# spliting, removing, remerging **URL:** \ **Category:** mothur bugs\ **Created:** [February 8, 2018, 9:15pm UTC](https://forum.mothur.org/t/spliting-removing-remerging/3489 "2018-02-08T21:15:08Z")\ **Posts on this page:** 9\ **Page:** 1
**Author:** ![Alex\_Thibodeau](https://avatars.discourse-cdn.com/v4/letter/a/e9a140/32.png) [@Alex\_Thibodeau](https://forum.mothur.org/u/Alex_Thibodeau)\ **Post date:** [February 8, 2018, 9:15pm UTC](https://forum.mothur.org/t/spliting-removing-remerging/3489/1 "2018-02-08T21:15:08Z")
Hello everybody. It is probably my brain that is freezing but I have a problem. For some reasons (too long to write), I need to split a fasta file and a count file (after chimera removal) in “2 dataset”. After I need to remove sequences from somes groups (negative controls) in dataset1 only, and to remerge the new fasta and count file with dataset 2. when I use merge.count, I get an error saying that [ERROR]: Your count table contains more than 1 sequence named M00833\_602\_000000000-BGWRN\_1\_1101\_10149\_9615, sequence names must be unique. Please correct. Which is weird because the original fasta and count are uniques… So please help. The workaround, I believe, would be to analyze dataset 1 and remove the sequences right after chimera removal, run data set 2 as usual, merge the two data sets, create OTUs, write a paper, live a happy life. But a faster approach would befit me. So please, if you have any cue, I could use some help. Here are my commands lines (yea I know, lots of groups to be removed we went frenzy on controls this time around). \*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\* #remove data set 2 from initial file to create dataset1 remove.groups(fasta=sandrine.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.pick.fasta, count=sandrine.trim.contigs.good.unique.good.filter.unique.precluster.denovo.vsearch.pick.pick.pick.count\_table, groups=48B14semF-48B1J0F-48B24semF-48B2J0F-48B34semF-48B3J0F-48B44semF-48B4J0F-48C14semF-48C1J0F-48C24semF-48C2J0F-48C34semF-48C3J0F-48C44semF-48C4J0F-48D14semF-48D1J0F-48D24semF-48D2J0F-48D34semF-48D3J0F-48D44semF-48D4J0F-714semF-71J0F-724semF-72J0F-734semF-73J0F-744semF-74J0F-HB314semF-HB31J0F-HB324semF-HB32J0F-HB334semF-HB33J0F-HB344semF-HB34J0F-LAND114semF-LAND11J0F-LAND124semF-LAND12J0F-LAND134semF-LAND13J0F-LAND14J0F-LAND414semF-LAND41J0F-LAND424semF-LAND42J0F-LAND434semF-LAND43J0F-LAND44J0F-LI114semF-LI11J0F-LI124semF-LI12J0F-LI134semF-LI13J0F-LI144semF-LI14J0F-LI214semF-LI21J0F-LI224semF-LI22J0F-LI234semF-LI23J0F-LI244semF-LI24J0F-M2214semF-M221J0F-M2224semF-M222J0F-M2234semF-M223J0F-M2244semF-M224J0F-M714semF-M71J0F-M724semF-M72J0F-M734semF-M73J0F-M744semF-M74J0F-M814semF-M81J0F-M824semF-M82J0F-M834semF-M83J0F-M844semF-M84J0F-Communautefeces) summary.seqs(fasta=current, count=current) count.groups(count=current) #remove what is not control from in dataset1 