Error finding *.depth file

[Mariaroviscomonteiro]

Hello,

I am trying to use LithoGenie to functionally annotate my MAGs.
The programme is working fine until I use the -bams option to normalise taking into account the coverage from read mapping (My MAGs were generated from a co-assembly and I made a bam.txt following your instructions for co-assembled genomes).

I keep getting this error:

---

processing... maxbin.031_sub.contigs.fa
Output depth matrix to maxbin.031_sub.contigs.fa.depth
jgi_summarize_bam_contig_depths 2.15 (Bioconda) 2020-07-03T13:02:15
Output matrix to maxbin.031_sub.contigs.fa.depth
0: Opening bam: /nesi/nobackup/nesi00465/raw_data/Chapter_2_version_Sep2/Chapter_2/MAGs/4.Qual_bins/bin_coverage/BT31.bam
12: Opening bam: 11: Opening bam: /nesi/nobackup/nesi00465/raw_data/Chapter_2_version_Sep2/Chapter_2/MAGs/4.Qual_bins/bin_coverage/BT52.bam56: Opening bam: /nesi/nobackup/nesi00465/raw_data/Chapter_2_version_Sep2/Chapter_2/MAGs/4.Qual_bins/bin_coverage/BT42.bam
/nesi/nobackup/nesi00465/raw_data/Chapter_2_version_Sep2/Chapter_2/MAGs/4.Qual_bins/bin_coverage/BT53.bam

8: Opening bam: /nesi/nobackup/nesi00465/raw_data/Chapter_2_version_Sep2/Chapter_2/MAGs/4.Qual_bins/bin_coverage/BT44.bam
: Opening bam: /nesi/nobackup/nesi00465/raw_data/Chapter_2_version_Sep2/Chapter_2/MAGs/4.Qual_bins/bin_coverage/BT41.bam
13: Opening bam: /nesi/nobackup/nesi00465/raw_data/Chapter_2_version_Sep2/Chapter_2/MAGs/4.Qual_bins/bin_coverage/BT54.bam
7: Opening bam: /nesi/nobackup/nesi00465/raw_data/Chapter_2_version_Sep2/Chapter_2/MAGs/4.Qual_bins/bin_coverage/BT43.bam
3: Opening bam: /nesi/nobackup/nesi00465/raw_data/Chapter_2_version_Sep2/Chapter_2/MAGs/4.Qual_bins/bin_coverage/BT34.bam
2: Opening bam: /nesi/nobackup/nesi00465/raw_data/Chapter_2_version_Sep2/Chapter_2/MAGs/4.Qual_bins/bin_coverage/BT33.bam
14: Opening bam: /nesi/nobackup/nesi00465/raw_data/Chapter_2_version_Sep2/Chapter_2/MAGs/4.Qual_bins/bin_coverage/BT55.bam
1: Opening bam: /nesi/nobackup/nesi00465/raw_data/Chapter_2_version_Sep2/Chapter_2/MAGs/4.Qual_bins/bin_coverage/BT32.bam
4: Opening bam: /nesi/nobackup/nesi00465/raw_data/Chapter_2_version_Sep2/Chapter_2/MAGs/4.Qual_bins/bin_coverage/BT35.bam
109: Opening bam: /nesi/nobackup/nesi00465/raw_data/Chapter_2_version_Sep2/Chapter_2/MAGs/4.Qual_bins/bin_coverage/BT51.bam
: Opening bam: /nesi/nobackup/nesi00465/raw_data/Chapter_2_version_Sep2/Chapter_2/MAGs/4.Qual_bins/bin_coverage/BT45.bam
Processing bam files
Thread 0 finished: BT31.bam with 41784108 reads and 2548900 readsWellMapped
Thread 13 finished: BT54.bam with 37818784 reads and 1818920 readsWellMapped
Thread 8 finished: BT44.bam with 47649368 reads and 8359982 readsWellMapped
Thread 12 finished: BT53.bam with 42732468 reads and 3793898 readsWellMapped
Thread 6 finished: BT42.bam with 41398298 reads and 4262408 readsWellMapped
Thread 14 finished: BT55.bam with 14976816 reads and 801879 readsWellMapped
Thread 7 finished: BT43.bam with 76231146 reads and 12109136 readsWellMapped
Thread 10 finished: BT51.bam with 20372246 reads and 805082 readsWellMapped
Thread 5 finished: BT41.bam with 52802668 reads and 3544574 readsWellMapped
Thread 11 finished: BT52.bam with 28965720 reads and 1986958 readsWellMapped
Thread 4 finished: BT35.bam with 34227688 reads and 5284176 readsWellMapped
Thread 2 finished: BT33.bam with 21982532 reads and 1772437 readsWellMapped
Thread 3 finished: BT34.bam with 33913086 reads and 3600508 readsWellMapped
Thread 1 finished: BT32.bam with 61539122 reads and 4501818 readsWellMapped
Thread 9 finished: BT45.bam with 77754398 reads and 11829835 readsWellMapped
Creating depth matrix file: maxbin.031_sub.contigs.fa.depth
Closing most bam files
Closing last bam file
Finished
processing... maxbin.031_sub.contigs.fa
Traceback (most recent call last):
File "/scale_wlg_nobackup/filesets/nobackup/nesi00465/raw_data/Chapter_2_version_Sep2/Chapter_2/MAGs/4.Qual_bins/1.Prodig_anno_renamed/MagicLamp/genies/LithoGenie.py", line 2253, in main
depth = open("%s/contigDepths/%s.depth" % (args.out, cell))
FileNotFoundError: [Errno 2] No such file or directory: 'lithogenie_output_bam/contigDepths/maxbin.031_sub.contigs.fa.depth'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "/nesi/nobackup/nesi00465/raw_data/Chapter_2_version_Sep2/Chapter_2/MAGs/4.Qual_bins/1.Prodig_anno_renamed/MagicLamp/MagicLamp.py", line 30, in
LithoGenie.main()
File "/scale_wlg_nobackup/filesets/nobackup/nesi00465/raw_data/Chapter_2_version_Sep2/Chapter_2/MAGs/4.Qual_bins/1.Prodig_anno_renamed/MagicLamp/genies/LithoGenie.py", line 2265, in main
depth = open("%s/contigDepths/%s.depth" % (args.out, cell))
FileNotFoundError: [Errno 2] No such file or directory: 'lithogenie_output_bam/contigDepths/maxbin.031_sub.contigs.fa.depth'

---

I have noticed that I generated the file "maxbin.031_sub.contigs.fa.depth", however it is not inside the output_directory.

This is the script I used:

MagicLamp.py LithoGenie -bin_dir /nesi/nobackup/nesi00465/raw_data/Chapter_2_version_Sep2/Chapter_2/MAGs/4.Qual_bins/1.Prodig_anno_renamed/MagicLamp/lithogenie_output/ORF_calls -bin_ext faa -out lithogenie_output_bam -bams bams3.txt --orfs

Cheers,

Maria