Hi,
Following the Schloss SOP for my pyrosequencing data and after running the trim.seqs and summary.seqs, I get the following:
error name of a sequence__ is not in your name or count file, please correct.
Thanks much for any help.
Could you post the exact commands you ran?
Thank you for your kind answer.
Here the commands I used:
Windows version
Running 64Bit Version
mothur v.1.29.0
Last updated: 1/14/2013
by
Patrick D. Schloss
Department of Microbiology & Immunology
University of Michigan
pschloss@umich.edu
When using, please cite:
Schloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported
software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75
(23):7537-41.
Distributed under the GNU General Public License
Type ‘help()’ for information on the commands that are available
Type ‘quit()’ to exit program
Interactive Mode
mothur > sffinfo(sff=HX774YY04.sff,fasta=true,sfftxt=true,flow=true) Extracting info from HX774YY04.sff ... 10000 20000 30000 40000 50000 60000 70000 80000 90000 100000 110000 120000 130000 140000 150000 155969 It took 1293 secs to extract 155969. Output File Names: HX774YY04.sff.txt HX774YY04.fasta HX774YY04.qual HX774YY04.flow
mothur > trim.flows(flow=HX774YY04.flow,oligos=A1_oligos.txt,pdiffs=2,bdiffs=1,processors=8)
Using 8 processors.
10000
20000
30000
40000
50000
60000
70000
80000
90000
100000
110000
120000
130000
140000
150000
155969
Output File Names:
HX774YY04.trim.flow
HX774YY04.scrap.flow
HX774YY04.AB.flow
HX774YY04.AW.flow
HX774YY04.AX.flow
HX774YY04.AE.flow
HX774YY04.A_BIOT_MIX.flow
HX774YY04.AS_MIX.flow
HX774YY04.A_BIOT_BLACK.flow
HX774YY04.AS_RED.flow
HX774YY04.AS_WHITE.flow
HX774YY04.flow.files
mothur > shhh.flows(file=HX774YY04.flow.files,processors=8,lookup=LookUp_Titanium.pat)
Using 8 processors.
Processing HX774YY04.AB.flow (file 1 of 9) <<<<<
Reading flowgrams…
Identifying unique flowgrams…
Calculating distances between flowgrams…
AFTER PROCESSING ALL FLOWGRAMS, I GOT ALL SAMPLES FILES
Finalizing... Total time to process not found: 4569 4568.53
Output File Names:
HX774YY04.AB.shhh.qual
HX774YY04.AB.shhh.fasta
HX774YY04.AB.shhh.names
HX774YY04.AB.shhh.counts
HX774YY04.AB.shhh.groups
HX774YY04.AW.shhh.qual
HX774YY04.AW.shhh.fasta
HX774YY04.AW.shhh.names
HX774YY04.AW.shhh.counts
HX774YY04.AW.shhh.groups
HX774YY04.AX.shhh.qual
HX774YY04.AX.shhh.fasta
HX774YY04.AX.shhh.names
HX774YY04.AX.shhh.counts
HX774YY04.AX.shhh.groups
HX774YY04.AE.shhh.qual
HX774YY04.AE.shhh.fasta
HX774YY04.AE.shhh.names
HX774YY04.AE.shhh.counts
HX774YY04.AE.shhh.groups
HX774YY04.A_BIOT_MIX.shhh.qual
HX774YY04.A_BIOT_MIX.shhh.fasta
HX774YY04.A_BIOT_MIX.shhh.names
HX774YY04.A_BIOT_MIX.shhh.counts
HX774YY04.A_BIOT_MIX.shhh.groups
HX774YY04.AS_MIX.shhh.qual
HX774YY04.AS_MIX.shhh.fasta
HX774YY04.AS_MIX.shhh.names
HX774YY04.AS_MIX.shhh.counts
HX774YY04.AS_MIX.shhh.groups
HX774YY04.A_BIOT_BLACK.shhh.qual
HX774YY04.A_BIOT_BLACK.shhh.fasta
HX774YY04.A_BIOT_BLACK.shhh.names
HX774YY04.A_BIOT_BLACK.shhh.counts
HX774YY04.A_BIOT_BLACK.shhh.groups
HX774YY04.AS_RED.shhh.qual
HX774YY04.AS_RED.shhh.fasta
HX774YY04.AS_RED.shhh.names
HX774YY04.AS_RED.shhh.counts
HX774YY04.AS_RED.shhh.groups
HX774YY04.AS_WHITE.shhh.qual
HX774YY04.AS_WHITE.shhh.fasta
HX774YY04.AS_WHITE.shhh.names
HX774YY04.AS_WHITE.shhh.counts
HX774YY04.AS_WHITE.shhh.groups
HX774YY04.shhh.fasta
HX774YY04.shhh.names
AFTER RUNNING THE TRIM.SEQS COMMAND, I GOT AN ERROR " SEQUENCE(S) NOT IN THE NAME OR COUNT FILE "
mothur > trim.seqs
(fasta=HX774YY04.shhh.fasta,name=HX774YY04.shhh.names,oligos=A1_oligos.txt,pdiffs=2,bdiffs=1,maxho
mop=8,minlength=200,flip=T,processors=8)
Using 8 processors.
00
00
00
1000
1000
1000
1000
1000
1000
20001000
1000
2000
2000
2000
2000
2846
2000
2000
2839
2000
2839
2839
2839
2839
2839
2839
Appending files from process 1
Appending files from process 2
Appending files from process 3
Appending files from process 4
Appending files from process 5
Appending files from process 6
Appending files from process 7
Group count:
121662
AS_WHITE 3098
Total of all groups is 124760
Output File Names:
HX774YY04.shhh.trim.fasta
HX774YY04.shhh.scrap.fasta
HX774YY04.shhh.trim.names
HX774YY04.shhh.scrap.names
HX774YY04.shhh.groups
mothur > summary.seqs(fasta=HX774YY04.shhh.trim.fasta,name=HX774YY04.shhh.trim.names)
Using 8 processors.
[ERROR]:
>HX774YY04IRUPJ is not in your name or count file,
please correct.
We had an issue with the Windows version of trim.seqs in 1.29.0 when using multiple processors. It has been corrected in the release of 1.29.1. Could you download the new version and see if the problem persists?
The trim.seqs (in Windows 7, 64 bit) worked fine with the new version 1.29.1.
Thank you for your help !