[galaxy-dev] Fastq_filter fails on large files

Hello,

The tool fastq_filter worked on 1M reads, but fails (hangs) on 15M reads. I had to kill the job after the user let it run for a whole day. The debug.txt file containing a python function "fastq_read_pass_filter" is created in the files/000/dataset_xxx_files directory. I am getting no error from the galaxy server.

I wonder what could cause fastq_filter to fail? The fastx equivalent tool works, but it misses all the options of fastq_filter.

I'd be grateful for any hints to help me get fastq_filter to work on large fastq files.

Thanks

Isabelle