:48 [base]�[0m�[0;35m Load file `transcript.sizes`�[0m
�[0;33m09:18:48 [base]�[0m�[0;35m Imported 65 records from `transcript.sizes`.�[0m
�[0;33m09:18:48 [base]�[0m�[0;35m Load file `transcript.sizes`�[0m
�[0;33m09:18:48 [base]�[0m�[0;35m Imported 65 records from `transcript.sizes`.�[0m
�[0;33m09:18:48 [stats]�[0m�[0;35m A total of 65 transcripts populated.�[0m
�[0;33m09:18:48 [__init__]�[0m�[0;35m $HOME=/home/runner�[0m
�[0;33m09:18:48 [__init__]�[0m�[0;35m matplotlib data path /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data�[0m
�[0;33m09:18:48 [__init__]�[0m�[0;35m loaded rc file /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/matplotlibrc�[0m
�[0;33m09:18:48 [__init__]�[0m�[0;35m matplotlib version 2.2.2�[0m
�[0;33m09:18:48 [__init__]�[0m�[0;35m interactive is False�[0m
�[0;33m09:18:48 [__init__]�[0m�[0;35m platform is linux2�[0m
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�[0;33m09:18:49 [font_manager]�[0m�[0;35m createFontDict: /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/pdfcorefonts/Courier-BoldOblique.afm�[0m
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�[0;33m09:18:49 [font_manager]�[0m�[0;35m createFontDict: /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/afm/pzdr.afm�[0m
�[0;33m09:18:49 [font_manager]�[0m�[0;35m createFontDict: /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/afm/phvr8a.afm�[0m
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�[0;33m09:18:49 [font_manager]�[0m�[0;35m createFontDict: /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/afm/pagko8a.afm�[0m
�[0;33m09:18:49 [font_manager]�[0m�[0;35m createFontDict: /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/pdfcorefonts/Times-Roman.afm�[0m
�[0;33m09:18:49 [font_manager]�[0m�[0;35m createFontDict: /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/afm/pbkdi8a.afm�[0m
�[0;33m09:18:49 [font_manager]�[0m�[0;35m createFontDict: /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/afm/pagdo8a.afm�[0m
�[0;33m09:18:49 [font_manager]�[0m�[0;35m createFontDict: /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/afm/pagk8a.afm�[0m
�[0;33m09:18:49 [font_manager]�[0m�[0;35m generated new fontManager�[0m
�[0;33m09:18:49 [__init__]�[0m�[0;35m backend agg version v2.2�[0m
�[0;33m09:18:49 [stats]�[0m�[0;35m Parsing files in `Exon_Length`..�[0m
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�[0;33m09:18:49 [base]�[0m�[0;35m Rscript /tmp/tmpa1bygd39/tmp/tmpev1x5a�[0m
Warning message:
Removed 21 rows containing non-finite values (stat_bin). 
Saving 7 x 7 in image
Warning message:
Removed 21 rows containing non-finite values (stat_bin). 
�[0;33m09:18:52 [stats]�[0m�[0;35m Parsing files in `Intron_Length`..�[0m
Intron_Length/input.txt: Min=50 Max=14088 N=205 Mean=547.107317073 SD=1467.30391824 Median=152.0 Sum=112157
�[0;33m09:18:52 [base]�[0m�[0;35m Rscript /tmp/tmpa1bygd39/tmp/tmp4_aDqK�[0m
Warning message:
Removed 23 rows containing non-finite values (stat_bin). 
Saving 7 x 7 in image
Warning message:
Removed 23 rows containing non-finite values (stat_bin). 
�[0;33m09:18:54 [stats]�[0m�[0;35m Parsing files in `Gene_Length`..�[0m
Gene_Length/input.txt: Min=111 Max=7371 N=65 Mean=1401.32307692 SD=1130.94596358 Median=1122.0 Sum=91086
�[0;33m09:18:54 [base]�[0m�[0;35m Rscript /tmp/tmpa1bygd39/tmp/tmpzqdRBr�[0m
Warning message:
Removed 2 rows containing non-finite values (stat_bin). 
Saving 7 x 7 in image
Warning message:
Removed 2 rows containing non-finite values (stat_bin). 
�[0;33m09:18:57 [stats]�[0m�[0;35m Parsing files in `Exon_Count`..�[0m
Exon_Count/input.txt: Min=1 Max=15 N=65 Mean=4.15384615385 SD=3.39334538463 Median=3.0 Sum=270
�[0;33m09:18:57 [base]�[0m�[0;35m Rscript /tmp/tmpa1bygd39/tmp/tmpmJMVDb�[0m
Saving 7 x 7 in image

              

              • 

            

            Traceback:
            

              

            • 

              

              • 

            

            Job Parameters:
            

              

            • 

              


              
Job parameter
Parameter value

              
              


              
__input_ext
"input"

              

              
__workflow_invocation_uuid__
"00011a22095911f08a577c1e52052d7f"

              

              
chromInfo
"/tmp/tmpa1bygd39/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"

              

              
dbkey
"?"

              

              
ref_genome
{"__current_case__": 1, "genome": {"values": [{"id": 1, "src": "hda"}]}, "genome_type_select": "history"}

              
              

              

              • 

            

            • 

          

          

          • 

        

        • 

      • 

        Step 6: JBrowse:
        

          

        • 

          step_state: scheduled
          

          • 

        • 

          Jobs

            

          • 

            Job 1:
            

              

            • Job state is ok
              • 

            

            Command Line:
            

              

            • 

              mkdir -p /tmp/tmpa1bygd39/job_working_directory/000/6/outputs/dataset_07cbc0ad-4786-4ed5-867a-b0e787edb734_files &&  cp /tmp/tmpa1bygd39/job_working_directory/000/6/configs/tmp91hiv23w /tmp/tmpa1bygd39/job_working_directory/000/6/outputs/dataset_07cbc0ad-4786-4ed5-867a-b0e787edb734_files/galaxy.xml &&  export JBROWSE_SOURCE_DIR=$(dirname $(which prepare-refseqs.pl))/../opt/jbrowse  &&  python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/a6e57ff585c0/jbrowse/jbrowse.py'  --jbrowse ${JBROWSE_SOURCE_DIR} --standalone 'minimal'  --outdir /tmp/tmpa1bygd39/job_working_directory/000/6/outputs/dataset_07cbc0ad-4786-4ed5-867a-b0e787edb734_files /tmp/tmpa1bygd39/job_working_directory/000/6/configs/tmp91hiv23w &&  cp /tmp/tmpa1bygd39/job_working_directory/000/6/outputs/dataset_07cbc0ad-4786-4ed5-867a-b0e787edb734_files/index.html /tmp/tmpa1bygd39/job_working_directory/000/6/outputs/dataset_07cbc0ad-4786-4ed5-867a-b0e787edb734.dat;
              

              • 

            

            Exit Code:
            

              

            • 

              0
              

              • 

            

            Standard Error:
            

              

            • 

              INFO:jbrowse:Processing Annotation / Helixer on data 1
WARNING: No feature names found for indexing, only reference sequence names will be indexed.

              

              • 

            

            Traceback:
            

              

            • 

              

              • 

            

            Job Parameters:
            

              

            • 

              


              
Job parameter
Parameter value

              
              


              
__input_ext
"fasta"

              

              
__workflow_invocation_uuid__
"00011a22095911f08a577c1e52052d7f"

              

              
action
{"__current_case__": 0, "action_select": "create"}

              

              
chromInfo
"/tmp/tmpa1bygd39/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"

              

              
dbkey
"?"

              

              
gencode
"1"

              

              
jbgen
{"aboutDescription": "", "defaultLocation": "", "hideGenomeOptions": false, "shareLink": true, "show_menu": true, "show_nav": true, "show_overview": true, "show_tracklist": true, "trackPadding": "20"}

              

              
plugins
{"BlastView": true, "ComboTrackSelector": false, "GCContent": false}

              

              
reference_genome
{"__current_case__": 1, "genome": {"values": [{"id": 1, "src": "hda"}]}, "genome_type_select": "history"}

              

              
standalone
"minimal"

              

              
track_groups
[{"__index__": 0, "category": "Annotation", "data_tracks": [{"__index__": 0, "data_format": {"__current_case__": 2, "annotation": {"values": [{"id": 2, "src": "hda"}]}, "data_format_select": "gene_calls", "index": false, "jb_custom_config": {"option": []}, "jbcolor_scale": {"color_score": {"__current_case__": 0, "color": {"__current_case__": 0, "color_select": "automatic"}, "color_score_select": "none"}}, "jbmenu": {"track_menu": []}, "jbstyle": {"max_height": "600", "style_classname": "feature", "style_description": "note,description", "style_height": "10px", "style_label": "product,name,id"}, "match_part": {"__current_case__": 1, "match_part_select": false}, "override_apollo_drag": "False", "override_apollo_plugins": "False", "track_config": {"__current_case__": 3, "html_options": {"topLevelFeatures": null}, "track_class": "NeatHTMLFeatures/View/Track/NeatFeatures"}, "track_visibility": "default_off"}}]}]

              

              
uglyTestingHack
""

              
              

              

              • 

            

            • 

          

          

          • 

        

        • 

      • 

        Step 7: Busco on protein:
        

          

        • 

          step_state: scheduled
          

          • 

        • 

          Jobs

            

          • 

            Job 1:
            

              

            • Job state is ok
              • 

            

            Command Line:
            

              

            • 

              busco --in '/tmp/tmpa1bygd39/files/4/0/5/dataset_4054ee06-dcac-471a-be6c-a3808a17ffe6.dat' --mode 'prot' --out busco_galaxy --cpu ${GALAXY_SLOTS:-4} --evalue 0.001 --limit 3 --contig_break 10  --offline --download_path /cvmfs/data.galaxyproject.org/byhand/busco/v5  --lineage_dataset 'mucorales_odb10'   && mkdir BUSCO_summaries && ls -l busco_galaxy/run_*/ && cp busco_galaxy/short_summary.*.txt BUSCO_summaries/ && generate_plot.py -wd BUSCO_summaries -rt specific  && echo "##gff-version 3" > busco_output.gff && cat busco_galaxy/run_*/busco_sequences/*busco_sequences/*.gff >> busco_output.gff 2> /dev/null || true
              

              • 

            

            Exit Code:
            

              

            • 

              0
              

              • 

            

            Standard Error:
            

              

            • 

              2025-03-25 09:25:33 ERROR:	
Warning message:
The `size` argument of `element_line()` is deprecated as of ggplot2 3.4.0.
ℹ Please use the `linewidth` argument instead. 


              

              • 

            

            Standard Output:
            

              

            • 

              2025-03-25 09:18:09 INFO:	***** Start a BUSCO v5.8.0 analysis, current time: 03/25/2025 09:18:09 *****
2025-03-25 09:18:09 INFO:	Configuring BUSCO with local environment
2025-03-25 09:18:09 INFO:	Running proteins mode
2025-03-25 09:18:09 INFO:	Input file is /tmp/tmpa1bygd39/files/4/0/5/dataset_4054ee06-dcac-471a-be6c-a3808a17ffe6.dat
2025-03-25 09:18:09 WARNING:	Option contig_break was provided but is not used in the selected run mode, proteins
2025-03-25 09:18:09 WARNING:	Option evalue was provided but is not used in the selected run mode, proteins
2025-03-25 09:18:09 WARNING:	Option limit was provided but is not used in the selected run mode, proteins
2025-03-25 09:18:09 INFO:	Running BUSCO using lineage dataset mucorales_odb10 (eukaryota, 2020-08-05)
2025-03-25 09:18:09 INFO:	***** Run HMMER on gene sequences *****
2025-03-25 09:18:10 INFO:	Running 2449 job(s) on hmmsearch, starting at 03/25/2025 09:18:10
2025-03-25 09:18:58 INFO:	[hmmsearch]	245 of 2449 task(s) completed
2025-03-25 09:19:43 INFO:	[hmmsearch]	490 of 2449 task(s) completed
2025-03-25 09:20:26 INFO:	[hmmsearch]	735 of 2449 task(s) completed
2025-03-25 09:21:07 INFO:	[hmmsearch]	980 of 2449 task(s) completed
2025-03-25 09:21:52 INFO:	[hmmsearch]	1225 of 2449 task(s) completed
2025-03-25 09:22:34 INFO:	[hmmsearch]	1470 of 2449 task(s) completed
2025-03-25 09:23:18 INFO:	[hmmsearch]	1715 of 2449 task(s) completed
2025-03-25 09:24:00 INFO:	[hmmsearch]	1960 of 2449 task(s) completed
2025-03-25 09:24:46 INFO:	[hmmsearch]	2205 of 2449 task(s) completed
2025-03-25 09:25:30 INFO:	[hmmsearch]	2449 of 2449 task(s) completed
2025-03-25 09:25:30 INFO:	

    ---------------------------------------------------
    |Results from dataset mucorales_odb10              |
    ---------------------------------------------------
    |C:0.1%[S:0.1%,D:0.0%],F:0.0%,M:99.9%,n:2449       |
    |2    Complete BUSCOs (C)                          |
    |2    Complete and single-copy BUSCOs (S)          |
    |0    Complete and duplicated BUSCOs (D)           |
    |0    Fragmented BUSCOs (F)                        |
    |2447    Missing BUSCOs (M)                        |
    |2449    Total BUSCO groups searched               |
    ---------------------------------------------------
2025-03-25 09:25:30 INFO:	BUSCO analysis done with WARNING(s). Total running time: 441 seconds

***** Summary of warnings: *****
2025-03-25 09:18:09 WARNING:busco.BuscoConfig	Option contig_break was provided but is not used in the selected run mode, proteins
2025-03-25 09:18:09 WARNING:busco.BuscoConfig	Option evalue was provided but is not used in the selected run mode, proteins
2025-03-25 09:18:09 WARNING:busco.BuscoConfig	Option limit was provided but is not used in the selected run mode, proteins

2025-03-25 09:25:30 INFO:	Results written in /tmp/tmpa1bygd39/job_working_directory/000/7/working/busco_galaxy
2025-03-25 09:25:30 INFO:	For assistance with interpreting the results, please consult the userguide: https://busco.ezlab.org/busco_userguide.html

2025-03-25 09:25:30 INFO:	Visit this page https://gitlab.com/ezlab/busco#how-to-cite-busco to see how to cite BUSCO
total 92
drwxr-xr-x 5 1001 118  4096 Mar 25 09:18 busco_sequences
-rw-r--r-- 1 1001 118 47714 Mar 25 09:25 full_table.tsv
drwxr-xr-x 4 1001 118  4096 Mar 25 09:25 hmmer_output
-rw-r--r-- 1 1001 118 27808 Mar 25 09:25 missing_busco_list.tsv
-rw-r--r-- 1 1001 118  2231 Mar 25 09:25 short_summary.json
-rw-r--r-- 1 1001 118   742 Mar 25 09:25 short_summary.txt
2025-03-25 09:25:31 INFO:	****************** Start plot generation at 03/25/2025 09:25:31 ******************
2025-03-25 09:25:31 INFO:	Load data ...
2025-03-25 09:25:31 INFO:	Loaded BUSCO_summaries/short_summary.specific.mucorales_odb10.busco_galaxy.txt successfully
2025-03-25 09:25:31 INFO:	Generate the R code ...
2025-03-25 09:25:31 INFO:	Run the R code ...
2025-03-25 09:25:33 INFO:	
[1] "Plotting the figure ..."
[1] "Done"

2025-03-25 09:25:33 INFO:	Plot generation done. Total running time: 2.1286838054656982 seconds
2025-03-25 09:25:33 INFO:	Results written in BUSCO_summaries/


              

              • 

            

            Traceback:
            

              

            • 

              

              • 

            

            Job Parameters:
            

              

            • 

              


              
Job parameter
Parameter value

              
              


              
__input_ext
"input"

              

              
__workflow_invocation_uuid__
"00011a22095911f08a577c1e52052d7f"

              

              
adv
{"contig_break": "10", "evalue": "0.001", "limit": "3"}

              

              
busco_mode
{"__current_case__": 2, "mode": "prot"}

              

              
chromInfo
"/tmp/tmpa1bygd39/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"

              

              
dbkey
"?"

              

              
lineage
{"__current_case__": 1, "lineage_dataset": "mucorales_odb10", "lineage_mode": "select_lineage"}

              

              
lineage_conditional
{"__current_case__": 0, "cached_db": "v5", "selector": "cached"}

              

              
outputs
["short_summary", "image", "gff", "missing"]

              
              

              

              • 

            

            • 

          

          

          • 

        

        • 

      • 

        Step 8: OMArk:
        

          

        • 

          step_state: scheduled
          

          • 

        • 

          Jobs

            

          • 

            Job 1:
            

              

            • Job state is error
              • 

            

            Command Line:
            

              

            • 

              omamer search --db '/cvmfs/data.galaxyproject.org/byhand/omamer/LUCA-v2.0.0.h5' --query '/tmp/tmpa1bygd39/files/4/0/5/dataset_4054ee06-dcac-471a-be6c-a3808a17ffe6.dat' --out 'output_omamer'  &&  omark -f 'output_omamer' -d '/cvmfs/data.galaxyproject.org/byhand/omamer/LUCA-v2.0.0.h5'      -o omark_galaxy
              

              • 

            

            Exit Code:
            

              

            • 

              1
              

              • 

            

            Standard Error:
            

              

            • 

              ================================================================================

   _____ _____ _____
  |     |     |  _  |_____ ___ ___
  |  |  | | | |     |     | -_|  _|
  |_____|_|_|_|__|__|_|_|_|___|_|   v2.1.0

  OMAmer is licensed under the GNU Lesser General Public License 3.0 (LGPL-3.0).
    
================================================================================

Loading required libraries  [DONE]

================================================================================

Running OMAmer on c40feb30d59a, using:
 - database: /cvmfs/data.galaxyproject.org/byhand/omamer/LUCA-v2.0.0.h5
 - query: /tmp/tmpa1bygd39/files/4/0/5/dataset_4054ee06-dcac-471a-be6c-a3808a17ffe6.dat
 - version: 2.1.0

================================================================================
WARNING: Database version mismatch: DB 2.0.0 / OMAmer 2.1.0

Loading data required for OMAmer search from database...
 - taxonomy information (6.5s) [DONE]
 - family information (6.7s) [DONE]
 - sub-family information (29.9s) [DONE]
 - family hierarchy (1.6s) [DONE]
 - k-mer index (56:20.6) [DONE]
 - family probability estimates (5.2s) [DONE]
 - sub-family probability estimates (14.1s) [DONE]

Finished loading required data

================================================================================

�[?25l
Searching -  0 queries in 0s (0.0 queries/s) 
Searching -  0 queries in 5s (0.0 queries/s) 
Searching -  0 queries in 10s (0.0 queries/s) 
Searching -  0 queries in 15s (0.0 queries/s) 
Searching -  0 queries in 20s (0.0 queries/s) 
Searching -  0 queries in 25s (0.0 queries/s) 
Searching -  0 queries in 30s (0.0 queries/s) 
Searching -  0 queries in 35s (0.0 queries/s) 
Searching -  0 queries in 40s (0.0 queries/s) 
Searching -  0 queries in 45s (0.0 queries/s) 
Searching -  0 queries in 50s (0.0 queries/s) 
Searching -  0 queries in 55s (0.0 queries/s) 
Searching -  0 queries in 1:00 (0.0 queries/s) 
Searching -  0 queries in 1:05 (0.0 queries/s) 
Searching -  0 queries in 1:10 (0.0 queries/s) �[?25h�[J
Searching -  65 queries in 1:15.1 (0.87 queries/s) 

================================================================================

OMAmer search complete:
 - results written to: output_omamer
 - total 3529.02 seconds
 - search phase only 0.89 queries/s


Note: family p-values are stated in negative log units.
================================================================================

Thank you for using OMAmer. If you use OMAmer in your research, please cite:

Victor Rossier, Alex Warwick Vesztrocy, Marc Robinson-Rechavi, Christophe Dessimoz, OMAmer: tree-driven and alignment-free protein assignment to subfamilies outperforms closest sequence approaches, Bioinformatics, Volume 37, Issue 18, September 2021, Pages 2866-2873, https://doi.org/10.1093/bioinformatics/btab219


OMAmer uses data from the OMA browser. Results can be interpreted further using:
 - OMA browser website (https://omabrowser.org)
 - PyOMADB, the Python OMA API client (https://github.com/DessimozLab/pyomadb)

================================================================================
WARNING: Database version mismatch: DB 2.0.0 / OMAmer 2.1.0
NCBI database not present yet (first time used?)
Downloading taxdump.tar.gz from NCBI FTP site (via HTTP)...
Done. Parsing...

