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IndexFeatureFile fails with compressed vcf on GCS #6348

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kachulis opened this issue Jan 6, 2020 · 1 comment
Closed
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IndexFeatureFile fails with compressed vcf on GCS #6348

kachulis opened this issue Jan 6, 2020 · 1 comment
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kachulis commented Jan 6, 2020

Bug Report

Affected tool(s) or class(es)

IndexFeatureFile

Affected version(s)

  • Latest master branch as of [1/6/2020]

Description

When running IndexFeatureFile on a compressed vcf stored on GCS, tool fails, error message:

  A USER ERROR has occurred: Error while trying to create index for dir/file.vcf.gz. Error was: 
  htsjdk.tribble.TribbleException.FeatureFileDoesntExist: Unable to open the input file, most 
  likely the file doesn't exist., for input source: /dir/file.vcf.gz

When running on an uncompressed vcf on GCS, the tool succeeds.

I've traced the issue to SeekableStreamFactory.getStreamFor in htsjdk, which gets called from IndexFactory.initIndexableBlockCompressedStream (also in htsdjk), and doesn't appear to handle GCS paths correctly.
@lbergelson lbergelson added the bug label Jan 6, 2020
@droazen droazen added this to the GATK-Triaged-Issues milestone Jan 6, 2020
This was referenced Jan 7, 2020
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lbergelson pushed a commit that referenced this issue Jan 27, 2020
@cmnbroad @lbergelson
Fixes for IndexFeatureFile error reporting. (#6367)
b5cbaac 
* Don't call toAbsolutePath on our Paths since it resolves paths that are not already absolute to a (implementation dependent) default location, which will often return an incorrect result for non-default file systems.
* Cosmetic improvement to the error reported in #6348
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Closed via #6462 (actually via htsjdk #6367) and #6367.

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@droazen @lbergelson @cmnbroad @kachulis