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Nextomics / NextDenovo

Fast and accurate de novo assembler for long reads

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nextgraph Floating point exception(core dumped)

guoqunfei opened this issue · comments

commented

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

commented

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.