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 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