Inserting synonyms:          0 
Inserting synonyms:       5000 
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Inserting taxid merges:      0 
Inserting taxid merges:   5000 
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Inserting taxids:           0 
Inserting taxids:        5000 
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Inserting taxids:       2630000 
Inserting taxids:       2635000 
Inserting taxids:       2640000 
Inserting taxids:       2645000 
Inserting taxids:       2650000 
Inserting taxids:       2655000 WARNING: Database version mismatch: DB 2.0.0 / OMAmer 2.1.0
Traceback (most recent call last):
  File "/usr/local/bin/omark", line 52, in <module>
    omark.launcher(arg)
  File "/usr/local/lib/python3.9/site-packages/omark/omark.py", line 269, in launcher
    get_omamer_qscore(omamerfile, dbpath, outdir, taxid, original_FASTA_file = original_fasta, isoform_file=isoform_file, taxonomic_rank=taxonomic_rank)
  File "/usr/local/lib/python3.9/site-packages/omark/omark.py", line 116, in get_omamer_qscore
    closest_corr = spd.get_sampled_taxa(likely_clade, 5 , tax_tab, sp_tab, tax_buff, taxonomic_rank)
  File "/usr/local/lib/python3.9/site-packages/omark/species_determination.py", line 403, in get_sampled_taxa
    ranks = ncbi.get_rank(lineage_ncbi)
  File "/usr/local/lib/python3.9/site-packages/ete3/ncbi_taxonomy/ncbiquery.py", line 201, in get_rank
    result = self.db.execute(cmd)
sqlite3.OperationalError: no such column: "6656" - should this be a string literal in single-quotes?
/usr/local/lib/python3.9/site-packages/tables/file.py:113: UnclosedFileWarning: Closing remaining open file: /cvmfs/data.galaxyproject.org/byhand/omamer/LUCA-v2.0.0.h5
  warnings.warn(UnclosedFileWarning(msg))

WARNING:galaxy.model:Datatype class not found for extension 'sum'
WARNING:galaxy.model:Datatype class not found for extension 'sum'
WARNING:galaxy.model:Datatype class not found for extension 'sum'
WARNING:galaxy.model:Datatype class not found for extension 'sum'
WARNING:galaxy.model:Datatype class not found for extension 'sum'
WARNING:galaxy.model:Datatype class not found for extension 'sum'

              

              • 

            

            Standard Output:
            

              

            • 

              Loading node names...
2656022 names loaded.
412380 synonyms loaded.
Loading nodes...
2656022 nodes loaded.
Linking nodes...
Tree is loaded.
Updating database: /tmp/tmpa1bygd39/job_working_directory/000/8/home/.etetoolkit/taxa.sqlite ...

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Uploading to /tmp/tmpa1bygd39/job_working_directory/000/8/home/.etetoolkit/taxa.sqlite





              

              • 

            

            Traceback:
            

              

            • 

              

              • 

            

            Job Parameters:
            

              

            • 

              


              
Job parameter
Parameter value

              
              


              
__input_ext
"input"

              

              
__workflow_invocation_uuid__
"00011a22095911f08a577c1e52052d7f"

              

              
chromInfo
"/tmp/tmpa1bygd39/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"

              

              
database
"LUCA-v2.0.0.h5"

              

              
dbkey
"?"

              

              
input_iso
None

              

              
omark_mode
false

              

              
outputs
"detail_sum"

              

              
r
None

              

              
t
None

              
              

              

              • 

            

            • 

          

          

          • 

        

        • 

      
 
      

      • 

    • 

      Other invocation details

        

      • 

        error_message
        

          

        • Failed to run workflow, at least one job is in [error] state.
          • 

        

        • 

      • 

        history_id
        

          

        • 9728d1f41d66ff64
          • 

        

        • 

      • 

        history_state
        

          

        • error
          • 

        

        • 

      • 

        invocation_id
        

          

        • 9728d1f41d66ff64
          • 

        

        • 

      • 

        invocation_state
        

          

        • scheduled
          • 

        

        • 

      • 

        workflow_id
        

          

        • 9728d1f41d66ff64
          • 

        

        • 

      

      

      • 

    
  
    

    • 




      		
    

  





        


            

            
            

              
            

        

      


      

            
  

    
  
    
    

  

  


    












      

  
      



  

  @mvdbeek





  


    

      

  

    

        
    
    

  


      
          
  
      
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            mvdbeek
  

      

      

      commented


        Mar 25, 2025


      
    


  





      


        


  
    

      
          
It looks like there's a problem with omark ?


Traceback (most recent call last):
  File "/usr/local/bin/omark", line 52, in <module>
    omark.launcher(arg)
  File "/usr/local/lib/python3.9/site-packages/omark/omark.py", line 269, in launcher
    get_omamer_qscore(omamerfile, dbpath, outdir, taxid, original_FASTA_file = original_fasta, isoform_file=isoform_file, taxonomic_rank=taxonomic_rank)
  File "/usr/local/lib/python3.9/site-packages/omark/omark.py", line 116, in get_omamer_qscore
    closest_corr = spd.get_sampled_taxa(likely_clade, 5 , tax_tab, sp_tab, tax_buff, taxonomic_rank)
  File "/usr/local/lib/python3.9/site-packages/omark/species_determination.py", line 403, in get_sampled_taxa
    ranks = ncbi.get_rank(lineage_ncbi)
  File "/usr/local/lib/python3.9/site-packages/ete3/ncbi_taxonomy/ncbiquery.py", line 201, in get_rank
    result = self.db.execute(cmd)
sqlite3.OperationalError: no such column: "6656" - should this be a string literal in single-quotes?
/usr/local/lib/python3.9/site-packages/tables/file.py:113: UnclosedFileWarning: Closing remaining open file: 


      		
    

  





        


            

            
            

              
            

        

      


      

            
  

    
  
    
    

  

  


    












      

  
      



  

  @rlibouba





  


    

      

  

    

        
    
    

  


      
          
  
      
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  Author


  


  

    

  





      


        


  
    

      
          
I think the problem is due to a version mismatch.

There is this warning : WARNING: Database version mismatch: DB 2.0.0 / OMAmer 2.1.0

      		
    

  





        


            

            
            

              
            

        

      


      

            
  

    
  
    
    

  

  


    












      

  
      



  

  @mvdbeek





  


    

      

  

    

        
    
    

  


      
          
  
      
            Copy link

  

      
    

  


  

      

  
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            mvdbeek
  

      

      

      commented


        Mar 25, 2025


      
    


  





      


        


  
    

      
          
I'll see if we can get the new data from somewhere

      		
    

  





        


            

            
            

              
            

        

      


      

            
  

    
  
    
    

  

  


    












      

  
        





      

  
      



  

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Test Results (powered by Planemo)


Test Summary



  

  

  

  

  

  








Test State
Count






Total
1




Passed
0




Error
1




Failure
0




Skipped
0






Errored Tests

    

  • 

    ❌ Galaxy-Workflow-annotation_helixer.ga_0
    

    Execution Problem:
    

      

    • 

      Failed to run workflow, at least one job is in [error] state.

      

      • 

    

    Workflow invocation details
    

      

    • 

      Invocation Messages
      

      • 

    • 

      Steps

        

      • 

        Step 1: Genome sequence:
        

          

        • step_state: scheduled
          • 

        

        • 

      • 

        Step 2: Helixer:
        

          

        • 

          step_state: scheduled
          

          • 

        • 

          Jobs

            

          • 

            Job 1:
            

              

            • Job state is ok
              • 

            

            Command Line:
            

              

            • 

              /usr/local/bin/fetch_helixer_models.py && Helixer.py --fasta-path '/tmp/tmppyertp20/files/3/e/5/dataset_3e51819b-6827-45ac-917f-d63d95da2525.dat' --species '' --gff-output-path '/tmp/tmppyertp20/job_working_directory/000/2/outputs/dataset_acc27a39-62d7-4a47-ae42-36f0ea99c6d7.dat' --temporary-dir ./   --lineage 'land_plant' --subsequence-length '106920'  --overlap-offset '53460'  --overlap-core-length '80190'  --batch-size 8 --window-size 100 --min-coding-length 100 --edge-threshold 0.1 --peak-threshold 0.8
              

              • 

            

            Exit Code:
            

              

            • 

              0
              

              • 

            

            Standard Error:
            

              

            • 

              2025-04-22 13:39:18.781552: I tensorflow/core/platform/cpu_feature_guard.cc:182] This TensorFlow binary is optimized to use available CPU instructions in performance-critical operations.
To enable the following instructions: AVX2 FMA, in other operations, rebuild TensorFlow with the appropriate compiler flags.
2025-04-22 13:39:19.531668: W tensorflow/compiler/tf2tensorrt/utils/py_utils.cc:38] TF-TRT Warning: Could not find TensorRT
2025-04-22 13:39:25.363427: W tensorflow/tsl/framework/cpu_allocator_impl.cc:83] Allocation of 205286400 exceeds 10% of free system memory.
2025-04-22 13:39:25.574317: W tensorflow/tsl/framework/cpu_allocator_impl.cc:83] Allocation of 205286400 exceeds 10% of free system memory.
2025-04-22 13:39:27.950303: W tensorflow/tsl/framework/cpu_allocator_impl.cc:83] Allocation of 205286400 exceeds 10% of free system memory.
2025-04-22 13:39:30.258940: W tensorflow/tsl/framework/cpu_allocator_impl.cc:83] Allocation of 205286400 exceeds 10% of free system memory.
2025-04-22 13:39:32.558626: W tensorflow/tsl/framework/cpu_allocator_impl.cc:83] Allocation of 205286400 exceeds 10% of free system memory.
/usr/local/lib/python3.8/dist-packages/tensorflow_addons/utils/tfa_eol_msg.py:23: UserWarning: 

TensorFlow Addons (TFA) has ended development and introduction of new features.
TFA has entered a minimal maintenance and release mode until a planned end of life in May 2024.
Please modify downstream libraries to take dependencies from other repositories in our TensorFlow community (e.g. Keras, Keras-CV, and Keras-NLP). 

For more information see: https://github.com/tensorflow/addons/issues/2807 

  warnings.warn(
Ignoring the following unexpected models in /tmp/tmppyertp20/job_working_directory/000/2/home/.local/share/Helixer/models:[].
You can set --model-filepath in Helixer.py if you wish to use these.

              

              • 

            

            Standard Output:
            

              

            • 

              ==========
== CUDA ==
==========

CUDA Version 11.8.0

Container image Copyright (c) 2016-2023, NVIDIA CORPORATION & AFFILIATES. All rights reserved.

This container image and its contents are governed by the NVIDIA Deep Learning Container License.
By pulling and using the container, you accept the terms and conditions of this license:
https://developer.nvidia.com/ngc/nvidia-deep-learning-container-license

A copy of this license is made available in this container at /NGC-DL-CONTAINER-LICENSE for your convenience.

WARNING: The NVIDIA Driver was not detected.  GPU functionality will not be available.
   Use the NVIDIA Container Toolkit to start this container with GPU support; see
   https://docs.nvidia.com/datacenter/cloud-native/ .

retrived list of available models from https://raw.githubusercontent.com/weberlab-hhu/Helixer/main/resources/model_list.csv
saved model land_plant_v0.3_a_0080.h5 to /tmp/tmppyertp20/job_working_directory/000/2/home/.local/share/Helixer/models
saved model vertebrate_v0.3_m_0080.h5 to /tmp/tmppyertp20/job_working_directory/000/2/home/.local/share/Helixer/models
saved model fungi_v0.3_a_0100.h5 to /tmp/tmppyertp20/job_working_directory/000/2/home/.local/share/Helixer/models
saved model invertebrate_v0.3_m_0100.h5 to /tmp/tmppyertp20/job_working_directory/000/2/home/.local/share/Helixer/models
HelixerPost <genome.h5> <predictions.h5> <windowSize> <edgeThresh> <peakThresh> <minCodingLength> <gff>
No config file found

retrived list of available models from https://raw.githubusercontent.com/weberlab-hhu/Helixer/main/resources/model_list.csv
Helixer.py config: 
{'batch_size': 8,
 'compression': 'gzip',
 'config_path': 'config/helixer_config.yaml',
 'debug': False,
 'edge_threshold': 0.1,
 'fasta_path': '/tmp/tmppyertp20/files/3/e/5/dataset_3e51819b-6827-45ac-917f-d63d95da2525.dat',
 'gff_output_path': '/tmp/tmppyertp20/job_working_directory/000/2/outputs/dataset_acc27a39-62d7-4a47-ae42-36f0ea99c6d7.dat',
 'lineage': 'land_plant',
 'min_coding_length': 100,
 'model_filepath': '/tmp/tmppyertp20/job_working_directory/000/2/home/.local/share/Helixer/models/land_plant/land_plant_v0.3_a_0080.h5',
 'no_multiprocess': False,
 'no_overlap': False,
 'overlap_core_length': 80190,
 'overlap_offset': 53460,
 'peak_threshold': 0.8,
 'species': '',
 'subsequence_length': 106920,
 'temporary_dir': './',
 'window_size': 100}

Testing whether helixer_post_bin is correctly installed
Helixer.py config loaded. Starting FASTA to H5 conversion.
storing temporary files under ./tmptj58zi5u
1 expected num of chunks to write in 19994040 bases to hdf5
Numerification of 0-720580 of the sequence of sample took 0.32 secs
1 Numerified Fasta only Coordinate (seqid: sample, len: 720580) in 0.47 secs

1 expected num of chunks to write in 19994040 bases to hdf5
Numerification of 0-2030 of the sequence of sample2 took 0.00 secs
2 Numerified Fasta only Coordinate (seqid: sample2, len: 2030) in 0.01 secs

1 expected num of chunks to write in 19994040 bases to hdf5
Numerification of 0-2100 of the sequence of sample3 took 0.00 secs
3 Numerified Fasta only Coordinate (seqid: sample3, len: 2100) in 0.01 secs

1 expected num of chunks to write in 19994040 bases to hdf5
Numerification of 0-7560 of the sequence of sample4 took 0.00 secs
4 Numerified Fasta only Coordinate (seqid: sample4, len: 7560) in 0.02 secs

logged installed version in place of git commit for geenuff
logged installed version in place of git commit for helixer
FASTA to H5 conversion done. Starting neural network prediction with overlapping.
HelixerModel config: 
{'batch_size': 8,
 'calculate_uncertainty': False,
 'check_every_nth_batch': 1000000,
 'class_weights': 'None',
 'clip_norm': 3.0,
 'cnn_layers': 1,
 'compression': 'gzip',
 'core_length': 80190,
 'coverage_norm': None,
 'coverage_offset': 0.0,
 'coverage_weights': False,
 'cpus': 8,
 'data_dir': None,
 'debug': False,
 'dropout1': 0.0,
 'dropout2': 0.0,
 'epochs': 10000,
 'eval': False,
 'filter_depth': 32,
 'fine_tune': False,
 'float_precision': 'float32',
 'gpu_id': -1,
 'input_coverage': False,
 'kernel_size': 26,
 'large_eval_folder': '',
 'learning_rate': 0.0003,
 'load_model_path': '/tmp/tmppyertp20/job_working_directory/000/2/home/.local/share/Helixer/models/land_plant/land_plant_v0.3_a_0080.h5',
 'load_predictions': False,
 'loss': '',
 'lstm_layers': 1,
 'nni': False,
 'no_utrs': False,
 'optimizer': 'adamw',
 'overlap': True,
 'overlap_offset': 53460,
 'patience': 3,
 'pool_size': 9,
 'post_coverage_hidden_layer': False,
 'predict_phase': False,
 'prediction_output_path': './tmptj58zi5u/tmp_predictions_.h5',
 'pretrained_model_path': None,
 'resume_training': False,
 'save_every_check': False,
 'save_model_path': './best_model.h5',
 'stretch_transition_weights': 0,
 'test_data': './tmptj58zi5u/tmp_species_.h5',
 'transition_weights': 'None',
 'units': 32,
 'val_test_batch_size': 8,
 'verbose': True,
 'weight_decay': 3.5e-05,
 'workers': 1}
No err_samples dataset found, correct samples will be set to 0
No fully_intergenic_samples dataset found, fully intergenic samples will be set to 0

Data config: 
[{'geenuff_commit': 'commit not found, version: 0.3.2', 'helixer_commit': 'commit not found, version: 0.3.3', 'input_path': '/tmp/tmppyertp20/files/3/e/5/dataset_3e51819b-6827-45ac-917f-d63d95da2525.dat', 'timestamp': '2025-04-22 13:39:22.414892'}]

Test data shape: (20, 106920)

Intergenic test seqs: 0.00%
Fully correct test seqs: 0.00%

Number of devices: 1
Current Helixer version: 0.3.3
Md5sum of the loaded model: f0e00efcbea83c66b69258d11119a691  /tmp/tmppyertp20/job_working_directory/000/2/home/.local/share/Helixer/models/land_plant/land_plant_v0.3_a_0080.h5

Model: "model"
__________________________________________________________________________________________________
 Layer (type)                Output Shape                 Param #   Connected to                  
==================================================================================================
 main_input (InputLayer)     [(None, None, 4)]            0         []                            
                                                                                                  
 conv1d (Conv1D)             (None, None, 96)             4704      ['main_input[0][0]']          
                                                                                                  
 batch_normalization (Batch  (None, None, 96)             384       ['conv1d[0][0]']              
 Normalization)                                                                                   
                                                                                                  
 conv1d_1 (Conv1D)           (None, None, 96)             110688    ['batch_normalization[0][0]'] 
                                                                                                  
 batch_normalization_1 (Bat  (None, None, 96)             384       ['conv1d_1[0][0]']            
 chNormalization)                                                                                 
                                                                                                  
 conv1d_2 (Conv1D)           (None, None, 96)             110688    ['batch_normalization_1[0][0]'
                                                                    ]                             
                                                                                                  
 batch_normalization_2 (Bat  (None, None, 96)             384       ['conv1d_2[0][0]']            
 chNormalization)                                                                                 
                                                                                                  
 conv1d_3 (Conv1D)           (None, None, 96)             110688    ['batch_normalization_2[0][0]'
                                                                    ]                             
                                                                                                  
 reshape (Reshape)           (None, None, 864)            0         ['conv1d_3[0][0]']            
                                                                                                  
 bidirectional (Bidirection  (None, None, 256)            1016832   ['reshape[0][0]']             
 al)                                                                                              
                                                                                                  
 bidirectional_1 (Bidirecti  (None, None, 256)            394240    ['bidirectional[0][0]']       
 onal)                                                                                            
                                                                                                  
 bidirectional_2 (Bidirecti  (None, None, 256)            394240    ['bidirectional_1[0][0]']     
 onal)                                                                                            
                                                                                                  
 dense (Dense)               (None, None, 72)             18504     ['bidirectional_2[0][0]']     
                                                                                                  
 tf.split (TFOpLambda)       [(None, None, 36),           0         ['dense[0][0]']               
                              (None, None, 36)]                                                   
                                                                                                  
 reshape_1 (Reshape)         (None, None, 9, 4)           0         ['tf.split[0][0]']            
                                                                                                  
 reshape_2 (Reshape)         (None, None, 9, 4)           0         ['tf.split[0][1]']            
                                                                                                  
 genic (Activation)          (None, None, 9, 4)           0         ['reshape_1[0][0]']           
                                                                                                  
 phase (Activation)          (None, None, 9, 4)           0         ['reshape_2[0][0]']           
                                                                                                  
==================================================================================================
Total params: 2161736 (8.25 MB)
Trainable params: 2161160 (8.24 MB)
Non-trainable params: 576 (2.25 KB)
__________________________________________________________________________________________________
HMM Config
  Splicing Flags: U:true US:true S:true SC:true C:true CS:true S:true SU:true U:true
  Splicing - Weights: Donor 1, Acceptor 1
  Splicing - Fixed Penalties: U2-GT-AG 0, U2-GT-AC 0 U12-GT-AG 0 U12-AT-AC 0
  Coding - Weights: Start 1000, Stop 1000
  Phase Mode: Implementation 1, Dilute to Total, Retention: 0.2

Sequences for Species  - 0
  BP_Extractor for Sequence sample - ID 0
Forward for Sequence sample - ID 0
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	      613530	         131	         479	         418		      Non Coding	      689510	        1069	        1104	        1091	
             UTR	         238	        5141	          87	         120		         Phase 0	         230	        9046	           2	           6	
          Coding	        1243	          82	       29647	         264		         Phase 1	         226	           8	        9014	           2	
          Intron	        1459	         120	         162	       67459		         Phase 2	         239	           2	           5	        9026	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     0.99523	     0.99833	     0.99678	            		      Non Coding	     0.99899	     0.99529	     0.99714	            	
             UTR	     0.93917	     0.92034	     0.92966	            		         Phase 0	     0.89343	     0.97436	     0.93214	            	
          Coding	     0.97603	     0.94913	     0.96239	            		         Phase 1	     0.89027	     0.97449	     0.93048	            	
          Intron	     0.98825	     0.97484	     0.98150	            		         Phase 2	     0.89146	     0.97347	     0.93066	            	

        Subgenic	     0.98449	     0.96684	     0.97559	            		          Coding	     0.89172	     0.97411	     0.93109	            	
           Genic	     0.98211	     0.96439	     0.97317	


Reverse for Sequence sample - ID 0
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	      555814	         209	         108	         776		      Non Coding	      659468	         985	         971	         987	
             UTR	         454	        9649	         137	         214		         Phase 0	         670	       18679	           9	          31	
          Coding	        2123	          49	       58497	         691		         Phase 1	         689	          33	       18702	          12	
          Intron	        8256	         265	         391	       82947		         Phase 2	         620	          14	          29	       18681	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     0.98088	     0.99804	     0.98939	            		      Non Coding	     0.99701	     0.99556	     0.99628	            	
             UTR	     0.94858	     0.92300	     0.93562	            		         Phase 0	     0.94764	     0.96338	     0.95545	            	
          Coding	     0.98924	     0.95334	     0.97096	            		         Phase 1	     0.94881	     0.96224	     0.95548	            	
          Intron	     0.98014	     0.90298	     0.93998	            		         Phase 2	     0.94774	     0.96573	     0.95665	            	

