Question: Error in MiModD variant caling
gravatar for 5mu
10 days ago by
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/", line 7, in <module>
  File "/cvmfs/", line 1197, in parse
    result = funcs[-1](**args)
  File "/cvmfs/", line 26, in catch_sigterm_wrapper
    ret = f(*args, **kwargs)
  File "/cvmfs/", line 389, in varcall
    call = '{0} | {1}'.format(call[0], call[1])
MiModD.SamtoolsRuntimeError: /cvmfs/ 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/ 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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