Error in reading your fastafile, at position -1. Blank name

1

Hello all,

I am a new user in mothur and I do not have any background and I hope you gonna help me.

I used this command:

mothur > screen.seqs(fasta=stability.trim.contigs.good.unique.abund.align,count=stability.trim.contigs.good.abund.count_table,summary=stability.trim.contigs.good.unique.abund.summary,start=3,end=11011,maxhomop=6)

and I get these output File Names:

stability.trim.contigs.good.unique.abund.good.summary
stability.trim.contigs.good.unique.abund.good.align
stability.trim.contigs.good.unique.abund.bad.accnos
stability.trim.contigs.good.abund.good.count_table

Then I run this command:

summary.seqs(fasta=stability.trim.contigs.good.unique.abund.good.align,count=stability.trim.contigs.good.abund.good.count_table)

and I get this Error

[ERROR]: stability.trim.contigs.good.unique.abund.good.align is blank. Please correct. Error in reading your fastafile, at position -1. Blank name.

I tried many time to remove all the output file and to start from the beginning and still I have the same problem. Then I tried to change the maxhomop=6 to maxhomop=8 and also one time without maxhomop and still the same Error.

I would be very happy If you help me.
Thank you

1 Like
2

it’s unlikely you really want start=3 in your screen.seqs command. can you post the summary.seqs just before this?

3

This is the summary

mothur > summary.seqs(fasta=stability.trim.contigs.good.unique.abund.align,count=stability.trim.contigs.good.abund.count_table)

	Start	End	NBases	Ambigs	Polymer	NumSeqs

Minimum: 1 524 1 0 1 1
2.5%-tile: 3 3352 52 0 4 43529
25%-tile: 3 11011 292 0 5 435288
Median: 3 11011 294 0 5 870575
75%-tile: 3 11011 294 0 5 1305862
97.5%-tile: 3 11011 297 0 6 1697621
Maximum: 11011 11011 302 0 9 1741149
Mean: 25.9466 10784.5 286.029 0 5.02185

of unique seqs: 120411

total # of seqs: 1741149

Output File Names:
stability.trim.contigs.good.unique.abund.summary

Thanks

4

your numbers are correct. either maxhomop should be fine. I’m not seeing a problem, you’ll have to wait till Pat or Sarah checks in.

1 Like
5

Hello, I am also getting the same error while running the chimera.vsearch program. Here’s the summary.
mothur > chimera.vsearch(fasta=stability.trim.contigs.good.unique.good.filter.unique.precluster.fasta, count=stability.trim.contigs.good.unique.good.filter.unique.precluster.count_table,processors=1, dereplicate=t)
Using 1 processors.
/usr/bin/vsearch file does not exist. Checking path…
Found vsearch in your path, using /home/srchoud/mothur/MiSeq_SOP/vsearch
Checking sequences from stability.trim.contigs.good.unique.good.filter.unique.precluster.fasta …
sh: 1: /home/srchoud/mothur/MiSeq_SOP/vsearch: Permission denied
Error in reading your fastafile, at position -1. Blank name.