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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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ctg_graph error, (core dumped), returned non-zero exit status 134". #209

Open usersHuangKun opened 1 month ago

usersHuangKun commented 1 month ago

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