# trim.seqs, only one group file from allfiles

**URL:** <https://forum.mothur.org/t/trim-seqs-only-one-group-file-from-allfiles/485>\
**Category:** mothur bugs\
**Created:** [March 2, 2011, 8:40pm UTC](https://forum.mothur.org/t/trim-seqs-only-one-group-file-from-allfiles/485 "2011-03-02T20:40:09Z")\
**Posts on this page:** 4\
**Page:** 1

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**Author:** ![jwhite](https://avatars.discourse-cdn.com/v4/letter/j/d26b3c/32.png) [@jwhite](https://forum.mothur.org/u/jwhite)\
**Post date:** [March 2, 2011, 8:40pm UTC](https://forum.mothur.org/t/trim-seqs-only-one-group-file-from-allfiles/485/1 "2011-03-02T20:40:09Z")

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Hello everyone,

Under 1.16, trim.seqs with allfiles=T would generate one groups file per sample, as is documented in the manual. However, the behavior has changed in 1.17 (affecting both 1.17.0 and 1.17.2) to only output a single groups file, regardless of the value of allfiles.

I suspect this is a bug, as there appears to have been major refactoring of trimseqscommand.cpp between 1.16 and 1.17, but please let me know if I’m misunderstanding what I should expect from allfiles.

Thank you very much!  
Jared

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**Author:** ![pschloss](https://yyz2.discourse-cdn.com/flex036/user_avatar/forum.mothur.org/pschloss/32/4_2.png) [@pschloss](https://forum.mothur.org/u/pschloss)\
**Post date:** [March 3, 2011, 12:46pm UTC](https://forum.mothur.org/t/trim-seqs-only-one-group-file-from-allfiles/485/2 "2011-03-03T12:46:48Z")

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Jared - thanks for bringing this to our attention - we’re on it. There was a big change between 1.16 and 1.17 in trim.seqs and I managed to screw up a few things (this is what happens when a PI starts mucking with stuff).

Pat

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**Author:** ![westcott](https://yyz2.discourse-cdn.com/flex036/user_avatar/forum.mothur.org/westcott/32/18_2.png) [@westcott](https://forum.mothur.org/u/westcott)\
**Post date:** [March 4, 2011, 4:01pm UTC](https://forum.mothur.org/t/trim-seqs-only-one-group-file-from-allfiles/485/3 "2011-03-04T16:01:17Z")

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We are working on this, but here’s a workaround that will get you the group files you want.

list.seqs(fasta=yourFasta.groupName.fasta)  
get.seqs(group=yourGroupfile, accnos=yourFasta.groupName.accnos)

This will ouput a yourGroupFile.pick.groups file which you will want to rename so that you know which fasta file it relates to.

example:  
list.seqs(fasta=f5m.700015283.v13.rep3.wu.fasta)  
get.seqs(group=f5m.groups, accnos=f5m.700015283.v13.rep3.wu.accnos)

creates f5m.pick.groups which I would rename to f5m.700015283.v13.rep3.wu.groups.

I hope this helps,

Sarah

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**Author:** ![jwhite](https://avatars.discourse-cdn.com/v4/letter/j/d26b3c/32.png) [@jwhite](https://forum.mothur.org/u/jwhite)\
**Post date:** [March 7, 2011, 3:18pm UTC](https://forum.mothur.org/t/trim-seqs-only-one-group-file-from-allfiles/485/4 "2011-03-07T15:18:25Z")

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Thank you both!

– jared