remove.groups(fasta=current, count=current, groups=M87J0-M86J0-M85J0-M84J0-M83J0-M82J0-M81J0-M77J0-M76J0-M75J0-M74J0-M73J0-M72J0-M71J0-LAND46J0-LAND45J0-LAND44J0-LAND43J0-LAND42J0-LAND41J0-LAND16J0-LAND15J0-LAND14J0-LAND13J0-LAND12J0-LAND11J0-48B7J0-48B6J0-48B5J0-48B4J0-48B3J0-48B2J0-48B1J0-M874sem-M864sem-M854sem-M844sem-M834sem-M824sem-M814sem-M774sem-M764sem-M754sem-M744sem-M734sem-M724sem-M714sem-LAND464sem-LAND454sem-LAND444sem-LAND434sem-LAND424sem-LAND414sem-LAND164sem-LAND154sem-LAND144sem-LAND134sem-LAND124sem-LAND114sem-48B74sem-48B64sem-48B54sem-48B44sem-48B34sem-48B24sem-48B14sem-48D1J0-48D2J0-48D3J0-48D4J0-48D5J0-48D6J0-48D7J0-48D14sem-48D24sem-48D34sem-48D44sem-48D54sem-48D64sem-48D74sem-M2274sem-M2264sem-M2254sem-M2244sem-M2234sem-M2224sem-M2214sem-LI27J0-LI26J0-LI25J0-LI24J0-LI23J0-LI22J0-LI21J0-LI17J0-LI16J0-LI15J0-LI14J0-LI13J0-LI12J0-LI11J0-LI274sem-LI264sem-LI254sem-LI244sem-LI234sem-LI224sem-LI214sem-LI174sem-LI164sem-LI154sem-LI144sem-LI134sem-LI124sem-LI114sem-HB374sem-HB364sem-HB354sem-HB344sem-HB334sem-HB324sem-HB314sem-774sem-764sem-754sem-744sem-734sem-724sem-714sem-48C1J0-48C2J0-48C3J0-48C4J0-48C5J0-48C6J0-71J0-72J0-73J0-74J0-75J0-76J0-HB31J0-HB32J0-HB33J0-HB34J0-HB35J0-HB36J0-M221J0-M222J0-M223J0-M224J0-M225J0-M226J0-48C7J0-77J0-HB37J0-M227J0-48C74sem-48C64sem-48C54sem-48C44sem-48C34sem-48C24sem-48C14sem-Communauteouef1-Communauteouef2) summary.seqs(fasta=current, count=current) count.groups(count=current) list.seqs(count=current) #remove sequences from full dataset1 remove.seqs(accnos=sandrine.trim.contigs.good.unique.good.filter.unique.precluster.denovo.vsearch.pick.pick.pick.pick.pick.accnos, fasta=sandrine.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.pick.pick.fasta, count=sandrine.trim.contigs.good.unique.good.filter.unique.precluster.denovo.vsearch.pick.pick.pick.pick.count\_table) summary.seqs(fasta=current, count=current) count.groups(count=current) unique.seqs(fasta=current, count=current) #remove dataset 1 from initial file to create dataset 2 remove.groups(fasta=sandrine.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.pick.fasta, count=sandrine.trim.contigs.good.unique.good.filter.unique.precluster.denovo.vsearch.pick.pick.pick.count\_table, groups=48B14sem-48B1J0-48B24sem-48B2J0-48B34sem-48B3J0-48B44sem-48B4J0-48B54sem-48B5J0-48B64sem-48B6J0-48B74sem-48B7J0-48B8ctrl4sem-48B8ctrlJ0-48C14sem-48C1J0-48C24sem-48C2J0-48C34sem-48C3J0-48C44sem-48C4J0-48C54sem-48C5J0-48C64sem-48C6J0-48C74sem-48C7J0-48C8ctrl4sem-48C8ctrlJ0-48D14sem-48D1J0-48D24sem-48D2J0-48D34sem-48D3J0-48D44sem-48D4J0-48D54sem-48D5J0-48D64sem-48D6J0-48D74sem-48D7J0-48D8ctrl4sem-48D8ctrlJ0-714sem-71J0-724sem-72J0-734sem-73J0-744sem-74J0-754sem-75J0-764sem-76J0-774sem-77J0-78ctrl4sem-78ctrlJ0-Communauteouef1-Communauteouef2-H20\_oeuf1-H20\_oeuf2-HB314sem-HB31J0-HB324sem-HB32J0-HB334sem-HB33J0-HB344sem-HB34J0-HB354sem-HB35J0-HB364sem-HB36J0-HB374sem-HB37J0-HB38ctrl4sem-HB38ctrlJ0-LAND114sem-LAND11J0-LAND124sem-LAND12J0-LAND134sem-LAND13J0-LAND144sem-LAND14J0-LAND154sem-LAND15J0-LAND164sem-LAND16J0-LAND18ctrlJ0-LAND414sem-LAND41J0-LAND424sem-LAND42J0-LAND434sem-LAND43J0-LAND444sem-LAND44J0-LAND454sem-LAND45J0-LAND464sem-LAND46J0-LAND48ctrl4sem-LAND48ctrlJ0-LI114sem-LI11J0-LI124sem-LI12J0-LI134sem-LI13J0-LI144sem-LI14J0-LI154sem-LI15J0-LI164sem-LI16J0-LI174sem-LI17J0-LI18ctrl4sem-LI18ctrlJ0-LI214sem-LI21J0-LI224sem-LI22J0-LI234sem-LI23J0-LI244sem-LI24J0-LI254sem-LI25J0-LI264sem-LI26J0-LI274sem-LI27J0-LI28ctrl4sem-LI28ctrlJ0-Land18ctrl4sem-M2214sem-M221J0-M2224sem-M222J0-M2234sem-M223J0-M2244sem-M224J0-M2254sem-M225J0-M2264sem-M226J0-M2274sem-M227J0-M228ctrl4sem-M228ctrlJ0-M714sem-M71J0-M724sem-M72J0-M734sem-M73J0-M744sem-M74J0-M754sem-M75J0-M764sem-M76J0-M774sem-M77J0-M78ctrl4sem-M78ctrlJ0-M814sem-M81J0-M824sem-M82J0-M834sem-M83J0-M844sem-M84J0-M854sem-M85J0-M864sem-M86J0-M874sem-M87J0-M87ctrl4sem-M88ctrlJ0) summary.seqs(fasta=current, count=current) count.groups(count=current) unique.seqs(fasta=current, count=current) #merge count merge.count(count=sandrine.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.pick.pick.pick.count\_table-sandrine.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.pick.pick.count\_table, output=merge.count\_table) #merge is not working so I did not went further. merge.files(input=sandrine.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.pick.pick.pick.unique.fasta-sandrine.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.pick.pick.unique.fasta, output=merge.fasta) unique.seqs(fasta=current, count=current) summary.seqs(fasta=merge.fasta, count=merge.fasta) * * * ---
**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:** [February 12, 2018, 9:47pm UTC](https://forum.mothur.org/t/spliting-removing-remerging/3489/2 "2018-02-12T21:47:21Z")
I think the issue you are having could be from the commands overwriting the files. Renaming should resolve it for you. #remove dataset 2 from initial file to create dataset1 remove.groups(fasta=sandrine.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.pick.fasta, count=sandrine.trim.contigs.good.unique.good.filter.unique.precluster.denovo.vsearch.pick.pick.pick.count\_table, groups=48B14semF-48B1J0F-48B24semF-48B2J0F-48B34semF-48B3J0F-48B44semF-48B4J0F-48C14semF-48C1J0F-48C24semF-48C2J0F-48C34semF-48C3J0F-48C44semF-48C4J0F-48D14semF-48D1J0F-48D24semF-48D2J0F-48D34semF-48D3J0F-48D44semF-48D4J0F-714semF-71J0F-724semF-72J0F-734semF-73J0F-744semF-74J0F-HB314semF-HB31J0F-HB324semF-HB32J0F-HB334semF-HB33J0F-HB344semF-HB34J0F-LAND114semF-LAND11J0F-LAND124semF-LAND12J0F-LAND134semF-LAND13J0F-LAND14J0F-LAND414semF-LAND41J0F-LAND424semF-LAND42J0F-LAND434semF-LAND43J0F-LAND44J0F-LI114semF-LI11J0F-LI124semF-LI12J0F-LI134semF-LI13J0F-LI144semF-LI14J0F-LI214semF-LI21J0F-LI224semF-LI22J0F-LI234semF-LI23J0F-LI244semF-LI24J0F-M2214semF-M221J0F-M2224semF-M222J0F-M2234semF-M223J0F-M2244semF-M224J0F-M714semF-M71J0F-M724semF-M72J0F-M734semF-M73J0F-M744semF-M74J0F-M814semF-M81J0F-M824semF-M82J0F-M834semF-M83J0F-M844semF-M84J0F-Communautefeces) #creates sandrine.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.pick.pick.fasta, lets’s rename it to help keep things straight. rename.file(fasta=current, count=current, prefix=dataset1\_control) summary.seqs(fasta=current, count=current) - dataset1\_control.fasta, dataset1\_control.count\_table count.groups(count=current) #remove what is not control from in dataset1 