Hi,
I am classifying Illumina sequences using mothur and PR2 database (18S sequences). I am running two sets of data but for the second set of data the classify.seqs() had no xxx.accnos output file and then the remove.lineage() did not remove anything.
Please find below these commands/results for the second set of data and then the one from the first set:
Second set:
classify.seqs(fasta=L_AIEQ_6.trim.contigs.good.unique.good.filter.good.unique.precluster.denovo.vsearch.fasta, count=L_AIEQ_6.trim.contigs.good.unique.good.filter.good.unique.precluster.denovo.vsearch.count_table, reference=pr2_version_4.14.0_SSU_mothur.fasta, taxonomy=pr2_version_4.14.0_SSU_mothur.tax, iters=1000, method=wang, ksize=8, cutoff=80, processors=96)
*It took 129793 secs to classify 549990 sequences.*
*It took 15 secs to create the summary file for 549990 sequences.*
*Output File Names: *
*L_AIEQ_6.trim.contigs.good.unique.good.filter.good.unique.precluster.denovo.vsearch.0_SSU_mothur.wang.taxonomy*
*L_AIEQ_6.trim.contigs.good.unique.good.filter.good.unique.precluster.denovo.vsearch.0_SSU_mothur.wang.tax.summary*
remove.lineage(fasta=L_AIEQ_6.trim.contigs.good.unique.good.filter.good.unique.precluster.denovo.vsearch.fasta, count=L_AIEQ_6.trim.contigs.good.unique.good.filter.good.unique.precluster.denovo.vsearch.count_table, taxonomy=L_AIEQ_6.trim.contigs.good.unique.good.filter.good.unique.precluster.denovo.vsearch.nr_v138_1.wang.taxonomy, taxon=unknown-Bacteria-Archaea-Eukaryota:nucl-Eukaryota:plas-Eukaryota:apic-Eukaryota:chrom-Eukaryota:mito)
*No contaminants to remove *
*Output File Names:*
*L_AIEQ_6.trim.contigs.good.unique.good.filter.good.unique.precluster.denovo.vsearch.nr_v138_1.wang.pick.taxonomy*
**First set:**
classify.seqs(fasta=L_AIEQ_5.trim.contigs.good.unique.good.filter.good.unique.precluster.denovo.vsearch.fasta, count=L_AIEQ_5.trim.contigs.good.unique.good.filter.good.unique.precluster.denovo.vsearch.count_table, reference
=pr2_version_4.14.0_SSU_mothur.fasta, taxonomy=pr2_version_4.14.0_SSU_mothur.tax, iters=1000, method=wang, ksize=8, cutoff=80, processors=96)
*[WARNING]: mothur reversed some your sequences for a better classification. If you would like to take a closer look, please check L_AIEQ_5.trim.contigs.good.unique.good.filter.good.unique.precluster.denovo.vsearch.0_SSU_mothur.wang.flip.accnos for the list of the sequences.*
*It took 110097 secs to classify 540511 sequences.*
*It took 15 secs to create the summary file for 540511 sequences.*
*Output File Names: *
*L_AIEQ_5.trim.contigs.good.unique.good.filter.good.unique.precluster.denovo.vsearch.0_SSU_mothur.wang.taxonomy*
*L_AIEQ_5.trim.contigs.good.unique.good.filter.good.unique.precluster.denovo.vsearch.0_SSU_mothur.wang.tax.summary*
*L_AIEQ_5.trim.contigs.good.unique.good.filter.good.unique.precluster.denovo.vsearch.0_SSU_mothur.wang.flip.accnos*
remove.lineage(fasta=L_AIEQ_5.trim.contigs.good.unique.good.filter.good.unique.precluster.denovo.vsearch.fasta, count=L_AIEQ_5.trim.contigs.good.unique.good.filter.good.unique.precluster.denovo.vsearch.count_table, taxonomy=L_AIEQ_5.trim.contigs.good.unique.good.filter.good.unique.precluster.denovo.vsearch.nr_v138_1.wang.taxonomy, taxon=unknown-Bacteria-Archaea-Eukaryota:nucl-Eukaryota:plas-Eukaryota:apic-Eukaryota:chrom-Eukaryota:mito)
`/******************************************/`
`Running command:
remove.seqs(accnos=L_AIEQ_5.trim.contigs.good.unique.good.filter.good.unique.precluster.denovo.vsearch.nr_v138_1.wang.accnos,
count=L_AIEQ_5.trim.contigs.good.unique.good.filter.good.unique.precluster.denovo.vsearch.count_table,
fasta=L_AIEQ_5.trim.contigs.good.unique.good.filter.good.unique.precluster.denovo.vsearch.fasta)`
`Removed
2 sequences from
L_AIEQ_5.trim.contigs.good.unique.good.filter.good.unique.precluster.denovo.vsearch.fasta.`
`Removed 2 sequences from L_AIEQ_5.trim.contigs.good.unique.good.filter.good.unique.precluster.denovo.vsearch.count_table.`
`OutputFile Names:`
`L_AIEQ_5.trim.contigs.good.unique.good.filter.good.unique.precluster.denovo.vsearch.pick.fasta`
`L_AIEQ_5.trim.contigs.good.unique.good.filter.good.unique.precluster.denovo.vsearch.pick.count_table`
`/******************************************/`
`Output File Names:`
`L_AIEQ_5.trim.contigs.good.unique.good.filter.good.unique.precluster.denovo.vsearch.nr_v138_1.wang.pick.taxonomy`
`L_AIEQ_5.trim.contigs.good.unique.good.filter.good.unique.precluster.denovo.vsearch.nr_v138_1.wang.accnos`
`L_AIEQ_5.trim.contigs.good.unique.good.filter.good.unique.precluster.denovo.vsearch.pick.count_table`
`L_AIEQ_5.trim.contigs.good.unique.good.filter.good.unique.precluster.denovo.vsearch.pick.fasta`
I am not sure which file I should use to continue the procedure: count.group(), cluster(), split.abund() …
Sincerely,
Pascal