        Subgenic	     0.98388	     0.92315	     0.95255	            		          Coding	     0.94807	     0.96378	     0.95586	            	
           Genic	     0.98155	     0.92314	     0.95145	


  BP_Extractor for Sequence sample2 - ID 1
Forward for Sequence sample2 - ID 1
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	        2026	           0	           0	           0		      Non Coding	        2029	           0	           0	           0	
             UTR	           0	           0	           0	           0		         Phase 0	           1	           0	           0	           0	
          Coding	           4	           0	           0	           0		         Phase 1	           0	           0	           0	           0	
          Intron	           0	           0	           0	           0		         Phase 2	           0	           0	           0	           0	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     0.99803	     1.00000	     0.99901	            		      Non Coding	     0.99951	     1.00000	     0.99975	            	
             UTR	         NaN	         NaN	         NaN	            		         Phase 0	         NaN	     0.00000	     0.00000	            	
          Coding	         NaN	     0.00000	     0.00000	            		         Phase 1	         NaN	         NaN	         NaN	            	
          Intron	         NaN	         NaN	         NaN	            		         Phase 2	         NaN	         NaN	         NaN	            	

        Subgenic	         NaN	     0.00000	     0.00000	            		          Coding	         NaN	     0.00000	     0.00000	            	
           Genic	         NaN	     0.00000	     0.00000	


Reverse for Sequence sample2 - ID 1
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	        2030	           0	           0	           0		      Non Coding	        2030	           0	           0	           0	
             UTR	           0	           0	           0	           0		         Phase 0	           0	           0	           0	           0	
          Coding	           0	           0	           0	           0		         Phase 1	           0	           0	           0	           0	
          Intron	           0	           0	           0	           0		         Phase 2	           0	           0	           0	           0	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     1.00000	     1.00000	     1.00000	            		      Non Coding	     1.00000	     1.00000	     1.00000	            	
             UTR	         NaN	         NaN	         NaN	            		         Phase 0	         NaN	         NaN	         NaN	            	
          Coding	         NaN	         NaN	         NaN	            		         Phase 1	         NaN	         NaN	         NaN	            	
          Intron	         NaN	         NaN	         NaN	            		         Phase 2	         NaN	         NaN	         NaN	            	

        Subgenic	         NaN	         NaN	         NaN	            		          Coding	         NaN	         NaN	         NaN	            	
           Genic	         NaN	         NaN	         NaN	


  BP_Extractor for Sequence sample3 - ID 2
Forward for Sequence sample3 - ID 2
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	        2098	           0	           0	           0		      Non Coding	        2099	           0	           0	           0	
             UTR	           0	           0	           0	           0		         Phase 0	           1	           0	           0	           0	
          Coding	           2	           0	           0	           0		         Phase 1	           0	           0	           0	           0	
          Intron	           0	           0	           0	           0		         Phase 2	           0	           0	           0	           0	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     0.99905	     1.00000	     0.99952	            		      Non Coding	     0.99952	     1.00000	     0.99976	            	
             UTR	         NaN	         NaN	         NaN	            		         Phase 0	         NaN	     0.00000	     0.00000	            	
          Coding	         NaN	     0.00000	     0.00000	            		         Phase 1	         NaN	         NaN	         NaN	            	
          Intron	         NaN	         NaN	         NaN	            		         Phase 2	         NaN	         NaN	         NaN	            	

        Subgenic	         NaN	     0.00000	     0.00000	            		          Coding	         NaN	     0.00000	     0.00000	            	
           Genic	         NaN	     0.00000	     0.00000	


Reverse for Sequence sample3 - ID 2
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	        2100	           0	           0	           0		      Non Coding	        2100	           0	           0	           0	
             UTR	           0	           0	           0	           0		         Phase 0	           0	           0	           0	           0	
          Coding	           0	           0	           0	           0		         Phase 1	           0	           0	           0	           0	
          Intron	           0	           0	           0	           0		         Phase 2	           0	           0	           0	           0	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     1.00000	     1.00000	     1.00000	            		      Non Coding	     1.00000	     1.00000	     1.00000	            	
             UTR	         NaN	         NaN	         NaN	            		         Phase 0	         NaN	         NaN	         NaN	            	
          Coding	         NaN	         NaN	         NaN	            		         Phase 1	         NaN	         NaN	         NaN	            	
          Intron	         NaN	         NaN	         NaN	            		         Phase 2	         NaN	         NaN	         NaN	            	

        Subgenic	         NaN	         NaN	         NaN	            		          Coding	         NaN	         NaN	         NaN	            	
           Genic	         NaN	         NaN	         NaN	


  BP_Extractor for Sequence sample4 - ID 3
Forward for Sequence sample4 - ID 3
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	        7535	           0	           0	           0		      Non Coding	        7553	           0	           0	           0	
             UTR	           3	           0	           0	           0		         Phase 0	           2	           0	           0	           0	
          Coding	           8	           0	           0	           0		         Phase 1	           2	           0	           0	           0	
          Intron	          14	           0	           0	           0		         Phase 2	           3	           0	           0	           0	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     0.99669	     1.00000	     0.99834	            		      Non Coding	     0.99907	     1.00000	     0.99954	            	
             UTR	         NaN	     0.00000	     0.00000	            		         Phase 0	         NaN	     0.00000	     0.00000	            	
          Coding	         NaN	     0.00000	     0.00000	            		         Phase 1	         NaN	     0.00000	     0.00000	            	
          Intron	         NaN	     0.00000	     0.00000	            		         Phase 2	         NaN	     0.00000	     0.00000	            	

        Subgenic	         NaN	     0.00000	     0.00000	            		          Coding	         NaN	     0.00000	     0.00000	            	
           Genic	         NaN	     0.00000	     0.00000	


Reverse for Sequence sample4 - ID 3
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	        4480	          19	           0	           0		      Non Coding	        5923	           2	           6	           4	
             UTR	          40	         453	           5	           0		         Phase 0	          17	         524	           0	           0	
          Coding	         321	           0	        1573	           1		         Phase 1	          17	           0	         520	           0	
          Intron	           0	           0	           0	         668		         Phase 2	          25	           0	           0	         522	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     0.92543	     0.99578	     0.95931	            		      Non Coding	     0.99014	     0.99798	     0.99404	            	
             UTR	     0.95975	     0.90964	     0.93402	            		         Phase 0	     0.99620	     0.96858	     0.98219	            	
          Coding	     0.99683	     0.83008	     0.90585	            		         Phase 1	     0.98859	     0.96834	     0.97836	            	
          Intron	     0.99851	     1.00000	     0.99925	            		         Phase 2	     0.99240	     0.95430	     0.97297	            	

        Subgenic	     0.99733	     0.87437	     0.93181	            		          Coding	     0.99240	     0.96369	     0.97783	            	
           Genic	     0.99081	     0.88010	     0.93218	


Forward for Species  - 0
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	      625189	         131	         479	         418		      Non Coding	      701191	        1069	        1104	        1091	
             UTR	         241	        5141	          87	         120		         Phase 0	         234	        9046	           2	           6	
          Coding	        1257	          82	       29647	         264		         Phase 1	         228	           8	        9014	           2	
          Intron	        1473	         120	         162	       67459		         Phase 2	         242	           2	           5	        9026	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     0.99527	     0.99836	     0.99681	            		      Non Coding	     0.99900	     0.99537	     0.99718	            	
             UTR	     0.93917	     0.91984	     0.92940	            		         Phase 0	     0.89343	     0.97394	     0.93195	            	
          Coding	     0.97603	     0.94870	     0.96217	            		         Phase 1	     0.89027	     0.97428	     0.93038	            	
          Intron	     0.98825	     0.97464	     0.98140	            		         Phase 2	     0.89146	     0.97315	     0.93052	            	

        Subgenic	     0.98449	     0.96658	     0.97545	            		          Coding	     0.89172	     0.97379	     0.93095	            	
           Genic	     0.98211	     0.96411	     0.97303	


Reverse for Species  - 0
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	      564424	         228	         108	         776		      Non Coding	      669521	         987	         977	         991	
             UTR	         494	       10102	         142	         214		         Phase 0	         687	       19203	           9	          31	
          Coding	        2444	          49	       60070	         692		         Phase 1	         706	          33	       19222	          12	
          Intron	        8256	         265	         391	       83615		         Phase 2	         645	          14	          29	       19203	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     0.98055	     0.99803	     0.98922	            		      Non Coding	     0.99697	     0.99561	     0.99629	            	
             UTR	     0.94908	     0.92239	     0.93554	            		         Phase 0	     0.94891	     0.96352	     0.95616	            	
          Coding	     0.98944	     0.94965	     0.96914	            		         Phase 1	     0.94984	     0.96240	     0.95608	            	
          Intron	     0.98028	     0.90368	     0.94042	            		         Phase 2	     0.94891	     0.96541	     0.95709	            	

        Subgenic	     0.98409	     0.92235	     0.95222	            		          Coding	     0.94922	     0.96378	     0.95644	            	
           Genic	     0.98171	     0.92235	     0.95110	


Total for Species  - 0
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	     1189613	         359	         587	        1194		      Non Coding	     1370712	        2056	        2081	        2082	
             UTR	         735	       15243	         229	         334		         Phase 0	         921	       28249	          11	          37	
          Coding	        3701	         131	       89717	         956		         Phase 1	         934	          41	       28236	          14	
          Intron	        9729	         385	         553	      151074		         Phase 2	         887	          16	          34	       28229	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     0.98823	     0.99820	     0.99319	            		      Non Coding	     0.99800	     0.99548	     0.99674	            	
             UTR	     0.94571	     0.92153	     0.93346	            		         Phase 0	     0.93041	     0.96684	     0.94827	            	
          Coding	     0.98497	     0.94934	     0.96682	            		         Phase 1	     0.92998	     0.96616	     0.94772	            	
          Intron	     0.98382	     0.93405	     0.95829	            		         Phase 2	     0.92975	     0.96787	     0.94843	            	

        Subgenic	     0.98425	     0.93969	     0.96145	            		          Coding	     0.93004	     0.96696	     0.94814	            	
           Genic	     0.98187	     0.93859	     0.95974	


Total: 482642bp across 25 windows
None

starting to load test data into memory..
For h5 starting with species = b'':
x shape: (20, 106920, 4)
Data loading of 20 (total so far 20) samples of data/X into memory took 0.06 secs
Compressed data size of data/X is at least 0.0008 GB

setting self.n_seqs to 20, bc that is len of data/X
0 / 8
1 / 8
2 / 8
3 / 8
4 / 8
5 / 8
6 / 8
7 / 8
Neural network prediction done. Starting post processing.

Helixer successfully finished the annotation of /tmp/tmppyertp20/files/3/e/5/dataset_3e51819b-6827-45ac-917f-d63d95da2525.dat in 0.07 hours. GFF file written to /tmp/tmppyertp20/job_working_directory/000/2/outputs/dataset_acc27a39-62d7-4a47-ae42-36f0ea99c6d7.dat.

              

              • 

            

            Traceback:
            

              

            • 

              

              • 

            

            Job Parameters:
            

              

            • 

              


              
Job parameter
Parameter value

              
              


              
__input_ext
"input"

              

              
__workflow_invocation_uuid__
"e3fb282c1f7e11f0be827c1e52674869"

              

              
chromInfo
"/tmp/tmppyertp20/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"

              

              
dbkey
"?"

              

              
input_model
None

              

              
lineages
"land_plant"

              

              
option_overlap
{"__current_case__": 0, "overlap_core_length": null, "overlap_offset": null, "use_overlap": "true"}

              

              
post_processing
{"edge_threshold": "0.1", "min_coding_length": "100", "peak_threshold": "0.8", "window_size": "100"}

              

              
size
"8"

              

              
species
None

              

              
subsequence_length
None

              
              

              

              • 

            

            • 

          

          

          • 

        

        • 

      • 

        Step 3: Busco on genome:
        

          

        • 

          step_state: scheduled
          

          • 

        • 

          Jobs

            

          • 

            Job 1:
            

              

            • Job state is ok
              • 

            

            Command Line:
            

              

            • 

              if [ -z "$AUGUSTUS_CONFIG_PATH" ] ; then BUSCO_PATH=$(dirname $(which busco)) ; export AUGUSTUS_CONFIG_PATH=$(realpath ${BUSCO_PATH}/../config) ; fi && cp -r "$AUGUSTUS_CONFIG_PATH/" augustus_dir/ && export AUGUSTUS_CONFIG_PATH=`pwd`/augustus_dir/ &&    busco --in '/tmp/tmppyertp20/files/3/e/5/dataset_3e51819b-6827-45ac-917f-d63d95da2525.dat' --mode 'geno' --out busco_galaxy --cpu ${GALAXY_SLOTS:-4} --evalue 0.001 --limit 3 --contig_break 10  --offline --download_path /cvmfs/data.galaxyproject.org/byhand/busco/v5  --lineage_dataset 'mucorales_odb10'   --augustus  && mkdir BUSCO_summaries && ls -l busco_galaxy/run_*/ && cp busco_galaxy/short_summary.*.txt BUSCO_summaries/ && generate_plot.py -wd BUSCO_summaries -rt specific  && echo "##gff-version 3" > busco_output.gff && cat busco_galaxy/run_*/busco_sequences/*busco_sequences/*.gff >> busco_output.gff 2> /dev/null || true
              

              • 

            

            Exit Code:
            

              

            • 

              0
              

              • 

            

            Standard Error:
            

              

            • 

              2025-04-22 13:51:17 ERROR:	
Warning message:
The `size` argument of `element_line()` is deprecated as of ggplot2 3.4.0.
ℹ Please use the `linewidth` argument instead. 


              

              • 

            

            Standard Output:
            

              

            • 

              2025-04-22 13:38:42 INFO:	***** Start a BUSCO v5.8.0 analysis, current time: 04/22/2025 13:38:42 *****
2025-04-22 13:38:42 INFO:	Configuring BUSCO with local environment
2025-04-22 13:38:42 INFO:	Running genome mode
2025-04-22 13:38:46 INFO:	Input file is /tmp/tmppyertp20/files/3/e/5/dataset_3e51819b-6827-45ac-917f-d63d95da2525.dat
2025-04-22 13:38:46 INFO:	Running BUSCO using lineage dataset mucorales_odb10 (eukaryota, 2020-08-05)
2025-04-22 13:38:46 INFO:	Running 1 job(s) on bbtools, starting at 04/22/2025 13:38:46
2025-04-22 13:38:47 INFO:	[bbtools]	1 of 1 task(s) completed
2025-04-22 13:38:47 INFO:	Running 1 job(s) on makeblastdb, starting at 04/22/2025 13:38:47
2025-04-22 13:38:48 INFO:	Creating BLAST database with input file
2025-04-22 13:38:48 INFO:	[makeblastdb]	1 of 1 task(s) completed
2025-04-22 13:38:48 INFO:	Running a BLAST search for BUSCOs against created database
2025-04-22 13:38:48 INFO:	Running 1 job(s) on tblastn, starting at 04/22/2025 13:38:48
2025-04-22 13:38:58 INFO:	[tblastn]	1 of 1 task(s) completed
2025-04-22 13:38:58 INFO:	Running Augustus gene predictor on BLAST search results.
2025-04-22 13:38:58 INFO:	Running Augustus prediction using aspergillus_nidulans as species:
2025-04-22 13:38:58 INFO:	Running 76 job(s) on augustus, starting at 04/22/2025 13:38:58
2025-04-22 13:41:06 INFO:	[augustus]	8 of 76 task(s) completed
2025-04-22 13:42:27 INFO:	[augustus]	16 of 76 task(s) completed
2025-04-22 13:43:08 INFO:	[augustus]	23 of 76 task(s) completed
2025-04-22 13:43:28 INFO:	[augustus]	31 of 76 task(s) completed
2025-04-22 13:43:49 INFO:	[augustus]	38 of 76 task(s) completed
2025-04-22 13:44:14 INFO:	[augustus]	46 of 76 task(s) completed
2025-04-22 13:44:34 INFO:	[augustus]	54 of 76 task(s) completed
2025-04-22 13:44:47 INFO:	[augustus]	61 of 76 task(s) completed
2025-04-22 13:45:00 INFO:	[augustus]	69 of 76 task(s) completed
2025-04-22 13:45:13 INFO:	[augustus]	76 of 76 task(s) completed
2025-04-22 13:45:13 INFO:	Extracting predicted proteins...
2025-04-22 13:45:13 INFO:	***** Run HMMER on gene sequences *****
2025-04-22 13:45:13 INFO:	Running 75 job(s) on hmmsearch, starting at 04/22/2025 13:45:13
2025-04-22 13:45:14 INFO:	[hmmsearch]	8 of 75 task(s) completed
2025-04-22 13:45:14 INFO:	[hmmsearch]	15 of 75 task(s) completed
2025-04-22 13:45:14 INFO:	[hmmsearch]	23 of 75 task(s) completed
2025-04-22 13:45:14 INFO:	[hmmsearch]	30 of 75 task(s) completed
2025-04-22 13:45:14 INFO:	[hmmsearch]	38 of 75 task(s) completed
2025-04-22 13:45:14 INFO:	[hmmsearch]	45 of 75 task(s) completed
2025-04-22 13:45:15 INFO:	[hmmsearch]	53 of 75 task(s) completed
2025-04-22 13:45:15 INFO:	[hmmsearch]	60 of 75 task(s) completed
2025-04-22 13:45:15 INFO:	[hmmsearch]	68 of 75 task(s) completed
2025-04-22 13:45:15 INFO:	[hmmsearch]	75 of 75 task(s) completed
2025-04-22 13:45:15 INFO:	0 exons in total
2025-04-22 13:45:15 INFO:	Starting second step of analysis. The gene predictor Augustus is retrained using the results from the initial run to yield more accurate results.
2025-04-22 13:45:15 INFO:	Extracting missing and fragmented buscos from the file ancestral_variants...
2025-04-22 13:45:19 INFO:	Running a BLAST search for BUSCOs against created database
2025-04-22 13:45:19 INFO:	Running 1 job(s) on tblastn, starting at 04/22/2025 13:45:19
2025-04-22 13:46:53 INFO:	[tblastn]	1 of 1 task(s) completed
2025-04-22 13:46:53 INFO:	Converting predicted genes to short genbank files
2025-04-22 13:46:53 INFO:	Running 1 job(s) on gff2gbSmallDNA.pl, starting at 04/22/2025 13:46:53
2025-04-22 13:46:53 INFO:	[gff2gbSmallDNA.pl]	1 of 1 task(s) completed
2025-04-22 13:46:53 INFO:	All files converted to short genbank files, now training Augustus using Single-Copy Complete BUSCOs
2025-04-22 13:46:53 INFO:	Running 1 job(s) on new_species.pl, starting at 04/22/2025 13:46:53
2025-04-22 13:46:54 INFO:	[new_species.pl]	1 of 1 task(s) completed
2025-04-22 13:46:54 INFO:	Running 1 job(s) on etraining, starting at 04/22/2025 13:46:54
2025-04-22 13:46:55 INFO:	[etraining]	1 of 1 task(s) completed
2025-04-22 13:46:55 INFO:	Re-running Augustus with the new metaparameters, number of target BUSCOs: 2448
2025-04-22 13:46:55 INFO:	Running Augustus gene predictor on BLAST search results.
2025-04-22 13:46:55 INFO:	Running Augustus prediction using BUSCO_busco_galaxy as species:
2025-04-22 13:46:55 INFO:	Running 100 job(s) on augustus, starting at 04/22/2025 13:46:55
2025-04-22 13:48:14 INFO:	[augustus]	10 of 100 task(s) completed
2025-04-22 13:49:21 INFO:	[augustus]	20 of 100 task(s) completed
2025-04-22 13:49:53 INFO:	[augustus]	30 of 100 task(s) completed
2025-04-22 13:50:06 INFO:	[augustus]	40 of 100 task(s) completed
2025-04-22 13:50:20 INFO:	[augustus]	50 of 100 task(s) completed
2025-04-22 13:50:32 INFO:	[augustus]	60 of 100 task(s) completed
2025-04-22 13:50:43 INFO:	[augustus]	70 of 100 task(s) completed
2025-04-22 13:50:53 INFO:	[augustus]	80 of 100 task(s) completed
2025-04-22 13:51:04 INFO:	[augustus]	90 of 100 task(s) completed
2025-04-22 13:51:14 INFO:	[augustus]	100 of 100 task(s) completed
2025-04-22 13:51:14 INFO:	Extracting predicted proteins...
2025-04-22 13:51:14 INFO:	***** Run HMMER on gene sequences *****
2025-04-22 13:51:14 WARNING:	No jobs to run on hmmsearch
2025-04-22 13:51:14 INFO:	0 exons in total
2025-04-22 13:51:14 INFO:	Results:	C:0.0%[S:0.0%,D:0.0%],F:0.0%,M:100.0%,n:2449	   

2025-04-22 13:51:14 INFO:	

