count.seqs ERROR

mothur bugs
1

Hi!
I’m running mothur v 1.33.3 and I have problems to make count_table after trim…

I have 22 samples from illumina, I have done at the beginning of my analysis a fasta and a groups file.
fasta=PUECHABON_merge.fasta
PUECHABON_mergegroups.groups


then trim.seqs and unique.seqs ;

trim.seqs(fasta=PUECHABON_merge.fasta,oligos=GH11.oligos.txt,pdiffs=2,checkorient=t,processors=20)

unique.seqs(fasta=PUECHABON_merge_GH11.trim.fasta)

count.seqs(name=PUECHABON_merge_GH11.trim.names,group=PUECHABON_mergegroups.groups)

and I’ve got this error:

Using 20 processors.
[ERROR]: processes reported processing 2362313 sequences, but group file indicates you have 6605628 sequences. Either you have a file mismatch or a process failed to complete the task assigned to it.

:?: I don’t know why… I have always done that in other version of mothur with less sequences and I never have this problem…

can you help me?

thanks a lot!

Claudia

2

If you are using mac/linux can you tell me the results of the following…

wc -l PUECHABON_mergegroups.groups
grep -c “>” PUECHABON_merge.fasta

If you are in windows I need to know how many lines in are in the group and fasta files

3

Dear Patrick,
thank you for your answer.

I’m using Linux,

the results you asked me is:

  1. wc -l PUECHABON_mergegroups.groups= 6605628

  2. grep -c “>” PUECHABON_merge.fasta= 6605628

4

Can you try the three steps with 1 processor?

5

Whit one processor it works…

Using 1 processors.
[ERROR]: processes reported processing 2298320 sequences, but group file indicates you have 6605628 sequences. Could you have a file mismatch?
It took 55 secs to create a table for 2298320 sequences.


Total number of sequences: 2298320

Output File Names:
PUECHABON_all.GH11trim.count_table

thnak you very much! :smiley:

6

Please send PUECHABON_mergegroups.groups and PUECHABON_merge.fasta to us at mothur.bugs@gmail.com along with the exact command you are running here.

Pat