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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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Segmentation fault (core dumped) #86

Open Morriyaty opened 4 years ago

Morriyaty commented 4 years ago

Hi, I run nextdenovo a few days, and i got an error now : [INFO] 2020-09-10 11:12:03,795 skip mkdir: /data/01/user152/nextdenovo/new_01_rundir [INFO] 2020-09-10 11:12:03,797 skip mkdir: /data/01/user152/nextdenovo/new_01_rundir/01.raw_align [INFO] 2020-09-10 11:12:03,798 skip mkdir: /data/01/user152/nextdenovo/new_01_rundir/02.cns_align [INFO] 2020-09-10 11:12:03,812 skip mkdir: /data/01/user152/nextdenovo/new_01_rundir/03.ctg_graph [INFO] 2020-09-10 11:12:05,071 analysis tasks done [INFO] 2020-09-10 11:12:05,073 skip step: db_split [INFO] 2020-09-10 11:12:07,531 analysis tasks done [INFO] 2020-09-10 11:12:18,435 skip step: raw_align [INFO] 2020-09-10 11:12:18,769 analysis tasks done [INFO] 2020-09-10 11:12:18,779 skip step: sort_align [INFO] 2020-09-10 11:12:18,814 analysis tasks done [INFO] 2020-09-10 11:12:18,822 skip step: seed_cns [INFO] 2020-09-10 11:12:18,823 seed_cns finished, and final corrected reads file: [INFO] 2020-09-10 11:12:18,824 /data/01/user152/nextdenovo/new_01_rundir/02.cns_align/01.seed_cns.sh.work/seed_cns*/cns.fasta [INFO] 2020-09-10 11:12:18,860 analysis tasks done [INFO] 2020-09-10 11:12:20,988 skip step: cns_align [INFO] 2020-09-10 11:12:20,992 analysis tasks done [INFO] 2020-09-10 11:12:21,128 total jobs: 1 [INFO] 2020-09-10 11:12:21,131 Throw jobID:[114955] jobCmd:[/data/01/user152/nextdenovo/new_01_rundir/03.ctg_graph/01.ctg_graph.sh.work/ctg_graph0/nextDenovo.sh] in the local_cycle. [ERROR] 2020-09-10 11:48:37,521 ctg_graph failed: please check the following logs: [ERROR] 2020-09-10 11:48:37,608 /data/01/user152/nextdenovo/new_01_rundir/03.ctg_graph/01.ctg_graph.sh.work/ctg_graph0/nextDenovo.sh.e

the wrong file :

hostname

my run.cfg : [General] job_type = local job_prefix = nextDenovo task = all # 'all', 'correct', 'assemble' rewrite = yes # yes/no deltmp = yes rerun = 3 parallel_jobs = 15 input_type = raw input_fofn = input.fofn workdir = new_01_rundir

cluster_options = -l vf={vf} -q all.q -pe smp {cpu} -S {bash} -w n

[correct_option] read_cutoff = 1k seed_cutoff = 22950 blocksize = 3g pa_correction = 20 seed_cutfiles = 20 sort_options = -m 20g -t 10 -k 60 minimap2_options_raw = -x ava-ont -t 8 correction_options = -p 15

[assemble_option] random_round = 20 minimap2_options_cns = -x ava-ont -t 8 -k17 -w17 nextgraph_options = -a 1

what should i do to fix the error ? thank you !

moold commented 4 years ago

Pls provide more details as https://github.com/Nextomics/NextDenovo/issues/new?assignees=&labels=&template=bug-or-error-report.md&title=

Morriyaty commented 4 years ago

the bug is ctg_graph failed ; /data/01/user152/nextdenovo/new_01_rundir/03.ctg_graph/01.ctg_graph.sh.work/ctg_graph0/nextDenovo.sh: line 5: 114961 Segmentation fault (core dumped) /data/01/user151/software/NextDenovo/bin/nextgraph -a 1 -f /data/01/user152/nextdenovo/new_01_rundir/03.ctg_graph/01.ctg_graph.input.seqs /data/01/user152/nextdenovo/new_01_rundir/03.ctg_graph/01.ctg_graph.input.ovls -o nd.asm.p.fasta

genome is about 2.3G nextdenovo version is 2.3.0

moold commented 4 years ago

Could you check whether all files in /data/01/user152/nextdenovo/new_01_rundir/03.ctg_graph/01.ctg_graph.input.seqs are not empty? and also use samtools faidx to check idx files are correct. BTW, pls provide your system and gcc version.

Morriyaty commented 4 years ago

All my files in /data/01/user152/nextdenovo/new_01_rundir/03.ctg_graph/01.ctg_graph.input.seqs are not empty. And all .fai and .idx files are not empty too. But how could I check the idx files are correct? Thank you . A months ago ,I have done another nextdenovo task, so it isn't the version problem . By the way, gcc version is 8.2.1. When I run 'lsb_release -a' , I get 'command not found' .

moold commented 4 years ago

Just check the first few lines and you will see that idx files are similar with the result of samtools faidx.

hanxue1994 commented 2 years ago

Have you solve this problem? We met the same thing