Segmentation fault in standalone ribopicker

[katyanne....@gmail.com]

Hello,

I have been trying to get RiboPicker to run on my mac, but I am having an error come up as follows:

$ perl ribopicker.pl -f Sample_paired_no_duplicates.fasta -dbs slr

sh: line 1: 4008 Segmentation fault: 11 ./bwaMAC bwasw -A -f /Users/piamoisander/ribopicker-standalone-0.4.3/1389975249_slr.tsv -z 1 db/slr108 Sample_paired_no_duplicates.fasta > /dev/null 2>&1
ERROR: system call "./bwaMAC bwasw -A -f /Users/piamoisander/ribopicker-standalone-0.4.3/1389975249_slr.tsv -z 1 db/slr108 Sample_paired_no_duplicates.fasta" failed: 35584.

Try 'perl ribopicker.pl -h' for more information.
Exit program.

I have no clue what the -A option is for that comes up in the error.

Anyone dealt with this before?

Thanks,
Katy

[Robert Schmieder]

You most likely have not sufficient resources (memory) to process the data.

The -A option is explained when running bwaMAC without input parameters or using the option -h to display the help. You can also find more information on the riboPicker FAQ page (http://ribopicker.sourceforge.net/faq.html) under "How was the BWA source code modified?":
"[...] parameters -A (generate alternative output), -R (output extended version of Cigar string with replacements) and -M (force to mismatch Ns in query sequence). [...]"

[asher...@gmail.com]

I've had a similar thing happen to me with the same error message, though I'm running it on a cluster with 256GB of RAM, so I don't understand the memory problem.

sh: line 1: 51666 Segmentation fault (core dumped) ./bwa64 bwasw -A -f ../ribofree/10966_8_1_a_ssr.tsv -z 1 db/ssr128 ../10966_8_1/10966_8_1_a_val_1.fq > /dev/null 2>&1
ERROR: system call "./bwa64 bwasw -A -f ../ribofree/10966_8_1_a_ssr.tsv -z 1 db/ssr128 ../10966_8_1/10966_8_1_a_val_1.fq" failed: 35584.

Any thoughts on what else might cause this?