Entering edit mode
7.7 years ago
Hans
▴
140
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.
Was this a warning (or an error)? Did you get a sam file after running the command or the program quit?
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.
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.
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.
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.