[ERROR] is in your groupfile and not your listfile

Commands in mothur
1

hello everybody, I am Juan and currently having a “small” inconvenient

When i executed make.shared command to get OTU from each group, its present a following ERROR

make.shared(list=manglar.cut.trim.contigs.good.unique.good.filter.unique.precluster.abund.pick.pick.an.unique_list.list, count=manglar.cut.trim.contigs.good.unique.good.filter.unique.precluster.abund.denovo.uchime.pick.pick.count_table, label=0.03)
[ERROR]: M01564_51_000000000-AG2K0_1_1102_20256_20354 is in your groupfile and not your listfile. Please correct.
Your group file contains 82403 sequences and list file contains 81279 sequences. Please correct.

Output File Names:
manglar.cut.trim.contigs.good.unique.good.filter.unique.precluster.abund.pick.pick.an.unique_list.shared

Previously commands were

cluster.split(fasta=manglar.cut.trim.contigs.good.unique.good.filter.unique.precluster.abund.pick.pick.fasta, count=manglar.cut.trim.contigs.good.unique.good.filter.unique.precluster.abund.denovo.uchime.pick.pick.count_table, taxonomy=manglar.cut.trim.contigs.good.unique.good.filter.unique.precluster.abund.pick.nr_v119.wang.pick.taxonomy, splitmethod=classify, taxlevel=6, cutoff=0.15, processors=8)

Clustering manglar.cut.trim.contigs.good.unique.good.filter.unique.precluster.abund.pick.pick.fasta.7.dist
Cutoff was 0.155 changed cutoff to 0.07
Cutoff was 0.155 changed cutoff to 0.07
Cutoff was 0.155 changed cutoff to 0.07
It took 159 seconds to cluster
Merging the clustered files…
It took 15 seconds to merge.

Output File Names:
manglar.cut.trim.contigs.good.unique.good.filter.unique.precluster.abund.pick.pick.an.unique_list.list

the count file was obtained with the following command

remove.lineage(fasta=manglar.cut.trim.contigs.good.unique.good.filter.unique.precluster.abund.pick.fasta, count=manglar.cut.trim.contigs.good.unique.good.filter.unique.precluster.abund.denovo.uchime.pick.count_table, taxonomy=manglar.cut.trim.contigs.good.unique.good.filter.unique.precluster.abund.pick.nr_v119.wang.taxonomy, taxon=Chloroplast-Mitochondria-unknown-Archaea-Eukaryota)

Output File Names:
manglar.cut.trim.contigs.good.unique.good.filter.unique.precluster.abund.pick.nr_v119.wang.pick.taxonomy
manglar.cut.trim.contigs.good.unique.good.filter.unique.precluster.abund.pick.pick.fasta
manglar.cut.trim.contigs.good.unique.good.filter.unique.precluster.abund.denovo.uchime.pick.pick.count_table


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Sorry if I missed relevant info, is my first time using mothur and although I believe that it is very helpful, this OTU step is freaking me out

thank you very muc

2

Could you post the uchime command and remove.seqs command you ran? I suspect you missed something there that is causing the file mismatch here.

3

hello

thank you for your reply

sure! the commands are the following

chimera.uchime(fasta=manglar.cut.trim.contigs.good.unique.good.filter.unique.precluster.abund.fasta, count=manglar.cut.trim.contigs.good.unique.good.filter.unique.precluster.abund.count_table, dereplicate=t)

remove.seqs(fasta=manglar.cut.trim.contigs.good.unique.good.filter.unique.precluster.abund.fasta, accnos=manglar.cut.trim.contigs.good.unique.good.filter.unique.precluster.abund.denovo.uchime.accnos)

4

As a workaround you can run:

mothur > list.seqs(list=yourListFile)
mothur > get.seqs(count=yourCountFile)