remove.groups(fasta=current, count=current, groups=M87J0-M86J0-M85J0-M84J0-M83J0-M82J0-M81J0-M77J0-M76J0-M75J0-M74J0-M73J0-M72J0-M71J0-LAND46J0-LAND45J0-LAND44J0-LAND43J0-LAND42J0-LAND41J0-LAND16J0-LAND15J0-LAND14J0-LAND13J0-LAND12J0-LAND11J0-48B7J0-48B6J0-48B5J0-48B4J0-48B3J0-48B2J0-48B1J0-M874sem-M864sem-M854sem-M844sem-M834sem-M824sem-M814sem-M774sem-M764sem-M754sem-M744sem-M734sem-M724sem-M714sem-LAND464sem-LAND454sem-LAND444sem-LAND434sem-LAND424sem-LAND414sem-LAND164sem-LAND154sem-LAND144sem-LAND134sem-LAND124sem-LAND114sem-48B74sem-48B64sem-48B54sem-48B44sem-48B34sem-48B24sem-48B14sem-48D1J0-48D2J0-48D3J0-48D4J0-48D5J0-48D6J0-48D7J0-48D14sem-48D24sem-48D34sem-48D44sem-48D54sem-48D64sem-48D74sem-M2274sem-M2264sem-M2254sem-M2244sem-M2234sem-M2224sem-M2214sem-LI27J0-LI26J0-LI25J0-LI24J0-LI23J0-LI22J0-LI21J0-LI17J0-LI16J0-LI15J0-LI14J0-LI13J0-LI12J0-LI11J0-LI274sem-LI264sem-LI254sem-LI244sem-LI234sem-LI224sem-LI214sem-LI174sem-LI164sem-LI154sem-LI144sem-LI134sem-LI124sem-LI114sem-HB374sem-HB364sem-HB354sem-HB344sem-HB334sem-HB324sem-HB314sem-774sem-764sem-754sem-744sem-734sem-724sem-714sem-48C1J0-48C2J0-48C3J0-48C4J0-48C5J0-48C6J0-71J0-72J0-73J0-74J0-75J0-76J0-HB31J0-HB32J0-HB33J0-HB34J0-HB35J0-HB36J0-M221J0-M222J0-M223J0-M224J0-M225J0-M226J0-48C7J0-77J0-HB37J0-M227J0-48C74sem-48C64sem-48C54sem-48C44sem-48C34sem-48C24sem-48C14sem-Communauteouef1-Communauteouef2) #creates dataset1\_control.pick.fasta, lets’s rename it to help keep things straight. rename.file(fasta=current, count=current, prefix=control) - control.fasta, control.count\_table summary.seqs(fasta=current, count=current) count.groups(count=current) list.seqs(count=current) - this should be all the sequences in the control set for dataset1 #remove control sequences from full dataset1 remove.seqs(accnos=control.accnos, fasta=dataset1\_control.fasta, count=dataset1\_control.count\_table) - creates a file containing only the dataset1 sequences #creates dataset1\_control.pick.fasta, lets’s rename it to help keep things straight. rename.file(fasta=current, count=current, prefix=dataset1) - dataset1.fasta, dataset1.count\_table summary.seqs(fasta=current, count=current) count.groups(count=current) unique.seqs(fasta=current, count=current) #remove dataset 1 from initial file to create dataset 2 - alternatively you could use the remove.seqs command here remove.groups(fasta=sandrine.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.pick.fasta, count=sandrine.trim.contigs.good.unique.good.filter.unique.precluster.denovo.vsearch.pick.pick.pick.count\_table, groups=48B14sem-48B1J0-48B24sem-48B2J0-48B34sem-48B3J0-48B44sem-48B4J0-48B54sem-48B5J0-48B64sem-48B6J0-48B74sem-48B7J0-48B8ctrl4sem-48B8ctrlJ0-48C14sem-48C1J0-48C24sem-48C2J0-48C34sem-48C3J0-48C44sem-48C4J0-48C54sem-48C5J0-48C64sem-48C6J0-48C74sem-48C7J0-48C8ctrl4sem-48C8ctrlJ0-48D14sem-48D1J0-48D24sem-48D2J0-48D34sem-48D3J0-48D44sem-48D4J0-48D54sem-48D5J0-48D64sem-48D6J0-48D74sem-48D7J0-48D8ctrl4sem-48D8ctrlJ0-714sem-71J0-724sem-72J0-734sem-73J0-744sem-74J0-754sem-75J0-764sem-76J0-774sem-77J0-78ctrl4sem-78ctrlJ0-Communauteouef1-Communauteouef2-H20\_oeuf1-H20\_oeuf2-HB314sem-HB31J0-HB324sem-HB32J0-HB334sem-HB33J0-HB344sem-HB34J0-HB354sem-HB35J0-HB364sem-HB36J0-HB374sem-HB37J0-HB38ctrl4sem