    ---------------------------------------------------
    |Results from dataset mucorales_odb10              |
    ---------------------------------------------------
    |C:0.0%[S:0.0%,D:0.0%],F:0.0%,M:100.0%,n:2449      |
    |1    Complete BUSCOs (C)                          |
    |1    Complete and single-copy BUSCOs (S)          |
    |0    Complete and duplicated BUSCOs (D)           |
    |0    Fragmented BUSCOs (F)                        |
    |2448    Missing BUSCOs (M)                        |
    |2449    Total BUSCO groups searched               |
    ---------------------------------------------------
2025-04-22 13:51:14 INFO:	BUSCO analysis done with WARNING(s). Total running time: 748 seconds

***** Summary of warnings: *****
2025-04-22 13:51:14 WARNING:busco.busco_tools.Toolset	No jobs to run on hmmsearch

2025-04-22 13:51:14 INFO:	Results written in /tmp/tmppyertp20/job_working_directory/000/3/working/busco_galaxy
2025-04-22 13:51:14 INFO:	For assistance with interpreting the results, please consult the userguide: https://busco.ezlab.org/busco_userguide.html

2025-04-22 13:51:14 INFO:	Visit this page https://gitlab.com/ezlab/busco#how-to-cite-busco to see how to cite BUSCO
total 100
drwxr-xr-x 8 1001 118  4096 Apr 22 13:51 augustus_output
drwxr-xr-x 3 1001 118  4096 Apr 22 13:46 blast_output
drwxr-xr-x 5 1001 118  4096 Apr 22 13:38 busco_sequences
-rw-r--r-- 1 1001 118 47630 Apr 22 13:51 full_table.tsv
drwxr-xr-x 4 1001 118  4096 Apr 22 13:45 hmmer_output
-rw-r--r-- 1 1001 118 27820 Apr 22 13:51 missing_busco_list.tsv
-rw-r--r-- 1 1001 118  3176 Apr 22 13:51 short_summary.json
-rw-r--r-- 1 1001 118  1067 Apr 22 13:51 short_summary.txt
2025-04-22 13:51:14 INFO:	****************** Start plot generation at 04/22/2025 13:51:14 ******************
2025-04-22 13:51:14 INFO:	Load data ...
2025-04-22 13:51:14 INFO:	Loaded BUSCO_summaries/short_summary.specific.mucorales_odb10.busco_galaxy.txt successfully
2025-04-22 13:51:14 INFO:	Generate the R code ...
2025-04-22 13:51:14 INFO:	Run the R code ...
2025-04-22 13:51:17 INFO:	
[1] "Plotting the figure ..."
[1] "Done"

2025-04-22 13:51:17 INFO:	Plot generation done. Total running time: 2.2885096073150635 seconds
2025-04-22 13:51:17 INFO:	Results written in BUSCO_summaries/


              

              • 

            

            Traceback:
            

              

            • 

              

              • 

            

            Job Parameters:
            

              

            • 

              


              
Job parameter
Parameter value

              
              


              
__input_ext
"input"

              

              
__workflow_invocation_uuid__
"e3fb282c1f7e11f0be827c1e52674869"

              

              
adv
{"contig_break": "10", "evalue": "0.001", "limit": "3"}

              

              
busco_mode
{"__current_case__": 0, "mode": "geno", "use_augustus": {"__current_case__": 2, "aug_prediction": {"__current_case__": 0, "augustus_mode": "no"}, "long": false, "use_augustus_selector": "augustus"}}

              

              
chromInfo
"/tmp/tmppyertp20/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"

              

              
dbkey
"?"

              

              
lineage
{"__current_case__": 1, "lineage_dataset": "mucorales_odb10", "lineage_mode": "select_lineage"}

              

              
lineage_conditional
{"__current_case__": 0, "cached_db": "v5", "selector": "cached"}

              

              
outputs
["short_summary", "image", "gff", "missing"]

              
              

              

              • 

            

            • 

          

          

          • 

        

        • 

      • 

        Step 4: Gffread:
        

          

        • 

          step_state: scheduled
          

          • 

        • 

          Jobs

            

          • 

            Job 1:
            

              

            • Job state is ok
              • 

            

            Command Line:
            

              

            • 

              ln -s '/tmp/tmppyertp20/files/3/e/5/dataset_3e51819b-6827-45ac-917f-d63d95da2525.dat' genomeref.fa &&  gffread '/tmp/tmppyertp20/files/a/c/c/dataset_acc27a39-62d7-4a47-ae42-36f0ea99c6d7.dat' -g genomeref.fa      -y pep.fa
              

              • 

            

            Exit Code:
            

              

            • 

              0
              

              • 

            

            Standard Error:
            

              

            • 

              FASTA index file genomeref.fa.fai created.

              

              • 

            

            Traceback:
            

              

            • 

              

              • 

            

            Job Parameters:
            

              

            • 

              


              
Job parameter
Parameter value

              
              


              
__input_ext
"input"

              

              
__workflow_invocation_uuid__
"e3fb282c1f7e11f0be827c1e52674869"

              

              
chr_replace
None

              

              
chromInfo
"/tmp/tmppyertp20/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"

              

              
dbkey
"?"

              

              
decode_url
false

              

              
expose
false

              

              
filtering
None

              

              
full_gff_attribute_preservation
false

              

              
gffs
{"__current_case__": 0, "gff_fmt": "none"}

              

              
maxintron
None

              

              
merging
{"__current_case__": 0, "merge_sel": "none"}

              

              
reference_genome
{"__current_case__": 2, "fa_outputs": ["-y pep.fa"], "genome_fasta": {"values": [{"id": 1, "src": "hda"}]}, "ref_filtering": null, "source": "history"}

              

              
region
{"__current_case__": 0, "region_filter": "none"}

              
              

              

              • 

            

            • 

          

          

          • 

        

        • 

      • 

        Step 5: Genome annotation statistics:
        

          

        • 

          step_state: scheduled
          

          • 

        • 

          Jobs

            

          • 

            Job 1:
            

              

            • Job state is ok
              • 

            

            Command Line:
            

              

            • 

              ln -s '/tmp/tmppyertp20/files/a/c/c/dataset_acc27a39-62d7-4a47-ae42-36f0ea99c6d7.dat' 'input.gff'  &&  python -m jcvi.annotation.stats genestats 'input.gff' > '/tmp/tmppyertp20/job_working_directory/000/5/outputs/dataset_9b0a43d5-9aee-4ea5-b611-40d04e3018ba.dat'  &&  python -m jcvi.annotation.stats summary 'input.gff' '/tmp/tmppyertp20/files/3/e/5/dataset_3e51819b-6827-45ac-917f-d63d95da2525.dat' 2>&1 | tail -n +3 >> '/tmp/tmppyertp20/job_working_directory/000/5/outputs/dataset_9b0a43d5-9aee-4ea5-b611-40d04e3018ba.dat'  &&  python -m jcvi.annotation.stats stats 'input.gff' 2>&1 | grep Mean >> '/tmp/tmppyertp20/job_working_directory/000/5/outputs/dataset_9b0a43d5-9aee-4ea5-b611-40d04e3018ba.dat'  &&  python -m jcvi.annotation.stats histogram 'input.gff'  &&  pdfunite *.input.pdf '/tmp/tmppyertp20/job_working_directory/000/5/outputs/dataset_016fe103-eec7-49b0-bb6b-73322b1ad748.dat'
              

              • 

            

            Exit Code:
            

              

            • 

              0
              

              • 

            

            Standard Error:
            

              

            • 

              �[0;33m13:44:14 [gff]�[0m�[0;35m Indexing `input.gff`�[0m
�[0;33m13:44:14 [base]�[0m�[0;35m Load file `transcript.sizes`�[0m
�[0;33m13:44:14 [base]�[0m�[0;35m Imported 65 records from `transcript.sizes`.�[0m
�[0;33m13:44:14 [base]�[0m�[0;35m Load file `transcript.sizes`�[0m
�[0;33m13:44:14 [base]�[0m�[0;35m Imported 65 records from `transcript.sizes`.�[0m
�[0;33m13:44:14 [stats]�[0m�[0;35m A total of 65 transcripts populated.�[0m
�[0;33m13:44:15 [__init__]�[0m�[0;35m $HOME=/home/runner�[0m
�[0;33m13:44:15 [__init__]�[0m�[0;35m matplotlib data path /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data�[0m
�[0;33m13:44:15 [__init__]�[0m�[0;35m loaded rc file /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/matplotlibrc�[0m
�[0;33m13:44:15 [__init__]�[0m�[0;35m matplotlib version 2.2.2�[0m
�[0;33m13:44:15 [__init__]�[0m�[0;35m interactive is False�[0m
�[0;33m13:44:15 [__init__]�[0m�[0;35m platform is linux2�[0m
�[0;33m13:44:15 [__init__]�[0m�[0;35m loaded modules: ['numpy.core.info', 'Bio.SeqIO.UniprotIO', 'jcvi.apps.base', 'ctypes.os', 'Bio.os', 'runpy', 'gc', 'distutils.sysconfig', 'matplotlib.cbook._backports', 'Bio._py3k.urllib2', 'logging.weakref', 'base64', 'jcvi.utils', 'jcvi.apps.signal', 'unittest.sys', 'numpy.core.umath', 'string', 'Bio.SeqIO.InsdcIO', 'numpy.lib.arraysetops', '_elementtree', 'xml.etree.warnings', 'xml.etree.sys', 'Bio.SeqUtils.binascii', 'json.encoder', 'Bio.SeqIO.QualityIO', 'numpy.core.machar', 'jcvi.formats.collections', 'unittest.StringIO', 'unittest.types', 'jcvi.apps.threading', 'numpy.ma.extras', 'numpy.fft.fftpack_lite', 'matplotlib.cbook', 'dis', 'zlib', 'logging.threading', 'jcvi.annotation', 'Bio.SeqIO.Bio', '_json', 'Bio.GenBank.warnings', 'matplotlib.cbook.warnings', 'pyparsing', 'matplotlib.cbook.textwrap', 'abc', 'numpy._globals', 'numpy.lib.npyio', 'xml.sax.io', 'Bio._py3k.sys', 'Bio.SeqIO.sys', 'numpy.fft.helper', 'matplotlib.rcsetup', 'optparse', 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�[0;33m13:44:15 [font_manager]�[0m�[0;35m createFontDict: /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/pdfcorefonts/Times-Italic.afm�[0m
�[0;33m13:44:15 [font_manager]�[0m�[0;35m createFontDict: /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/afm/ptmb8a.afm�[0m
�[0;33m13:44:15 [font_manager]�[0m�[0;35m createFontDict: /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/afm/ptmr8a.afm�[0m
�[0;33m13:44:15 [font_manager]�[0m�[0;35m createFontDict: /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/afm/phvl8a.afm�[0m
�[0;33m13:44:15 [font_manager]�[0m�[0;35m createFontDict: /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/afm/pbkl8a.afm�[0m
�[0;33m13:44:15 [font_manager]�[0m�[0;35m createFontDict: /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/afm/pncri8a.afm�[0m
�[0;33m13:44:15 [font_manager]�[0m�[0;35m createFontDict: /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/afm/cmr10.afm�[0m
�[0;33m13:44:15 [font_manager]�[0m�[0;35m createFontDict: /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/afm/putbi8a.afm�[0m
�[0;33m13:44:15 [font_manager]�[0m�[0;35m createFontDict: /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/pdfcorefonts/Helvetica-Oblique.afm�[0m
�[0;33m13:44:15 [font_manager]�[0m�[0;35m createFontDict: /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/pdfcorefonts/Times-BoldItalic.afm�[0m
�[0;33m13:44:15 [font_manager]�[0m�[0;35m createFontDict: /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/afm/phvlo8a.afm�[0m
�[0;33m13:44:15 [font_manager]�[0m�[0;35m createFontDict: /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/afm/pcrbo8a.afm�[0m
�[0;33m13:44:15 [font_manager]�[0m�[0;35m createFontDict: /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/afm/pplri8a.afm�[0m
�[0;33m13:44:15 [font_manager]�[0m�[0;35m createFontDict: /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/pdfcorefonts/Courier-Bold.afm�[0m
�[0;33m13:44:15 [font_manager]�[0m�[0;35m createFontDict: /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/afm/pplbi8a.afm�[0m
�[0;33m13:44:15 [font_manager]�[0m�[0;35m createFontDict: /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/afm/ptmbi8a.afm�[0m
�[0;33m13:44:15 [font_manager]�[0m�[0;35m createFontDict: /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/afm/pcrb8a.afm�[0m
�[0;33m13:44:15 [font_manager]�[0m�[0;35m createFontDict: /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/afm/phvbo8a.afm�[0m
�[0;33m13:44:15 [font_manager]�[0m�[0;35m createFontDict: /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/afm/pncr8a.afm�[0m
�[0;33m13:44:15 [font_manager]�[0m�[0;35m createFontDict: /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/afm/pcrro8a.afm�[0m
�[0;33m13:44:15 [font_manager]�[0m�[0;35m createFontDict: /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/pdfcorefonts/ZapfDingbats.afm�[0m
�[0;33m13:44:15 [font_manager]�[0m�[0;35m createFontDict: /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/afm/cmmi10.afm�[0m
�[0;33m13:44:15 [font_manager]�[0m�[0;35m createFontDict: /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/afm/pcrr8a.afm�[0m
�[0;33m13:44:15 [font_manager]�[0m�[0;35m createFontDict: /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/afm/pncb8a.afm�[0m
�[0;33m13:44:15 [font_manager]�[0m�[0;35m createFontDict: /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/afm/pbkd8a.afm�[0m
�[0;33m13:44:15 [font_manager]�[0m�[0;35m createFontDict: /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/afm/pzcmi8a.afm�[0m
�[0;33m13:44:15 [font_manager]�[0m�[0;35m createFontDict: /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/afm/pagko8a.afm�[0m
�[0;33m13:44:15 [font_manager]�[0m�[0;35m createFontDict: /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/pdfcorefonts/Times-Roman.afm�[0m
�[0;33m13:44:15 [font_manager]�[0m�[0;35m createFontDict: /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/afm/pbkdi8a.afm�[0m
�[0;33m13:44:15 [font_manager]�[0m�[0;35m createFontDict: /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/afm/pagdo8a.afm�[0m
�[0;33m13:44:15 [font_manager]�[0m�[0;35m createFontDict: /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/afm/pagk8a.afm�[0m
�[0;33m13:44:15 [font_manager]�[0m�[0;35m generated new fontManager�[0m
�[0;33m13:44:15 [__init__]�[0m�[0;35m backend agg version v2.2�[0m
�[0;33m13:44:15 [stats]�[0m�[0;35m Parsing files in `Exon_Length`..�[0m
Exon_Length/input.txt: Min=1 Max=2026 N=270 Mean=337.355555556 SD=399.160349598 Median=198.0 Sum=91086
�[0;33m13:44:15 [base]�[0m�[0;35m Rscript /tmp/tmppyertp20/tmp/tmpUYShre�[0m
Warning message:
Removed 21 rows containing non-finite values (stat_bin). 
Saving 7 x 7 in image
Warning message:
Removed 21 rows containing non-finite values (stat_bin). 
�[0;33m13:44:19 [stats]�[0m�[0;35m Parsing files in `Intron_Length`..�[0m
Intron_Length/input.txt: Min=50 Max=14088 N=205 Mean=547.107317073 SD=1467.30391824 Median=152.0 Sum=112157
�[0;33m13:44:19 [base]�[0m�[0;35m Rscript /tmp/tmppyertp20/tmp/tmpYP7KX2�[0m
Warning message:
Removed 23 rows containing non-finite values (stat_bin). 
Saving 7 x 7 in image
Warning message:
Removed 23 rows containing non-finite values (stat_bin). 
�[0;33m13:44:22 [stats]�[0m�[0;35m Parsing files in `Gene_Length`..�[0m
Gene_Length/input.txt: Min=111 Max=7371 N=65 Mean=1401.32307692 SD=1130.94596358 Median=1122.0 Sum=91086
�[0;33m13:44:22 [base]�[0m�[0;35m Rscript /tmp/tmppyertp20/tmp/tmpD9tOOI�[0m
Warning message:
Removed 2 rows containing non-finite values (stat_bin). 
Saving 7 x 7 in image
Warning message:
Removed 2 rows containing non-finite values (stat_bin). 
�[0;33m13:44:26 [stats]�[0m�[0;35m Parsing files in `Exon_Count`..�[0m
Exon_Count/input.txt: Min=1 Max=15 N=65 Mean=4.15384615385 SD=3.39334538463 Median=3.0 Sum=270
�[0;33m13:44:26 [base]�[0m�[0;35m Rscript /tmp/tmppyertp20/tmp/tmpodJSt4�[0m
Saving 7 x 7 in image

              

              • 

            

            Traceback:
            

              

            • 

              

              • 

            

            Job Parameters:
            

              

            • 

              


              
Job parameter
Parameter value

              
              


              
__input_ext
"input"

              

              
__workflow_invocation_uuid__
"e3fb282c1f7e11f0be827c1e52674869"

              

              
chromInfo
"/tmp/tmppyertp20/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"

              

              
dbkey
"?"

              

              
ref_genome
{"__current_case__": 1, "genome": {"values": [{"id": 1, "src": "hda"}]}, "genome_type_select": "history"}

              
              

              

              • 

            

            • 

          

          

          • 

        

        • 

      • 

        Step 6: JBrowse:
        

          

        • 

          step_state: scheduled
          

          • 

        • 

          Jobs

            

          • 

            Job 1:
            

              

            • Job state is ok
              • 

            

            Command Line:
            

              

            • 

              mkdir -p /tmp/tmppyertp20/job_working_directory/000/6/outputs/dataset_6e15de53-aaec-4a2f-8731-3bd3c378507f_files &&  cp /tmp/tmppyertp20/job_working_directory/000/6/configs/tmpzjgvwfel /tmp/tmppyertp20/job_working_directory/000/6/outputs/dataset_6e15de53-aaec-4a2f-8731-3bd3c378507f_files/galaxy.xml &&  export JBROWSE_SOURCE_DIR=$(dirname $(which prepare-refseqs.pl))/../opt/jbrowse  &&  python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/a6e57ff585c0/jbrowse/jbrowse.py'  --jbrowse ${JBROWSE_SOURCE_DIR} --standalone 'minimal'  --outdir /tmp/tmppyertp20/job_working_directory/000/6/outputs/dataset_6e15de53-aaec-4a2f-8731-3bd3c378507f_files /tmp/tmppyertp20/job_working_directory/000/6/configs/tmpzjgvwfel &&  cp /tmp/tmppyertp20/job_working_directory/000/6/outputs/dataset_6e15de53-aaec-4a2f-8731-3bd3c378507f_files/index.html /tmp/tmppyertp20/job_working_directory/000/6/outputs/dataset_6e15de53-aaec-4a2f-8731-3bd3c378507f.dat;
              

              • 

            

            Exit Code:
            

              

            • 

              0
              

              • 

            

            Standard Error:
            

              

            • 

              INFO:jbrowse:Processing Annotation / Helixer on data 1
WARNING: No feature names found for indexing, only reference sequence names will be indexed.

              

              • 

            

            Traceback:
            

              

            • 

              

              • 

            

            Job Parameters:
            

              

            • 

              


              
Job parameter
Parameter value

              
              


              
__input_ext
"fasta"

              

              
__workflow_invocation_uuid__
"e3fb282c1f7e11f0be827c1e52674869"

              

              
action
{"__current_case__": 0, "action_select": "create"}

              

              
chromInfo
"/tmp/tmppyertp20/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"

              

              
dbkey
"?"

              

              
gencode
"1"

              

              
jbgen
{"aboutDescription": "", "defaultLocation": "", "hideGenomeOptions": false, "shareLink": true, "show_menu": true, "show_nav": true, "show_overview": true, "show_tracklist": true, "trackPadding": "20"}

              

              
plugins
{"BlastView": true, "ComboTrackSelector": false, "GCContent": false}

              

              
reference_genome
{"__current_case__": 1, "genome": {"values": [{"id": 1, "src": "hda"}]}, "genome_type_select": "history"}

              

              
standalone
"minimal"

              

              
track_groups
[{"__index__": 0, "category": "Annotation", "data_tracks": [{"__index__": 0, "data_format": {"__current_case__": 2, "annotation": {"values": [{"id": 2, "src": "hda"}]}, "data_format_select": "gene_calls", "index": false, "jb_custom_config": {"option": []}, "jbcolor_scale": {"color_score": {"__current_case__": 0, "color": {"__current_case__": 0, "color_select": "automatic"}, "color_score_select": "none"}}, "jbmenu": {"track_menu": []}, "jbstyle": {"max_height": "600", "style_classname": "feature", "style_description": "note,description", "style_height": "10px", "style_label": "product,name,id"}, "match_part": {"__current_case__": 1, "match_part_select": false}, "override_apollo_drag": "False", "override_apollo_plugins": "False", "track_config": {"__current_case__": 3, "html_options": {"topLevelFeatures": null}, "track_class": "NeatHTMLFeatures/View/Track/NeatFeatures"}, "track_visibility": "default_off"}}]}]

              

              
uglyTestingHack
""

              
              

              

              • 

            

            • 

          

          

          • 

        

        • 

      • 

        Step 7: Busco on protein:
        

          

        • 

          step_state: scheduled
          

          • 

        • 

          Jobs

            

          • 

            Job 1:
            

              

            • Job state is ok
              • 

            

            Command Line:
            

              

            • 

              busco --in '/tmp/tmppyertp20/files/7/1/4/dataset_714c71cf-2bcc-4788-b5c7-031e464430c6.dat' --mode 'prot' --out busco_galaxy --cpu ${GALAXY_SLOTS:-4} --evalue 0.001 --limit 3 --contig_break 10  --offline --download_path /cvmfs/data.galaxyproject.org/byhand/busco/v5  --lineage_dataset 'mucorales_odb10'   && mkdir BUSCO_summaries && ls -l busco_galaxy/run_*/ && cp busco_galaxy/short_summary.*.txt BUSCO_summaries/ && generate_plot.py -wd BUSCO_summaries -rt specific  && echo "##gff-version 3" > busco_output.gff && cat busco_galaxy/run_*/busco_sequences/*busco_sequences/*.gff >> busco_output.gff 2> /dev/null || true
              

              • 

            

            Exit Code:
            

              

            • 

              0
              

              • 

            

            Standard Error:
            

              

            • 

              2025-04-22 13:47:18 ERROR:	
Warning message:
The `size` argument of `element_line()` is deprecated as of ggplot2 3.4.0.
ℹ Please use the `linewidth` argument instead. 


