Illegal instruction (core dumped) - calib_cons

[awsdd]

Hi there, wondering if any ideas on the following.

I'm running calib installed with conda on a Linux server. I've successfully run the calib command and generated a cluster file. The problem occurs when I try to run calib_cons. The following is the full command and output:

calib_cons -c B5-testgz.cluster -q B5_3_1_S5_L001_R1_UMI_full.fastq B5_3_1_S5_L001_R2_UMI_full.fastq -t 4 -o B5gz-R1 B5gz-R2

Reading cluster file: B5-testgz.cluster
Reading fastq file: B5_3_1_S5_L001_R1_UMI_full.fastq
Writing output files: B5gz-R1
Illegal instruction (core dumped)

I end up with 6 empty files in my directory (.msa, .msa1, .fastq and .fast0/1/2).

A factor here is that some preprocessing occurred before the data was passed to me and the UMIs had been removed from the front of the read sequences - I have had to copy them back to the sequence start from the read header and put dummy characters (!!!!!!!!!!!) in the quality scores line so that the lengths match the sequences. Not sure if something here could be problematic. An example read:

@A01439:100:HC3VHDRX2:1:2101:2808:1000:CTTGCATCTTA 1:N:0:CGGCATTA+TGACTGAC CTTGCATCTTACTTAAAAACCTACAAATGAAACCCAGCATGCATACACACACCCCTCCATACCCTCACATAAATTATATATACCCTTATCTATACTAACTATAAAATGTAT + !!!!!!!!!!!F:F:FFF,:F,:F::FFFF::FF:F,,FFFFF:FFF,F:FF,:FFFFF,FFFFFFFFFFFFFFF:F:FFFFFFFFFFFFFFF::FFFFFFFFFFFFFFFF

results of head B5-testgz.cluster if it helps:
26551449 34947546 10 @A01439:100:HC3VHDRX2:1:2101:12319:1000:GGAAACTGTCT GGAAACTGTCTAGTCAGTTTTCTAAATCTATAATGGAAAAGAAAATCGAATCTCGTCTTTATTTTTAAAAAGGGAAGGATGTTCAAGATCGGAAGAGCACACGTCTGAA !!!!!!!!!!!FF::FFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF @A01439:100:HC3VHDRX2:1:2101:12319:1000:GGAAACTGTCT GGAAACTGTCTTGAACATCCTTCCCTTTTTAAAAATAAAGACGAGATTCGATTTTCTTTTCCATTATAGATTTAGAAAACTGACTTAGATCGGAAGAGCGTCGTGTAGGGAA !!!!!!!!!!!FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF 11104884 14491263 46 @A01439:100:HC3VHDRX2:1:2101:6777:1016:CGGATTCATCA CGGATTCATCAGTACTGGAAAGTCCCATTTTTCTCTGCACTGAACAGCCAGAAAAAGAAACAACGTTTCTAACTTAATTGGCTAGATCGGAAGAGCACACGTCTGAACTC !!!!!!!!!!!,,FF:FFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF @A01439:100:HC3VHDRX2:1:2101:6777:1016:CGGATTCATCA CGGATTCATCAAGCCAATTAAGTTAGAAACGTTGTTTCTTTTTCTGGCTGTTCAGTGCAGAGAAAAATGGGACTTTCCAGTACAAGATCGGAAGAGCGTCGTGTTGGGAAAG !!!!!!!!!!!FFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFF:FFFFFFFFFFFFFFF:FFF,FF,,FF,,:F 15253236 19933987 47 @A01439:100:HC3VHDRX2:1:2101:7229:1016:GGAAATCGGTT GGAAATCGGTTGCATAACACAGCAGAGCCACTATGAAATTCAGCTCTTATAGCAAACATTTAAATGATTTTTGTTGGATATTTTCTCTCAGTTGGCATGTGAACAAATGTG !!!!!!!!!!!F,,,FFFFFFFFFF:FFF:FFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF @A01439:100:HC3VHDRX2:1:2101:7229:1016:GGAAATCGGTT GGAAATCGGTTCACATTTGTTCACATGCCAACTGAGAGAAAATATCCAACAAAAATCATTTAAATGTTTGCTATAAGAGCTGAATTTCATAGTGGCTCTGCTGTGTTATG !!!!!!!!!!!FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

any thoughts on what may be leading to this error?

[baraaorabi]

I don't think using dummy !'s is the problem. Do you mind sharing your OS and the command you used to install Calib?

[awsdd]

I installed using the conda command as per this page i.e.
conda install -c bioconda calib
onto a remote server running Red Hat Enterprise Linux v8.6 (Ootpa)

[Joon-Klaps]

I also encounterd this issue
https://github.com/Joon-Klaps/viralgenie/actions/runs/7729194129/job/21071816540?pr=87#step:4:311:

 .command.sh: line 12:    95 Illegal instruction     (core dumped) calib_cons --threads 2 -c SRR11140748.cluster -q SRR11140748_R1.fastq.gz SRR11140748_R2.fastq.gz -o SRR11140748_dedup1. SRR11140748_dedup2.

Using a docker container I build with wave: wave --conda-package calib --conda-package pigz --freeze --platform linux/amd64 as I didn't find an official container for calib.