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Nextomics / NextPolish

Fast and accurately polish the genome generated by long reads.
GNU General Public License v3.0
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db_split failed: #119

Open YDD99 opened 1 year ago

YDD99 commented 1 year ago

"/home/xly/soft/NextPolish/nextPolish" run.cfg [1941029 INFO] 2023-08-16 13:07:01 NextPolish start... [1941029 INFO] 2023-08-16 13:07:01 version:v1.4.1 logfile:pid1941029.log.info [1941029 WARNING] 2023-08-16 13:07:01 Re-write workdir [1941029 WARNING] 2023-08-16 13:07:01 Delete task: 5 due to missing lgs_fofn. [1941029 WARNING] 2023-08-16 13:07:01 Delete task: 5 due to missing lgs_fofn. [1941029 WARNING] 2023-08-16 13:07:01 Delete task: 6 due to missing hifi_fofn. [1941029 WARNING] 2023-08-16 13:07:01 Delete task: 6 due to missing hifi_fofn. [1941029 INFO] 2023-08-16 13:07:01 scheduled tasks: [1, 2, 1, 2] [1941029 INFO] 2023-08-16 13:07:01 options: [1941029 INFO] 2023-08-16 13:07:01 rerun: 3 rewrite: 1 kill: None cleantmp: 0 use_drmaa: 0 submit: None deltmp: False job_type: local sgs_unpaired: 0 sgs_rm_nread: 1 lgs_read_type: parallel_jobs: 5 align_threads: 2 check_alive: None task: [1, 2, 1, 2] job_id_regex: None sgs_max_depth: 100 lgs_max_depth: 100 multithread_jobs: 2 lgs_max_read_len: 0 hifi_max_depth: 100 polish_options: -p 2 lgs_block_size: 500M lgs_min_read_len: 1k hifi_max_read_len: 0 genome_size: 44463965 hifi_block_size: 500M hifi_min_read_len: 1k job_prefix: nextPolish sgs_block_size: 500000000 sgs_use_duplicate_reads: 0 lgs_minimap2_options: -x map-ont hifi_minimap2_options: -x map-pb sgs_align_options: bwa mem -p -t 2 workdir: /home/xly/work8/313/finalfasta/./rundir sgs_fofn: /home/xly/work8/313/finalfasta/sgs.fofn genome: /home/xly/work8/313/finalfasta/WYBBLT7.final.fasta snp_phase: /home/xly/work8/313/finalfasta/./rundir/%02d.snp_phase snp_valid: /home/xly/work8/313/finalfasta/./rundir/%02d.snp_valid lgs_polish: /home/xly/work8/313/finalfasta/./rundir/%02d.lgs_polish kmer_count: /home/xly/work8/313/finalfasta/./rundir/%02d.kmer_count hifi_polish: /home/xly/work8/313/finalfasta/./rundir/%02d.hifi_polish score_chain: /home/xly/work8/313/finalfasta/./rundir/%02d.score_chain [1941029 INFO] 2023-08-16 13:07:01 step 0 and task 1 start: [1941029 INFO] 2023-08-16 13:07:06 Total jobs: 3 [1941029 INFO] 2023-08-16 13:07:06 Submitted jobID:[1941100] jobCmd:[/home/xly/work8/313/finalfasta/rundir/00.score_chain/01.db_split.sh.work/db_split1/nextPolish.sh] in the local_cycle. [1941100 CRITICAL] 2023-08-16 13:07:06 Command '/bin/bash /home/xly/work8/313/finalfasta/rundir/00.score_chain/01.db_split.sh.work/db_split1/nextPolish.sh > /home/xly/work8/313/finalfasta/rundir/00.score_chain/01.db_split.sh.work/db_split1/nextPolish.sh.o 2> /home/xly/work8/313/finalfasta/rundir/00.score_chain/01.db_split.sh.work/db_split1/nextPolish.sh.e' returned non-zero exit status 1, error info: . Traceback (most recent call last): File "/home/xly/soft/NextPolish/nextPolish", line 553, in main(args) File "/home/xly/soft/NextPolish/nextPolish", line 403, in main task.run.start() File "/home/xly/mambaforge/lib/python3.10/site-packages/paralleltask/task_control.py", line 350, in start self._start() File "/home/xly/mambaforge/lib/python3.10/site-packages/paralleltask/task_control.py", line 374, in _start self.submit(job) File "/home/xly/mambaforge/lib/python3.10/site-packages/paralleltask/taskcontrol.py", line 254, in submit , stdout, _ = self.run(job.cmd) File "/home/xly/mambaforge/lib/python3.10/site-packages/paralleltask/task_control.py", line 294, in run log.critical("Command '%s' returned non-zero exit status %d, error info: %s." % (cmd, p.returncode, stderr)) File "/home/xly/mambaforge/lib/python3.10/logging/init.py", line 1524, in critical self._log(CRITICAL, msg, args, **kwargs) File "/home/xly/mambaforge/lib/python3.10/logging/init.py", line 1624, in _log self.handle(record) File "/home/xly/mambaforge/lib/python3.10/logging/init.py", line 1634, in handle self.callHandlers(record) File "/home/xly/mambaforge/lib/python3.10/logging/init.py", line 1696, in callHandlers hdlr.handle(record) File "/home/xly/mambaforge/lib/python3.10/logging/init.py", line 968, in handle self.emit(record) File "/home/xly/mambaforge/lib/python3.10/site-packages/paralleltask/kit.py", line 42, in emit raise Exception(record.msg) Exception: Command '/bin/bash /home/xly/work8/313/finalfasta/rundir/00.score_chain/01.db_split.sh.work/db_split1/nextPolish.sh > /home/xly/work8/313/finalfasta/rundir/00.score_chain/01.db_split.sh.work/db_split1/nextPolish.sh.o 2> /home/xly/work8/313/finalfasta/rundir/00.score_chain/01.db_split.sh.work/db_split1/nextPolish.sh.e' returned non-zero exit status 1, error info: . [1941029 INFO] 2023-08-16 13:07:07 Submitted jobID:[1941106] jobCmd:[/home/xly/work8/313/finalfasta/rundir/00.score_chain/01.db_split.sh.work/db_split2/nextPolish.sh] in the local_cycle. [1941029 INFO] 2023-08-16 13:07:07 Submitted jobID:[1941112] jobCmd:[/home/xly/work8/313/finalfasta/rundir/00.score_chain/01.db_split.sh.work/db_split3/nextPolish.sh] in the local_cycle. [1941029 ERROR] 2023-08-16 13:08:11 db_split failed: please check the following logs: [1941029 ERROR] 2023-08-16 13:08:11 /home/xly/work8/313/finalfasta/rundir/00.score_chain/01.db_split.sh.work/db_split1/nextPolish.sh.e