              

              • 

            

            Standard Output:
            

              

            • 

              2025-04-22 13:43:55 INFO:	***** Start a BUSCO v5.8.0 analysis, current time: 04/22/2025 13:43:55 *****
2025-04-22 13:43:55 INFO:	Configuring BUSCO with local environment
2025-04-22 13:43:55 INFO:	Running proteins mode
2025-04-22 13:43:55 INFO:	Input file is /tmp/tmppyertp20/files/7/1/4/dataset_714c71cf-2bcc-4788-b5c7-031e464430c6.dat
2025-04-22 13:43:55 WARNING:	Option contig_break was provided but is not used in the selected run mode, proteins
2025-04-22 13:43:55 WARNING:	Option evalue was provided but is not used in the selected run mode, proteins
2025-04-22 13:43:55 WARNING:	Option limit was provided but is not used in the selected run mode, proteins
2025-04-22 13:43:55 INFO:	Running BUSCO using lineage dataset mucorales_odb10 (eukaryota, 2020-08-05)
2025-04-22 13:43:55 INFO:	***** Run HMMER on gene sequences *****
2025-04-22 13:43:55 INFO:	Running 2449 job(s) on hmmsearch, starting at 04/22/2025 13:43:55
2025-04-22 13:44:18 INFO:	[hmmsearch]	245 of 2449 task(s) completed
2025-04-22 13:44:36 INFO:	[hmmsearch]	490 of 2449 task(s) completed
2025-04-22 13:45:07 INFO:	[hmmsearch]	735 of 2449 task(s) completed
2025-04-22 13:45:25 INFO:	[hmmsearch]	980 of 2449 task(s) completed
2025-04-22 13:45:43 INFO:	[hmmsearch]	1225 of 2449 task(s) completed
2025-04-22 13:46:02 INFO:	[hmmsearch]	1470 of 2449 task(s) completed
2025-04-22 13:46:21 INFO:	[hmmsearch]	1715 of 2449 task(s) completed
2025-04-22 13:46:38 INFO:	[hmmsearch]	1960 of 2449 task(s) completed
2025-04-22 13:46:57 INFO:	[hmmsearch]	2205 of 2449 task(s) completed
2025-04-22 13:47:14 INFO:	[hmmsearch]	2449 of 2449 task(s) completed
2025-04-22 13:47:15 INFO:	

    ---------------------------------------------------
    |Results from dataset mucorales_odb10              |
    ---------------------------------------------------
    |C:0.1%[S:0.1%,D:0.0%],F:0.0%,M:99.9%,n:2449       |
    |2    Complete BUSCOs (C)                          |
    |2    Complete and single-copy BUSCOs (S)          |
    |0    Complete and duplicated BUSCOs (D)           |
    |0    Fragmented BUSCOs (F)                        |
    |2447    Missing BUSCOs (M)                        |
    |2449    Total BUSCO groups searched               |
    ---------------------------------------------------
2025-04-22 13:47:15 INFO:	BUSCO analysis done with WARNING(s). Total running time: 200 seconds

***** Summary of warnings: *****
2025-04-22 13:43:55 WARNING:busco.BuscoConfig	Option contig_break was provided but is not used in the selected run mode, proteins
2025-04-22 13:43:55 WARNING:busco.BuscoConfig	Option evalue was provided but is not used in the selected run mode, proteins
2025-04-22 13:43:55 WARNING:busco.BuscoConfig	Option limit was provided but is not used in the selected run mode, proteins

2025-04-22 13:47:15 INFO:	Results written in /tmp/tmppyertp20/job_working_directory/000/7/working/busco_galaxy
2025-04-22 13:47:15 INFO:	For assistance with interpreting the results, please consult the userguide: https://busco.ezlab.org/busco_userguide.html

2025-04-22 13:47:15 INFO:	Visit this page https://gitlab.com/ezlab/busco#how-to-cite-busco to see how to cite BUSCO
total 92
drwxr-xr-x 5 1001 118  4096 Apr 22 13:43 busco_sequences
-rw-r--r-- 1 1001 118 47714 Apr 22 13:47 full_table.tsv
drwxr-xr-x 4 1001 118  4096 Apr 22 13:47 hmmer_output
-rw-r--r-- 1 1001 118 27808 Apr 22 13:47 missing_busco_list.tsv
-rw-r--r-- 1 1001 118  2231 Apr 22 13:47 short_summary.json
-rw-r--r-- 1 1001 118   742 Apr 22 13:47 short_summary.txt
2025-04-22 13:47:16 INFO:	****************** Start plot generation at 04/22/2025 13:47:16 ******************
2025-04-22 13:47:16 INFO:	Load data ...
2025-04-22 13:47:16 INFO:	Loaded BUSCO_summaries/short_summary.specific.mucorales_odb10.busco_galaxy.txt successfully
2025-04-22 13:47:16 INFO:	Generate the R code ...
2025-04-22 13:47:16 INFO:	Run the R code ...
2025-04-22 13:47:18 INFO:	
[1] "Plotting the figure ..."
[1] "Done"

2025-04-22 13:47:18 INFO:	Plot generation done. Total running time: 2.636357069015503 seconds
2025-04-22 13:47:18 INFO:	Results written in BUSCO_summaries/


              

              • 

            

            Traceback:
            

              

            • 

              

              • 

            

            Job Parameters:
            

              

            • 

              


              
Job parameter
Parameter value

              
              


              
__input_ext
"input"

              

              
__workflow_invocation_uuid__
"e3fb282c1f7e11f0be827c1e52674869"

              

              
adv
{"contig_break": "10", "evalue": "0.001", "limit": "3"}

              

              
busco_mode
{"__current_case__": 2, "mode": "prot"}

              

              
chromInfo
"/tmp/tmppyertp20/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"

              

              
dbkey
"?"

              

              
lineage
{"__current_case__": 1, "lineage_dataset": "mucorales_odb10", "lineage_mode": "select_lineage"}

              

              
lineage_conditional
{"__current_case__": 0, "cached_db": "v5", "selector": "cached"}

              

              
outputs
["short_summary", "image", "gff", "missing"]

              
              

              

              • 

            

            • 

          

          

          • 

        

        • 

      • 

        Step 8: OMArk:
        

          

        • 

          step_state: scheduled
          

          • 

        • 

          Jobs

            

          • 

            Job 1:
            

              

            • Job state is error
              • 

            

            Command Line:
            

              

            • 

              omamer search --db '/cvmfs/data.galaxyproject.org/byhand/omamer/LUCA-v2.0.0.h5' --query '/tmp/tmppyertp20/files/7/1/4/dataset_714c71cf-2bcc-4788-b5c7-031e464430c6.dat' --out 'output_omamer'  &&  omark -f 'output_omamer' -d '/cvmfs/data.galaxyproject.org/byhand/omamer/LUCA-v2.0.0.h5'      -o omark_galaxy
              

              • 

            

            Exit Code:
            

              

            • 

              1
              

              • 

            

            Standard Error:
            

              

            • 

              ================================================================================

   _____ _____ _____
  |     |     |  _  |_____ ___ ___
  |  |  | | | |     |     | -_|  _|
  |_____|_|_|_|__|__|_|_|_|___|_|   v2.1.0

  OMAmer is licensed under the GNU Lesser General Public License 3.0 (LGPL-3.0).
    
================================================================================

Loading required libraries  [DONE]

================================================================================

Running OMAmer on 2f4010d01343, using:
 - database: /cvmfs/data.galaxyproject.org/byhand/omamer/LUCA-v2.0.0.h5
 - query: /tmp/tmppyertp20/files/7/1/4/dataset_714c71cf-2bcc-4788-b5c7-031e464430c6.dat
 - version: 2.1.0

================================================================================
WARNING: Database version mismatch: DB 2.0.0 / OMAmer 2.1.0

Loading data required for OMAmer search from database...
 - taxonomy information (1.1s) [DONE]
 - family information (0.7s) [DONE]
 - sub-family information (16.7s) [DONE]
 - family hierarchy (0.3s) [DONE]
 - k-mer index (10:59.6) [DONE]
 - family probability estimates (0.4s) [DONE]
 - sub-family probability estimates (1.5s) [DONE]

Finished loading required data

================================================================================

�[?25l
Searching -  0 queries in 0s (0.0 queries/s) 
Searching -  0 queries in 5s (0.0 queries/s) 
Searching -  0 queries in 10s (0.0 queries/s) 
Searching -  0 queries in 15s (0.0 queries/s) 
Searching -  0 queries in 20s (0.0 queries/s) 
Searching -  0 queries in 25s (0.0 queries/s) 
Searching -  0 queries in 30s (0.0 queries/s) 
Searching -  0 queries in 35s (0.0 queries/s) 
Searching -  0 queries in 40s (0.0 queries/s) �[?25h�[J
Searching -  65 queries in 45.0s (1.44 queries/s) 

================================================================================

OMAmer search complete:
 - results written to: output_omamer
 - total 735.87 seconds
 - search phase only 1.46 queries/s


Note: family p-values are stated in negative log units.
================================================================================

Thank you for using OMAmer. If you use OMAmer in your research, please cite:

Victor Rossier, Alex Warwick Vesztrocy, Marc Robinson-Rechavi, Christophe Dessimoz, OMAmer: tree-driven and alignment-free protein assignment to subfamilies outperforms closest sequence approaches, Bioinformatics, Volume 37, Issue 18, September 2021, Pages 2866-2873, https://doi.org/10.1093/bioinformatics/btab219


OMAmer uses data from the OMA browser. Results can be interpreted further using:
 - OMA browser website (https://omabrowser.org)
 - PyOMADB, the Python OMA API client (https://github.com/DessimozLab/pyomadb)

================================================================================
WARNING: Database version mismatch: DB 2.0.0 / OMAmer 2.1.0
NCBI database not present yet (first time used?)
Downloading taxdump.tar.gz from NCBI FTP site (via HTTP)...
Done. Parsing...

Inserting synonyms:          0 
Inserting synonyms:       5000 
Inserting synonyms:      10000 
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Inserting synonyms:      410000 
Inserting taxid merges:      0 
Inserting taxid merges:   5000 
Inserting taxid merges:  10000 
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Inserting taxid merges:  20000 
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Inserting taxid merges:  35000 
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Inserting taxids:           0 
Inserting taxids:        5000 
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Inserting taxids:       100000 
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Inserting taxids:       150000 
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Inserting taxids:       165000 
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Inserting taxids:       2660000 WARNING: Database version mismatch: DB 2.0.0 / OMAmer 2.1.0
Traceback (most recent call last):
  File "/usr/local/bin/omark", line 52, in <module>
    omark.launcher(arg)
  File "/usr/local/lib/python3.9/site-packages/omark/omark.py", line 269, in launcher
    get_omamer_qscore(omamerfile, dbpath, outdir, taxid, original_FASTA_file = original_fasta, isoform_file=isoform_file, taxonomic_rank=taxonomic_rank)
  File "/usr/local/lib/python3.9/site-packages/omark/omark.py", line 116, in get_omamer_qscore
    closest_corr = spd.get_sampled_taxa(likely_clade, 5 , tax_tab, sp_tab, tax_buff, taxonomic_rank)
  File "/usr/local/lib/python3.9/site-packages/omark/species_determination.py", line 403, in get_sampled_taxa
    ranks = ncbi.get_rank(lineage_ncbi)
  File "/usr/local/lib/python3.9/site-packages/ete3/ncbi_taxonomy/ncbiquery.py", line 201, in get_rank
    result = self.db.execute(cmd)
sqlite3.OperationalError: no such column: "6656" - should this be a string literal in single-quotes?
/usr/local/lib/python3.9/site-packages/tables/file.py:113: UnclosedFileWarning: Closing remaining open file: /cvmfs/data.galaxyproject.org/byhand/omamer/LUCA-v2.0.0.h5
  warnings.warn(UnclosedFileWarning(msg))

WARNING:galaxy.model:Datatype class not found for extension 'sum'
WARNING:galaxy.model:Datatype class not found for extension 'sum'
WARNING:galaxy.model:Datatype class not found for extension 'sum'
WARNING:galaxy.model:Datatype class not found for extension 'sum'
WARNING:galaxy.model:Datatype class not found for extension 'sum'
WARNING:galaxy.model:Datatype class not found for extension 'sum'

              

              • 

            

            Standard Output:
            

              

            • 

              Loading node names...
2662596 names loaded.
414788 synonyms loaded.
Loading nodes...
2662596 nodes loaded.
Linking nodes...
Tree is loaded.
Updating database: /tmp/tmppyertp20/job_working_directory/000/8/home/.etetoolkit/taxa.sqlite ...

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Uploading to /tmp/tmppyertp20/job_working_directory/000/8/home/.etetoolkit/taxa.sqlite





              

              • 

            

            Traceback:
            

              

            • 

              

              • 

            

            Job Parameters:
            

              

            • 

              


              
Job parameter
Parameter value

              
              


              
__input_ext
"input"

              

              
__workflow_invocation_uuid__
"e3fb282c1f7e11f0be827c1e52674869"

              

              
chromInfo
"/tmp/tmppyertp20/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"

              

              
database
"LUCA-v2.0.0.h5"

              

              
dbkey
"?"

              

              
input_iso
None

              

              
omark_mode
false

              

              
outputs
"detail_sum"

              

              
r
None

              

              
t
None

              
              

              

              • 

            

            • 

          

          

          • 

        

        • 

      
 
      

      • 

    • 

      Other invocation details

        

      • 

        error_message
        

          

        • Failed to run workflow, at least one job is in [error] state.
          • 

        

        • 

      • 

        history_id
        

          

        • 8d27a077f7f3ce9e
          • 

        

        • 

      • 

        history_state
        

          

        • error
          • 

        

        • 

      • 

        invocation_id
        

          

        • 8d27a077f7f3ce9e
          • 

        

        • 

      • 

        invocation_state
        

          

        • scheduled
          • 

        

        • 

      • 

        workflow_id
        

          

        • 8d27a077f7f3ce9e
          • 

        

        • 

      

      

      • 

    
  
    

    • 




      		
    

  





        


            

            
            

              
            

        

      


      

            
  

    
  
    
    

  

  


    












      

  
      



  

  @rlibouba





  


    

      

  

    

        
    
    

  


      
          
  
      
            Copy link

  

      
    

  


  

      

  
    Contributor


      

  Author


  


  

    

  





      


        


  
    

      
          
Hello @mvdbeek , were you able to get the new data for OMArk?

      		
    

  





        


            

            
            

              
            

        

      


      

            
  

    
  
    
    

  

  


    












      

  
      



  

  @mvdbeek





  


    

      

  

    

        
    
    

  


      
          
  
      
            Copy link

  

      
    

  


  

      

  
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            mvdbeek
  

      

      

      commented


        Apr 29, 2025


      
    


  





      


        


  
    

      
          
I only see 2.0.0 at usegalaxy.eu. Are you sure the warning is an indication of the error ? Where would we get a newer database from ?

      		
    

  





        


            

            
            

              
            

        

      


      

            
  

    
  
    
    

  

  


    












      

  
        





      

  
      



  

  @github-actions

    
      GitHub Actions
    




  


    

      

  

    

        
    
    

  


      
          
  
      
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Test Results (powered by Planemo)


Test Summary



  

  

  

  

  

  








Test State
Count






Total
1




Passed
0




Error
1




Failure
0




Skipped
0






Errored Tests

    

  • 

    ❌ Galaxy-Workflow-annotation_helixer.ga_0
    

    Execution Problem:
    

      

    • 

      Failed to run workflow, at least one job is in [error] state.

      

      • 

    

    Workflow invocation details
    

      

    • 

      Invocation Messages
      

      • 

    • 

      Steps

        

      • 

        Step 1: Genome sequence:
        

          

        • step_state: scheduled
          • 

        

        • 

      • 

        Step 2: Helixer:
        

          

        • 

          step_state: scheduled
          

          • 

        • 

          Jobs

            

          • 

            Job 1:
            

              

            • Job state is ok
              • 

            

            Command Line:
            

              

            • 

              /usr/local/bin/fetch_helixer_models.py && Helixer.py --fasta-path '/tmp/tmp_egrp8er/files/6/c/2/dataset_6c2d21bd-224b-4fc3-9a72-222c53390e5e.dat' --species '' --gff-output-path '/tmp/tmp_egrp8er/job_working_directory/000/2/outputs/dataset_a818b70f-8789-47de-a9b6-14913e4af365.dat' --temporary-dir ./   --lineage 'land_plant' --subsequence-length '106920'  --overlap-offset '53460'  --overlap-core-length '80190'  --batch-size 8 --window-size 100 --min-coding-length 100 --edge-threshold 0.1 --peak-threshold 0.8
              

              • 

            

            Exit Code:
            

              

            • 

              0
              

              • 

            

            Standard Error:
            

              

            • 

              2025-05-12 08:55:24.319503: I tensorflow/core/platform/cpu_feature_guard.cc:182] This TensorFlow binary is optimized to use available CPU instructions in performance-critical operations.
To enable the following instructions: AVX2 FMA, in other operations, rebuild TensorFlow with the appropriate compiler flags.
2025-05-12 08:55:25.022044: W tensorflow/compiler/tf2tensorrt/utils/py_utils.cc:38] TF-TRT Warning: Could not find TensorRT
2025-05-12 08:55:30.497991: W tensorflow/tsl/framework/cpu_allocator_impl.cc:83] Allocation of 205286400 exceeds 10% of free system memory.
2025-05-12 08:55:30.711849: W tensorflow/tsl/framework/cpu_allocator_impl.cc:83] Allocation of 205286400 exceeds 10% of free system memory.
2025-05-12 08:55:33.012661: W tensorflow/tsl/framework/cpu_allocator_impl.cc:83] Allocation of 205286400 exceeds 10% of free system memory.
2025-05-12 08:55:35.117091: W tensorflow/tsl/framework/cpu_allocator_impl.cc:83] Allocation of 205286400 exceeds 10% of free system memory.
2025-05-12 08:55:37.406721: W tensorflow/tsl/framework/cpu_allocator_impl.cc:83] Allocation of 205286400 exceeds 10% of free system memory.
/usr/local/lib/python3.8/dist-packages/tensorflow_addons/utils/tfa_eol_msg.py:23: UserWarning: 

TensorFlow Addons (TFA) has ended development and introduction of new features.
TFA has entered a minimal maintenance and release mode until a planned end of life in May 2024.
Please modify downstream libraries to take dependencies from other repositories in our TensorFlow community (e.g. Keras, Keras-CV, and Keras-NLP). 

For more information see: https://github.com/tensorflow/addons/issues/2807 

  warnings.warn(
Ignoring the following unexpected models in /tmp/tmp_egrp8er/job_working_directory/000/2/home/.local/share/Helixer/models:[].
You can set --model-filepath in Helixer.py if you wish to use these.

              

              • 

            

            Standard Output:
            

              

            • 

              ==========
== CUDA ==
==========

CUDA Version 11.8.0

Container image Copyright (c) 2016-2023, NVIDIA CORPORATION & AFFILIATES. All rights reserved.

This container image and its contents are governed by the NVIDIA Deep Learning Container License.
By pulling and using the container, you accept the terms and conditions of this license:
https://developer.nvidia.com/ngc/nvidia-deep-learning-container-license

A copy of this license is made available in this container at /NGC-DL-CONTAINER-LICENSE for your convenience.

