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MAFFT binary returns exit code 0 when its own child process is killed (OOM) #34

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ebolyen opened this issue Jun 28, 2017 · 3 comments
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MAFFT binary returns exit code 0 when its own child process is killed (OOM) #34

ebolyen opened this issue Jun 28, 2017 · 3 comments
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type:bug Something is wrong.

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@ebolyen
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ebolyen commented Jun 28, 2017

This came up on the forum.

I believe upgrading our mafft binary will fix this, as there is a changelog note that says:

  • Fixed a long-standing problem on exit code.

But as of right now users will get this error:

InPath('/tmp/q2-AlignedDNAFASTAFormat-e5oap_ts') is not formatted as a
  AlignedDNAFASTAFormat file.

which is misleading.
@ebolyen ebolyen added the type:bug Something is wrong. label Jun 28, 2017
@ebolyen ebolyen mentioned this issue Jun 28, 2017
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@jairideout jairideout self-assigned this Aug 25, 2017
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jairideout commented Aug 25, 2017 •
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I tried out mafft 7.310 (latest version available from bioconda) and the exit code issue is resolved! 🎉

We can't upgrade from mafft 7.221 yet because deblur requires that exact version. I'll get in touch with the deblur devs to see about updating.

@jairideout jairideout mentioned this issue Aug 25, 2017
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This issue came up on the forum again today.

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Fixed in #39

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