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nextgraph floating point exception error #159

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kanchond opened this issue Dec 23, 2022 · 2 comments
Open

nextgraph floating point exception error #159

kanchond opened this issue Dec 23, 2022 · 2 comments

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@kanchond
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Describe the bug
Floating point exception during nextgraph

Error message
Main task log
[6250 INFO] 2022-12-23 12:41:12 skip step: db_split
[6250 INFO] 2022-12-23 12:41:12 skip step: raw_align
[6250 INFO] 2022-12-23 12:41:12 skip step: sort_align
[6250 INFO] 2022-12-23 12:41:13 skip step: seed_cns
[6250 INFO] 2022-12-23 12:41:13 seed_cns finished, and final corrected reads file:
[6250 INFO] 2022-12-23 12:41:13 /mnt/lustre/groups/biol-specgen-2018/kanchon/masurca_assemblies/hypothyris_anastasia/batch_1_2_pass/./01_rundir/02.cns_align/01.seed_cns.sh.work/seed_cns*/cns.fasta
[6250 INFO] 2022-12-23 12:41:13 skip step: cns_align
[6250 INFO] 2022-12-23 12:41:18 Total jobs: 1
[6250 INFO] 2022-12-23 12:41:18 Submitted jobID:[6267] jobCmd:[/mnt/lustre/groups/biol-specgen-2018/kanchon/masurca_assemblies/hypothyris_anastasia/batch_1_2_pass/01_rundir/03.ctg_graph/01.ctg_graph.sh.work/ctg_graph1/nextDenovo.sh] in the local_cycle.
[6267 CRITICAL] 2022-12-23 12:41:33 Command '/bin/sh /mnt/lustre/groups/biol-specgen-2018/kanchon/masurca_assemblies/hypothyris_anastasia/batch_1_2_pass/01_rundir/03.ctg_graph/01.ctg_graph.sh.work/ctg_graph1/nextDenovo.sh > /mnt/lustre/groups/biol-specgen-2018/kanchon/masurca_assemblies/hypothyris_anastasia/batch_1_2_pass/01_rundir/03.ctg_graph/01.ctg_graph.sh.work/ctg_graph1/nextDenovo.sh.o 2> /mnt/lustre/groups/biol-specgen-2018/kanchon/masurca_assemblies/hypothyris_anastasia/batch_1_2_pass/01_rundir/03.ctg_graph/01.ctg_graph.sh.work/ctg_graph1/nextDenovo.sh.e' returned non-zero exit status 136, error info: .
[6250 ERROR] 2022-12-23 12:41:38 ctg_graph failed: please check the following logs:
[6250 ERROR] 2022-12-23 12:41:38 /mnt/lustre/groups/biol-specgen-2018/kanchon/masurca_assemblies/hypothyris_anastasia/batch_1_2_pass/01_rundir/03.ctg_graph/01.ctg_graph.sh.work/ctg_graph1/nextDenovo.sh.e

