Error in reading fastafile

Commands in mothur
1

Hi,

I’m a new mothur user. I tried to follow MiSeq SOP tutorial with my own data.
My problem satared after the alignment step. When I ran summary after the alignment i got this Warnning
[WARNING]: This command can take a namefile and you did not provide one. The current namefile is FullPrewk 1.trim.contigs.good.names which seems to match FullPrewk 1.trim.contigs.good.unique.align.
Error in reading your fastafile, at position -1. Blank name.
[ERROR]: process 0 only processed 1 of 267996 sequences assigned to it, quitting.

This was my input
mothur > summary.seqs(fasta=current)
Using FullPrewk 1.trim.contigs.good.unique.align as input file for the fasta parameter.

Regards
Fathalla

1 Like
2

Welcome to the mothur community! The warning is nothing to be concerned about. Mothur is just alerting you that if you want the entire dataset included in your summary you need to provide the name file. It is not required. The error you are getting indicates one of the processes failed. What version of mothur are you running? Have you tried running it with processors=1?

3

Hi,

Thank you for your answer.
I found myself using this version v.1.34.4.
I downloaded the latest version and doing my analysis with the latest version v.1.35.0.
Am I required to repeat my analysis with latest version or I can continue with the latest version?
Now I’m using processors=1 and got this results. Could you please tell me if I’m doing well with my data or not?
Here is my work

mothur >
summary.seqs(fasta=current)
Using FullPrewk 1.trim.contigs.good.unique.align as input file for the fasta parameter.

Using 1 processors.

Start End NBases Ambigs Polymer NumSeqs
Minimum: -1 -1 0 0 1 1
2.5%-tile: 1 13422 290 0 4 13400
25%-tile: 1 13422 291 0 4 133999
Median: 1 13422 291 0 6 267997
75%-tile: 1 13422 291 0 6 401995
97.5%-tile: 1 13422 291 0 6 522594
Maximum: 13425 13425 311 0 29 535993
Mean: 10.3686 13418 290.467 0 5.06695

of Seqs: 535993

mothur >
screen.seqs(fasta=FullPrewk 1.trim.contigs.good.unique.align, count=FullPrewk 1.trim.contigs.good.count_table, summary=FullPrewk 1.trim.contigs.good.unique.summary, start=1, end=13422, maxhomop=8)

mothur >
summary.seqs(fasta=current, count=current)
Using FullPrewk 1.trim.contigs.good.good.count_table as input file for the count parameter.
Using FullPrewk 1.trim.contigs.good.unique.good.align as input file for the fasta parameter.

Using 1 processors.

Start End NBases Ambigs Polymer NumSeqs
Minimum: 1 13422 263 0 3 1
2.5%-tile: 1 13422 290 0 4 48919
25%-tile: 1 13422 291 0 4 489189
Median: 1 13422 291 0 6 978377
75%-tile: 1 13422 291 0 6 1467565
97.5%-tile: 1 13422 291 0 6 1907834
Maximum: 1 13425 311 0 8 1956752
Mean: 1 13422 290.794 0 5.0688

of unique seqs: 528750

total # of seqs: 1956752

mothur >
filter.seqs(fasta=FullPrewk 1.trim.contigs.good.unique.good.align, vertical=T, trump=.)

Using 1 processors.
Creating Filter…

Running Filter…

Length of filtered alignment: 563
Number of columns removed: 12862
Length of the original alignment: 13425
Number of sequences used to construct filter: 528750

mothur >
unique.seqs(fasta=FullPrewk 1.trim.contigs.good.unique.good.filter.fasta, count=FullPrewk 1.trim.contigs.good.good.count_table)
528750 197391

mothur >
pre.cluster(fasta=FullPrewk 1.trim.contigs.good.unique.good.filter.unique.fasta, count=FullPrewk 1.trim.contigs.good.unique.good.filter.count_table, diffs=2)

mothur >
chimera.uchime(fasta=FullPrewk 1.trim.contigs.good.unique.good.filter.unique.precluster.fasta, count=FullPrewk 1.trim.contigs.good.unique.good.filter.unique.precluster.count_table, dereplicate=t)

mothur >
remove.seqs(fasta=FullPrewk 1.trim.contigs.good.unique.good.filter.unique.precluster.fasta, accnos=FullPrewk 1.trim.contigs.good.unique.good.filter.unique.precluster.uchime.accnos)
Removed 4898 sequences from your fasta file.