WARNING: The NVIDIA Driver was not detected.  GPU functionality will not be available.
   Use the NVIDIA Container Toolkit to start this container with GPU support; see
   https://docs.nvidia.com/datacenter/cloud-native/ .

retrived list of available models from https://raw.githubusercontent.com/weberlab-hhu/Helixer/main/resources/model_list.csv
saved model land_plant_v0.3_a_0080.h5 to /tmp/tmp_egrp8er/job_working_directory/000/2/home/.local/share/Helixer/models
saved model vertebrate_v0.3_m_0080.h5 to /tmp/tmp_egrp8er/job_working_directory/000/2/home/.local/share/Helixer/models
saved model fungi_v0.3_a_0100.h5 to /tmp/tmp_egrp8er/job_working_directory/000/2/home/.local/share/Helixer/models
saved model invertebrate_v0.3_m_0100.h5 to /tmp/tmp_egrp8er/job_working_directory/000/2/home/.local/share/Helixer/models
HelixerPost <genome.h5> <predictions.h5> <windowSize> <edgeThresh> <peakThresh> <minCodingLength> <gff>
No config file found

retrived list of available models from https://raw.githubusercontent.com/weberlab-hhu/Helixer/main/resources/model_list.csv
Helixer.py config: 
{'batch_size': 8,
 'compression': 'gzip',
 'config_path': 'config/helixer_config.yaml',
 'debug': False,
 'edge_threshold': 0.1,
 'fasta_path': '/tmp/tmp_egrp8er/files/6/c/2/dataset_6c2d21bd-224b-4fc3-9a72-222c53390e5e.dat',
 'gff_output_path': '/tmp/tmp_egrp8er/job_working_directory/000/2/outputs/dataset_a818b70f-8789-47de-a9b6-14913e4af365.dat',
 'lineage': 'land_plant',
 'min_coding_length': 100,
 'model_filepath': '/tmp/tmp_egrp8er/job_working_directory/000/2/home/.local/share/Helixer/models/land_plant/land_plant_v0.3_a_0080.h5',
 'no_multiprocess': False,
 'no_overlap': False,
 'overlap_core_length': 80190,
 'overlap_offset': 53460,
 'peak_threshold': 0.8,
 'species': '',
 'subsequence_length': 106920,
 'temporary_dir': './',
 'window_size': 100}

Testing whether helixer_post_bin is correctly installed
Helixer.py config loaded. Starting FASTA to H5 conversion.
storing temporary files under ./tmpx6g4lap7
1 expected num of chunks to write in 19994040 bases to hdf5
Numerification of 0-720580 of the sequence of sample took 0.25 secs
1 Numerified Fasta only Coordinate (seqid: sample, len: 720580) in 0.40 secs

1 expected num of chunks to write in 19994040 bases to hdf5
Numerification of 0-2030 of the sequence of sample2 took 0.00 secs
2 Numerified Fasta only Coordinate (seqid: sample2, len: 2030) in 0.02 secs

1 expected num of chunks to write in 19994040 bases to hdf5
Numerification of 0-2100 of the sequence of sample3 took 0.00 secs
3 Numerified Fasta only Coordinate (seqid: sample3, len: 2100) in 0.01 secs

1 expected num of chunks to write in 19994040 bases to hdf5
Numerification of 0-7560 of the sequence of sample4 took 0.00 secs
4 Numerified Fasta only Coordinate (seqid: sample4, len: 7560) in 0.02 secs

logged installed version in place of git commit for geenuff
logged installed version in place of git commit for helixer
FASTA to H5 conversion done. Starting neural network prediction with overlapping.
HelixerModel config: 
{'batch_size': 8,
 'calculate_uncertainty': False,
 'check_every_nth_batch': 1000000,
 'class_weights': 'None',
 'clip_norm': 3.0,
 'cnn_layers': 1,
 'compression': 'gzip',
 'core_length': 80190,
 'coverage_norm': None,
 'coverage_offset': 0.0,
 'coverage_weights': False,
 'cpus': 8,
 'data_dir': None,
 'debug': False,
 'dropout1': 0.0,
 'dropout2': 0.0,
 'epochs': 10000,
 'eval': False,
 'filter_depth': 32,
 'fine_tune': False,
 'float_precision': 'float32',
 'gpu_id': -1,
 'input_coverage': False,
 'kernel_size': 26,
 'large_eval_folder': '',
 'learning_rate': 0.0003,
 'load_model_path': '/tmp/tmp_egrp8er/job_working_directory/000/2/home/.local/share/Helixer/models/land_plant/land_plant_v0.3_a_0080.h5',
 'load_predictions': False,
 'loss': '',
 'lstm_layers': 1,
 'nni': False,
 'no_utrs': False,
 'optimizer': 'adamw',
 'overlap': True,
 'overlap_offset': 53460,
 'patience': 3,
 'pool_size': 9,
 'post_coverage_hidden_layer': False,
 'predict_phase': False,
 'prediction_output_path': './tmpx6g4lap7/tmp_predictions_.h5',
 'pretrained_model_path': None,
 'resume_training': False,
 'save_every_check': False,
 'save_model_path': './best_model.h5',
 'stretch_transition_weights': 0,
 'test_data': './tmpx6g4lap7/tmp_species_.h5',
 'transition_weights': 'None',
 'units': 32,
 'val_test_batch_size': 8,
 'verbose': True,
 'weight_decay': 3.5e-05,
 'workers': 1}
No err_samples dataset found, correct samples will be set to 0
No fully_intergenic_samples dataset found, fully intergenic samples will be set to 0

Data config: 
[{'geenuff_commit': 'commit not found, version: 0.3.2', 'helixer_commit': 'commit not found, version: 0.3.3', 'input_path': '/tmp/tmp_egrp8er/files/6/c/2/dataset_6c2d21bd-224b-4fc3-9a72-222c53390e5e.dat', 'timestamp': '2025-05-12 08:55:27.715162'}]

Test data shape: (20, 106920)

Intergenic test seqs: 0.00%
Fully correct test seqs: 0.00%

Number of devices: 1
Current Helixer version: 0.3.3
Md5sum of the loaded model: f0e00efcbea83c66b69258d11119a691  /tmp/tmp_egrp8er/job_working_directory/000/2/home/.local/share/Helixer/models/land_plant/land_plant_v0.3_a_0080.h5

Model: "model"
__________________________________________________________________________________________________
 Layer (type)                Output Shape                 Param #   Connected to                  
==================================================================================================
 main_input (InputLayer)     [(None, None, 4)]            0         []                            
                                                                                                  
 conv1d (Conv1D)             (None, None, 96)             4704      ['main_input[0][0]']          
                                                                                                  
 batch_normalization (Batch  (None, None, 96)             384       ['conv1d[0][0]']              
 Normalization)                                                                                   
                                                                                                  
 conv1d_1 (Conv1D)           (None, None, 96)             110688    ['batch_normalization[0][0]'] 
                                                                                                  
 batch_normalization_1 (Bat  (None, None, 96)             384       ['conv1d_1[0][0]']            
 chNormalization)                                                                                 
                                                                                                  
 conv1d_2 (Conv1D)           (None, None, 96)             110688    ['batch_normalization_1[0][0]'
                                                                    ]                             
                                                                                                  
 batch_normalization_2 (Bat  (None, None, 96)             384       ['conv1d_2[0][0]']            
 chNormalization)                                                                                 
                                                                                                  
 conv1d_3 (Conv1D)           (None, None, 96)             110688    ['batch_normalization_2[0][0]'
                                                                    ]                             
                                                                                                  
 reshape (Reshape)           (None, None, 864)            0         ['conv1d_3[0][0]']            
                                                                                                  
 bidirectional (Bidirection  (None, None, 256)            1016832   ['reshape[0][0]']             
 al)                                                                                              
                                                                                                  
 bidirectional_1 (Bidirecti  (None, None, 256)            394240    ['bidirectional[0][0]']       
 onal)                                                                                            
                                                                                                  
 bidirectional_2 (Bidirecti  (None, None, 256)            394240    ['bidirectional_1[0][0]']     
 onal)                                                                                            
                                                                                                  
 dense (Dense)               (None, None, 72)             18504     ['bidirectional_2[0][0]']     
                                                                                                  
 tf.split (TFOpLambda)       [(None, None, 36),           0         ['dense[0][0]']               
                              (None, None, 36)]                                                   
                                                                                                  
 reshape_1 (Reshape)         (None, None, 9, 4)           0         ['tf.split[0][0]']            
                                                                                                  
 reshape_2 (Reshape)         (None, None, 9, 4)           0         ['tf.split[0][1]']            
                                                                                                  
 genic (Activation)          (None, None, 9, 4)           0         ['reshape_1[0][0]']           
                                                                                                  
 phase (Activation)          (None, None, 9, 4)           0         ['reshape_2[0][0]']           
                                                                                                  
==================================================================================================
Total params: 2161736 (8.25 MB)
Trainable params: 2161160 (8.24 MB)
Non-trainable params: 576 (2.25 KB)
__________________________________________________________________________________________________
HMM Config
  Splicing Flags: U:true US:true S:true SC:true C:true CS:true S:true SU:true U:true
  Splicing - Weights: Donor 1, Acceptor 1
  Splicing - Fixed Penalties: U2-GT-AG 0, U2-GT-AC 0 U12-GT-AG 0 U12-AT-AC 0
  Coding - Weights: Start 1000, Stop 1000
  Phase Mode: Implementation 1, Dilute to Total, Retention: 0.2

Sequences for Species  - 0
  BP_Extractor for Sequence sample - ID 0
Forward for Sequence sample - ID 0
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	      613530	         131	         479	         418		      Non Coding	      689510	        1069	        1104	        1091	
             UTR	         238	        5141	          87	         120		         Phase 0	         230	        9046	           2	           6	
          Coding	        1243	          82	       29647	         264		         Phase 1	         226	           8	        9014	           2	
          Intron	        1459	         120	         162	       67459		         Phase 2	         239	           2	           5	        9026	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     0.99523	     0.99833	     0.99678	            		      Non Coding	     0.99899	     0.99529	     0.99714	            	
             UTR	     0.93917	     0.92034	     0.92966	            		         Phase 0	     0.89343	     0.97436	     0.93214	            	
          Coding	     0.97603	     0.94913	     0.96239	            		         Phase 1	     0.89027	     0.97449	     0.93048	            	
          Intron	     0.98825	     0.97484	     0.98150	            		         Phase 2	     0.89146	     0.97347	     0.93066	            	

        Subgenic	     0.98449	     0.96684	     0.97559	            		          Coding	     0.89172	     0.97411	     0.93109	            	
           Genic	     0.98211	     0.96439	     0.97317	


Reverse for Sequence sample - ID 0
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	      555814	         209	         108	         776		      Non Coding	      659468	         985	         971	         987	
             UTR	         454	        9649	         137	         214		         Phase 0	         670	       18679	           9	          31	
          Coding	        2123	          49	       58497	         691		         Phase 1	         689	          33	       18702	          12	
          Intron	        8256	         265	         391	       82947		         Phase 2	         620	          14	          29	       18681	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     0.98088	     0.99804	     0.98939	            		      Non Coding	     0.99701	     0.99556	     0.99628	            	
             UTR	     0.94858	     0.92300	     0.93562	            		         Phase 0	     0.94764	     0.96338	     0.95545	            	
          Coding	     0.98924	     0.95334	     0.97096	            		         Phase 1	     0.94881	     0.96224	     0.95548	            	
          Intron	     0.98014	     0.90298	     0.93998	            		         Phase 2	     0.94774	     0.96573	     0.95665	            	

        Subgenic	     0.98388	     0.92315	     0.95255	            		          Coding	     0.94807	     0.96378	     0.95586	            	
           Genic	     0.98155	     0.92314	     0.95145	


  BP_Extractor for Sequence sample2 - ID 1
Forward for Sequence sample2 - ID 1
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	        2026	           0	           0	           0		      Non Coding	        2029	           0	           0	           0	
             UTR	           0	           0	           0	           0		         Phase 0	           1	           0	           0	           0	
          Coding	           4	           0	           0	           0		         Phase 1	           0	           0	           0	           0	
          Intron	           0	           0	           0	           0		         Phase 2	           0	           0	           0	           0	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     0.99803	     1.00000	     0.99901	            		      Non Coding	     0.99951	     1.00000	     0.99975	            	
             UTR	         NaN	         NaN	         NaN	            		         Phase 0	         NaN	     0.00000	     0.00000	            	
          Coding	         NaN	     0.00000	     0.00000	            		         Phase 1	         NaN	         NaN	         NaN	            	
          Intron	         NaN	         NaN	         NaN	            		         Phase 2	         NaN	         NaN	         NaN	            	

        Subgenic	         NaN	     0.00000	     0.00000	            		          Coding	         NaN	     0.00000	     0.00000	            	
           Genic	         NaN	     0.00000	     0.00000	


Reverse for Sequence sample2 - ID 1
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	        2030	           0	           0	           0		      Non Coding	        2030	           0	           0	           0	
             UTR	           0	           0	           0	           0		         Phase 0	           0	           0	           0	           0	
          Coding	           0	           0	           0	           0		         Phase 1	           0	           0	           0	           0	
          Intron	           0	           0	           0	           0		         Phase 2	           0	           0	           0	           0	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     1.00000	     1.00000	     1.00000	            		      Non Coding	     1.00000	     1.00000	     1.00000	            	
             UTR	         NaN	         NaN	         NaN	            		         Phase 0	         NaN	         NaN	         NaN	            	
          Coding	         NaN	         NaN	         NaN	            		         Phase 1	         NaN	         NaN	         NaN	            	
          Intron	         NaN	         NaN	         NaN	            		         Phase 2	         NaN	         NaN	         NaN	            	

        Subgenic	         NaN	         NaN	         NaN	            		          Coding	         NaN	         NaN	         NaN	            	
           Genic	         NaN	         NaN	         NaN	


  BP_Extractor for Sequence sample3 - ID 2
Forward for Sequence sample3 - ID 2
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	        2098	           0	           0	           0		      Non Coding	        2099	           0	           0	           0	
             UTR	           0	           0	           0	           0		         Phase 0	           1	           0	           0	           0	
          Coding	           2	           0	           0	           0		         Phase 1	           0	           0	           0	           0	
          Intron	           0	           0	           0	           0		         Phase 2	           0	           0	           0	           0	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     0.99905	     1.00000	     0.99952	            		      Non Coding	     0.99952	     1.00000	     0.99976	            	
             UTR	         NaN	         NaN	         NaN	            		         Phase 0	         NaN	     0.00000	     0.00000	            	
          Coding	         NaN	     0.00000	     0.00000	            		         Phase 1	         NaN	         NaN	         NaN	            	
          Intron	         NaN	         NaN	         NaN	            		         Phase 2	         NaN	         NaN	         NaN	            	

        Subgenic	         NaN	     0.00000	     0.00000	            		          Coding	         NaN	     0.00000	     0.00000	            	
           Genic	         NaN	     0.00000	     0.00000	


Reverse for Sequence sample3 - ID 2
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	        2100	           0	           0	           0		      Non Coding	        2100	           0	           0	           0	
             UTR	           0	           0	           0	           0		         Phase 0	           0	           0	           0	           0	
          Coding	           0	           0	           0	           0		         Phase 1	           0	           0	           0	           0	
          Intron	           0	           0	           0	           0		         Phase 2	           0	           0	           0	           0	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     1.00000	     1.00000	     1.00000	            		      Non Coding	     1.00000	     1.00000	     1.00000	            	
             UTR	         NaN	         NaN	         NaN	            		         Phase 0	         NaN	         NaN	         NaN	            	
          Coding	         NaN	         NaN	         NaN	            		         Phase 1	         NaN	         NaN	         NaN	            	
          Intron	         NaN	         NaN	         NaN	            		         Phase 2	         NaN	         NaN	         NaN	            	

        Subgenic	         NaN	         NaN	         NaN	            		          Coding	         NaN	         NaN	         NaN	            	
           Genic	         NaN	         NaN	         NaN	


  BP_Extractor for Sequence sample4 - ID 3
Forward for Sequence sample4 - ID 3
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	        7535	           0	           0	           0		      Non Coding	        7553	           0	           0	           0	
             UTR	           3	           0	           0	           0		         Phase 0	           2	           0	           0	           0	
          Coding	           8	           0	           0	           0		         Phase 1	           2	           0	           0	           0	
          Intron	          14	           0	           0	           0		         Phase 2	           3	           0	           0	           0	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     0.99669	     1.00000	     0.99834	            		      Non Coding	     0.99907	     1.00000	     0.99954	            	
             UTR	         NaN	     0.00000	     0.00000	            		         Phase 0	         NaN	     0.00000	     0.00000	            	
          Coding	         NaN	     0.00000	     0.00000	            		         Phase 1	         NaN	     0.00000	     0.00000	            	
          Intron	         NaN	     0.00000	     0.00000	            		         Phase 2	         NaN	     0.00000	     0.00000	            	

        Subgenic	         NaN	     0.00000	     0.00000	            		          Coding	         NaN	     0.00000	     0.00000	            	
           Genic	         NaN	     0.00000	     0.00000	


Reverse for Sequence sample4 - ID 3
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	        4480	          19	           0	           0		      Non Coding	        5923	           2	           6	           4	
             UTR	          40	         453	           5	           0		         Phase 0	          17	         524	           0	           0	
          Coding	         321	           0	        1573	           1		         Phase 1	          17	           0	         520	           0	
          Intron	           0	           0	           0	         668		         Phase 2	          25	           0	           0	         522	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     0.92543	     0.99578	     0.95931	            		      Non Coding	     0.99014	     0.99798	     0.99404	            	
             UTR	     0.95975	     0.90964	     0.93402	            		         Phase 0	     0.99620	     0.96858	     0.98219	            	
          Coding	     0.99683	     0.83008	     0.90585	            		         Phase 1	     0.98859	     0.96834	     0.97836	            	
          Intron	     0.99851	     1.00000	     0.99925	            		         Phase 2	     0.99240	     0.95430	     0.97297	            	

        Subgenic	     0.99733	     0.87437	     0.93181	            		          Coding	     0.99240	     0.96369	     0.97783	            	
           Genic	     0.99081	     0.88010	     0.93218	


Forward for Species  - 0
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	      625189	         131	         479	         418		      Non Coding	      701191	        1069	        1104	        1091	
             UTR	         241	        5141	          87	         120		         Phase 0	         234	        9046	           2	           6	
          Coding	        1257	          82	       29647	         264		         Phase 1	         228	           8	        9014	           2	
          Intron	        1473	         120	         162	       67459		         Phase 2	         242	           2	           5	        9026	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     0.99527	     0.99836	     0.99681	            		      Non Coding	     0.99900	     0.99537	     0.99718	            	
             UTR	     0.93917	     0.91984	     0.92940	            		         Phase 0	     0.89343	     0.97394	     0.93195	            	
          Coding	     0.97603	     0.94870	     0.96217	            		         Phase 1	     0.89027	     0.97428	     0.93038	            	
          Intron	     0.98825	     0.97464	     0.98140	            		         Phase 2	     0.89146	     0.97315	     0.93052	            	

        Subgenic	     0.98449	     0.96658	     0.97545	            		          Coding	     0.89172	     0.97379	     0.93095	            	
           Genic	     0.98211	     0.96411	     0.97303	


Reverse for Species  - 0
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	      564424	         228	         108	         776		      Non Coding	      669521	         987	         977	         991	
             UTR	         494	       10102	         142	         214		         Phase 0	         687	       19203	           9	          31	
          Coding	        2444	          49	       60070	         692		         Phase 1	         706	          33	       19222	          12	
          Intron	        8256	         265	         391	       83615		         Phase 2	         645	          14	          29	       19203	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     0.98055	     0.99803	     0.98922	            		      Non Coding	     0.99697	     0.99561	     0.99629	            	
             UTR	     0.94908	     0.92239	     0.93554	            		         Phase 0	     0.94891	     0.96352	     0.95616	            	
          Coding	     0.98944	     0.94965	     0.96914	            		         Phase 1	     0.94984	     0.96240	     0.95608	            	
          Intron	     0.98028	     0.90368	     0.94042	            		         Phase 2	     0.94891	     0.96541	     0.95709	            	

        Subgenic	     0.98409	     0.92235	     0.95222	            		          Coding	     0.94922	     0.96378	     0.95644	            	
           Genic	     0.98171	     0.92235	     0.95110	


Total for Species  - 0
   ML v HP Class	  Intergenic	         UTR	      Coding	      Intron		   ML v HP Phase	  Non Coding	     Phase 0	     Phase 1	     Phase 2	
      Intergenic	     1189613	         359	         587	        1194		      Non Coding	     1370712	        2056	        2081	        2082	
             UTR	         735	       15243	         229	         334		         Phase 0	         921	       28249	          11	          37	
          Coding	        3701	         131	       89717	         956		         Phase 1	         934	          41	       28236	          14	
          Intron	        9729	         385	         553	      151074		         Phase 2	         887	          16	          34	       28229	

                	   Precision	      Recall	          F1	            		                	   Precision	      Recall	          F1	            	
      Intergenic	     0.98823	     0.99820	     0.99319	            		      Non Coding	     0.99800	     0.99548	     0.99674	            	
             UTR	     0.94571	     0.92153	     0.93346	            		         Phase 0	     0.93041	     0.96684	     0.94827	            	
          Coding	     0.98497	     0.94934	     0.96682	            		         Phase 1	     0.92998	     0.96616	     0.94772	            	
          Intron	     0.98382	     0.93405	     0.95829	            		         Phase 2	     0.92975	     0.96787	     0.94843	            	

        Subgenic	     0.98425	     0.93969	     0.96145	            		          Coding	     0.93004	     0.96696	     0.94814	            	
           Genic	     0.98187	     0.93859	     0.95974	


Total: 482642bp across 25 windows
None

starting to load test data into memory..
For h5 starting with species = b'':
x shape: (20, 106920, 4)
Data loading of 20 (total so far 20) samples of data/X into memory took 0.06 secs
Compressed data size of data/X is at least 0.0008 GB

setting self.n_seqs to 20, bc that is len of data/X
0 / 8
1 / 8
2 / 8
3 / 8
4 / 8
5 / 8
6 / 8
7 / 8
Neural network prediction done. Starting post processing.

