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?