mothur

AAError: Sequence 'M02220_29' was not found in the name or count file, please correct

Dear Mothur friends:
An error code was reported (showed as following) and terminated in an analysis running with a batch mode (showing after the terminal error message). I think there is something related the the message one line before the AAError “It took 1128853 seconds to split the distance file.” Suggestions will be highly appreciated.

sincerely

Jrhau

/******************************************/
Running command: dist.seqs(fasta=/media/mpiu/a93b0b36-e288-45ef-b21f-acc26e4b0af9/tooth-16S/test/stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.pick.fasta.70.temp, processors=1, cutoff=0.15)

Using 1 processors.
/******************************************/

Sequence	Time	Num_Dists_Below_Cutoff
0	0	0
2	0	0

It took 0 secs to find distances for 3 sequences. 0 distances below cutoff 0.15.

/media/mpiu/a93b0b36-e288-45ef-b21f-acc26e4b0af9/tooth-16S/test/stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.pick.fasta.70.dist is blank. This can result if there are no distances below your cutoff.

Output File Names: 
/media/mpiu/a93b0b36-e288-45ef-b21f-acc26e4b0af9/tooth-16S/test/stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.pick.fasta.70.dist

/******************************************/
Running command: dist.seqs(fasta=/media/mpiu/a93b0b36-e288-45ef-b21f-acc26e4b0af9/tooth-16S/test/stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.pick.fasta.71.temp, processors=1, cutoff=0.15)

Using 1 processors.
/******************************************/

Sequence	Time	Num_Dists_Below_Cutoff
0	0	0
2	0	3

It took 0 secs to find distances for 3 sequences. 3 distances below cutoff 0.15.


Output File Names: 
/media/mpiu/a93b0b36-e288-45ef-b21f-acc26e4b0af9/tooth-16S/test/stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.pick.fasta.71.dist

/******************************************/
Running command: dist.seqs(fasta=/media/mpiu/a93b0b36-e288-45ef-b21f-acc26e4b0af9/tooth-16S/test/stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.pick.fasta.72.temp, processors=1, cutoff=0.15)

Using 1 processors.
/******************************************/

Sequence	Time	Num_Dists_Below_Cutoff
0	0	0
3	0	6

It took 0 secs to find distances for 4 sequences. 6 distances below cutoff 0.15.


Output File Names: 
/media/mpiu/a93b0b36-e288-45ef-b21f-acc26e4b0af9/tooth-16S/test/stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.pick.fasta.72.dist

/******************************************/
Running command: dist.seqs(fasta=/media/mpiu/a93b0b36-e288-45ef-b21f-acc26e4b0af9/tooth-16S/test/stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.pick.fasta.73.temp, processors=1, cutoff=0.15)

Using 1 processors.
/******************************************/

Sequence	Time	Num_Dists_Below_Cutoff
0	0	0
1	0	1

It took 0 secs to find distances for 2 sequences. 1 distances below cutoff 0.15.


Output File Names: 
/media/mpiu/a93b0b36-e288-45ef-b21f-acc26e4b0af9/tooth-16S/test/stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.pick.fasta.73.dist

It took 1128853 seconds to split the distance file.
AAError: Sequence 'M02220_29' was not found in the name or count file, please correct

REFERENCE_LOCATION=/media/mpiu/a93b0b36-e288-45ef-b21f-acc26e4b0af9/Bacteria-16S-Ref
ALIGNREF=silva.full_v138.fasta
TAXONREF_FASTA=trainset9_032012.pds.fasta
TAXONREF_TAX=trainset9_032012.pds.tax
CONTAMINENTS=Chloroplast-Mitochondria-unknown-Archaea-Eukaryota
LOGNAME=20201026-trial2
DATA=/media/mpiu/a93b0b36-e288-45ef-b21f-acc26e4b0af9/tooth-16S/test
TYPE=fastq

#batch commands
set.logfile(name=$LOGNAME)
make.file(inputdir=$DATA, type=$TYPE, prefix=stability)
make.contigs(file=current, processors=56)
screen.seqs(fasta=current, group=current, maxambig=0, maxlength=500, processors=56)
unique.seqs()
count.seqs(name=current, group=current)
align.seqs(fasta=current, reference=$REFERENCE_LOCATION/$ALIGNREF, processors=56)
# screen.seqs(fasta=current, count=current, start=6000, end=26000, maxhomop=8)
screen.seqs(fasta=current, count=current, start=6388, end=25316, maxhomop=8, processors=56)
filter.seqs(fasta=current, vertical=T, trump=.)
unique.seqs(fasta=current, count=current)
pre.cluster(fasta=current, count=current, diffs=2, processors=56)
chimera.vsearch(fasta=current, count=current, dereplicate=t, processors=56)
remove.seqs(fasta=current, accnos=current)
classify.seqs(fasta=current, count=current, reference=$REFERENCE_LOCATION/$TAXONREF_FASTA, taxonomy=$REFERENCE_LOCATION/$TAXONREF_TAX, cutoff=80, processors=56)
remove.lineage(fasta=current, count=current, taxonomy=current, taxon=$CONTAMINENTS)
remove.groups(count=current, fasta=current, taxonomy=current, groups=Mock)
cluster.split(fasta=current, count=current, taxonomy=current, splitmethod=classify, taxlevel=4, cutoff=0.15, processors=1)
make.shared(list=current, count=current, label=0.03)
classify.otu(list=current, count=current, taxonomy=current, label=0.03)
phylotype(taxonomy=current)
make.shared(list=current, count=current, label=1)
classify.otu(list=current, count=current, taxonomy=current, label=1)

Can you try to re-run it but use cutoff=0.03 in cluster.split?

Thanks,
Pat

Dear Professor Scholoss:

The cutoff=0.03 does solve the issue. Thanks for all your help.

Sincerely,

Jrhau

Pat Schloss via mothur <mothur@discoursemail.com> 於 2021年2月2日 週二 下午10:49寫道: