Bowtie error message

[nncy1105]

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

[GenoMax]

Are you doing this on unix or some other OS?

Have you looked in the sequence files to see where that offending read is? It may be the first one. Sounds like there is something about that read bowtie does not like.

You can grep the read name out of the file and post it here so we can see if there is something odd about it.

$cat F3.csfasta | grep "1_5_66_F3"

It also seems that the number of entries in your csfasta files do not seem to match .qual file.

Can you check the following?

$cat F3.csfasta | grep ">"| wc -l
$cat F3.QV.qual | grep ">"| wc -l

Are those numbers identical for both sets of files?

[nncy1105]

Hi GenoMax,

I'm running this on a server: GNU/Linux (I believe RedHat).

I tried your codes and I can't see anything wrong still:

code: $cat F3.csfasta | grep "1_5_66_F3"
and it returned:
>1_5_66_F3

code:$cat F3.csfasta | grep ">"| wc -l
$cat F3.QV.qual | grep ">"| wc -l
and it returned:
23693204
23693204

[GenoMax]

Hi GenoMax,

I'm running this on a server: GNU/Linux (I believe RedHat).

I tried your codes and I can't see anything wrong still:

code: $cat F3.csfasta | grep "1_5_66_F3"
and it returned:
>1_5_66_F3

code:$cat F3.csfasta | grep ">"| wc -l
$cat F3.QV.qual | grep ">"| wc -l
and it returned:
23693204
23693204

Those stats look ok.

Were these files saved on a PC/Mac and then transferred to the unix server? Did you try to open them in an editor on a PC/Mac? If that was the case then see this: http://kb.iu.edu/data/acux.html

[nncy1105]

Those stats look ok.

Were these files saved on a PC/Mac and then transferred to the unix server? Did you try to open them in an editor on a PC/Mac? If that was the case then see this: http://kb.iu.edu/data/acux.html

GenoMax, those were saved from a ftp site to my external harddrive attached to a MacOSX 10.5 then sftp transferred to the Linux server. I'll try the Cyberduck or OpenSSH program on the page you recommended and transfer those files again. Hopefully that will solve this. Thanks!