mothur

Fasta and count files don't match after split.abund

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.

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I am not able to reproduce this error with our test files using our current version, https://github.com/mothur/mothur/releases/tag/v1.44.3.

If you send your logfile and input files to mothur.bugs@gmail.com I can take a closer look for you.

Alternatively, you could try the remove.rare command, https://mothur.org/wiki/remove.rare/.

mothur > remove.rare(list=stability.trim.contigs.pcr.good.unique.pick.trim.precluster.opti_mcc.list, nseqs=1, count=stability.trim.contigs.pcr.good.unique.pick.trim.precluster.count_table) - remove singletons

mothur > list.seqs(list=current) - list names of abundant sequences

mothur > get.seqs(fasta=stability.trim.contigs.pcr.good.unique.pick.trim.precluster.fasta) - select abundant sequences from fasta file

Kindly,
Sarah