# remove.lineage output file reverts to size 0

**URL:** <https://forum.mothur.org/t/remove-lineage-output-file-reverts-to-size-0/1893>\
**Category:** mothur bugs\
**Created:** [June 13, 2014, 9:59pm UTC](https://forum.mothur.org/t/remove-lineage-output-file-reverts-to-size-0/1893 "2014-06-13T21:59:10Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![mbakker](https://avatars.discourse-cdn.com/v4/letter/m/82dd89/32.png) [@mbakker](https://forum.mothur.org/u/mbakker)\
**Post date:** [June 13, 2014, 9:59pm UTC](https://forum.mothur.org/t/remove-lineage-output-file-reverts-to-size-0/1893/1 "2014-06-13T21:59:10Z")

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Had a funny thing happen with remove.lineage (windows version 1.33.3). I had thrown in all the different file types together. Checking on the progress of the command, I saw the \*.names file accumulate size, but when the command was done, it was listed as 0 bytes.

From the logfile:

mothur \> remove.lineage(taxonomy=MiSeq\_flipped.unique.pick.subsample.silva.wang.taxonomy, fasta=MiSeq\_flipped.unique.pick.subsample.fasta, name=MiSeq\_flipped.unique.pick.subsample.names, group=MiSeq.pick.subsample.groups, taxon=‘unknown;’)

Output File Names:  
H:\ManuscriptsPresentations\CSU\_SoilAmendments\NewDataAnalysis\MiSeq\_flipped.unique.pick.subsample.silva.wang.pick.taxonomy  
H:\ManuscriptsPresentations\CSU\_SoilAmendments\NewDataAnalysis\MiSeq\_flipped.unique.pick.subsample.pick.names  
H:\ManuscriptsPresentations\CSU\_SoilAmendments\NewDataAnalysis\MiSeq\_flipped.unique.pick.subsample.pick.fasta  
H:\ManuscriptsPresentations\CSU\_SoilAmendments\NewDataAnalysis\MiSeq.pick.subsample.pick.groups

[WARNING]: your sequence names contained ‘:’. I changed them to ‘\_’ to avoid problems in your downstream analysis.

mothur \>  
[ERROR]: You are missing (  
Invalid.  
[WARNING]: your sequence names contained ‘:’. I changed them to ‘\_’ to avoid problems in your downstream analysis.

mothur \>  
[ERROR]: You are missing (  
Invalid.  
[WARNING]: your sequence names contained ‘:’. I changed them to ‘\_’ to avoid problems in your downstream analysis.

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<div class="post-metadata">

**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:** [June 17, 2014, 8:30pm UTC](https://forum.mothur.org/t/remove-lineage-output-file-reverts-to-size-0/1893/2 "2014-06-17T20:30:09Z")

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Can you try it without the single quote marks? Just put taxon=unknown. Ideally there won’t be anything removed.