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Old 10-08-2012, 07:45 PM   #1
vallejov
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Location: Michigan

Join Date: Jul 2011
Posts: 10
Default Problem with FastXtool kit

I'm a complete newbie to bioinformatics and have just started analyzing my RNA-seq data (illumina HiSeq2000 100 bp reads) and have hit a snag. I'm trying to run the fastx_quality_stats and I keep getting this error message:

fastx_quality_stats: failed to open input file '/home/vallejov/stevia_R1.fastq': Value too large for defined data type

I get the same message if I try to run fastx_trimmer. Does this mean that my file is too large? my file is 48G. Do I need to parse it? If I parse it, when do I need to merge the output files again?

Veronica
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Old 10-09-2012, 04:18 AM   #2
GenoMax
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Default

Did you compile the fastx toolkit yourself or get the pre-compiled binaries?

It is possible that you are either using a 32-bit operating system or you downloaded the 32-bit fastx toolkit binaries and thus running into the error above.
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