segmentation fault (terminated by singal 11)

[jychoilab]

Hello

I was interested in using svmu for my genome assembly of interest and I ran into a seg fault error. Could you take a look at this error? The genome assembly of my organism is a plant ~400Mbp but I hard masked my sample genome and hard masked my reference genome. The reference genome has 12 chromosomes but my sample genome is still a draft so it has ~2000 contigs. I initially thought the seg fault occured due to running out of memory so I just took one chromosome of the ref genome and used numcer to align all of the possible sample genome contigs. I'm running the commands on a server where I gave 140GB of memory and still ran into seg fault error.

Heres what I get with /usr/bin/time -v

Command terminated by signal 11 Command being timed: "/home/PROGRAMS_AND_SCRIPTS/PROGRAMS/svmu/svmu sam2ref.mr.delta RM.chr01.fa sample.fasta 5 h" User time (seconds): 82.17 System time (seconds): 6.53 Percent of CPU this job got: 89% Elapsed (wall clock) time (h:mm:ss or m:ss): 1:38.90 Average shared text size (kbytes): 0 Average unshared data size (kbytes): 0 Average stack size (kbytes): 0 Average total size (kbytes): 0 Maximum resident set size (kbytes): 6509976 Average resident set size (kbytes): 0 Major (requiring I/O) page faults: 0 Minor (reclaiming a frame) page faults: 1890746 Voluntary context switches: 1553260 Involuntary context switches: 900 Swaps: 0 File system inputs: 0 File system outputs: 1880 Socket messages sent: 0 Socket messages received: 0 Signals delivered: 0 Page size (bytes): 4096 Exit status: 0

And here's what I got from running

gdb

GNU gdb (GDB) Red Hat Enterprise Linux 7.6.1-94.el7 Copyright (C) 2013 Free Software Foundation, Inc. License GPLv3+: GNU GPL version 3 or later http://gnu.org/licenses/gpl.html This is free software: you are free to change and redistribute it. There is NO WARRANTY, to the extent permitted by law. Type "show copying" and "show warranty" for details. This GDB was configured as "x86_64-redhat-linux-gnu". For bug reporting instructions, please see: http://www.gnu.org/software/gdb/bugs/... Reading symbols from /home/PROGRAMS_AND_SCRIPTS/PROGRAMS/svmu/svmu...done. [New LWP 4636] Core was generated by `/home/PROGRAMS_AND_SCRIPTS/PROGRAMS/svmu/svmu sam2ref.mr.delta /scratch/'. Program terminated with signal 11, Segmentation fault.

0 0x00002b29496f2fdc in std::string::assign(std::string const&) () from /lib64/libstdc++.so.6

Missing separate debuginfos, use: debuginfo-install glibc-2.17-157.el7_3.1.x86_64 libgcc-4.8.5-11.el7.x86_64 libstdc++-4.8.5-11.el7.x86_64

Thanks in advance for the help.

Jae

[mahulchak]

I don't think memory is the problem. Will you be able to share your sequences so that I can replicate the error?

[navajeet123]

Hi, I executed the following commands.

1. nucmer -mumreference -noextend -prefix sam2ref.mm ref.fasta Scaf.fasta nucmer version version 3.1
2. ./svmu sam2ref.mm.delta ref.fasta Scaf.fasta 5 h

It ended with an error msg ! munmap_chunk(): invalid pointer: 0x0000001957d578b0 ***

OutFiles Generated: trans.txt, cm.txt, cords.txt(blank)

Can You Please help. Navajeet

[mahulchak]

Sorry somehow I missed this message. Hopefully you were able to find a solution. If there are any outstanding problems, I'll be happy to help. I am closing it for now.