hello,
running bwa v0.5.9 i get this error:
fail to open file 'long_path/filename.fastq'. Abort!
Abort (core dumped)
yes, the file does actually exist. i think the problem is that it's too big - 4.6G.
this is one side of illumina paired end reads - 100bp reads and there are 18,517,594 reads in the file. i shortened the file to ~2 million reads and bwa handled it just fine. is there a limit to the size of the fastq input file?
if there is a limit i was thinking i could break up each of the paired end files and create multiple .sai files - but i think that would be problematic on the 'bwa sampe' end. i don't think the 'sampe' command supports multiple pairs of .sai files. maybe i could cat all the .sai files together?
anyone else have a problem like this? too much data!
thanks,
mike
running bwa v0.5.9 i get this error:
fail to open file 'long_path/filename.fastq'. Abort!
Abort (core dumped)
yes, the file does actually exist. i think the problem is that it's too big - 4.6G.
this is one side of illumina paired end reads - 100bp reads and there are 18,517,594 reads in the file. i shortened the file to ~2 million reads and bwa handled it just fine. is there a limit to the size of the fastq input file?
if there is a limit i was thinking i could break up each of the paired end files and create multiple .sai files - but i think that would be problematic on the 'bwa sampe' end. i don't think the 'sampe' command supports multiple pairs of .sai files. maybe i could cat all the .sai files together?
anyone else have a problem like this? too much data!
thanks,
mike
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