Nextomics/NextDenovo

ctg_graph error, (core dumped), returned non-zero exit status 134".

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usersHuangKun commented

Dear author, hello. I encountered a "(core dumped), returned non-zero exit status 134" issue in 03.ctg_graph/01.ctg_graph.sh.work/. I am reaching out to you for assistance regarding this matter.

Question or Expected behavior
ctg_graph error, (core dumped), returned non-zero exit status 134.

Operating system
Which operating system and version are you using?
CentOS Linux release 7.9.2009 (Core)

GCC
What version of GCC are you using?
gcc version 8.3.1 20190311 (Red Hat 8.3.1-3) (GCC)

Python
What version of Python are you using?
Python 3.10.14

NextDenovo
What version of NextDenovo are you using?
nextDenovo 2.5.2

Additional context (Optional)

run.cfg:

[General]
job_type = local
job_prefix = nextDenovo
task = all
rewrite = yes
deltmp = yes
rerun = 3
parallel_jobs = 10
input_type = raw # raw, corrected
read_type = ont
input_fofn = input.fofn
workdir = 01_rundir
submit = auto
kill = auto
check_alive = auto
job_id_regex = auto
use_drmaa = no

[correct_option]
read_cutoff = 1k
seed_cutoff = 10000
blocksize = 10g
genome_size = 4.59g
seed_depth = 30
seed_cutfiles = 20
sort_options = -m 100g -t 20 -k 40
minimap2_options_raw = -x ava-ont -t 20
pa_correction = 1
correction_options = -p 20 -s

[assemble_option]

random_round = 20

minimap2_options_cns = -x ava-ont -t 10
minimap2_options_map = -x map-ont -t 10
nextgraph_options = -a 1 -q 10

cat 2/b.assembing/nextdenove/01_rundir/03.ctg_graph/01.ctg_graph.sh.work/ctg_graph1/nextDenovo.sh.e
hostname
hostname

