Accepted a killed signal and killing all running jobs, please wait...
WengangXbio opened this issue · comments
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:
Try to kill all subtasks and main task, then re-run with the same command, it will skip the finisehd subtasks.