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Cannot identify error cause in make_examples stage

See original GitHub issue

I’m running a pipeline but get an error on “make_examples” stage. Could you help me to debug possible cause, please?

Here is a log:

[W::hts_idx_load2] The index file is older than the data file: /mnt/google/.google/input/cannabis-3k-results/manual/merged_bam/SRS1107973_LKUA01.sorted.merged.bam.bai
2019-08-14 12:36:51.456603: W third_party/nucleus/io/sam_reader.cc:531] Unrecognized SAM header type, ignoring: 
WARNING: Logging before flag parsing goes to stderr.
I0814 12:36:53.581777 140158089049856 genomics_reader.py:174] Reading /mnt/google/.google/input/cannabis-3k-results/manual/merged_bam/SRS1107973_LKUA01.sorted.merged.bam with NativeSamReader
I0814 12:36:54.201131 140158089049856 make_examples.py:1024] Preparing inputs
[W::hts_idx_load2] The index file is older than the data file: /mnt/google/.google/input/cannabis-3k-results/manual/merged_bam/SRS1107973_LKUA01.sorted.merged.bam.bai
2019-08-14 12:36:58.286794: W third_party/nucleus/io/sam_reader.cc:531] Unrecognized SAM header type, ignoring: 
I0814 12:36:59.914532 140158089049856 genomics_reader.py:174] Reading /mnt/google/.google/input/cannabis-3k-results/manual/merged_bam/SRS1107973_LKUA01.sorted.merged.bam with NativeSamReader
I0814 12:45:36.568115 140158089049856 make_examples.py:946] Common contigs are [u'LKUA01000001.1', u'LKUA01000002.1', ...<ANOTHER 300k NAMES>..., u'LKUA01311038.1', u'LKUA01311039.1']
parallel: This job failed:
/opt/deepvariant/bin/make_examples --mode calling --examples /mnt/google/.google/output/cannabis-3k-vcf/staging/SRS1107973_LKUA01/staging/examples/0/examples_output.tfrecord@512.gz --reads /mnt/google/.google/input/cannabis-3k-results/manual/merged_bam/SRS1107973_LKUA01.sorted.merged.bam --ref /mnt/google/.google/input/cannabis-3k/reference/LKUA01/LKUA01.fa --task 8

For me it looks that the error message is parallel: This job failed: and failure doesn’t relate to the warnings at the beginning of the file?

Regards,

Issue Analytics

State:
Created 4 years ago
Comments:5 (3 by maintainers)

Top GitHub Comments

1reaction

obshcommented, Sep 3, 2019

Hi @gunjanbaid, thank you! I’ll try the v0.8.0 release and other recommendations.

I’m working on a cannabis variants project with a Googler @allenday. We consulted @AndrewCarroll previously, from his preliminary analysis - seems that default DeepVariant model should work fine with our data.

0reactions

gunjanbaidcommented, Sep 4, 2019

@obsh sounds good. I’ll close this issue for now, but feel free to reopen if you run into any other errors.

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