mothur >
summary.seqs(fasta=current, count=current)
Using FullPrewk 1.trim.contigs.good.unique.good.filter.unique.precluster.uchime.pick.count_table as input file for the count parameter.
Using FullPrewk 1.trim.contigs.good.unique.good.filter.unique.precluster.pick.fasta as input file for the fasta parameter.

Using 1 processors.

Start End NBases Ambigs Polymer NumSeqs
Minimum: 1 563 277 0 3 1
2.5%-tile: 1 563 290 0 4 48203
25%-tile: 1 563 291 0 4 482022
Median: 1 563 291 0 6 964044
75%-tile: 1 563 291 0 6 1446065
97.5%-tile: 1 563 291 0 6 1879884
Maximum: 1 563 297 0 8 1928086
Mean: 1 563 290.801 0 5.07098

of unique seqs: 53761

total # of seqs: 1928086

mothur >
classify.seqs(fasta=FullPrewk 1.trim.contigs.good.unique.good.filter.unique.precluster.pick.fasta, count=FullPrewk 1.trim.contigs.good.unique.good.filter.unique.precluster.uchime.pick.count_table, reference=trainset9_032012.pds.fasta, taxonomy=trainset9_032012.pds.tax, cutoff=80)

mothur >
classify.seqs(fasta=FullPrewk 1.trim.contigs.good.unique.good.filter.unique.precluster.pick.fasta, count=FullPrewk 1.trim.contigs.good.unique.good.filter.unique.precluster.uchime.pick.count_table, reference=trainset9_032012.pds.fasta, taxonomy=trainset9_032012.pds.tax, cutoff=80)

mothur >
remove.lineage(fasta=FullPrewk 1.trim.contigs.good.unique.good.filter.unique.precluster.pick.fasta, count=FullPrewk 1.trim.contigs.good.unique.good.filter.unique.precluster.uchime.pick.count_table, taxonomy=FullPrewk 1.trim.contigs.good.unique.good.filter.unique.precluster.pick.pds.wang.taxonomy, taxon=Chloroplast-Mitochondria-unknown-Archaea-Eukaryota)

mothur >
summary.seqs(fasta=current, count=current)
Using FullPrewk 1.trim.contigs.good.unique.good.filter.unique.precluster.uchime.pick.pick.count_table as input file for the count parameter.
Using FullPrewk 1.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta as input file for the fasta parameter.

Using 1 processors.

Start End NBases Ambigs Polymer NumSeqs
Minimum: 1 563 277 0 3 1
2.5%-tile: 1 563 290 0 4 48203
25%-tile: 1 563 291 0 4 482021
Median: 1 563 291 0 6 964041
75%-tile: 1 563 291 0 6 1446061
97.5%-tile: 1 563 291 0 6 1879879
Maximum: 1 563 297 0 8 1928081
Mean: 1 563 290.801 0 5.07098

of unique seqs: 53757

total # of seqs: 1928081

Regards
Fathalla

4

It looks like everything is behaving in the output you posted - where are you seeing a problem?

5

Hi,
Is there any problem on the first line of his summery?
The minimum (-1)
Start End NBases Ambigs Polymer NumSeqs
Minimum: -1 -1 0 0 1 1
2.5%-tile: 1 13422 290 0 4 13400
25%-tile: 1 13422 291 0 4 133999
Median: 1 13422 291 0 6 267997
75%-tile: 1 13422 291 0 6 401995
97.5%-tile: 1 13422 291 0 6 522594
Maximum: 13425 13425 311 0 29 535993
Mean: 10.3686 13418 290.467 0 5.06695

of Seqs: 535993

Thank you

6

The -1/-1 and 13425/13425 sequence(s) are those that did not align to the region. We generally see that when we get something non-specific to amplify. It looks like screen.seqs took care of those for you and you should be in good shape now.

pat

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