SunPengChuan / wgdi

WGDI: A user-friendly toolkit for evolutionary analyses of whole-genome duplications and ancestral karyotypes
https://wgdi.readthedocs.io/en/latest/
BSD 2-Clause "Simplified" License
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wgdi -d get Segmentation fault (core dumped) #10

Closed dailing57 closed 3 years ago

dailing57 commented 3 years ago

I tried to run wgdi -d grape.total.conf, It shows like this:

blast  =  grape.blast.txt
gff1  =  grape_Chr_uniq.gff
gff2  =  grape_Chr_uniq.gff
lens1  =  grape_Chr.len
lens2  =  grape_Chr.len
genome1_name  =  Vitis_vinifera
genome2_name  =  Vitis_vinifera
multiple  =  1
score  =  100
evalue  =  1e-5
repeat_number  =  10
position  =  order
blast_reverse  =  false
ancestor_left  =  none
ancestor_top  =  none
markersize  =  0.5
figsize  =  10,10
savefig  =  grape.dot.png
failed to get the current screen resources
Segmentation fault (core dumped)

and I run gdb core.76309:

(base) [root@localhost colinearlity]# gdb core.76309 
GNU gdb (GDB) Red Hat Enterprise Linux 7.6.1-114.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 76309]
[New LWP 76396]
Core was generated by `/home/qinsong/anaconda3/bin/python /home/qinsong/anaconda3/bin/wgdi -d grape.to'.
Program terminated with signal 11, Segmentation fault.
#0  0x00007f9d55cd9f03 in ?? ()
"/home/qinsong/WGDI/colinearlity/core.76309" is a core file.
Please specify an executable to debug.

How should I pinpoint the wrong location?

SunPengChuan commented 3 years ago

It may be a memory problem. Can you provide the way you run and error information?

dailing57 commented 3 years ago

Thanks for your reply. The run and error information is stated as the issue. I created a new environment and reintalled wgdi, and I get through the trouble. Maybe the causes of the problem is that I messed up the environment.