fastq_to_fasta segmentation fault (core dumped)

[smitra]

Hi, I am trying to convert my fastq files which have been stitched using multiple_join_paired_ends.py under qiime-1.9.1
Now my fastq joined files look okay, but when I try to convert them to fasta I am having trouble. for a single file test I get the error

less fastq2fasta.single.file.sh.e378704

/var/spool/sge_prod/hb01s2b15/job_scripts/378704: line 7: 26760 Segmentation fault      (core dumped) fastq_to_fasta -i RIFSAMPLEA_S1.join.fastq -o RIFSAMPLEA_S1.join.fasta
fastq2fasta.single.file.sh.e378704 (END)

This is the job script that I used.

less fastq2fasta.single.file.sh

#$ -l h_rt=24:00:00
#$ -cwd
#$ -V
#$ -l h_vmem=8G
#$ -M s.mitra@leeds.ac.uk

 fastq_to_fasta -i RIFSAMPLEA_S1.join.fastq -o RIFSAMPLEA_S1.join.fasta


fastq2fasta.single.file.sh (END)

I have looked at the log for the job so I can see that it fails as it is setting up and probably fails at the very beginning of that. Also the log indicates that no memory has been used. I heard, that a segmentation fault is often a problem with allocating memory but it normally occurs late on in the execution of a program when nearly all of the memory has been used and the programm asks for more memory than there is left. But this is definitely not a case here.

Can anybody please help me how to fix this problem?
Thanks,
Mitra

[aprice67]

First thing I'd try is throwing a ton of memory at it. See if it runs with 64G of memory. If it does maybe slim it down for other jobs. Segmentation faults say to me that the problem has something to do with memory allocation and not necessarily the task itself. I know that you know that, and so suspect that there is something else going on, but even still, I would keep digging into the memory issue as being the problem for a long while. Permissions and memory. Good luck!

[Brian Bushnell]

Fastq to fasta should not require much memory. Try BBMap's reformat.sh:

reformat.sh in=file.fastq out=file.fasta -Xmx1g