Segmentation fault (core dumped)

[gvic628]

Hi,

I have been able to install LtrDetector on our local cluster; however, I keep getting the following error message:

var/spool/gridengine/perun17/job_scripts/59630: line 8: 23093 Segmentation fault (core dumped) LtrDetector -fasta /scratch3/ginaf/Phaeo_minION/LTR_programs/ltrdetector/REF/Phatr2_chromosomes_assembly_chromosomes_bd.fasta -destDir /scratch3/ginaf/Phaeo_minION/LTR_programs/ltrdetector/REF -nThreads 4 -rawScores -cleanedScores -nested -seqLevel

[6046401.982155] LtrDetector[23093]: segfault at 4 ip 000015042859ac12 sp 00007ffc1a105cd0 error 6 in libc-2.27.so[1504284bb000+1e7000]

I'm wondering if this is possibly a ram issue? Any insight would be appreciated!
Gina

[hani-girgis]

Hi, Gina.

First, the -fasta option is not used correctly; this option takes a directory/folder not a file. Files under this directory must have the ".fa" extension.

If this does not fix the error. I am wondering which option is causing this error. I suggest to run LtrDetector without the last 4 options, then add each of these options one by one. If none of this works, it would be helpful if you share with me the input file(s) that caused this error. You may contact me at hzgirgis at buffalo dot edu.

Best,

Hani Zakaria

[gvic628]

Hi Hani,
Thanks very much for your help. I fixed the -fasta option so that it represents a directory and changed the extension to ".fa". I was able to get the program running using the options -rawScores, -cleanedScores, -seqLevel separately and together.

The option -nested seems to be the parameter resulting in the core dump. I've attached the bash script that I used as well as the resulting error and output files.

thanks! Gina
detect_test3.txt
detect_test3.sh.e59688.txt
detect_test3.sh.o59688.txt