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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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Accepted a killed signal and killing all running jobs, please wait... #213

Closed WengangXbio closed 2 months ago

WengangXbio commented 3 months ago

Question or Expected behavior Hi developer, It ran 3days ended without assembly generated, the log file is pasted as below, would be appreciate if you can help me on this, many thanks!

Operating system LSB Version: Distributor ID: CentOS Description: CentOS Linux release 7.9.2009 (Core) Release: 7.9.2009 Codename: Core

GCC Using built-in specs. COLLECT_GCC=gcc COLLECT_LTO_WRAPPER=/usr/libexec/gcc/x86_64-redhat-linux/4.8.5/lto-wrapper Target: x86_64-redhat-linux Configured with: ../configure --prefix=/usr --mandir=/usr/share/man --infodir=/usr/share/info --with-bugurl=http://bugzilla.redhat.com/bugzilla --enable-bootstrap --enable-shared --enable-threads=posix --enable-checking=release --with-system-zlib --enable-__cxa_atexit --disable-libunwind-exceptions --enable-gnu-unique-object --enable-linker-build-id --with-linker-hash-style=gnu --enable-languages=c,c++,objc,obj-c++,java,fortran,ada,go,lto --enable-plugin --enable-initfini-array --disable-libgcj --with-isl=/builddir/build/BUILD/gcc-4.8.5-20150702/obj-x86_64-redhat-linux/isl-install --with-cloog=/builddir/build/BUILD/gcc-4.8.5-20150702/obj-x86_64-redhat-linux/cloog-install --enable-gnu-indirect-function --with-tune=generic --with-arch_32=x86-64 --build=x86_64-redhat-linux Thread model: posix gcc version 4.8.5 20150623 (Red Hat 4.8.5-44) (GCC)

Python Python 3.12.3

NextDenovo nextDenovo 2.5.2

Additional context (Optional)

