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Picard MergeBamAlignment issue #186

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vdauwera opened this issue Mar 30, 2015 · 7 comments

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@vdauwera
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commented Mar 30, 2015

Exception merging bam alignment due to sort error. User has provided snippets for debugging.

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commented Apr 26, 2015

@chandrans Would you be able to process this bug report?

@vdauwera vdauwera added the 1 - Ready label Apr 26, 2015

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commented Apr 26, 2015

Yes, I think I can handle it.

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commented Jul 27, 2015

It looks like his ALIGNED_BAM input is missing read group information. When I run Validate Sam File, it gives a long list of reads missing read group information.

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commented Jul 27, 2015

@chandrans Please post a representative section of the validation error output.

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commented Jul 27, 2015

The error message I get from MergeBamAlignment is:
Exception in thread "main" java.lang.IllegalStateException: Aligned record iterator (HS3:608:C6LNLACXX:7:1101:10082:8616) is behind the unmapped reads (HS3:608:C6LNLACXX:7:1101:10083:36394)

The error message from ValidateSamFile:
ERROR: Read groups is empty
WARNING: Read name HS3:608:C6LNLACXX:7:1316:15889:69616, A record is missing a read group
WARNING: Read name HS3:608:C6LNLACXX:7:1107:13342:90541, A record is missing a read group
WARNING: Read name HS3:608:C6LNLACXX:7:2208:4239:16257, A record is missing a read group
WARNING: Read name HS3:608:C6LNLACXX:7:2303:18152:26068, A record is missing a read group
WARNING: Read name HS3:608:C6LNLACXX:7:1209:14098:5489, A record is missing a read group
WARNING: Read name HS3:608:C6LNLACXX:7:2105:15796:95595, A record is missing a read group
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up to 100 (max) errors for record missing read group. This is for the ALIGNED_BAM that goes into MergeBamAlignment.

@vdauwera vdauwera removed the 1 - Ready label Feb 12, 2016

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commented May 27, 2016

I've seen this MergeBamAlignment error. If this is not resolved, let me know and I can dig through my notes on what this was about.

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commented May 30, 2016

OOh it looks like your suggestion resolved the latest user's error @sooheelee 👍

@chandrans chandrans closed this May 30, 2016

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