I'm using bowtie 12.7 and am aligning Solid colorspace sequencing files to hg19. I have ran two similar datasets using the same script and it went fine, but ran into a wall with this set. I've been trying to find the source of the error given it refers to a specific tag/tags. When I look for the sequence tag identities in the .csfasta or .QV.qual files, they look fine - no typo, nothing glaring. I'm not sure where else to go at this point. If anyone can offer me suggestions on where the source of this error could be or anything to help, that would be great. I have no prior bioinformatics experience so this hiccup here is a bit daunting so thank you for bearing with my laymen explanation and trying to help.
Input Script:
bowtie -C /index/hg19_c -B 1 -p 6 -v 0 -m 1 --col-keepend --fr -f -1 F3.csfasta -2 F5.csfasta --Q1 F3.QV.qual --Q2 F5.QV.qual --max multiple_V0 --un notMatch_V0 > map_V0.txt
Error message:
Warning: one or more mismatched read names between FASTA and quality files
Warning: one or more mismatched read names between FASTA and quality files
Warning: one or more mismatched read names between FASTA and quality files
Warning: one or more mismatched read names between FASTA and quality files
Warning: one or more mismatched read names between FASTA and quality files
Warning: one or more mismatched read names between FASTA and quality files
Offending read name: "1_5_66_F3"
Too few quality values for read: 1_5_66_F3
are you sure this is a FASTQ-int file?
terminate called after throwing an instance of 'int'
getAlignment.sh: line 22: 3579 Aborted
Input Script:
bowtie -C /index/hg19_c -B 1 -p 6 -v 0 -m 1 --col-keepend --fr -f -1 F3.csfasta -2 F5.csfasta --Q1 F3.QV.qual --Q2 F5.QV.qual --max multiple_V0 --un notMatch_V0 > map_V0.txt
Error message:
Warning: one or more mismatched read names between FASTA and quality files
Warning: one or more mismatched read names between FASTA and quality files
Warning: one or more mismatched read names between FASTA and quality files
Warning: one or more mismatched read names between FASTA and quality files
Warning: one or more mismatched read names between FASTA and quality files
Warning: one or more mismatched read names between FASTA and quality files
Offending read name: "1_5_66_F3"
Too few quality values for read: 1_5_66_F3
are you sure this is a FASTQ-int file?
terminate called after throwing an instance of 'int'
getAlignment.sh: line 22: 3579 Aborted
Comment