-HB38ctrlJ0-LAND114sem-LAND11J0-LAND124sem-LAND12J0-LAND134sem-LAND13J0-LAND144sem-LAND14J0-LAND154sem-LAND15J0-LAND164sem-LAND16J0-LAND18ctrlJ0-LAND414sem-LAND41J0-LAND424sem-LAND42J0-LAND434sem-LAND43J0-LAND444sem-LAND44J0-LAND454sem-LAND45J0-LAND464sem-LAND46J0-LAND48ctrl4sem-LAND48ctrlJ0-LI114sem-LI11J0-LI124sem-LI12J0-LI134sem-LI13J0-LI144sem-LI14J0-LI154sem-LI15J0-LI164sem-LI16J0-LI174sem-LI17J0-LI18ctrl4sem-LI18ctrlJ0-LI214sem-LI21J0-LI224sem-LI22J0-LI234sem-LI23J0-LI244sem-LI24J0-LI254sem-LI25J0-LI264sem-LI26J0-LI274sem-LI27J0-LI28ctrl4sem-LI28ctrlJ0-Land18ctrl4sem-M2214sem-M221J0-M2224sem-M222J0-M2234sem-M223J0-M2244sem-M224J0-M2254sem-M225J0-M2264sem-M226J0-M2274sem-M227J0-M228ctrl4sem-M228ctrlJ0-M714sem-M71J0-M724sem-M72J0-M734sem-M73J0-M744sem-M74J0-M754sem-M75J0-M764sem-M76J0-M774sem-M77J0-M78ctrl4sem-M78ctrlJ0-M814sem-M81J0-M824sem-M82J0-M834sem-M83J0-M844sem-M84J0-M854sem-M85J0-M864sem-M86J0-M874sem-M87J0-M87ctrl4sem-M88ctrlJ0) #creates sandrine.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.pick.pick.fasta, lets’s rename it to help keep things straight. rename.file(fasta=current, count=current, prefix=dataset2) dataset2.fasta, dataset2.count\_table summary.seqs(fasta=current, count=current) count.groups(count=current) unique.seqs(fasta=current, count=current) #merge counts of dataset1 and dataset2 merge.count(count=current-dataset1.unique.count\_table, output=merge.count\_table) merge.files(input=dataset1.unique.fasta-dataset2.unique.fasta, output=merge.fasta) unique.seqs(fasta=merge.fasta, count=merge.count\_table) summary.seqs(fasta=current, count=current) ---
**Author:** ![Alex\_Thibodeau](https://avatars.discourse-cdn.com/v4/letter/a/e9a140/32.png) [@Alex\_Thibodeau](https://forum.mothur.org/u/Alex_Thibodeau)\ **Post date:** [February 13, 2018, 3:42pm UTC](https://forum.mothur.org/t/spliting-removing-remerging/3489/3 "2018-02-13T15:42:32Z")
Thank Sarah for pointing that out, I will try this and will post the results back. ---
**Author:** ![Alex\_Thibodeau](https://avatars.discourse-cdn.com/v4/letter/a/e9a140/32.png) [@Alex\_Thibodeau](https://forum.mothur.org/u/Alex_Thibodeau)\ **Post date:** [February 13, 2018, 4:06pm UTC](https://forum.mothur.org/t/spliting-removing-remerging/3489/4 "2018-02-13T16:06:11Z")
It, unfortunately, was not the case. I still have the same error message. I will try the long road. I will report back. ---
**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:** [February 13, 2018, 5:27pm UTC](https://forum.mothur.org/t/spliting-removing-remerging/3489/5 "2018-02-13T17:27:44Z")
If you send your input files to [mothur.bugs@gmail.com](mailto:mothur.bugs@gmail.com), I will take a look. ---
**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:** [February 13, 2018, 7:39pm UTC](https://forum.mothur.org/t/spliting-removing-remerging/3489/6 "2018-02-13T19:39:56Z")
Hi Alexandre, Thanks for sending your files. When I take a closer look at sequence M00833\_602\_000000000-BGWRN\_1\_1101\_10149\_9615, I can see it belongs to dataset1 and dataset2. M00833\_602\_000000000-BGWRN\_1\_1101\_10149\_9615 is represented in 5 groups as follows: 48C44sem = dataset1 48D24sem = dataset1 48D4J0 = dataset1 LI12J0 = dataset1 LI21J0F = dataset2 When mothur tries to merge the files, it fails because it’s not sure which counts for M00833\_602\_000000000-BGWRN\_1\_1101\_10149\_9615 you want to keep. M00833\_602\_000000000-BGWRN\_1\_1101\_10149\_9615 … 0 0 0 0 4 … or M00833\_602\_000000000-BGWRN\_1\_1101\_10149\_9615 … 1 2 1 3 0 … Kindly, Sarah Westcott ---
