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IO Error while running MergeBamAlignment on Terra

lraolrao Member


I'm currently running a sample through snapshot 8 of the "processing-for-variant-discovery-gatk4" workflow on Terra, and I'm consistently hitting the following error on the MergeBamAlignment step:

INFO 2019-07-02 03:36:35 AbstractAlignmentMerger Merged 375,000,000 records. Elapsed time: 02:27:06s. Time for last 1,000,000: 23s. Last read position: chr8:137,530,448
INFO 2019-07-02 03:36:35 AbstractAlignmentMerger 24457599 Reads have been unmapped due to being suspected of being Cross-species contamination.
[Tue Jul 02 03:36:52 UTC 2019] picard.sam.MergeBamAlignment done. Elapsed time: 147.42 minutes.
To get help, see
htsjdk.samtools.util.RuntimeIOException: Write error; BinaryCodec in writemode; streamed file (filename not available)
at htsjdk.samtools.util.BinaryCodec.writeBytes(
at htsjdk.samtools.util.BlockCompressedOutputStream.writeGzipBlock(
at htsjdk.samtools.util.BlockCompressedOutputStream.deflateBlock(
at htsjdk.samtools.util.BlockCompressedOutputStream.write(
at htsjdk.samt

A few notes:
1. I've tried increasing the java_opt and mem_size inputs of MergeBamAlignment to "-Xms7000m" and "7500 MB" respectively. Unsurprisingly, this didn't work, as the error seems to be in writing the output of MergeBamAlignment.
2. I've shared the workspace "pd-wgs-workspace" in the project "pd-wgs-project" with the FireCloud support group. The offending sample is "HDF111iPS501_D0_r1".
3. Attached is the full stderr log.

Thank you!


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