I encounter a problem when I use igblastn (ncbi-igblast-1.4.0-x64-linux.tar.gz) in my server(Ubuntu). When I set organism as human, the script died with "Segmentation fault", while it is ok for organisms with mouse and rabbit. My command is below. Anyone can give me some hints to deal with the problem?
igblastn -germline_db_V IMGT_refseq/human_IMGT_V -germline_db_J IMGT_refseq/human_IMGT_J -germline_db_D IMGT_refseq/human_IMGT_D -organism human -domain_system imgt -query temp.fa -auxiliary_data optional_file/human_gl.aux
Segmentation fault
igblastn -germline_db_V IMGT_refseq/human_IMGT_V -germline_db_J IMGT_refseq/human_IMGT_J -germline_db_D IMGT_refseq/human_IMGT_D -organism mouse -domain_system imgt -query temp.fa -auxiliary_data optional_file/human_gl.aux
#it is ok to run
Here is similar thread: segmentation fault (core dumped) in IGBlast
Your query might be too large.
•
written
by
marina.v.yurieva
Thanks for your answer. I have viewed that post and don't think that can solve my question. In fact, I just put one seq into temp.fa (as below) to test this error. I used different versions of the igblast, and found same question.
>HWI-M941
TCACGTCATGGTATTCGGCGGCGGGACCAAGCTGACCGTCCTTGGTCAGCCCAAGGCTGCCCCCTCGGTCACTCTGTTCCCACCCTCCTCTCTCTCTCTCCTC
Log in to answer this question.
