Segmentation fault for Igblastn with species human
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9.1 years ago
lye210 • 0

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
igblast • 2.0k views
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9.1 years ago

Here is similar thread: segmentation fault (core dumped) in IGBlast

Your query might be too large.

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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
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Entering edit mode
9.1 years ago
lye210 • 0

I got the reason why it is wrong. My downloading file "internal_data/human/human_V.nsi" is not right, when I redownload it, igblastn works well and the problem is solved

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