# Pick.pick output file **URL:** \ **Category:** Commands in mothur\ **Created:** [May 14, 2019, 1:51am UTC](https://forum.mothur.org/t/pick-pick-output-file/19893 "2019-05-14T01:51:04Z")\ **Posts on this page:** 8\ **Page:** 1
**Author:** ![Yogiara](https://avatars.discourse-cdn.com/v4/letter/y/a183cd/32.png) [@Yogiara](https://forum.mothur.org/u/Yogiara)\ **Post date:** [May 14, 2019, 1:51am UTC](https://forum.mothur.org/t/pick-pick-output-file/19893/1 "2019-05-14T01:51:05Z")
After command line remove.lineage, I want to proceed to get.groups step, but I can’t find \*.pick.pick.count\_table and \*.pick.pick fasta in my output file. Are there any steps that I missed? ---
**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:** [May 16, 2019, 5:08pm UTC](https://forum.mothur.org/t/pick-pick-output-file/19893/2 "2019-05-16T17:08:00Z")
What files does mothur tell you were generated as part of `remove.lineage`? Those should be the inputs to `get.groups`. Pat ---
**Author:** ![Yogiara](https://avatars.discourse-cdn.com/v4/letter/y/a183cd/32.png) [@Yogiara](https://forum.mothur.org/u/Yogiara)\ **Post date:** [May 20, 2019, 1:17am UTC](https://forum.mothur.org/t/pick-pick-output-file/19893/3 "2019-05-20T01:17:09Z")
The output file from remove.lineage is… oncom.trim.contigs.good.unique.good.filter.unique.precluster.pick.ezbiocloud\_id\_taxonomy.wang.pick.taxonomy For get.groups command, it needs count=oncom.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.count\_table and fasta=oncom.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta Those two files I couldn’t find in my output file. ---
**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:** [May 20, 2019, 4:55pm UTC](https://forum.mothur.org/t/pick-pick-output-file/19893/4 "2019-05-20T16:55:20Z")
did you include oncom.trim.contigs.good.unique.good.filter.unique.precluster.pick.fasta and oncom.trim.contigs.good.unique.good.filter.unique.precluster.pick.count\_table as parameter values when you ran `remove.lineage`? ---
**Author:** ![Yogiara](https://avatars.discourse-cdn.com/v4/letter/y/a183cd/32.png) [@Yogiara](https://forum.mothur.org/u/Yogiara)\ **Post date:** [May 22, 2019, 8:52am UTC](https://forum.mothur.org/t/pick-pick-output-file/19893/5 "2019-05-22T08:52:59Z")
Yes I did. I tried to repeat and resulted in the same output file : oncom.trim.contigs.good.unique.good.filter.unique.precluster.pick.ezbiocloud\_id\_taxonomy.wang.pick.taxonomy . ---
**Author:** ![catquart](https://avatars.discourse-cdn.com/v4/letter/c/b5ac83/32.png) [@catquart](https://forum.mothur.org/u/catquart)\ **Post date:** [May 22, 2019, 6:05pm UTC](https://forum.mothur.org/t/pick-pick-output-file/19893/6 "2019-05-22T18:05:38Z")
I am encountering a similar issue; the only output that I receive from remove.lineage is a pick.taxonomy file, NOT the \*pick.pick.count\_table or the \*pick.pick.fasta. Example below: > remove.lineage(fasta=pilot.trim.contigs.renamed.trim.unique.precluster.pick.fasta, count=pilot.trim.contigs.renamed.trim.unique.precluster.denovo.vsearch.pick.count\_table, taxonomy=pilot.trim.contigs.renamed.trim.unique.precluster.pick.UNITEv8\_sh\_dynamic.wang.taxonomy, taxon=unknown-Protista-Plantae) Output File Names: pilot.trim.contigs.renamed.trim.unique.precluster.pick.UNITEv8\_sh\_dynamic.wang.pick.taxonomy ---
**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:** [May 23, 2019, 5:25pm UTC](https://forum.mothur.org/t/pick-pick-output-file/19893/7 "2019-05-23T17:25:17Z")
Are you using our current version? Are all your reads removed? Or none of them? Could you send your log, fasta, count and taxonomy files to [mothur.bugs@gmail.com](mailto:mothur.bugs@gmail.com)? ---
**Author:** ![system](https://yyz2.discourse-cdn.com/flex036/user_avatar/forum.mothur.org/system/32/2_2.png) [@system](https://forum.mothur.org/u/system)\ **Post date:** [June 2, 2019, 5:25pm UTC](https://forum.mothur.org/t/pick-pick-output-file/19893/8 "2019-06-02T17:25:25Z")
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