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postprocess_variants: Found multiple file patterns in input filename space #818
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I do not run it step by step. I run "run_deepvariant". This is my command:
I have now added the following command, which is a workaround for the problem ...
Eventually this workaround sets --infile to "./call_variants_output@1.tfrecord.gz" and --nonvariant_site_tfrecord_path to "./gvcf.tfrecord@8.gz" (see directory listing above). |
I could extract the three commands make_examples, call_variants and postprocess_variants from the output. Here it is:
And here are the two last commands with std out ...
|
@MiWitt , Given that you are using |
This can not be the point. I am working in a cluster environment using slurm and the dir "." is the job specific scratch dir, which is located at "/scratch/SlurmTMP/JobSpecificFolder" (${TMPDIR})
|
@MiWitt , Can you use |
Hi, do you have any updates on this issue? |
Have you checked the FAQ? https://github.com/google/deepvariant/blob/r1.6.1/docs/FAQ.md:
Describe the issue:
The postprocess_variants step fails with following error message:
ValueError: ('Found multiple file patterns in input filename space: ', './call_variants_output.tfrecord.gz')
Setup
Steps to reproduce:
Traceback (most recent call last):
File "/tmp/Bazel.runfiles_t3t5ek8u/runfiles/com_google_deepvariant/deepvariant/postprocess_variants.py", line 1419, in
app.run(main)
File "/tmp/Bazel.runfiles_t3t5ek8u/runfiles/absl_py/absl/app.py", line 312, in run
_run_main(main, args)
File "/tmp/Bazel.runfiles_t3t5ek8u/runfiles/absl_py/absl/app.py", line 258, in _run_main
sys.exit(main(argv))
File "/tmp/Bazel.runfiles_t3t5ek8u/runfiles/com_google_deepvariant/deepvariant/postprocess_variants.py", line 1300, in main
sample_name = get_sample_name()
File "/tmp/Bazel.runfiles_t3t5ek8u/runfiles/com_google_deepvariant/deepvariant/postprocess_variants.py", line 1203, in get_sample_name
_, record = get_cvo_paths_and_first_record()
File "/tmp/Bazel.runfiles_t3t5ek8u/runfiles/com_google_deepvariant/deepvariant/postprocess_variants.py", line 1179, in get_cvo_paths_and_first_record
raise ValueError(
ValueError: ('Found multiple file patterns in input filename space: ', './call_variants_output.tfrecord.gz')
Does the quick start test work on your system?
Please test with https://github.com/google/deepvariant/blob/r1.6/docs/deepvariant-quick-start.md.
Is there any way to reproduce the issue by using the quick start?
???
Any additional context:
Yes. I can change the parameter "--infile" of the postprocess_variants.py call from "./call_variants_output.tfrecord.gz" to "./call_variants_output@1.tfrecord.gz" and it works. Anyway, the call of postprocess_variants.py is auto-generated by "/opt/deepvariant/bin/run_deepvariant". The error does not occur for every sample ...
directory content of intermediate_results_dir after the error occured:
call_variants.log
call_variants_output-00000-of-00001.tfrecord.gz
gvcf.tfrecord-00000-of-00008.gz
gvcf.tfrecord-00001-of-00008.gz
gvcf.tfrecord-00002-of-00008.gz
gvcf.tfrecord-00003-of-00008.gz
gvcf.tfrecord-00004-of-00008.gz
gvcf.tfrecord-00005-of-00008.gz
gvcf.tfrecord-00006-of-00008.gz
gvcf.tfrecord-00007-of-00008.gz
make_examples.log
make_examples.tfrecord-00000-of-00008.gz
make_examples.tfrecord-00000-of-00008.gz.example_info.json
make_examples.tfrecord-00001-of-00008.gz
make_examples.tfrecord-00001-of-00008.gz.example_info.json
make_examples.tfrecord-00002-of-00008.gz
make_examples.tfrecord-00002-of-00008.gz.example_info.json
make_examples.tfrecord-00003-of-00008.gz
make_examples.tfrecord-00003-of-00008.gz.example_info.json
make_examples.tfrecord-00004-of-00008.gz
make_examples.tfrecord-00004-of-00008.gz.example_info.json
make_examples.tfrecord-00005-of-00008.gz
make_examples.tfrecord-00005-of-00008.gz.example_info.json
make_examples.tfrecord-00006-of-00008.gz
make_examples.tfrecord-00006-of-00008.gz.example_info.json
make_examples.tfrecord-00007-of-00008.gz
make_examples.tfrecord-00007-of-00008.gz.example_info.json
postprocess_variants.log
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