*Suggested seed_cutoff (genome size: 3000.00Mb, expected seed depth: 45, real seed depth: 26.45): 10000 bp
[54486 INFO] 2024-06-20 12:36:16 Total jobs: 1
[54486 INFO] 2024-06-20 12:36:16 Submitted jobID:[4732] jobCmd:[/share/home/yzwl_zhangwg/YLcattle_asm/nextdenovo/01_rundir/01.raw_align/02.db_split.sh.work/db_split1/nextDenovo.sh] in the local_cycle.
[54486 INFO] 2024-06-20 12:53:59 db_split done
[54486 INFO] 2024-06-20 12:53:59 Total jobs: 15
[54486 INFO] 2024-06-20 12:53:59 Submitted jobID:[13964] jobCmd:[/share/home/yzwl_zhangwg/YLcattle_asm/nextdenovo/01_rundir/01.raw_align/03.raw_align.sh.work/raw_align01/nextDenovo.sh] in the local_cycle.
[54486 INFO] 2024-06-20 12:54:00 Submitted jobID:[13970] jobCmd:[/share/home/yzwl_zhangwg/YLcattle_asm/nextdenovo/01_rundir/01.raw_align/03.raw_align.sh.work/raw_align02/nextDenovo.sh] in the local_cycle.
[54486 INFO] 2024-06-20 12:54:00 Submitted jobID:[13975] jobCmd:[/share/home/yzwl_zhangwg/YLcattle_asm/nextdenovo/01_rundir/01.raw_align/03.raw_align.sh.work/raw_align03/nextDenovo.sh] in the local_cycle.
[54486 INFO] 2024-06-20 12:54:01 Submitted jobID:[13986] jobCmd:[/share/home/yzwl_zhangwg/YLcattle_asm/nextdenovo/01_rundir/01.raw_align/03.raw_align.sh.work/raw_align04/nextDenovo.sh] in the local_cycle.
[54486 INFO] 2024-06-20 12:54:01 Submitted jobID:[14021] jobCmd:[/share/home/yzwl_zhangwg/YLcattle_asm/nextdenovo/01_rundir/01.raw_align/03.raw_align.sh.work/raw_align05/nextDenovo.sh] in the local_cycle.
[54486 INFO] 2024-06-20 13:33:48 Submitted jobID:[32438] jobCmd:[/share/home/yzwl_zhangwg/YLcattle_asm/nextdenovo/01_rundir/01.raw_align/03.raw_align.sh.work/raw_align06/nextDenovo.sh] in the local_cycle.
[54486 INFO] 2024-06-20 13:33:57 Submitted jobID:[32528] jobCmd:[/share/home/yzwl_zhangwg/YLcattle_asm/nextdenovo/01_rundir/01.raw_align/03.raw_align.sh.work/raw_align07/nextDenovo.sh] in the local_cycle.
[54486 INFO] 2024-06-20 13:36:10 Submitted jobID:[33591] jobCmd:[/share/home/yzwl_zhangwg/YLcattle_asm/nextdenovo/01_rundir/01.raw_align/03.raw_align.sh.work/raw_align08/nextDenovo.sh] in the local_cycle.
[54486 INFO] 2024-06-20 14:14:32 Submitted jobID:[51512] jobCmd:[/share/home/yzwl_zhangwg/YLcattle_asm/nextdenovo/01_rundir/01.raw_align/03.raw_align.sh.work/raw_align09/nextDenovo.sh] in the local_cycle.
[54486 INFO] 2024-06-20 14:17:21 Submitted jobID:[52898] jobCmd:[/share/home/yzwl_zhangwg/YLcattle_asm/nextdenovo/01_rundir/01.raw_align/03.raw_align.sh.work/raw_align10/nextDenovo.sh] in the local_cycle.
[54486 INFO] 2024-06-20 14:56:00 Submitted jobID:[14406] jobCmd:[/share/home/yzwl_zhangwg/YLcattle_asm/nextdenovo/01_rundir/01.raw_align/03.raw_align.sh.work/raw_align11/nextDenovo.sh] in the local_cycle.
[54486 INFO] 2024-06-22 02:36:25 Submitted jobID:[56430] jobCmd:[/share/home/yzwl_zhangwg/YLcattle_asm/nextdenovo/01_rundir/01.raw_align/03.raw_align.sh.work/raw_align12/nextDenovo.sh] in the local_cycle.
[54486 INFO] 2024-06-22 03:18:14 Submitted jobID:[18865] jobCmd:[/share/home/yzwl_zhangwg/YLcattle_asm/nextdenovo/01_rundir/01.raw_align/03.raw_align.sh.work/raw_align13/nextDenovo.sh] in the local_cycle.
[54486 INFO] 2024-06-22 04:00:20 Submitted jobID:[37394] jobCmd:[/share/home/yzwl_zhangwg/YLcattle_asm/nextdenovo/01_rundir/01.raw_align/03.raw_align.sh.work/raw_align14/nextDenovo.sh] in the local_cycle.
[54486 INFO] 2024-06-22 04:18:00 Submitted jobID:[45351] jobCmd:[/share/home/yzwl_zhangwg/YLcattle_asm/nextdenovo/01_rundir/01.raw_align/03.raw_align.sh.work/raw_align15/nextDenovo.sh] in the local_cycle.
[54486 INFO] 2024-06-23 16:54:24 raw_align done
[54486 INFO] 2024-06-23 16:54:29 Total jobs: 3
[54486 INFO] 2024-06-23 16:54:29 Submitted jobID:[33266] jobCmd:[/share/home/yzwl_zhangwg/YLcattle_asm/nextdenovo/01_rundir/01.raw_align/04.sort_align.sh.work/sort_align1/nextDenovo.sh] in the local_cycle.
[54486 INFO] 2024-06-23 16:54:30 Submitted jobID:[33272] jobCmd:[/share/home/yzwl_zhangwg/YLcattle_asm/nextdenovo/01_rundir/01.raw_align/04.sort_align.sh.work/sort_align2/nextDenovo.sh] in the local_cycle.
[54486 INFO] 2024-06-23 16:54:30 Submitted jobID:[33277] jobCmd:[/share/home/yzwl_zhangwg/YLcattle_asm/nextdenovo/01_rundir/01.raw_align/04.sort_align.sh.work/sort_align3/nextDenovo.sh] in the local_cycle.
[54486 INFO] 2024-06-23 17:14:47 sort_align done
