DEEP VARIANT RETURNS ERROR PLZHELP

[hze...@gmail.com]

Dear life sciences team

 i am facing error whats is wrong

real    0m5.182s

user    0m34.334s

sys     0m5.397s

I0224 23:40:18.695070 139629147019008 run_deepvariant.py:416] None

Traceback (most recent call last):

  File "/opt/deepvariant/bin/run_deepvariant.py", line 421, in <module>

    app.run(main)

  File "/usr/local/lib/python3.6/dist-packages/absl/app.py", line 299, in run

    _run_main(main, args)

  File "/usr/local/lib/python3.6/dist-packages/absl/app.py", line 250, in _run_main

    sys.exit(main(argv))

  File "/opt/deepvariant/bin/run_deepvariant.py", line 414, in main

    subprocess.check_call(command, shell=True, executable='/bin/bash')

  File "/usr/lib/python3.6/subprocess.py", line 311, in check_call

    raise CalledProcessError(retcode, cmd)

subprocess.CalledProcessError: Command '( time seq 0 7 | parallel -q --halt 2 --line-buffer /opt/deepvariant/bin/make_examples --mode calling --ref "/input/sequences (12).fasta" --reads "/input/SRR11953670.bam" --examples "/output/intermediate_results_dir/make_examples.tfrecord.gz" --add_hp_channel --alt_aligned_pileup "diff_channels" --gvcf "/output/intermediate_results_dir/gvcf.tfrecord8.gz" --noparse_sam_aux_fields --norealign_reads --regions "chr20" --nosort_by_haplotypes --vsc_min_fraction_indels "0.12" --task {} )' returned non-zero exit status 1.

thanks in advance

haroon zeb

[Andrew Carroll]

Hi Haroon,

First, the commands that you are using  --noparse_sam_aux_fields --norealign_reads are typically used for PacBio HiFi data. Are these sequence samples PacBio HiFi? If not, it is better to run using the case study for WGS or exome: https://github.com/google/deepvariant/blob/r1.1/docs/deepvariant-case-study.md

Are you able to paste the command that you use to execute the Docker image?

Thank you,

Andrew

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