Open kanchond opened 1 year ago
moold
commented
1 year ago 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
commented
1 year ago I am afraid that did not seem to help, and I get the same error:
cat /mnt/lustre/groups/biol-specgen-2018/kanchon/masurca_assemblies/hypothyris_anastasia/batch_1_2_pass/01_rundir_again/03.ctg_graph/ 01.ctg_graph.sh.work/ctg_graph1/nextDenovo.sh.e
hostname
On Tue, 27 Dec 2022 at 01:19, Hu Jiang @.***> wrote:
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 ?
— Reply to this email directly, view it on GitHub https://github.com/Nextomics/NextDenovo/issues/159#issuecomment-1365539290, or unsubscribe https://github.com/notifications/unsubscribe-auth/AL3AFL54Q4SMYRV2GANZ77LWPI73HANCNFSM6AAAAAATHXJK24 . You are receiving this because you authored the thread.Message ID: @.***>
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
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