Entering edit mode
6.2 years ago
c.clarido
▴
110
Hello,
I was trying to map my reads as follow:
bowtie2 -x dbref -1 /home/s1104230/output/tR1.fastq -2 /home/s1104230/output/tR2.fastq -S eq2.sam
However I got the following the errors:
perl: warning: Setting locale failed.
perl: warning: Please check that your locale settings:
LANGUAGE = (unset),
LC_ALL = (unset),
LC_CTYPE = "UTF-8",
LANG = "en_US.UTF-8"
are supported and installed on your system.
perl: warning: Falling back to a fallback locale ("en_US.UTF-8").
Error: Read D00476:230:C8TCRANXX:8:2214:1156:2230 1:N:0:ACAGTGA+GATCTAC has more quality values than read characters.
Error: Encountered exception: 'Unidentified exception'
Command: /usr/bin/bowtie2-align-s --wrapper basic-0 -x dbref -S eq2.sam -1 /home/s1104230/output/tR1.fastq -2 /home/s1104230/output/tR2.fastq
(ERR): bowtie2-align exited with value 1
Any suggestion how I could solve this?
What does
grep -A 3 "D00476:230:C8TCRANXX:8:2214:1156:2230" /home/s1104230/output/tR1.fastq
show? Looks like a malformed file.