gsMapper failed to create ace or bam file

[dnajuice]

Hi,

I encountered a problem with gsMapper (v2.6) when I tried to align 10M Illumina paired end reads on to 100 large contigs. Even though I set the parameters to output file in ACE and BAM format, neither was generated. Can anybody give me a clue?

Also, is there any way to use the gsMapper output files to generate scaffolds based on paired end information?

Thanks!

[jimmybee]

Why are you using gsMapper with Illumina data? Its a GSFLX tool, so I would have thought it would be much easier to use programs designed to work with smaller reads and Illumina tech