bowtie2 chomp error

[frej.tulin]

Hi

I just received a number of fastq files from Illumina sequencing.

When I try to align these with bowtie2 I get this error message for a subset of the fastq files:

Use of uninitialized value $l in scalar chomp at /home/fcross/frej/bowtie2-2.0.4/bowtie2 line 408, <BT> line 828339.
Use of uninitialized value $l in substitution (s///) at /home/fcross/frej/bowtie2-2.0.4/bowtie2 line 409, <BT> line 828339.

This is the perl-wrapper script (bowtie2) complaining at line 408 when trying to perform chomp on an empty line i belive.

I'm guessig the error comes from some a bad line somewhere in my fastq file, but I haven't been able to find where. It looks fine as far as I can tell.

Questions:
1. Has anyone seen this error before? What is the likely the problem?
2. Does anyone have a script (perl preferably) to check integrity of a fastq file?


Many thanks

/frej

[wenxuezhao]

I used bowtie in Galaxy, but I didn't have this problem.

[kcchan]

Does this only happen when you use the perl script or does it also show up when you run Bowtie via the command line?

If you want a program to check the fastq files itself, you can use something like FastQValidator or run a QC using FastX-Toolkit.