Segmentation fault in 'uncalled sim'

[WeipengMO]

Hello

I ran the uncalled simulation and got 278742 Segmentation fault (core dumped). I tried it on different HPCs and got the same problem. Any ideas to solve this?

I ran the simulation like this:

uncalled sim index/col_non_cen.fasta fast5/ --ctl-seqsum sequencing_summary.txt --unc-seqsum 20190809_zymo_seqsum.txt --unc-paf 20190809_zymo_uncalled.paf -t 4 --deplete --sim-speed 0.25 > sim_uncalled_out.paf 2> uncalled_err.txt

Resource usage summary:

    CPU time :                                   10876.19 sec.
    Max Memory :                                 40303 MB
    Average Memory :                             39679.36 MB
    Total Requested Memory :                     -
    Delta Memory :                               -
    Max Swap :                                   1 MB
    Max Processes :                              4
    Max Threads :                                9
    Run time :                                   30601 sec.
    Turnaround time :                            30602 sec.

It return a core file core.278742:

$ gdb -c core.278742

GNU gdb (GDB) Red Hat Enterprise Linux 7.6.1-110.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/>.
[New LWP 278742]
[New LWP 280323]
[New LWP 280324]
[New LWP 280325]
[New LWP 280326]
Core was generated by `/scem/work/mowp/anaconda3/envs/uncalled/bin/python3 /scem/work/mowp/anaconda3/e'.
Program terminated with signal 11, Segmentation fault.
#0  0x00002ae7e2ad8554 in ?? ()

The uncalled_err.txt is attached. (uncalled_err.txt)

Any help very much appreciated. Weipeng

[WeipengMO]

22

[skovaka]

Sorry for the issue! I'm not sure what's causing it. I don't think it's the same error as #22, since that segfaulted immediately after loading reads, while yours looks like it runs for a few hours before failing. Would you be able to share your fast5 files with me? I know that might be a lot of data, but the simulator is hard to debug, and I'm not sure if I can help without it. Feel free to email me at skovaka1 jhu edu

[WeipengMO]

Sorry for the issue! I'm not sure what's causing it. I don't think it's the same error as #22, since that segfaulted immediately after loading reads, while yours looks like it runs for a few hours before failing. Would you be able to share your fast5 files with me? I know that might be a lot of data, but the simulator is hard to debug, and I'm not sure if I can help without it. Feel free to email me at skovaka1 jhu edu

Thank you very much. I have sent you an email.