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Nextomics / NextDenovo

Fast and accurate de novo assembler for long reads
GNU General Public License v3.0
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nextgraph Floating point exception(core dumped) #131

Open guoqunfei opened 2 years ago

guoqunfei commented 2 years ago

Hi developer,

Describe the bug The downloaded NextDenovo process can be tested on the provided test data set without any problems. Then I use my own data set to run the three steps of the NextDenovo process separately, and there is no problem in the first two steps. But I meet an error with 03.ctg_graph/01.ctg_graph.sh.work/ctg_graph0/nextDenovo.sh

Error message /NextDenovo/01_rundir/03.ctg_graph/01.ctg_graph.sh.work/ctg_graph0/nextDenovo.sh.e

hostname
+ hostname
cd /NextDenovo/01_rundir/03.ctg_graph/01.ctg_graph.sh.work/ctg_graph1
+ cd /NextDenovo/01_rundir/03.ctg_graph/01.ctg_graph.sh.work/ctg_graph1
time /NextDenovo/bin/nextgraph -a 1 -R 0.7 -f /NextDenovo/01_rundir/03.ctg_graph/01.ctg_graph.input.seqs /NextDenovo/01_rundir/03.ctg_graph/01.ctg_graph.input.ovls -o nd.asm.p.fasta;
+ /NextDenovo/bin/nextgraph -a 1 -R 0.7 -f /NextDenovo/01_rundir/03.ctg_graph/01.ctg_graph.input.seqs /NextDenovo/01_rundir/03.ctg_graph/01.ctg_graph.input.ovls -o nd.asm.p.fasta
[INFO] 2021-10-23 08:43:30 Initialize graph and reading...
[INFO] 2021-10-23 09:01:24 Initial Node(s): 10539239, Edge(s): 103652853
[INFO] 2021-10-23 09:11:33 Depth stat, Mid: 17.000 Max: 34000.000 Repeat: 25.500 L:N:H: 0.137:0.819:0.044
[INFO] 2021-10-23 09:11:33 Outdegree stat, Mid: 3.000 Max: 6000.000 Repeat: 4.500 L:N:H: 0.500:0.496:0.004
[INFO] 2021-10-23 09:14:23 Chimeric node ratio: 2.256% (candidate: 4.991%)
[INFO] 2021-10-23 09:30:53 Assembly done and outputting...
/NextDenovo/01_rundir/03.ctg_graph/01.ctg_graph.sh.work/ctg_graph1/nextDenovo.sh: line 5: 14783 **Floating point exception(core dumped)** /NextDenovo/bin/nextgraph -a 1 -R 0.7 -f /NextDenovo/01_rundir/03.ctg_graph/01.ctg_graph.input.seqs /NextDenovo/01_rundir/03.ctg_graph/01.ctg_graph.input.ovls -o nd.asm.p.fasta

Genome characteristics genome size: 15G

Input data pacbio HiFi reads、sequence depth: 30X

Operating system Which operating system and version are you using? Linux SGE

GCC What version of GCC are you using? gcc version 5.2.0 (GCC)

Python What version of Python are you using? Python 3.8.1

NextDenovo What version of NextDenovo are you using? nextDenovo v2.5.0

moold commented 2 years ago

I can not fix it by now unless I can reproduce this core dumped problem, so I suggest you try other assemblies first, I will keep this issue opening until I fix it.