Failed subtask log:
hostname

  • hostname
    cd /mnt/lustre/groups/biol-specgen-2018/kanchon/masurca_assemblies/hypothyris_anastasia/batch_1_2_pass/01_rundir/03.ctg_graph/01.ctg_graph.sh.work/ctg_graph1
  • cd /mnt/lustre/groups/biol-specgen-2018/kanchon/masurca_assemblies/hypothyris_anastasia/batch_1_2_pass/01_rundir/03.ctg_graph/01.ctg_graph.sh.work/ctg_graph1
    time /mnt/lustre/users/kd684/applications/NextDenovo/bin/nextgraph -a 1 -f /mnt/lustre/groups/biol-specgen-2018/kanchon/masurca_assemblies/hypothyris_anastasia/batch_1_2_pass/./01_rundir/03.ctg_graph/01.ctg_graph.input.seqs /mnt/lustre/groups/biol-specgen-2018/kanchon/masurca_assemblies/hypothyris_anastasia/batch_1_2_pass/./01_rundir/03.ctg_graph/01.ctg_graph.input.ovls -o nd.asm.p.fasta;
  • /mnt/lustre/users/kd684/applications/NextDenovo/bin/nextgraph -a 1 -f /mnt/lustre/groups/biol-specgen-2018/kanchon/masurca_assemblies/hypothyris_anastasia/batch_1_2_pass/./01_rundir/03.ctg_graph/01.ctg_graph.input.seqs /mnt/lustre/groups/biol-specgen-2018/kanchon/masurca_assemblies/hypothyris_anastasia/batch_1_2_pass/./01_rundir/03.ctg_graph/01.ctg_graph.input.ovls -o nd.asm.p.fasta
    [INFO] 2022-12-23 12:41:18 Initialize graph and reading...
    [INFO] 2022-12-23 12:41:27 Initial Node(s): 208456, Edge(s): 1482244
    [INFO] 2022-12-23 12:41:28 Depth stat, Mid: 12.000 Max: 24000.000 Repeat: 18.000 L:N:H: 0.060:0.888:0.052
    [INFO] 2022-12-23 12:41:28 Outdegree stat, Mid: 5.000 Max: 10000.000 Repeat: 7.500 L:N:H: 0.161:0.839:0.000
    [INFO] 2022-12-23 12:41:29 Chimeric node ratio: 0.883% (candidate: 2.370%)
    [INFO] 2022-12-23 12:41:33 Assembly done and outputting...
    /mnt/lustre/groups/biol-specgen-2018/kanchon/masurca_assemblies/hypothyris_anastasia/batch_1_2_pass/01_rundir/03.ctg_graph/01.ctg_graph.sh.work/ctg_graph1/nextDenovo.sh: line 5: 6271 Floating point exception/mnt/lustre/users/kd684/applications/NextDenovo/bin/nextgraph -a 1 -f /mnt/lustre/groups/biol-specgen-2018/kanchon/masurca_assemblies/hypothyris_anastasia/batch_1_2_pass/./01_rundir/03.ctg_graph/01.ctg_graph.input.seqs /mnt/lustre/groups/biol-specgen-2018/kanchon/masurca_assemblies/hypothyris_anastasia/batch_1_2_pass/./01_rundir/03.ctg_graph/01.ctg_graph.input.ovls -o nd.asm.p.fasta

Genome characteristics
genome size = 850Mb

Input data
sequencing depth = 80x
N50 read length = 17100

Config file
[General]
job_type = local
job_prefix = nextDenovo
task = all # 'all', 'correct', 'assemble'
rewrite = yes # yes/no
deltmp = yes
rerun = 3
parallel_jobs = 1
input_type = raw
read_type = ont
input_fofn = ./input.fofn
workdir = ./01_rundir

[correct_option]
read_cutoff = 1k
genome_size = 0.7g
pa_correction = 5
sort_options = -m 17g -t 4
minimap2_options_raw = -t 20
correction_options = -p 4

[assemble_option]
minimap2_options_cns = -t 20
nextgraph_options = -a 1

Operating system
lsb_release -a
LSB Version: :core-4.1-amd64:core-4.1-noarch
Distributor ID: CentOS
Description: CentOS Linux release 7.9.2009 (Core)
Release: 7.9.2009
Codename: Core

GCC
gcc version 4.8.5 20150623 (Red Hat 4.8.5-44) (GCC)

Python
Python 3.9.13

NextDenovo
nextDenovo v2.5.0

Additional context (Optional)
I have successfully run nextdenovo using a slightly larger input sequence dataset that included all the nanopore reads. The dataset that keeps failing comprises only the "pass" nanopore sequences.

Thanks,
Kanchon
@moold
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moold commented Dec 27, 2022 •
edited
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Could you try to run /mnt/lustre/groups/biol-specgen-2018/kanchon/masurca_assemblies/hypothyris_anastasia/batch_1_2_pass/01_rundir/03.ctg_graph/01.ctg_graph.sh.work/ctg_graph1/nextDenovo.sh with -a 0 to see if there is still an error?

@kanchond
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kanchond commented Dec 27, 2022 via email

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@moold @kanchond