Helixer successfully finished the annotation of /tmp/tmp_egrp8er/files/6/c/2/dataset_6c2d21bd-224b-4fc3-9a72-222c53390e5e.dat in 0.06 hours. GFF file written to /tmp/tmp_egrp8er/job_working_directory/000/2/outputs/dataset_a818b70f-8789-47de-a9b6-14913e4af365.dat.

              

              • 

            

            Traceback:
            

              

            • 

              

              • 

            

            Job Parameters:
            

              

            • 

              


              
Job parameter
Parameter value

              
              


              
__input_ext
"input"

              

              
__workflow_invocation_uuid__
"3d77199e2f0e11f0a4527c1e52252d76"

              

              
chromInfo
"/tmp/tmp_egrp8er/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"

              

              
dbkey
"?"

              

              
input_model
None

              

              
lineages
"land_plant"

              

              
option_overlap
{"__current_case__": 0, "overlap_core_length": null, "overlap_offset": null, "use_overlap": "true"}

              

              
post_processing
{"edge_threshold": "0.1", "min_coding_length": "100", "peak_threshold": "0.8", "window_size": "100"}

              

              
size
"8"

              

              
species
None

              

              
subsequence_length
None

              
              

              

              • 

            

            • 

          

          

          • 

        

        • 

      • 

        Step 3: Busco on genome:
        

          

        • 

          step_state: scheduled
          

          • 

        • 

          Jobs

            

          • 

            Job 1:
            

              

            • Job state is ok
              • 

            

            Command Line:
            

              

            • 

              if [ -z "$AUGUSTUS_CONFIG_PATH" ] ; then BUSCO_PATH=$(dirname $(which busco)) ; export AUGUSTUS_CONFIG_PATH=$(realpath ${BUSCO_PATH}/../config) ; fi && cp -r "$AUGUSTUS_CONFIG_PATH/" augustus_dir/ && export AUGUSTUS_CONFIG_PATH=`pwd`/augustus_dir/ &&    busco --in '/tmp/tmp_egrp8er/files/6/c/2/dataset_6c2d21bd-224b-4fc3-9a72-222c53390e5e.dat' --mode 'geno' --out busco_galaxy --cpu ${GALAXY_SLOTS:-4} --evalue 0.001 --limit 3 --contig_break 10  --offline --download_path /cvmfs/data.galaxyproject.org/byhand/busco/v5  --lineage_dataset 'mucorales_odb10'   --augustus  && mkdir BUSCO_summaries && ls -l busco_galaxy/run_*/ && cp busco_galaxy/short_summary.*.txt BUSCO_summaries/ && generate_plot.py -wd BUSCO_summaries -rt specific  && echo "##gff-version 3" > busco_output.gff && cat busco_galaxy/run_*/busco_sequences/*busco_sequences/*.gff >> busco_output.gff 2> /dev/null || true
              

              • 

            

            Exit Code:
            

              

            • 

              0
              

              • 

            

            Standard Error:
            

              

            • 

              2025-05-12 09:05:03 ERROR:	
Warning message:
The `size` argument of `element_line()` is deprecated as of ggplot2 3.4.0.
ℹ Please use the `linewidth` argument instead. 


              

              • 

            

            Standard Output:
            

              

            • 

              2025-05-12 08:53:14 INFO:	***** Start a BUSCO v5.8.0 analysis, current time: 05/12/2025 08:53:14 *****
2025-05-12 08:53:14 INFO:	Configuring BUSCO with local environment
2025-05-12 08:53:14 INFO:	Running genome mode
2025-05-12 08:53:18 INFO:	Input file is /tmp/tmp_egrp8er/files/6/c/2/dataset_6c2d21bd-224b-4fc3-9a72-222c53390e5e.dat
2025-05-12 08:53:18 INFO:	Running BUSCO using lineage dataset mucorales_odb10 (eukaryota, 2020-08-05)
2025-05-12 08:53:18 INFO:	Running 1 job(s) on bbtools, starting at 05/12/2025 08:53:18
2025-05-12 08:53:19 INFO:	[bbtools]	1 of 1 task(s) completed
2025-05-12 08:53:19 INFO:	Running 1 job(s) on makeblastdb, starting at 05/12/2025 08:53:19
2025-05-12 08:53:20 INFO:	Creating BLAST database with input file
2025-05-12 08:53:20 INFO:	[makeblastdb]	1 of 1 task(s) completed
2025-05-12 08:53:20 INFO:	Running a BLAST search for BUSCOs against created database
2025-05-12 08:53:20 INFO:	Running 1 job(s) on tblastn, starting at 05/12/2025 08:53:20
2025-05-12 08:53:31 INFO:	[tblastn]	1 of 1 task(s) completed
2025-05-12 08:53:31 INFO:	Running Augustus gene predictor on BLAST search results.
2025-05-12 08:53:31 INFO:	Running Augustus prediction using aspergillus_nidulans as species:
2025-05-12 08:53:31 INFO:	Running 76 job(s) on augustus, starting at 05/12/2025 08:53:31
2025-05-12 08:55:14 INFO:	[augustus]	8 of 76 task(s) completed
2025-05-12 08:56:25 INFO:	[augustus]	16 of 76 task(s) completed
2025-05-12 08:57:01 INFO:	[augustus]	23 of 76 task(s) completed
2025-05-12 08:57:22 INFO:	[augustus]	31 of 76 task(s) completed
2025-05-12 08:57:41 INFO:	[augustus]	38 of 76 task(s) completed
2025-05-12 08:58:00 INFO:	[augustus]	46 of 76 task(s) completed
2025-05-12 08:58:20 INFO:	[augustus]	54 of 76 task(s) completed
2025-05-12 08:58:30 INFO:	[augustus]	61 of 76 task(s) completed
2025-05-12 08:58:42 INFO:	[augustus]	69 of 76 task(s) completed
2025-05-12 08:58:56 INFO:	[augustus]	76 of 76 task(s) completed
2025-05-12 08:58:56 INFO:	Extracting predicted proteins...
2025-05-12 08:58:56 INFO:	***** Run HMMER on gene sequences *****
2025-05-12 08:58:57 INFO:	Running 75 job(s) on hmmsearch, starting at 05/12/2025 08:58:57
2025-05-12 08:58:59 INFO:	[hmmsearch]	8 of 75 task(s) completed
2025-05-12 08:59:00 INFO:	[hmmsearch]	15 of 75 task(s) completed
2025-05-12 08:59:02 INFO:	[hmmsearch]	23 of 75 task(s) completed
2025-05-12 08:59:04 INFO:	[hmmsearch]	30 of 75 task(s) completed
2025-05-12 08:59:06 INFO:	[hmmsearch]	38 of 75 task(s) completed
2025-05-12 08:59:07 INFO:	[hmmsearch]	45 of 75 task(s) completed
2025-05-12 08:59:09 INFO:	[hmmsearch]	53 of 75 task(s) completed
2025-05-12 08:59:10 INFO:	[hmmsearch]	60 of 75 task(s) completed
2025-05-12 08:59:12 INFO:	[hmmsearch]	68 of 75 task(s) completed
2025-05-12 08:59:14 INFO:	[hmmsearch]	75 of 75 task(s) completed
2025-05-12 08:59:14 INFO:	0 exons in total
2025-05-12 08:59:14 INFO:	Starting second step of analysis. The gene predictor Augustus is retrained using the results from the initial run to yield more accurate results.
2025-05-12 08:59:14 INFO:	Extracting missing and fragmented buscos from the file ancestral_variants...
2025-05-12 08:59:27 INFO:	Running a BLAST search for BUSCOs against created database
2025-05-12 08:59:27 INFO:	Running 1 job(s) on tblastn, starting at 05/12/2025 08:59:27
2025-05-12 09:01:10 INFO:	[tblastn]	1 of 1 task(s) completed
2025-05-12 09:01:11 INFO:	Converting predicted genes to short genbank files
2025-05-12 09:01:11 INFO:	Running 1 job(s) on gff2gbSmallDNA.pl, starting at 05/12/2025 09:01:11
2025-05-12 09:01:11 INFO:	[gff2gbSmallDNA.pl]	1 of 1 task(s) completed
2025-05-12 09:01:11 INFO:	All files converted to short genbank files, now training Augustus using Single-Copy Complete BUSCOs
2025-05-12 09:01:11 INFO:	Running 1 job(s) on new_species.pl, starting at 05/12/2025 09:01:11
2025-05-12 09:01:11 INFO:	[new_species.pl]	1 of 1 task(s) completed
2025-05-12 09:01:11 INFO:	Running 1 job(s) on etraining, starting at 05/12/2025 09:01:11
2025-05-12 09:01:12 INFO:	[etraining]	1 of 1 task(s) completed
2025-05-12 09:01:12 INFO:	Re-running Augustus with the new metaparameters, number of target BUSCOs: 2448
2025-05-12 09:01:12 INFO:	Running Augustus gene predictor on BLAST search results.
2025-05-12 09:01:12 INFO:	Running Augustus prediction using BUSCO_busco_galaxy as species:
2025-05-12 09:01:12 INFO:	Running 100 job(s) on augustus, starting at 05/12/2025 09:01:12
2025-05-12 09:02:16 INFO:	[augustus]	10 of 100 task(s) completed
2025-05-12 09:03:14 INFO:	[augustus]	20 of 100 task(s) completed
2025-05-12 09:03:42 INFO:	[augustus]	30 of 100 task(s) completed
2025-05-12 09:03:54 INFO:	[augustus]	40 of 100 task(s) completed
2025-05-12 09:04:07 INFO:	[augustus]	50 of 100 task(s) completed
2025-05-12 09:04:19 INFO:	[augustus]	60 of 100 task(s) completed
2025-05-12 09:04:30 INFO:	[augustus]	70 of 100 task(s) completed
2025-05-12 09:04:39 INFO:	[augustus]	80 of 100 task(s) completed
2025-05-12 09:04:50 INFO:	[augustus]	90 of 100 task(s) completed
2025-05-12 09:05:00 INFO:	[augustus]	100 of 100 task(s) completed
2025-05-12 09:05:00 INFO:	Extracting predicted proteins...
2025-05-12 09:05:00 INFO:	***** Run HMMER on gene sequences *****
2025-05-12 09:05:00 WARNING:	No jobs to run on hmmsearch
2025-05-12 09:05:00 INFO:	0 exons in total
2025-05-12 09:05:00 INFO:	Results:	C:0.0%[S:0.0%,D:0.0%],F:0.0%,M:100.0%,n:2449	   

2025-05-12 09:05:00 INFO:	

    ---------------------------------------------------
    |Results from dataset mucorales_odb10              |
    ---------------------------------------------------
    |C:0.0%[S:0.0%,D:0.0%],F:0.0%,M:100.0%,n:2449      |
    |1    Complete BUSCOs (C)                          |
    |1    Complete and single-copy BUSCOs (S)          |
    |0    Complete and duplicated BUSCOs (D)           |
    |0    Fragmented BUSCOs (F)                        |
    |2448    Missing BUSCOs (M)                        |
    |2449    Total BUSCO groups searched               |
    ---------------------------------------------------
2025-05-12 09:05:00 INFO:	BUSCO analysis done with WARNING(s). Total running time: 702 seconds

***** Summary of warnings: *****
2025-05-12 09:05:00 WARNING:busco.busco_tools.Toolset	No jobs to run on hmmsearch

2025-05-12 09:05:00 INFO:	Results written in /tmp/tmp_egrp8er/job_working_directory/000/3/working/busco_galaxy
2025-05-12 09:05:00 INFO:	For assistance with interpreting the results, please consult the userguide: https://busco.ezlab.org/busco_userguide.html

2025-05-12 09:05:00 INFO:	Visit this page https://gitlab.com/ezlab/busco#how-to-cite-busco to see how to cite BUSCO
total 100
drwxr-xr-x 8 1001 118  4096 May 12 09:05 augustus_output
drwxr-xr-x 3 1001 118  4096 May 12 09:01 blast_output
drwxr-xr-x 5 1001 118  4096 May 12 08:53 busco_sequences
-rw-r--r-- 1 1001 118 47630 May 12 09:05 full_table.tsv
drwxr-xr-x 4 1001 118  4096 May 12 08:59 hmmer_output
-rw-r--r-- 1 1001 118 27820 May 12 09:05 missing_busco_list.tsv
-rw-r--r-- 1 1001 118  3176 May 12 09:05 short_summary.json
-rw-r--r-- 1 1001 118  1067 May 12 09:05 short_summary.txt
2025-05-12 09:05:01 INFO:	****************** Start plot generation at 05/12/2025 09:05:01 ******************
2025-05-12 09:05:01 INFO:	Load data ...
2025-05-12 09:05:01 INFO:	Loaded BUSCO_summaries/short_summary.specific.mucorales_odb10.busco_galaxy.txt successfully
2025-05-12 09:05:01 INFO:	Generate the R code ...
2025-05-12 09:05:01 INFO:	Run the R code ...
2025-05-12 09:05:03 INFO:	
[1] "Plotting the figure ..."
[1] "Done"

2025-05-12 09:05:03 INFO:	Plot generation done. Total running time: 2.0223093032836914 seconds
2025-05-12 09:05:03 INFO:	Results written in BUSCO_summaries/


              

              • 

            

            Traceback:
            

              

            • 

              

              • 

            

            Job Parameters:
            

              

            • 

              


              
Job parameter
Parameter value

              
              


              
__input_ext
"input"

              

              
__workflow_invocation_uuid__
"3d77199e2f0e11f0a4527c1e52252d76"

              

              
adv
{"contig_break": "10", "evalue": "0.001", "limit": "3"}

              

              
busco_mode
{"__current_case__": 0, "mode": "geno", "use_augustus": {"__current_case__": 2, "aug_prediction": {"__current_case__": 0, "augustus_mode": "no"}, "long": false, "use_augustus_selector": "augustus"}}

              

              
chromInfo
"/tmp/tmp_egrp8er/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"

              

              
dbkey
"?"

              

              
lineage
{"__current_case__": 1, "lineage_dataset": "mucorales_odb10", "lineage_mode": "select_lineage"}

              

              
lineage_conditional
{"__current_case__": 0, "cached_db": "v5", "selector": "cached"}

              

              
outputs
["short_summary", "image", "gff", "missing"]

              
              

              

              • 

            

            • 

          

          

          • 

        

        • 

      • 

        Step 4: Gffread:
        

          

        • 

          step_state: scheduled
          

          • 

        • 

          Jobs

            

          • 

            Job 1:
            

              

            • Job state is ok
              • 

            

            Command Line:
            

              

            • 

              ln -s '/tmp/tmp_egrp8er/files/6/c/2/dataset_6c2d21bd-224b-4fc3-9a72-222c53390e5e.dat' genomeref.fa &&  gffread '/tmp/tmp_egrp8er/files/a/8/1/dataset_a818b70f-8789-47de-a9b6-14913e4af365.dat' -g genomeref.fa      -y pep.fa
              

              • 

            

            Exit Code:
            

              

            • 

              0
              

              • 

            

            Standard Error:
            

              

            • 

              FASTA index file genomeref.fa.fai created.

              

              • 

            

            Traceback:
            

              

            • 

              

              • 

            

            Job Parameters:
            

              

            • 

              


              
Job parameter
Parameter value

              
              


              
__input_ext
"input"

              

              
__workflow_invocation_uuid__
"3d77199e2f0e11f0a4527c1e52252d76"

              

              
chr_replace
None

              

              
chromInfo
"/tmp/tmp_egrp8er/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"

              

              
dbkey
"?"

              

              
decode_url
false

              

              
expose
false

              

              
filtering
None

              

              
full_gff_attribute_preservation
false

              

              
gffs
{"__current_case__": 0, "gff_fmt": "none"}

              

              
maxintron
None

              

              
merging
{"__current_case__": 0, "merge_sel": "none"}

              

              
reference_genome
{"__current_case__": 2, "fa_outputs": ["-y pep.fa"], "genome_fasta": {"values": [{"id": 1, "src": "hda"}]}, "ref_filtering": null, "source": "history"}

              

              
region
{"__current_case__": 0, "region_filter": "none"}

              
              

              

              • 

            

            • 

          

          

          • 

        

        • 

      • 

        Step 5: Genome annotation statistics:
        

          

        • 

          step_state: scheduled
          

          • 

        • 

          Jobs

            

          • 

            Job 1:
            

              

            • Job state is ok
              • 

            

            Command Line:
            

              

            • 

              ln -s '/tmp/tmp_egrp8er/files/a/8/1/dataset_a818b70f-8789-47de-a9b6-14913e4af365.dat' 'input.gff'  &&  python -m jcvi.annotation.stats genestats 'input.gff' > '/tmp/tmp_egrp8er/job_working_directory/000/5/outputs/dataset_7c524762-68ce-4048-b534-a35e41de6ebc.dat'  &&  python -m jcvi.annotation.stats summary 'input.gff' '/tmp/tmp_egrp8er/files/6/c/2/dataset_6c2d21bd-224b-4fc3-9a72-222c53390e5e.dat' 2>&1 | tail -n +3 >> '/tmp/tmp_egrp8er/job_working_directory/000/5/outputs/dataset_7c524762-68ce-4048-b534-a35e41de6ebc.dat'  &&  python -m jcvi.annotation.stats stats 'input.gff' 2>&1 | grep Mean >> '/tmp/tmp_egrp8er/job_working_directory/000/5/outputs/dataset_7c524762-68ce-4048-b534-a35e41de6ebc.dat'  &&  python -m jcvi.annotation.stats histogram 'input.gff'  &&  pdfunite *.input.pdf '/tmp/tmp_egrp8er/job_working_directory/000/5/outputs/dataset_fcc89c2e-deb0-439f-9064-1e70e24005dd.dat'
              

              • 

            

            Exit Code:
            

              

            • 

              0
              

              • 

            

            Standard Error:
            

              

            • 

              �[0;33m09:00:18 [gff]�[0m�[0;35m Indexing `input.gff`�[0m
�[0;33m09:00:18 [base]�[0m�[0;35m Load file `transcript.sizes`�[0m
�[0;33m09:00:18 [base]�[0m�[0;35m Imported 65 records from `transcript.sizes`.�[0m
�[0;33m09:00:18 [base]�[0m�[0;35m Load file `transcript.sizes`�[0m
�[0;33m09:00:18 [base]�[0m�[0;35m Imported 65 records from `transcript.sizes`.�[0m
�[0;33m09:00:18 [stats]�[0m�[0;35m A total of 65 transcripts populated.�[0m
�[0;33m09:00:19 [__init__]�[0m�[0;35m $HOME=/home/runner�[0m
�[0;33m09:00:19 [__init__]�[0m�[0;35m matplotlib data path /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data�[0m
�[0;33m09:00:19 [__init__]�[0m�[0;35m loaded rc file /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/matplotlibrc�[0m
�[0;33m09:00:19 [__init__]�[0m�[0;35m matplotlib version 2.2.2�[0m
�[0;33m09:00:19 [__init__]�[0m�[0;35m interactive is False�[0m
�[0;33m09:00:19 [__init__]�[0m�[0;35m platform is linux2�[0m
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�[0;33m09:00:19 [font_manager]�[0m�[0;35m createFontDict: /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/pdfcorefonts/Times-Roman.afm�[0m
�[0;33m09:00:19 [font_manager]�[0m�[0;35m createFontDict: /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/afm/pbkdi8a.afm�[0m
�[0;33m09:00:19 [font_manager]�[0m�[0;35m createFontDict: /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/afm/pagdo8a.afm�[0m
�[0;33m09:00:19 [font_manager]�[0m�[0;35m createFontDict: /usr/local/lib/python2.7/site-packages/matplotlib/mpl-data/fonts/afm/pagk8a.afm�[0m
�[0;33m09:00:19 [font_manager]�[0m�[0;35m generated new fontManager�[0m
�[0;33m09:00:19 [__init__]�[0m�[0;35m backend agg version v2.2�[0m
�[0;33m09:00:19 [stats]�[0m�[0;35m Parsing files in `Exon_Length`..�[0m
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�[0;33m09:00:19 [base]�[0m�[0;35m Rscript /tmp/tmp_egrp8er/tmp/tmp9PPFwC�[0m
Warning message:
Removed 21 rows containing non-finite values (stat_bin). 
Saving 7 x 7 in image
Warning message:
Removed 21 rows containing non-finite values (stat_bin). 
�[0;33m09:00:22 [stats]�[0m�[0;35m Parsing files in `Intron_Length`..�[0m
Intron_Length/input.txt: Min=50 Max=14088 N=205 Mean=547.107317073 SD=1467.30391824 Median=152.0 Sum=112157
�[0;33m09:00:22 [base]�[0m�[0;35m Rscript /tmp/tmp_egrp8er/tmp/tmp2uYT2w�[0m
Warning message:
Removed 23 rows containing non-finite values (stat_bin). 
Saving 7 x 7 in image
Warning message:
Removed 23 rows containing non-finite values (stat_bin). 
�[0;33m09:00:25 [stats]�[0m�[0;35m Parsing files in `Gene_Length`..�[0m
Gene_Length/input.txt: Min=111 Max=7371 N=65 Mean=1401.32307692 SD=1130.94596358 Median=1122.0 Sum=91086
�[0;33m09:00:25 [base]�[0m�[0;35m Rscript /tmp/tmp_egrp8er/tmp/tmpvkdK1F�[0m
Warning message:
Removed 2 rows containing non-finite values (stat_bin). 
Saving 7 x 7 in image
Warning message:
Removed 2 rows containing non-finite values (stat_bin). 
�[0;33m09:00:28 [stats]�[0m�[0;35m Parsing files in `Exon_Count`..�[0m
Exon_Count/input.txt: Min=1 Max=15 N=65 Mean=4.15384615385 SD=3.39334538463 Median=3.0 Sum=270
�[0;33m09:00:28 [base]�[0m�[0;35m Rscript /tmp/tmp_egrp8er/tmp/tmpoK9tf3�[0m
Saving 7 x 7 in image

              

              • 

            

            Traceback:
            

              

            • 

              

              • 

            

            Job Parameters:
            

              

            • 

              


              
Job parameter
Parameter value

              
              


              
__input_ext
"input"

              

              
__workflow_invocation_uuid__
"3d77199e2f0e11f0a4527c1e52252d76"

              

              
chromInfo
"/tmp/tmp_egrp8er/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"

              

              
dbkey
"?"

