Hi,
i was wondering if anyone else has come up with the same issue as i have encountered today
i am running a sff.multiple command on a project containing 20 different sequencing reactions (i have already completed this analysis on two alternate species with no issues, although sff files were produced from a separate sequencing run).
however, for the third time now, my analysis halts once the final shhh.flows, trim.seqs and summary.seqs commands have run from within sff.multiple. the last commandline output is as follows
_Running command: trim.seqs(fasta=png10c3.shhh.fasta, name=png10c3.shhh.names, oligos=pngbacteria3.txt, allfiles=t, flip=f, keepforward=f, pdiffs=2, bdiffs=0, ldiffs=0, sdiffs=0, tdiffs=2, maxambig=-1, minlength=200, maxlength=0, processors=1)
Using 1 processors.
1000
1401
Group count:
png10c3 6967
Total of all groups is 6967
Output File Names:
png10c3.shhh.trim.fasta
png10c3.shhh.scrap.fasta
png10c3.shhh.trim.names
png10c3.shhh.scrap.names
png10c3.shhh.png10c3.fasta
png10c3.shhh.png10c3.names
png10c3.shhh.groups
png10c3.shhh.png10c3.groups
Running command: summary.seqs(fasta=png10c3.shhh.trim.fasta, processors=1, name=png10c3.shhh.trim.names)
Using 1 processors.
Start End NBases Ambigs Polymer NumSeqs
Minimum: 1 200 200 0 3 1
2.5%-tile: 1 205 205 0 4 175
25%-tile: 1 224 224 0 5 1742
Median: 1 226 226 0 5 3484
75%-tile: 1 226 226 0 5 5226
97.5%-tile: 1 236 236 0 6 6793
Maximum: 1 249 249 0 7 6967
Mean: 1 223.711 223.711 0 4.91388
of unique seqs: 1393
total # of seqs: 6967
Output File Names:
png10c3.shhh.trim.summary
/******************************************/
plaffy@plaffy-Precision-T7600:~/projects/PNGproject/originaldata/work/bacteria/species3$_
as you can see, the process jumps straight out of mothur and does not provide me with any error information so i am not sure why this error keeps occuring.
i thought this could be due to the original input file format or the.oligos file format, but i have checked these and cannot find the issue
i have also performed the analysis on the final sff file, and i have been able to complete these steps without issue
i have noticed there was a similar sounding post a week or so ago, but i cant seem to figure out what the issue is from that post
http://mothur.ltcmp.net/t/shhh-flows-error-for-one-file/1296/6
any help you can provide on solving this problem would be greatly appreciated
thanks
Patrick Laffy