Question: "Paired-end accessions do not match" error in gsnapl
0
gravatar for Hanan
3.8 years ago by
Hanan70
Tel Aviv University
Hanan70 wrote:

Hello, I was running this command of gsnapl: gsnapl -t 12 -d CSPSE -D ~/zav/ S1.trimmed-paired-1.fq S1.trimmed-paired-2.fq S2.trimmed-paired-1.fq S2.trimmed-paired-2.fq S3.trimmed-paired-1.fq S3.trimmed-paired-2.fq > S.sam

and I get this error message: "Paired-end accessions HWI-D00525:193:C6DFKANXX:2:1101:1233:2170 and @HWI-D00525:193:C6DFKANXX:2:1101:1233:2170 do not match" As you can see, they do match, except for the "@" at the first line. However, the "@" is present in the fastq file. I got this message twice, each time on different file, and in both cases, these were the first lines of the file.
Thank you for your help.

gsnapl • 1.4k views
ADD COMMENTlink modified 3.8 years ago • written 3.8 years ago by Hanan70

Was this a warning (or an error)? Did you get a sam file after running the command or the program quit?

ADD REPLYlink written 3.8 years ago by genomax83k

I seems like an error, even though there is no "error" in the message. The program quits. When gsanp ends normally, I get this message: "Processed 40630662 queries in 7573.52 seconds (5364.83 queries/sec)". Moreover, the sam file I get is smaller than I expect.

ADD REPLYlink written 3.8 years ago by Hanan70

I found this flag --allow-pe-name-mismatch that allows accession names of reads to mismatch in paired-end files. This flag overcomes the problem.

ADD REPLYlink modified 3.8 years ago • written 3.8 years ago by Hanan70

If you are sure that there is no real PE name mismatch then great. It may be a bug of some kind. You can report it back to the authors.

ADD REPLYlink written 3.8 years ago by genomax83k

Hi, It was a bug. I have reported to the author, Thomas Wu, and he was able to reproduce it and fix it. The last version 2016-06-30.v3 runs smoothly. Thank you Tom.

ADD REPLYlink modified 3.8 years ago • written 3.8 years ago by Hanan70
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