[54486 INFO] 2024-06-23 17:14:47 remove temporary result: /share/home/yzwl_zhangwg/YLcattle_asm/nextdenovo/01_rundir/01.raw_align/03.raw_align.sh.work/raw_align06/input.seed.003.2bit.5.ovl
[54486 INFO] 2024-06-23 17:14:47 remove temporary result: /share/home/yzwl_zhangwg/YLcattle_asm/nextdenovo/01_rundir/01.raw_align/03.raw_align.sh.work/raw_align11/input.seed.003.2bit.10.ovl
[54486 INFO] 2024-06-23 17:14:47 remove temporary result: /share/home/yzwl_zhangwg/YLcattle_asm/nextdenovo/01_rundir/01.raw_align/03.raw_align.sh.work/raw_align12/input.seed.003.2bit.11.ovl
[54486 INFO] 2024-06-23 17:14:47 remove temporary result: /share/home/yzwl_zhangwg/YLcattle_asm/nextdenovo/01_rundir/01.raw_align/03.raw_align.sh.work/raw_align13/input.seed.003.2bit.12.ovl
[54486 INFO] 2024-06-23 17:14:47 remove temporary result: /share/home/yzwl_zhangwg/YLcattle_asm/nextdenovo/01_rundir/01.raw_align/03.raw_align.sh.work/raw_align14/input.seed.003.2bit.13.ovl
[54486 INFO] 2024-06-23 17:14:47 remove temporary result: /share/home/yzwl_zhangwg/YLcattle_asm/nextdenovo/01_rundir/01.raw_align/03.raw_align.sh.work/raw_align15/input.seed.003.2bit.14.ovl
[54486 INFO] 2024-06-23 17:14:47 remove temporary result: /share/home/yzwl_zhangwg/YLcattle_asm/nextdenovo/01_rundir/01.raw_align/03.raw_align.sh.work/raw_align05/input.seed.001.2bit.4.ovl
[54486 INFO] 2024-06-23 17:14:47 remove temporary result: /share/home/yzwl_zhangwg/YLcattle_asm/nextdenovo/01_rundir/01.raw_align/03.raw_align.sh.work/raw_align07/input.seed.001.2bit.6.ovl
[54486 INFO] 2024-06-23 17:14:47 remove temporary result: /share/home/yzwl_zhangwg/YLcattle_asm/nextdenovo/01_rundir/01.raw_align/03.raw_align.sh.work/raw_align08/input.seed.001.2bit.7.ovl
[54486 INFO] 2024-06-23 17:14:47 remove temporary result: /share/home/yzwl_zhangwg/YLcattle_asm/nextdenovo/01_rundir/01.raw_align/03.raw_align.sh.work/raw_align09/input.seed.001.2bit.8.ovl
[54486 INFO] 2024-06-23 17:14:47 remove temporary result: /share/home/yzwl_zhangwg/YLcattle_asm/nextdenovo/01_rundir/01.raw_align/03.raw_align.sh.work/raw_align10/input.seed.001.2bit.9.ovl
[54486 INFO] 2024-06-23 17:14:47 remove temporary result: /share/home/yzwl_zhangwg/YLcattle_asm/nextdenovo/01_rundir/01.raw_align/03.raw_align.sh.work/raw_align11/input.seed.001.2bit.10.ovl
[54486 INFO] 2024-06-23 17:14:47 remove temporary result: /share/home/yzwl_zhangwg/YLcattle_asm/nextdenovo/01_rundir/01.raw_align/03.raw_align.sh.work/raw_align01/input.seed.002.2bit.0.ovl
[54486 INFO] 2024-06-23 17:14:47 remove temporary result: /share/home/yzwl_zhangwg/YLcattle_asm/nextdenovo/01_rundir/01.raw_align/03.raw_align.sh.work/raw_align02/input.seed.002.2bit.1.ovl
[54486 INFO] 2024-06-23 17:14:47 remove temporary result: /share/home/yzwl_zhangwg/YLcattle_asm/nextdenovo/01_rundir/01.raw_align/03.raw_align.sh.work/raw_align03/input.seed.002.2bit.2.ovl
[54486 INFO] 2024-06-23 17:14:47 remove temporary result: /share/home/yzwl_zhangwg/YLcattle_asm/nextdenovo/01_rundir/01.raw_align/03.raw_align.sh.work/raw_align04/input.seed.002.2bit.3.ovl
[54486 INFO] 2024-06-23 17:14:47 remove temporary result: /share/home/yzwl_zhangwg/YLcattle_asm/nextdenovo/01_rundir/01.raw_align/03.raw_align.sh.work/raw_align05/input.seed.002.2bit.4.ovl
[54486 INFO] 2024-06-23 17:14:47 remove temporary result: /share/home/yzwl_zhangwg/YLcattle_asm/nextdenovo/01_rundir/01.raw_align/03.raw_align.sh.work/raw_align06/input.seed.002.2bit.5.ovl
[54486 INFO] 2024-06-23 17:14:53 Total jobs: 3
[54486 INFO] 2024-06-23 17:14:53 Submitted jobID:[42733] jobCmd:[/share/home/yzwl_zhangwg/YLcattle_asm/nextdenovo/01_rundir/02.cns_align/01.seed_cns.sh.work/seed_cns1/nextDenovo.sh] in the local_cycle.
[54486 INFO] 2024-06-23 17:14:53 Submitted jobID:[42756] jobCmd:[/share/home/yzwl_zhangwg/YLcattle_asm/nextdenovo/01_rundir/02.cns_align/01.seed_cns.sh.work/seed_cns2/nextDenovo.sh] in the local_cycle.
[54486 INFO] 2024-06-23 17:14:54 Submitted jobID:[42761] jobCmd:[/share/home/yzwl_zhangwg/YLcattle_asm/nextdenovo/01_rundir/02.cns_align/01.seed_cns.sh.work/seed_cns3/nextDenovo.sh] in the local_cycle.
[54486 WARNING] 2024-06-23 17:15:11 Accepted a killed signal and killing all running jobs, please wait...
[54486 WARNING] 2024-06-23 17:15:11 Killed all running jobs done
[54486 WARNING] 2024-06-23 17:15:11 Exit!
Job 10842884 stderr output:
moold commented 2 months ago

Try to kill all subtasks and main task, then re-run with the same command, it will skip the finisehd subtasks.