**Author:** ![Alex\_Thibodeau](https://avatars.discourse-cdn.com/v4/letter/a/e9a140/32.png) [@Alex\_Thibodeau](https://forum.mothur.org/u/Alex_Thibodeau)\ **Post date:** [February 16, 2018, 5:45pm UTC](https://forum.mothur.org/t/spliting-removing-remerging/3489/7 "2018-02-16T17:45:21Z")
Ok, so I took the long way and analyzed each dataset separately. I still have the same error message, which is weird. My understanding was that each sequence name was unique to the sample/sequencing run so I do not get why some sequence names are shared between the 2 datasets. Was I wrong? ---
**Author:** ![Alex\_Thibodeau](https://avatars.discourse-cdn.com/v4/letter/a/e9a140/32.png) [@Alex\_Thibodeau](https://forum.mothur.org/u/Alex_Thibodeau)\ **Post date:** [February 16, 2018, 6:42pm UTC](https://forum.mothur.org/t/spliting-removing-remerging/3489/8 "2018-02-16T18:42:50Z")
Ok, I went back to my \*.files. Two groups are in both dataset, that’s why. ---
**Author:** ![mikeschhirn](https://avatars.discourse-cdn.com/v4/letter/m/df788c/32.png) [@mikeschhirn](https://forum.mothur.org/u/mikeschhirn)\ **Post date:** [February 21, 2018, 12:03am UTC](https://forum.mothur.org/t/spliting-removing-remerging/3489/9 "2018-02-21T00:03:41Z")
Hi, I also was struggling with exactly the same problem and have encountered the merge.count error with different files, even with the split and reassembly of count\_tables containing only 2 groups. Similar to Alex’s example, I had split my analysis into several runs and re-merged before clustering without problems. However, below the example were I have tried to split and re-merge count\_files without any further manipulation between split and merging, nevertheless it always results in error. :shock: Any help would be greatly appreciated, Cheers, Thomas #-------------------------------- #test with equal split, verification of base files unique.seqs(count=test.main.count\_table, fasta=test.main.fasta) 2178329 2178329 #no more new uniques summary.seqs(count=test.main.count\_table, fasta=test.main.fasta) Start End NBases Ambigs Polymer NumSeqs Minimum: 1 635 226 0 3 1 2.5%-tile: 1 635 253 0 4 764358 25%-tile: 1 635 253 0 4 7643580 Median: 1 635 253 0 5 15287160 75%-tile: 1 635 253 0 5 22930739 97.5%-tile: 1 635 254 0 6 29809961 Maximum: 1 635 275 0 8 30574318 Mean: 1 635 253.064 0 4.59494 # of unique seqs: 2178329 total # of seqs: 30574318 count.groups(count=test.main.count\_table) #get randomly chosen 1/2 of all groups #--------------------------------------------------- #get groups from base files get.groups(count=test.main.count\_table, fasta=test.main.fasta, accnos=rd.groups.74.accnos) system(mv test.main.pick.count\_table test.main.accnos.count\_table) system(mv test.main.pick.fasta