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error: no reads in first split: bad BAM file or tiny split size? #896

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astewart-twist opened this Issue Dec 7, 2015 · 8 comments

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astewart-twist commented Dec 7, 2015

I keep receiving the following error while trying to convert a bam file into adam format.

java.io.IOException: 'file:/my.bam': no reads in first split: bad BAM file or tiny split size?

Additional info:

  • I'm able to run the small.sam test set
  • I've regenerated my bam file multiple times and checked for any kind of corruption, etc
  • I've repeated this experiment on both a local environment (spark in single machine mode), and in EMR.
  • spark-1.5.2-bin-hadoop2.6
  • adam-distribution_2.10-0.18.2
  • scala version 2.10.6

Full stack trace: https://gist.github.com/astewart-twist/ceb36e492f96fe2a2500

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heuermh Feb 25, 2016

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@fnothaft @jpdna I was never able to reproduce this, might it be related to #962?

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heuermh commented Feb 25, 2016

@fnothaft @jpdna I was never able to reproduce this, might it be related to #962?

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fnothaft Feb 25, 2016

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Nah, #962 would be output only, not input.

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fnothaft commented Feb 25, 2016

Nah, #962 would be output only, not input.

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heuermh Feb 25, 2016

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Ah right, sorry, wasn't looking closely enough

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heuermh commented Feb 25, 2016

Ah right, sorry, wasn't looking closely enough

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heuermh Mar 29, 2016

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Fixed by HadoopGenomics/Hadoop-BAM#80 upstream, will have to wait for an update of Hadoop-BAM dependency version to 7.4.1 (or later as appropriate) to pick it up.

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heuermh commented Mar 29, 2016

Fixed by HadoopGenomics/Hadoop-BAM#80 upstream, will have to wait for an update of Hadoop-BAM dependency version to 7.4.1 (or later as appropriate) to pick it up.

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heuermh Apr 7, 2016

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See #989 which uses Hadoop-BAM version 7.4.1-SNAPSHOT to pick up the fix for this issue. Currently blocked on Jenkins environment changes.

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heuermh commented Apr 7, 2016

See #989 which uses Hadoop-BAM version 7.4.1-SNAPSHOT to pick up the fix for this issue. Currently blocked on Jenkins environment changes.

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fnothaft Apr 7, 2016

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@shaneknapp should be back online tomorrow. I looked and alas, I do not have permissions to make the @AmplabJenkins changes.

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fnothaft commented Apr 7, 2016

@shaneknapp should be back online tomorrow. I looked and alas, I do not have permissions to make the @AmplabJenkins changes.

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heuermh May 18, 2016

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May be fixed by #989, please retest if possible.

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heuermh commented May 18, 2016

May be fixed by #989, please retest if possible.

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fnothaft Jul 17, 2016

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Closing as fixed by #989.

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fnothaft commented Jul 17, 2016

Closing as fixed by #989.

@fnothaft fnothaft closed this Jul 17, 2016

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