# Mothur removing group after screen.seqs command? **URL:** \ **Category:** Theory behind mothur\ **Created:** [October 23, 2017, 10:32pm UTC](https://forum.mothur.org/t/mothur-removing-group-after-screen-seqs-command/3428 "2017-10-23T22:32:31Z")\ **Posts on this page:** 5\ **Page:** 1
**Author:** ![sekhwal](https://avatars.discourse-cdn.com/v4/letter/s/b38774/32.png) [@sekhwal](https://forum.mothur.org/u/sekhwal)\ **Post date:** [October 23, 2017, 10:32pm UTC](https://forum.mothur.org/t/mothur-removing-group-after-screen-seqs-command/3428/1 "2017-10-23T22:32:31Z")
Hi, I am analyzing MiSeq data of nifH gene with a nifH databasein fasta format [http://www.css.cornell.edu/faculty/buckley/nifh.htm](http://www.css.cornell.edu/faculty/buckley/nifh.htm). But, Mothur removing all sequences in the groups with following message— “Removing group: CB1\_NP because all sequences have been removed” while using screen.seqs command. Please suggest. ---
**Author:** ![campenr](https://avatars.discourse-cdn.com/v4/letter/c/8dc957/32.png) [@campenr](https://forum.mothur.org/u/campenr)\ **Post date:** [October 24, 2017, 1:01pm UTC](https://forum.mothur.org/t/mothur-removing-group-after-screen-seqs-command/3428/2 "2017-10-24T13:01:14Z")
The message would appear to indicate that your screen.seqs command is too harsh, and is removing all of your sequences. Perhaps you need to alter some of the parameters to be more relaxed? ---
**Author:** ![sekhwal](https://avatars.discourse-cdn.com/v4/letter/s/b38774/32.png) [@sekhwal](https://forum.mothur.org/u/sekhwal)\ **Post date:** [October 24, 2017, 4:20pm UTC](https://forum.mothur.org/t/mothur-removing-group-after-screen-seqs-command/3428/3 "2017-10-24T16:20:42Z")
Yes, i am just running command without any parameters. Further, while using filter.seqs and unique.seqs commands, Mothur removing all data and making blank output file for chimera.uchime command. Let me show the process------------ summary.seqs(fasta=stability.trim.contigs.good.unique.align, count=stability.trim.contigs.good.count\_table) Using 1 processors. Start End NBases Ambigs Polymer NumSeqs Minimum: 0 0 0 0 1 1 2.5%-tile: 247 247 1 0 1 184 25%-tile: 358 1097 8 0 2 1837 Median: 364 1103 367 0 6 3673 75%-tile: 534 1103 386 0 7 5509 97.5%-tile: 1686 1772 392 0 7 7161 Maximum: 1772 1772 427 0 12 7344 Mean: 635.301 1109.05 237.035 0 4.57979 # of unique seqs: 6840 total # of seqs: 7344 screen.seqs(fasta=stability.trim.contigs.good.unique.align, count=stability.trim.contigs.good.count\_table, summary=stability.trim.contigs.good.unique.summary) Output File Names: stability.trim.contigs.good.unique.good.summary stability.trim.contigs.good.unique.good.align stability.trim.contigs.good.unique.bad.accnos stability.trim.contigs.good.good.count\_table It took 2 secs to screen 6840 sequences. filter.seqs(fasta=stability.trim.contigs.good.unique.good.align, vertical=T, trump=.) Length of filtered alignment: 0 Number of columns removed: 1772 Length of the original alignment: 1772 Number of sequences used to construct filter: 4808 Output File Names: stability.filter stability.trim.contigs.good.unique.good.filter.fasta unique.seqs(fasta=stability.trim.contigs.good.unique.good.filter.fasta, count=stability.trim.contigs.good.good.count\_table) Output File Names: stability.trim.contigs.good.unique.good.filter.count\_table stability.trim.contigs.good.unique.good.filter.unique.fasta pre.cluster(fasta=stability.trim.contigs.good.unique.good.filter.unique.fasta, count=stability.trim.contigs.good.unique.good.filter.count\_table, diffs=0) Output File Names: stability.trim.contigs.good.unique.good.filter.unique.precluster.fasta stability.trim.contigs.good.unique.good.filter.unique.precluster.count\_table stability.trim.contigs.good.unique.good.filter.unique.precluster.W1\_100.map stability.trim.contigs.good.unique.good.filter.unique.precluster.W4\_100.map stability.trim.contigs.good.unique.good.filter.unique.precluster.W5\_100.map chimera.uchime(fasta=stability.trim.contigs.good.unique.good.filter.unique.precluster.fasta, count=stability.trim.contigs.good.unique.good.filter.unique.precluster.count\_table, dereplicate=t) [ERROR]: stability.trim.contigs.good.unique.good.filter.unique.precluster.denovo.uchime.chimerasW5\_100 is blank. Please correct. ---
**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:** [October 30, 2017, 10:53am UTC](https://forum.mothur.org/t/mothur-removing-group-after-screen-seqs-command/3428/4 "2017-10-30T10:53:59Z")
You have to select start and end positions in screen.seqs. you might try start=534 / end=1103. This will keep anything that starts before 534 and ends after 1103. Pat ---
**Author:** ![sekhwal](https://avatars.discourse-cdn.com/v4/letter/s/b38774/32.png) [@sekhwal](https://forum.mothur.org/u/sekhwal)\ **Post date:** [November 2, 2017, 5:22pm UTC](https://forum.mothur.org/t/mothur-removing-group-after-screen-seqs-command/3428/5 "2017-11-02T17:22:42Z")
Thanks, I got understand. 🙂