chimera.uchime, Just got confused

mothur bugs
1

Hi,
There are so many problems when I use mothur, anyone had similar enconter? May renpin of mine be so bad :evil: ?
look at this

_mothur > chimera.uchime(fasta=YU.shhh.trim.unique.good.filter.unique.precluste
r.fasta,reference=silva.gold.ng.fasta,processors=2)


Using 2 processors.

uchime by Robert C. Edgar
http://drive5.com/uchime
This code is donated to the public domain.

Checking sequences from YU.shhh.trim.unique.good.filter.unique.precluster.fast
a …
‘K:\mothur\5月454测序\æ–°flow\预实验\uchime.exe" --input “YU.shhh.trim.unique.g
ood.filter.unique.precluster.fasta1.temp” --db “silva.gold.ng.fasta” --uchimeout
"YU.shhh.trim.unique.good.filter.unique.precluster.uchime.chimeras1.temp’ 不
是内部或外部命令，也不是可运行的程序
或批处理文件。
[ERROR]: Could not open YU.shhh.trim.unique.good.filter.unique.precluster.uchi
me.chimeras1.temp
uchime v4.2.40
by Robert C. Edgar
http://drive5.com/uchime
This code is donated to the public domain.

00:00 0.1% Reading YU.shhh.trim.unique.good.filter.unique.precluster.fasta0
00:00 0.1% Reading YU.shhh.trim.unique.good.filter.unique.precluster.fasta0
.temp
WARNING: Ignoring gaps in FASTA file ‘YU.shhh.trim.unique.good.filter.unique.p
recluster.fasta0.temp’
00:00 100.0% Reading YU.shhh.trim.unique.good.filter.unique.precluster.fasta0
.temp
00:00 2481 sequences

00:00 100.0% Reading silva.gold.ng.fasta
00:00 5181 sequences
40:37 100.0% 279/2480 chimeras found (11.2%)_


Seemingly it only does a half of jobs(2481 of the *.fasta0 .temp ), but, why? what's the problem? and why did it split my fasta file to fasta0.temp and fasta1.temp while only fasta0.temp would it do.

Any kinds of explanation helping me out will be appreciated!

2

It looks like one of your processes is crashing. This usually occurs when there is an error in the input file. Can you try running it with processors=1? Mothur splits the file to divide the work between the two processors.