8000 postprocess variants failed !!! · Issue #485 · google/deepvariant · GitHub
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leedchou opened this issue Sep 12, 2021 · 5 comments
Closed

postprocess variants failed !!! #485

leedchou opened this issue Sep 12, 2021 · 5 comments

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@leedchou
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leedchou commented Sep 12, 2021 •
edited
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Have you checked the FAQ? https://github.com/google/deepvariant/blob/r1.2/docs/FAQ.md: YES

Describe the issue:

Manually selected regions (a single region is formed by a locus extending 500 bp to both sides) were used in my project to make examples, and it was also succeed in calling variants. However, when I running postprocess_variants, something went wrong. I check the log, and I guess it was related to the wrong "call_variant_outputs". So I printed one "call_variant_outputs" out of the whole tfrecord, and found out there are several repeated variant in one call. Where did I go wrong?

The log file is attached.
postprocess_variants.log

Setup

  • Operating system: ubuntu 16
  • DeepVariant version: 0.7.0
  • Installation method (Docker, built from source, etc.): built from source
  • Type of data: (sequencing instrument, reference genome, anything special that is unlike the case studies?) NO

Steps to reproduce:

  • Command:
  • Error trace: (if applicable)

W0912 23:51:01.891268 140429229119232 postprocess_variants.py:331] Alt allele indices found from call_variants_outputs for variant reference_bases: "C"
alternate_bases: "A"
calls {
info {
key: "AD"
value {
values {
int_value: 17
}
values {
int_value: 4
}
}
}
info {
key: "DP"
value {
values {
int_value: 21
}
}
}
info {
key: "VAF"
value {
values {
number_value: 0.190476190476
}
}
}
genotype: -1
genotype: -1
call_set_name: "XY406-1"
}
end: 10147
reference_name: "1"
start: 10146
is [[0], [0], [0]], which is invalid.
Traceback (most recent call last):
File "/tmp/Bazel.runfiles_4jh3iyl1/runfiles/com_google_deepvariant/deepvariant/postprocess_variants.py", line 874, in
tf.app.run()
File "/usr/local/lib/python2.7/dist-packages/tensorflow/python/platform/app.py", line 125, in run
_sys.exit(main(argv))
File "/tmp/Bazel.runfiles_4jh3iyl1/runfiles/com_google_deepvariant/deepvariant/postprocess_variants.py", line 851, in main
header=header)
File "/tmp/Bazel.runfiles_4jh3iyl1/runfiles/com_google_deepvariant/deepvariant/postprocess_variants.py", line 595, in write_variants_to_vcf
for variant in variant_generator:
File "/tmp/Bazel.runfiles_4jh3iyl1/runfiles/com_google_deepvariant/deepvariant/haplotypes.py", line 91, in maybe_resolve_conflicting_variants
for overlapping_candidates in _group_overlapping_variants(sorted_variants):
File "/tmp/Bazel.runfiles_4jh3iyl1/runfiles/com_google_deepvariant/deepvariant/haplotypes.py", line 110, in _group_overlapping_variants
for variant in sorted_variants:
File "/tmp/Bazel.runfiles_4jh3iyl1/runfiles/com_google_deepvariant/deepvariant/postprocess_variants.py", line 631, in _transform_call_variants_output_to_variants
outputs, multi_allelic_qual_filter)
File "/tmp/Bazel.runfiles_4jh3iyl1/runfiles/com_google_deepvariant/deepvariant/postprocess_variants.py", line 559, in merge_predictions
raise ValueError('call_variants_outputs did not pass sanity check.')
ValueError: call_variants_outputs did not pass sanity check.

Does the quick start test work on your system?
YES
@MariaNattestad
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Can you include all the commands you ran? Also can you try with the latest version of DeepVariant?

@leedchou
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leedchou commented Sep 15, 2021 •
edited
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Hi, @MariaNattestad

Thank you very much for your kind advice. I have figured out what caused this error and it did work.

Additionally, I don't understand how DeepVariant defines those candidate variants when making examples. I know it is implemented by the file "allelecounter.cilf", but I get limited information from this file.
Could you please tell me more information about the candidate variants part?

Thank you again for your help.

@akolesnikov
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For the detailed explanation of how candidates are generated please see https://www.biorxiv.org/content/10.1101/092890v6.full.pdf (starting at page 14).
Also, main code is in allelecounter.cc and variant_calling.cc.

@leedchou
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Soga, thank you@akolesnikov

@NagaComBio NagaComBio mentioned this issue Feb 18, 2022
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@MariaNattestad
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@leedchou can you share what you figured out was the cause of the error?

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@akolesnikov @MariaNattestad @leedchou
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