picard 2.10.7 fails pipelining SortSam and SetNmAndUqTags

[sooheelee]

From a forum user a bug in v2.10.7 that is not in v2.10.6.

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My findings:

• Picard 2.10.6 works fine with pipelined SortSam and SetNmMdAndUqTags/SetNmAndUqTags at the moment.
• Picard 2.10.7 fails both pipelined configurations.
• Picard 2.10.7 works both configurations without pipelining.

This Issue was generated from your [forums]
[forums]: https://gatkforums.broadinstitute.org/gatk/discussion/comment/41160#Comment_41160

[sooheelee]

I'm not sure who's attention to bring this to. @ktibbett, can you please pass on to the appropriate developer?

[sooheelee]

User follows up:

Looks like the problem is solved in later versions now. I tested only 2.10.9 and pipelining works properly.

So I will close this issue.