Question: Error in MiModD variant caling
0
gravatar for 5mu
10 days ago by
5mu0
5mu0 wrote:

Hi I am using MiModD on galaxy to do mapping-by-sequencing. I used bowtie2 to do the alignments and then used the BAM files to generate the joint BCFfile from MiModD variant calling tool.

Following is the error I get:

Fatal error: Exit code 1 ()
[fai_load] fail to open FASTA file.
 Failed to open -: unknown file type

Traceback (most recent call last):
  File "/cvmfs/main.galaxyproject.org/deps/_conda/envs/__MiModD@0.1.9/bin/mimodd", line 7, in <module>
    __main__.parse()
  File "/cvmfs/main.galaxyproject.org/deps/_conda/envs/__MiModD@0.1.9/lib/python3.6/site-packages/MiModD/__main__.py", line 1197, in parse
    result = funcs[-1](**args)
  File "/cvmfs/main.galaxyproject.org/deps/_conda/envs/__MiModD@0.1.9/lib/python3.6/site-packages/MiModD/tmpfiles.py", line 26, in catch_sigterm_wrapper
    ret = f(*args, **kwargs)
  File "/cvmfs/main.galaxyproject.org/deps/_conda/envs/__MiModD@0.1.9/lib/python3.6/site-packages/MiModD/variant_calling.py", line 389, in varcall
    call = '{0} | {1}'.format(call[0], call[1])
MiModD.SamtoolsRuntimeError: /cvmfs/main.galaxyproject.org/deps/_conda/envs/__MiModD@0.1.9/lib/python3.6/site-packages/MiModD/bin/samtools mpileup -d 250 -r chr3: -t DP,DPR -gu -f /galaxy-repl/main/jobdir/020/282/20282112/working/tmp_genome1207.fa /galaxy-repl/main/jobdir/020/282/20282112/working/tmp_indexed_bam_9454.bam /galaxy-repl/main/jobdir/020/282/20282112/working/tmp_indexed_bam_6989.bam /galaxy-repl/main/jobdir/020/282/20282112/working/tmp_indexed_bam_8072.bam | /cvmfs/main.galaxyproject.org/deps/_conda/envs/__MiModD@0.1.9/lib/python3.6/site-packages/MiModD/bin/bcftools call -m -A -f GQ -O b - failed.
No further information about this error is available.

Variant Calling for contig chr3 failed.
python: : Unknown error 72105920

How can I figure this error out? Thank you, Midhat

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