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
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
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