              

              
ref_genome
{"__current_case__": 1, "genome": {"values": [{"id": 1, "src": "hda"}]}, "genome_type_select": "history"}

              
              

              

              • 

            

            • 

          

          

          • 

        

        • 

      • 

        Step 6: JBrowse:
        

          

        • 

          step_state: scheduled
          

          • 

        • 

          Jobs

            

          • 

            Job 1:
            

              

            • Job state is ok
              • 

            

            Command Line:
            

              

            • 

              mkdir -p /tmp/tmp_egrp8er/job_working_directory/000/6/outputs/dataset_0c390b9a-924b-437b-b7ec-fd2c69d29bff_files &&  cp /tmp/tmp_egrp8er/job_working_directory/000/6/configs/tmp1i3hp7hu /tmp/tmp_egrp8er/job_working_directory/000/6/outputs/dataset_0c390b9a-924b-437b-b7ec-fd2c69d29bff_files/galaxy.xml &&  export JBROWSE_SOURCE_DIR=$(dirname $(which prepare-refseqs.pl))/../opt/jbrowse  &&  python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/a6e57ff585c0/jbrowse/jbrowse.py'  --jbrowse ${JBROWSE_SOURCE_DIR} --standalone 'minimal'  --outdir /tmp/tmp_egrp8er/job_working_directory/000/6/outputs/dataset_0c390b9a-924b-437b-b7ec-fd2c69d29bff_files /tmp/tmp_egrp8er/job_working_directory/000/6/configs/tmp1i3hp7hu &&  cp /tmp/tmp_egrp8er/job_working_directory/000/6/outputs/dataset_0c390b9a-924b-437b-b7ec-fd2c69d29bff_files/index.html /tmp/tmp_egrp8er/job_working_directory/000/6/outputs/dataset_0c390b9a-924b-437b-b7ec-fd2c69d29bff.dat;
              

              • 

            

            Exit Code:
            

              

            • 

              0
              

              • 

            

            Standard Error:
            

              

            • 

              INFO:jbrowse:Processing Annotation / Helixer on data 1
WARNING: No feature names found for indexing, only reference sequence names will be indexed.

              

              • 

            

            Traceback:
            

              

            • 

              

              • 

            

            Job Parameters:
            

              

            • 

              


              
Job parameter
Parameter value

              
              


              
__input_ext
"fasta"

              

              
__workflow_invocation_uuid__
"3d77199e2f0e11f0a4527c1e52252d76"

              

              
action
{"__current_case__": 0, "action_select": "create"}

              

              
chromInfo
"/tmp/tmp_egrp8er/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"

              

              
dbkey
"?"

              

              
gencode
"1"

              

              
jbgen
{"aboutDescription": "", "defaultLocation": "", "hideGenomeOptions": false, "shareLink": true, "show_menu": true, "show_nav": true, "show_overview": true, "show_tracklist": true, "trackPadding": "20"}

              

              
plugins
{"BlastView": true, "ComboTrackSelector": false, "GCContent": false}

              

              
reference_genome
{"__current_case__": 1, "genome": {"values": [{"id": 1, "src": "hda"}]}, "genome_type_select": "history"}

              

              
standalone
"minimal"

              

              
track_groups
[{"__index__": 0, "category": "Annotation", "data_tracks": [{"__index__": 0, "data_format": {"__current_case__": 2, "annotation": {"values": [{"id": 2, "src": "hda"}]}, "data_format_select": "gene_calls", "index": false, "jb_custom_config": {"option": []}, "jbcolor_scale": {"color_score": {"__current_case__": 0, "color": {"__current_case__": 0, "color_select": "automatic"}, "color_score_select": "none"}}, "jbmenu": {"track_menu": []}, "jbstyle": {"max_height": "600", "style_classname": "feature", "style_description": "note,description", "style_height": "10px", "style_label": "product,name,id"}, "match_part": {"__current_case__": 1, "match_part_select": false}, "override_apollo_drag": "False", "override_apollo_plugins": "False", "track_config": {"__current_case__": 3, "html_options": {"topLevelFeatures": null}, "track_class": "NeatHTMLFeatures/View/Track/NeatFeatures"}, "track_visibility": "default_off"}}]}]

              

              
uglyTestingHack
""

              
              

              

              • 

            

            • 

          

          

          • 

        

        • 

      • 

        Step 7: Busco on protein:
        

          

        • 

          step_state: scheduled
          

          • 

        • 

          Jobs

            

          • 

            Job 1:
            

              

            • Job state is ok
              • 

            

            Command Line:
            

              

            • 

              busco --in '/tmp/tmp_egrp8er/files/6/8/4/dataset_684bde41-4dbb-4a6d-9f11-8ca3b26e9c8f.dat' --mode 'prot' --out busco_galaxy --cpu ${GALAXY_SLOTS:-4} --evalue 0.001 --limit 3 --contig_break 10  --offline --download_path /cvmfs/data.galaxyproject.org/byhand/busco/v5  --lineage_dataset 'mucorales_odb10'   && mkdir BUSCO_summaries && ls -l busco_galaxy/run_*/ && cp busco_galaxy/short_summary.*.txt BUSCO_summaries/ && generate_plot.py -wd BUSCO_summaries -rt specific  && echo "##gff-version 3" > busco_output.gff && cat busco_galaxy/run_*/busco_sequences/*busco_sequences/*.gff >> busco_output.gff 2> /dev/null || true
              

              • 

            

            Exit Code:
            

              

            • 

              0
              

              • 

            

            Standard Error:
            

              

            • 

              2025-05-12 09:07:30 ERROR:	
Warning message:
The `size` argument of `element_line()` is deprecated as of ggplot2 3.4.0.
ℹ Please use the `linewidth` argument instead. 


              

              • 

            

            Standard Output:
            

              

            • 

              2025-05-12 08:59:42 INFO:	***** Start a BUSCO v5.8.0 analysis, current time: 05/12/2025 08:59:42 *****
2025-05-12 08:59:42 INFO:	Configuring BUSCO with local environment
2025-05-12 08:59:42 INFO:	Running proteins mode
2025-05-12 08:59:42 INFO:	Input file is /tmp/tmp_egrp8er/files/6/8/4/dataset_684bde41-4dbb-4a6d-9f11-8ca3b26e9c8f.dat
2025-05-12 08:59:42 WARNING:	Option contig_break was provided but is not used in the selected run mode, proteins
2025-05-12 08:59:42 WARNING:	Option evalue was provided but is not used in the selected run mode, proteins
2025-05-12 08:59:42 WARNING:	Option limit was provided but is not used in the selected run mode, proteins
2025-05-12 08:59:42 INFO:	Running BUSCO using lineage dataset mucorales_odb10 (eukaryota, 2020-08-05)
2025-05-12 08:59:42 INFO:	***** Run HMMER on gene sequences *****
2025-05-12 08:59:42 INFO:	Running 2449 job(s) on hmmsearch, starting at 05/12/2025 08:59:42
2025-05-12 09:00:32 INFO:	[hmmsearch]	245 of 2449 task(s) completed
2025-05-12 09:01:19 INFO:	[hmmsearch]	490 of 2449 task(s) completed
2025-05-12 09:02:05 INFO:	[hmmsearch]	735 of 2449 task(s) completed
2025-05-12 09:02:49 INFO:	[hmmsearch]	980 of 2449 task(s) completed
2025-05-12 09:03:35 INFO:	[hmmsearch]	1225 of 2449 task(s) completed
2025-05-12 09:04:20 INFO:	[hmmsearch]	1470 of 2449 task(s) completed
2025-05-12 09:05:08 INFO:	[hmmsearch]	1715 of 2449 task(s) completed
2025-05-12 09:05:54 INFO:	[hmmsearch]	1960 of 2449 task(s) completed
2025-05-12 09:06:40 INFO:	[hmmsearch]	2205 of 2449 task(s) completed
2025-05-12 09:07:26 INFO:	[hmmsearch]	2449 of 2449 task(s) completed
2025-05-12 09:07:27 INFO:	

    ---------------------------------------------------
    |Results from dataset mucorales_odb10              |
    ---------------------------------------------------
    |C:0.1%[S:0.1%,D:0.0%],F:0.0%,M:99.9%,n:2449       |
    |2    Complete BUSCOs (C)                          |
    |2    Complete and single-copy BUSCOs (S)          |
    |0    Complete and duplicated BUSCOs (D)           |
    |0    Fragmented BUSCOs (F)                        |
    |2447    Missing BUSCOs (M)                        |
    |2449    Total BUSCO groups searched               |
    ---------------------------------------------------
2025-05-12 09:07:27 INFO:	BUSCO analysis done with WARNING(s). Total running time: 465 seconds

***** Summary of warnings: *****
2025-05-12 08:59:42 WARNING:busco.BuscoConfig	Option contig_break was provided but is not used in the selected run mode, proteins
2025-05-12 08:59:42 WARNING:busco.BuscoConfig	Option evalue was provided but is not used in the selected run mode, proteins
2025-05-12 08:59:42 WARNING:busco.BuscoConfig	Option limit was provided but is not used in the selected run mode, proteins

2025-05-12 09:07:27 INFO:	Results written in /tmp/tmp_egrp8er/job_working_directory/000/7/working/busco_galaxy
2025-05-12 09:07:27 INFO:	For assistance with interpreting the results, please consult the userguide: https://busco.ezlab.org/busco_userguide.html

2025-05-12 09:07:27 INFO:	Visit this page https://gitlab.com/ezlab/busco#how-to-cite-busco to see how to cite BUSCO
total 92
drwxr-xr-x 5 1001 118  4096 May 12 08:59 busco_sequences
-rw-r--r-- 1 1001 118 47714 May 12 09:07 full_table.tsv
drwxr-xr-x 4 1001 118  4096 May 12 09:07 hmmer_output
-rw-r--r-- 1 1001 118 27808 May 12 09:07 missing_busco_list.tsv
-rw-r--r-- 1 1001 118  2231 May 12 09:07 short_summary.json
-rw-r--r-- 1 1001 118   742 May 12 09:07 short_summary.txt
2025-05-12 09:07:28 INFO:	****************** Start plot generation at 05/12/2025 09:07:28 ******************
2025-05-12 09:07:28 INFO:	Load data ...
2025-05-12 09:07:28 INFO:	Loaded BUSCO_summaries/short_summary.specific.mucorales_odb10.busco_galaxy.txt successfully
2025-05-12 09:07:28 INFO:	Generate the R code ...
2025-05-12 09:07:28 INFO:	Run the R code ...
2025-05-12 09:07:30 INFO:	
[1] "Plotting the figure ..."
[1] "Done"

2025-05-12 09:07:30 INFO:	Plot generation done. Total running time: 2.171099901199341 seconds
2025-05-12 09:07:30 INFO:	Results written in BUSCO_summaries/


              

              • 

            

            Traceback:
            

              

            • 

              

              • 

            

            Job Parameters:
            

              

            • 

              


              
Job parameter
Parameter value

              
              


              
__input_ext
"input"

              

              
__workflow_invocation_uuid__
"3d77199e2f0e11f0a4527c1e52252d76"

              

              
adv
{"contig_break": "10", "evalue": "0.001", "limit": "3"}

              

              
busco_mode
{"__current_case__": 2, "mode": "prot"}

              

              
chromInfo
"/tmp/tmp_egrp8er/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"

              

              
dbkey
"?"

              

              
lineage
{"__current_case__": 1, "lineage_dataset": "mucorales_odb10", "lineage_mode": "select_lineage"}

              

              
lineage_conditional
{"__current_case__": 0, "cached_db": "v5", "selector": "cached"}

              

              
outputs
["short_summary", "image", "gff", "missing"]

              
              

              

              • 

            

            • 

          

          

          • 

        

        • 

      • 

        Step 8: OMArk:
        

          

        • 

          step_state: scheduled
          

          • 

        • 

          Jobs

            

          • 

            Job 1:
            

              

            • Job state is error
              • 

            

            Command Line:
            

              

            • 

              omamer search --db '/cvmfs/data.galaxyproject.org/byhand/omamer/LUCA-v2.0.0.h5' --query '/tmp/tmp_egrp8er/files/6/8/4/dataset_684bde41-4dbb-4a6d-9f11-8ca3b26e9c8f.dat' --out 'output_omamer'  &&  omark -f 'output_omamer' -d '/cvmfs/data.galaxyproject.org/byhand/omamer/LUCA-v2.0.0.h5'      -o omark_galaxy
              

              • 

            

            Exit Code:
            

              

            • 

              1
              

              • 

            

            Standard Error:
            

              

            • 

              ================================================================================

   _____ _____ _____
  |     |     |  _  |_____ ___ ___
  |  |  | | | |     |     | -_|  _|
  |_____|_|_|_|__|__|_|_|_|___|_|   v2.1.0

  OMAmer is licensed under the GNU Lesser General Public License 3.0 (LGPL-3.0).
    
================================================================================

Loading required libraries  [DONE]

================================================================================

Running OMAmer on c5cc4a7a2030, using:
 - database: /cvmfs/data.galaxyproject.org/byhand/omamer/LUCA-v2.0.0.h5
 - query: /tmp/tmp_egrp8er/files/6/8/4/dataset_684bde41-4dbb-4a6d-9f11-8ca3b26e9c8f.dat
 - version: 2.1.0

================================================================================
WARNING: Database version mismatch: DB 2.0.0 / OMAmer 2.1.0

Loading data required for OMAmer search from database...
 - taxonomy information (4.3s) [DONE]
 - family information (5.5s) [DONE]
 - sub-family information (1:37.2) [DONE]
 - family hierarchy (7.6s) [DONE]
 - k-mer index (1:03:09.4) [DONE]
 - family probability estimates (1.2s) [DONE]
 - sub-family probability estimates (18.0s) [DONE]

Finished loading required data

================================================================================

�[?25l
Searching -  0 queries in 0s (0.0 queries/s) 
Searching -  0 queries in 5s (0.0 queries/s) 
Searching -  0 queries in 10s (0.0 queries/s) 
Searching -  0 queries in 15s (0.0 queries/s) 
Searching -  0 queries in 20s (0.0 queries/s) 
Searching -  0 queries in 25s (0.0 queries/s) 
Searching -  0 queries in 30s (0.0 queries/s) 
Searching -  0 queries in 35s (0.0 queries/s) 
Searching -  0 queries in 40s (0.0 queries/s) 
Searching -  0 queries in 45s (0.0 queries/s) 
Searching -  0 queries in 50s (0.0 queries/s) 
Searching -  0 queries in 55s (0.0 queries/s) 
Searching -  0 queries in 1:00 (0.0 queries/s) 
Searching -  0 queries in 1:05 (0.0 queries/s) �[?25h�[J
Searching -  65 queries in 1:10.0 (0.93 queries/s) 

================================================================================

OMAmer search complete:
 - results written to: output_omamer
 - total 4018.78 seconds
 - search phase only 0.93 queries/s


Note: family p-values are stated in negative log units.
================================================================================

Thank you for using OMAmer. If you use OMAmer in your research, please cite:

Victor Rossier, Alex Warwick Vesztrocy, Marc Robinson-Rechavi, Christophe Dessimoz, OMAmer: tree-driven and alignment-free protein assignment to subfamilies outperforms closest sequence approaches, Bioinformatics, Volume 37, Issue 18, September 2021, Pages 2866-2873, https://doi.org/10.1093/bioinformatics/btab219


OMAmer uses data from the OMA browser. Results can be interpreted further using:
 - OMA browser website (https://omabrowser.org)
 - PyOMADB, the Python OMA API client (https://github.com/DessimozLab/pyomadb)

================================================================================
WARNING: Database version mismatch: DB 2.0.0 / OMAmer 2.1.0
NCBI database not present yet (first time used?)
Downloading taxdump.tar.gz from NCBI FTP site (via HTTP)...
Done. Parsing...

Inserting synonyms:          0 
Inserting synonyms:       5000 
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Inserting taxid merges:      0 
Inserting taxid merges:   5000 
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Inserting taxids:           0 
Inserting taxids:        5000 
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Inserting taxids:       2655000 
Inserting taxids:       2660000 
Inserting taxids:       2665000 WARNING: Database version mismatch: DB 2.0.0 / OMAmer 2.1.0
Traceback (most recent call last):
  File "/usr/local/bin/omark", line 52, in <module>
    omark.launcher(arg)
  File "/usr/local/lib/python3.9/site-packages/omark/omark.py", line 269, in launcher
    get_omamer_qscore(omamerfile, dbpath, outdir, taxid, original_FASTA_file = original_fasta, isoform_file=isoform_file, taxonomic_rank=taxonomic_rank)
  File "/usr/local/lib/python3.9/site-packages/omark/omark.py", line 116, in get_omamer_qscore
    closest_corr = spd.get_sampled_taxa(likely_clade, 5 , tax_tab, sp_tab, tax_buff, taxonomic_rank)
  File "/usr/local/lib/python3.9/site-packages/omark/species_determination.py", line 403, in get_sampled_taxa
    ranks = ncbi.get_rank(lineage_ncbi)
  File "/usr/local/lib/python3.9/site-packages/ete3/ncbi_taxonomy/ncbiquery.py", line 201, in get_rank
    result = self.db.execute(cmd)
sqlite3.OperationalError: no such column: "6656" - should this be a string literal in single-quotes?
/usr/local/lib/python3.9/site-packages/tables/file.py:113: UnclosedFileWarning: Closing remaining open file: /cvmfs/data.galaxyproject.org/byhand/omamer/LUCA-v2.0.0.h5
  warnings.warn(UnclosedFileWarning(msg))

WARNING:galaxy.model:Datatype class not found for extension 'sum'
WARNING:galaxy.model:Datatype class not found for extension 'sum'
WARNING:galaxy.model:Datatype class not found for extension 'sum'
WARNING:galaxy.model:Datatype class not found for extension 'sum'
WARNING:galaxy.model:Datatype class not found for extension 'sum'
WARNING:galaxy.model:Datatype class not found for extension 'sum'

              

              • 

            

            Standard Output:
            

              

            • 

              Loading node names...
2665637 names loaded.
415531 synonyms loaded.
Loading nodes...
2665637 nodes loaded.
Linking nodes...
Tree is loaded.
Updating database: /tmp/tmp_egrp8er/job_working_directory/000/8/home/.etetoolkit/taxa.sqlite ...

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Uploading to /tmp/tmp_egrp8er/job_working_directory/000/8/home/.etetoolkit/taxa.sqlite





              

              • 

            

            Traceback:
            

              

            • 

              

              • 

            

            Job Parameters:
            

              

            • 

              


              
Job parameter
Parameter value

              
              


              
__input_ext
"input"

              

              
__workflow_invocation_uuid__
"3d77199e2f0e11f0a4527c1e52252d76"

              

              
chromInfo
"/tmp/tmp_egrp8er/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"

              

              
database
"LUCA-v2.0.0.h5"

              

              
dbkey
"?"

              

              
input_iso
None

              

              
omark_mode
false

              

              
outputs
"detail_sum"

              

              
r
None

              

              
t
None

              
              

              

              • 

            

            • 

          

          

          • 

        

        • 

      
 
      

      • 

    • 

      Other invocation details

        

      • 

        error_message
        

          

        • Failed to run workflow, at least one job is in [error] state.
          • 

        

        • 

      • 

        history_id
        

          

        • 377d4e67e4846376
          • 

        

        • 

      • 

        history_state
        

          

        • error
          • 

        

        • 

      • 

        invocation_id
        

          

        • 377d4e67e4846376
          • 

        

        • 

      • 

        invocation_state
        

          

        • scheduled
          • 

        

        • 

      • 

        workflow_id
        

          

        • 377d4e67e4846376
          • 

        

        • 

      

      

      • 

    
  
    

    • 




      		
    

  





        


            

            
            

              
            

        

      


      

            
  

    
  
    
    

  

  


    












      

  
          

  

    
  


  

      

  This was referenced May 13, 2025





  


  

      
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      2 participants
    

    

        
          @rlibouba 
        
          @mvdbeek