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RNA Seq failed exit status 247

See original GitHub issue

I thought I should be able to call variants from short reads aligned to the human genome (hg19) with hisat2. So I gave it a try.

Windows 10 Docker desktop.

/opt/deepvariant/bin/run_deepvariant --model_type=WGS --output_vcf=CDAR-016_run0124_deepvariant.vcf --reads=CDAR-016_human37_align.bam --ref=./CFM032/human_g1k_v37.fasta --novcf_stats_report --num_shards=5 --call_variants_extra_args "use_openvino=true"

Error:

I0123 08:06:11.771944 139769488508672 make_examples.py:535] Task 1/5: 9704 candidates (9978 examples) [651.40s elapsed]
I0123 08:07:25.050816 140120745805568 make_examples.py:535] Task 3/5: 9400 candidates (9710 examples) [246.46s elapsed]
I0123 08:09:37.633983 140665948894976 make_examples.py:535] Task 4/5: 6501 candidates (6671 examples) [1447.91s elapsed]
I0123 08:10:30.871732 140590877263616 make_examples.py:535] Task 2/5: 7503 candidates (7798 examples) [1754.74s elapsed]
I0123 08:14:47.526611 139645822764800 make_examples.py:535] Task 0/5: 8701 candidates (9015 examples) [4857.13s elapsed]
I0123 08:16:17.660391 140590877263616 make_examples.py:535] Task 2/5: 7600 candidates (7895 examples) [346.79s elapsed]
I0123 08:17:25.425076 140120745805568 make_examples.py:535] Task 3/5: 9501 candidates (9813 examples) [600.37s elapsed]
I0123 08:23:17.762356 140590877263616 make_examples.py:535] Task 2/5: 7700 candidates (8000 examples) [420.10s elapsed]
I0123 08:28:08.231647 140590877263616 make_examples.py:535] Task 2/5: 7800 candidates (8102 examples) [290.47s elapsed]
I0123 08:33:41.777438 139769488508672 make_examples.py:535] Task 1/5: 9800 candidates (10074 examples) [1650.01s elapsed]
parallel: This job failed:
/opt/deepvariant/bin/make_examples --mode calling --ref ./CFM032/human_g1k_v37.fasta --reads run0124_lane9_indexUDI0001-UDI0001=CDAR-016_human37_align.bam --examples /tmp/tmpfh_b9v77/make_examples.tfrecord@5.gz --task 1

real    2480m8.473s
user    2463m44.983s
sys     2m30.474s
I0123 08:51:28.346467 139763485337344 run_deepvariant.py:321] None
Traceback (most recent call last):
  File "/opt/deepvariant/bin/run_deepvariant.py", line 332, 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 319, 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 4 | parallel --halt 2 --line-buffer /opt/deepvariant/bin/make_examples --mode calling --ref "./CFM032/human_g1k_v37.fasta" --reads "run0124_lane9_indexUDI0001-UDI0001=CDAR-016_human37_align.bam" --examples "/tmp/tmpfh_b9v77/make_examples.tfrecord@5.gz" --task {}' returned non-zero exit status 247.

Issue Analytics

State:
Created 3 years ago
Comments:10

Top GitHub Comments

2reactions

pgrosucommented, Jan 26, 2021

@husamia Basically what you are seeing is that you’re running out of memory. Try it on a machine with more memory.

0reactions

danielecookcommented, Oct 21, 2022

@husamia we have not tried it, but I would expect it to work. Please let us know if you run into any issues.

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