I am running the split.abund to remove the singleton. The abund.fasta and abund.count_table did not match each other. I tried all the possible ways e.g.using list.seqs from .abund.fasta, then using get.seqs to generate new .abund.count_talbe. Still not working. Help highly appreciated.
The fasta and count_talbe have beaning working fine before split.abund.
below is the split.abund :
mothur > split.abund(fasta=stability.trim.contigs.pcr.good.unique.pick.trim.precluster.fasta,list=stability.trim.contigs.pcr.good.unique.pick.trim.precluster.opti_mcc.list,count=stability.trim.contigs.pcr.good.unique.pick.trim.precluster.count_table,cutoff=1, label=0.03)
0.03
/******************************************/
Running command: get.otus(accnos=stability.trim.contigs.pcr.good.unique.pick.trim.precluster.opti_mcc.0.03_OTUS.rare.accnos, list=stability.trim.contigs.pcr.good.unique.pick.trim.precluster.opti_mcc.list, label=0.03)
Selected 30640 OTUs from your list file.
Output File Names:
stability.trim.contigs.pcr.good.unique.pick.trim.precluster.opti_mcc.0.03.pick.list
/******************************************/
Done.
/******************************************/
Running command: get.otus(accnos=stability.trim.contigs.pcr.good.unique.pick.trim.precluster.opti_mcc.0.03_OTUS.abund.accnos, list=stability.trim.contigs.pcr.good.unique.pick.trim.precluster.opti_mcc.list, label=0.03)
Selected 13867 OTUs from your list file.
Output File Names:
stability.trim.contigs.pcr.good.unique.pick.trim.precluster.opti_mcc.0.03.pick.list
/******************************************/
Done.
/******************************************/
Running command: get.seqs(dups=t, accnos=stability.trim.contigs.pcr.good.unique.pick.trim.precluster.opti_mcc.0.03.rare.accnos, count=stability.trim.contigs.pcr.good.unique.pick.trim.precluster.count_table, fasta=stability.trim.contigs.pcr.good.unique.pick.trim.precluster.fasta)
Selected 30640 sequences from your fasta file.
Selected 30640 sequences from your count file.
Output File Names:
stability.trim.contigs.pcr.good.unique.pick.trim.precluster.pick.fasta
stability.trim.contigs.pcr.good.unique.pick.trim.precluster.pick.count_table
/******************************************/
Done.
/******************************************/
Running command: get.seqs(dups=t, accnos=stability.trim.contigs.pcr.good.unique.pick.trim.precluster.opti_mcc.0.03.abund.accnos, count=stability.trim.contigs.pcr.good.unique.pick.trim.precluster.count_table, fasta=stability.trim.contigs.pcr.good.unique.pick.trim.precluster.fasta)
Selected 13882 sequences from your fasta file.
Selected 12598008 sequences from your count file.
Output File Names:
stability.trim.contigs.pcr.good.unique.pick.trim.precluster.pick.fasta
stability.trim.contigs.pcr.good.unique.pick.trim.precluster.pick.count_table
/******************************************/
Done.
Output File Names:
stability.trim.contigs.pcr.good.unique.pick.trim.precluster.opti_mcc.0.03_OTUS.rare.accnos
stability.trim.contigs.pcr.good.unique.pick.trim.precluster.opti_mcc.0.03_OTUS.abund.accnos
stability.trim.contigs.pcr.good.unique.pick.trim.precluster.opti_mcc.0.03.rare.list
stability.trim.contigs.pcr.good.unique.pick.trim.precluster.opti_mcc.0.03.abund.list
stability.trim.contigs.pcr.good.unique.pick.trim.precluster.opti_mcc.0.03.rare.accnos
stability.trim.contigs.pcr.good.unique.pick.trim.precluster.opti_mcc.0.03.abund.accnos
stability.trim.contigs.pcr.good.unique.pick.trim.precluster.0.03.rare.count_table
stability.trim.contigs.pcr.good.unique.pick.trim.precluster.0.03.rare.fasta
stability.trim.contigs.pcr.good.unique.pick.trim.precluster.0.03.abund.count_table
stability.trim.contigs.pcr.good.unique.pick.trim.precluster.0.03.abund.fasta
mothur > summary.seqs(fasta=stability.trim.contigs.pcr.good.unique.pick.trim.precluster.0.03.abund.fasta)
Using 40 processors.
Start End NBases Ambigs Polymer NumSeqs
Minimum: 1 230 230 0 3 1
2.5%-tile: 1 230 230 0 4 348
25%-tile: 1 230 230 0 4 3471
Median: 1 230 230 0 5 6942
75%-tile: 1 230 230 0 6 10412
97.5%-tile: 1 230 230 0 8 13535
Maximum: 1 230 230 0 8 13882
Mean: 1 230 230 0 5
of Seqs: 13882
mothur > summary.seqs(fasta=stability.trim.contigs.pcr.good.unique.pick.trim.precluster.0.03.abund.fasta,count=stability.trim.contigs.pcr.good.unique.pick.trim.precluster.0.03.abund.count_table)
Using 40 processors.
[ERROR]: ‘A01045_232_HM5J5DRXX_1_2130_8260_17018’ is not in your name or count file, please correct.
[ERROR]: Your count file contains 1238 unique sequences, but your fasta file contains 1. File mismatch detected, quitting command.