test.main.accnos.fasta) unique.seqs(fasta=test.main.accnos.fasta, count=test.main.accnos.count\_table) #1184814 1184814 #no new uniques summary.seqs(fasta=test.main.accnos.fasta, count=test.main.accnos.count\_table) Start End NBases Ambigs Polymer NumSeqs Minimum: 1 635 226 0 3 1 2.5%-tile: 1 635 253 0 4 384930 25%-tile: 1 635 253 0 4 3849291 Median: 1 635 253 0 5 7698581 75%-tile: 1 635 253 0 5 11547871 97.5%-tile: 1 635 254 0 6 15012232 Maximum: 1 635 275 0 8 15397161 Mean: 1 635 253.066 0 4.58229 # of unique seqs: 1184814 total # of seqs: 15397161 #================================================== #remove same groups from base files remove.groups(count=test.main.count\_table, fasta=test.main.fasta, accnos=rd.groups.74.accnos) system(mv test.main.pick.count\_table test.main.remaining.groups.count\_table) system(mv test.main.pick.fasta test.main.remaining.groups.fasta) unique.seqs(fasta=test.main.remaining.groups.fasta, count=test.main.remaining.groups.count\_table) #1138837 1138837 # no new uniques summary.seqs(fasta=test.main.remaining.groups.fasta, count=test.main.remaining.groups.count\_table) Start End NBases Ambigs Polymer NumSeqs Minimum: 1 635 233 0 3 1 2.5%-tile: 1 635 253 0 4 379429 25%-tile: 1 635 253 0 4 3794290 Median: 1 635 253 0 5 7588579 75%-tile: 1 635 253 0 5 11382868 97.5%-tile: 1 635 254 0 6 14797729 Maximum: 1 635 275 0 8 15177157 Mean: 1 635 253.063 0 4.60777 # of unique seqs: 1138837 total # of seqs: 15177157 count.groups(count=test.main.remaining.groups.count\_table) count.groups(count=test.main.accnos.count\_table) #no duplication of groups #====================================================== merge.count(count=test.main.accnos.unique.count\_table-test.main.remaining.groups.unique.count\_table, output=test.main.reassembled.count\_table) [ERROR]: Your count table contains more than 1 sequence named M01157\_11\_000000000-B48TH\_1\_1101\_10742\_22525, sequence names must be unique. Please correct. #================================================================================================= #2nd test: split of files containing only two groups: split.groups(fasta=TWA\_STO.unique.fasta, count=TWA\_STO.unique.count\_table) Output File Names: TWA\_STO.unique.STO.fasta TWA\_STO.unique.STO.count\_table TWA\_STO.unique.TWA.fasta TWA\_STO.unique.TWA.count\_table # verifying extracted groups unique.seqs(fasta=TWA\_STO.unique.TWA.fasta, count=TWA\_STO.unique.TWA.count\_table) 13547 13547 Output File Names: TWA\_STO.unique.TWA.unique.count\_table TWA\_STO.unique.TWA.unique.fasta unique.seqs(fasta=TWA\_STO.unique.STO.fasta, count=TWA\_STO.unique.STO.count\_table) 15204 15204 Output File Names: TWA\_STO.unique.STO.unique.count\_table TWA\_STO.unique.STO.unique.fasta # reassembling extracted and split groups merge.count(count=TWA\_STO.unique.STO.unique.count\_table-TWA\_STO.unique.TWA.unique.count\_table, output=test.reassemble.count\_table) [ERROR]: Your count table contains more than 1 sequence named M01157\_11\_000000000-B48TH\_1\_1103\_19550\_12172, sequence names must be unique. Please correct. ==========================================================