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ddunlap4 / ea-utils

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Error opening file 'GFI-410.fastq': Value too large for defined data type #6

Closed GoogleCodeExporter closed 8 years ago

GoogleCodeExporter commented 8 years ago 
I just ran fastq-multx tool to demultiplex barcodes from the fastq file and got 
this error. 

Error opening file 'GFI-410.fastq': Value too large for defined data type

I am using ea-utilsv1.1.258 on Ubuntu 8.04.4 LTS/Linux 2.6.24-25-generic i686

This is the command I used:
fastq-multx -B barcode-list.txt GFI-410.fastq -o barcode.%.fq -b

My fastq file consist of about 170 million reads and of size 41 GB size. My 
barcode list consist of 56 lines of different barcodes 

Is there a size limit for the fastq file to be used / should I use different 
version. Any help would be much appreciated. 

Thank you

Original issue reported on code.google.com by janu.fl...@gmail.com on 11 Jan 2012 at 9:12

GoogleCodeExporter commented 8 years ago 
I just pushed 258 after fixing a bug... but it may have caused a problem.   You 
may want to use an older release for now.   However, can you attach a sample of 
the fastq used?

Original comment by earone...@gmail.com on 11 Jan 2012 at 10:29

GoogleCodeExporter commented 8 years ago 
Thanks for the reply. Please find the attached sample of the fastq file and 
barcode list. I installed the previous release of ea-utils 1.1.237 version- but 
still get the same error.

Original comment by janu.fl...@gmail.com on 11 Jan 2012 at 11:50

Attachments:

GoogleCodeExporter commented 8 years ago 
Does the program fail for you on the small samples?

OK, I *think* the new release might work (273) for you ... not sure exactly 
because I didn't reproduce the error.  But I cleaned up a lot of misc stuff.

Original comment by earone...@gmail.com on 12 Jan 2012 at 5:31

GoogleCodeExporter commented 8 years ago 
Thanks for that. Yes, it indeed worked for the small samples. I tried with the 
new release 273, but still getting the same error. "Error opening fastq file : 
Value too large for defined datatype. Any suggestions?

Original comment by janu.fl...@gmail.com on 13 Jan 2012 at 1:05

GoogleCodeExporter commented 8 years ago 
Sorry for my previous comment. The new release 273 seems to be working with 
gzipped fastq file. Many thanks for that.

Original comment by janu.fl...@gmail.com on 13 Jan 2012 at 1:51

GoogleCodeExporter commented 8 years ago 
For now, the gz version should work, for 32 bit system support

I'm adding this for future version which should work on Max os X and Lion as 
well.

#if defined(__i386__)
#define _FILE_OFFSET_BITS 64
#endif

Original comment by earone...@gmail.com on 13 Jan 2012 at 2:17

GoogleCodeExporter commented 8 years ago 
New code should work for gz and non-gz files on Lion.

Original comment by earone...@gmail.com on 16 Jan 2012 at 3:00