#8 Ribopicker segmentation fault:11

[Anonymous]

When I run the test_input file, ribopicker seems to run just fine. However, when I give my sequence file as input, I get the following error

sh: line 1: 17463 Segmentation fault: 11 ./bwaMAC bwasw -A -f /tmp/nsar/ribopicker/119_filtered_0.5_reject_slr.tsv -z 1 /tmp/nsar/ribopicker/db/slr108 119_R1.filter_0.5_reject.fa > /dev/null 2>&1
ERROR: system call "./bwaMAC bwasw -A -f /tmp/nsarode3/ribopicker/119_filtered_0.5_reject_slr.tsv -z 1 /tmp/nsar/ribopicker/db/slr108 119_R1.filter_0.5_reject.fa" failed: 35584.

My sequence files are in fasta format, and I don't see any obvious mistake in the file format itself.

[Anonymous]

• Description has changed:

Diff:

--- old
+++ new
@@ -1,4 +1,4 @@
-When I run the test_input file, ribopicker seems to run just fine. However, when I give me sequence file as input, I get the following error
+When I run the test_input file, ribopicker seems to run just fine. However, when I give my sequence file as input, I get the following error

 sh: line 1: 17463 Segmentation fault: 11  ./bwaMAC bwasw -A -f /tmp/nsar/ribopicker/119_filtered_0.5_reject_slr.tsv -z 1 /tmp/nsar/ribopicker/db/slr108 119_R1.filter_0.5_reject.fa > /dev/null 2>&1
 ERROR: system call "./bwaMAC bwasw -A -f /tmp/nsarode3/ribopicker/119_filtered_0.5_reject_slr.tsv -z 1 /tmp/nsar/ribopicker/db/slr108 119_R1.filter_0.5_reject.fa" failed: 35584.

[Robert Schmieder]

The "Segmentation fault" error suggests that you most likely did not have sufficient memory to run the file through BWA-SW. Can you monitor the memory usage and let me know if this is not the case? Thanks!

[Anonymous]

Thanks.
I managed to run the program on our server (ubuntu machine) without any errors. On my Mac machine (8Gb RAM and almost 800Gb) space, it kept giving this error. I monitored the memory usage during the run (only other program running being the browser) and though there was a spike in memory usage, I am not sure if it appeared to require something beyond the available resources.

[Anonymous]

[Anonymous]