  • hostname
    cd /data/2/b.assembing/nextdenove/01_rundir/03.ctg_graph/01.ctg_graph.sh.work/ctg_graph1
  • cd /data/2/b.assembing/nextdenove/01_rundir/03.ctg_graph/01.ctg_graph.sh.work/ctg_graph1
    time /opt/biosoft/anaconda3/envs/nextdenovo/lib/python3.10/site-packages/nextdenovo/bin/nextgraph -a 1 -q 10 -f /data/2/b.assembing/nextdenove/01_rundir/03.ctg_graph/01.ctg_graph.input.seqs /data/2/b.assembing/nextdenove/01_rundir/03.ctg_graph/01.ctg_graph.input.ovls -o nd.asm.p.fasta;
  • /opt/biosoft/anaconda3/envs/nextdenovo/lib/python3.10/site-packages/nextdenovo/bin/nextgraph -a 1 -q 10 -f /data/2/b.assembing/nextdenove/01_rundir/03.ctg_graph/01.ctg_graph.input.seqs /data/2/b.assembing/nextdenove/01_rundir/03.ctg_graph/01.ctg_graph.input.ovls -o nd.asm.p.fasta
    [INFO] 2024-05-22 10:42:26 Initialize graph and reading...
    [INFO] 2024-05-22 10:43:26 Initial Node(s): 354136, Edge(s): 6540909
    [INFO] 2024-05-22 10:43:42 Depth stat, Mid: 3.000 Max: 6000.000 Repeat: 4.500 L:N:H: 0.442:0.473:0.085
    [INFO] 2024-05-22 10:43:42 Outdegree stat, Mid: 1.000 Max: 2000.000 Repeat: 1.500 L:N:H: 0.806:0.187:0.008
    [INFO] 2024-05-22 10:43:47 Chimeric node ratio: 3.621% (candidate: 4.214%)
    [INFO] 2024-05-22 10:44:00 Assembly done and outputting...
    *** Error in `/opt/biosoft/anaconda3/envs/nextdenovo/lib/python3.10/site-packages/nextdenovo/bin/nextgraph': munmap_chunk(): invalid pointer: 0x00002b849e013010 ***
    ======= Backtrace: =========
    /lib64/libc.so.6(+0x7f474)[0x2b84895c3474]
    /opt/biosoft/anaconda3/envs/nextdenovo/lib/python3.10/site-packages/nextdenovo/bin/nextgraph[0x4184bc]
    /opt/biosoft/anaconda3/envs/nextdenovo/lib/python3.10/site-packages/nextdenovo/bin/nextgraph[0x41775a]
    /opt/biosoft/anaconda3/envs/nextdenovo/lib/python3.10/site-packages/nextdenovo/bin/nextgraph[0x402c52]
    /lib64/libc.so.6(__libc_start_main+0xf5)[0x2b8489566555]
    /opt/biosoft/anaconda3/envs/nextdenovo/lib/python3.10/site-packages/nextdenovo/bin/nextgraph[0x403243]
    ======= Memory map: ========
    003ff000-00400000 rw-p 00000000 08:11 581310978
    /opt/biosoft/anaconda3/envs/nextdenovo/lib/python3.10/site-packages/nextdenovo/bin/nextgraph
    00400000-00421000 r-xp 00001000 08:11 581310978
    /opt/biosoft/anaconda3/envs/nextdenovo/lib/python3.10/site-packages/nextdenovo/bin/nextgraph
    00621000-00622000 r--p 00022000 08:11 581310978
    /opt/biosoft/anaconda3/envs/nextdenovo/lib/python3.10/site-packages/nextdenovo/bin/nextgraph
    00622000-00623000 rw-p 00023000 08:11 581310978
    /opt/biosoft/anaconda3/envs/nextdenovo/lib/python3.10/site-packages/nextdenovo/bin/nextgraph
    022ec000-6a903000 rw-p 00000000 00:00 0 [heap]
    2b848901e000-2b8489040000 r-xp 00000000 fd:00 2369070 /usr/lib64/ld-2.17.so
    2b8489040000-2b8489058000 rw-p 00000000 00:00 0
    2b848905e000-2b848905f000 rw-p 00000000 00:00 0
    2b848905f000-2b8489062000 r--p 00000000 08:11 581310856
    /opt/biosoft/anaconda3/envs/nextdenovo/lib/libz.so.1.2.13
    2b8489062000-2b8489071000 r-xp 00003000 08:11 581310856
    /opt/biosoft/anaconda3/envs/nextdenovo/lib/libz.so.1.2.13
    2b8489071000-2b8489078000 r--p 00012000 08:11 581310856
    /opt/biosoft/anaconda3/envs/nextdenovo/lib/libz.so.1.2.13
    2b8489078000-2b8489079000 r--p 00018000 08:11 581310856
    /opt/biosoft/anaconda3/envs/nextdenovo/lib/libz.so.1.2.13
    2b8489079000-2b848907a000 rw-p 00019000 08:11 581310856
    /opt/biosoft/anaconda3/envs/nextdenovo/lib/libz.so.1.2.13
    2b848907a000-2b848907d000 rw-p 00000000 00:00 0
    2b848907d000-2b8489081000 r--p 00000000 08:11 581316217
    /opt/biosoft/anaconda3/envs/nextdenovo/lib/libgcc_s.so.1
    2b8489081000-2b8489093000 r-xp 00004000 08:11 581316217
    /opt/biosoft/anaconda3/envs/nextdenovo/lib/libgcc_s.so.1
    2b8489093000-2b8489096000 r--p 00016000 08:11 581316217
    /opt/biosoft/anaconda3/envs/nextdenovo/lib/libgcc_s.so.1
    2b8489096000-2b8489097000 r--p 00019000 08:11 581316217
    /opt/biosoft/anaconda3/envs/nextdenovo/lib/libgcc_s.so.1
    2b8489097000-2b8489098000 rw-p 0001a000 08:11 581316217
    /opt/biosoft/anaconda3/envs/nextdenovo/lib/libgcc_s.so.1
    2b848923f000-2b8489240000 r--p 00021000 fd:00 2369070 /usr/lib64/ld-2.17.so
    2b8489240000-2b8489241000 rw-p 00022000 fd:00 2369070 /usr/lib64/ld-2.17.so
    2b8489241000-2b8489242000 rw-p 00000000 00:00 0
    2b8489242000-2b8489343000 r-xp 00000000 fd:00 2360418 /usr/lib64/libm-2.17.so
    2b8489343000-2b8489542000 ---p 00101000 fd:00 2360418 /usr/lib64/libm-2.17.so
    2b8489542000-2b8489543000 r--p 00100000 fd:00 2360418 /usr/lib64/libm-2.17.so
    2b8489543000-2b8489544000 rw-p 00101000 fd:00 2360418 /usr/lib64/libm-2.17.so
    2b8489544000-2b8489708000 r-xp 00000000 fd:00 2360410 /usr/lib64/libc-2.17.so
    2b8489708000-2b8489907000 ---p 001c4000 fd:00 2360410 /usr/lib64/libc-2.17.so
    2b8489907000-2b848990b000 r--p 001c3000 fd:00 2360410 /usr/lib64/libc-2.17.so
    2b848990b000-2b848990d000 rw-p 001c7000 fd:00 2360410 /usr/lib64/libc-2.17.so
    2b848990d000-2b859e014000 rw-p 00000000 00:00 0
    7ffc46aff000-7ffc46b21000 rw-p 00000000 00:00 0 [stack]
    7ffc46bf5000-7ffc46bf7000 r-xp 00000000 00:00 0 [vdso]
    ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0 [vsyscall]
    /data/2/b.assembing/nextdenove/01_rundir/03.ctg_graph/01.ctg_graph.sh.work/ctg_graph1/nextDenovo.sh: line 5: 162326 Aborted (core dumped)
    /opt/biosoft/anaconda3/envs/nextdenovo/lib/python3.10/site-packages/nextdenovo/bin/nextgraph -a 1 -q 10 -f /data/2/b.assembing/nextdenove/01_rundir/03.ctg_graph/01.ctg_graph.input.seqs /data/2/b.assembing/nextdenove/01_rundir/03.ctg_graph/01.ctg_graph.input.ovls -o nd.asm.p.fasta