YDD99 commented 1 year ago

run.cfg [General] job_type = local job_prefix = nextPolish task = best rewrite = yes rerun = 3 parallel_jobs = 5 multithread_jobs = 2 genome = /home/xly/work8/313/finalfasta/WYBBLT7.final.fasta #genome file genome_size = auto workdir = ./rundir polish_options = -p {multithread_jobs}

[sgs_option] sgs_fofn = /home/xly/work8/313/finalfasta/sgs.fofn sgs_options = -max_depth 100 -bwa

sgs.fofn /home/xly/work8/313/WYBBLT7/WYBBLT7_1.clean.fq.gz /home/xly/work8/313/WYBBLT7/WYBBLT7_2.clean.fq.gz

YDD99 commented 1 year ago

gcc -v Using built-in specs. COLLECT_GCC=gcc COLLECT_LTO_WRAPPER=/usr/lib/gcc/x86_64-linux-gnu/9/lto-wrapper OFFLOAD_TARGET_NAMES=nvptx-none:hsa OFFLOAD_TARGET_DEFAULT=1 Target: x86_64-linux-gnu Configured with: ../src/configure -v --with-pkgversion='Ubuntu 9.5.0-1ubuntu1~22.04' --with-bugurl=file:///usr/share/doc/gcc-9/README.Bugs --enable-languages=c,ada,c++,go,brig,d,fortran,objc,obj-c++,gm2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-9 --program-prefix=x86_64-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-vtable-verify --enable-plugin --enable-default-pie --with-system-zlib --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-werror --with-arch-32=i686 --with-abi=m64 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-offload-targets=nvptx-none=/build/gcc-9-5Q4PKF/gcc-9-9.5.0/debian/tmp-nvptx/usr,hsa --without-cuda-driver --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu --with-build-config=bootstrap-lto-lean --enable-link-mutex Thread model: posix gcc version 9.5.0 (Ubuntu 9.5.0-1ubuntu1~22.04)

python --version Python 3.10.10

moold commented 1 year ago

Could you paste the content of file /home/xly/work8/313/finalfasta/rundir/00.score_chain/01.db_split.sh.work/db_split1/nextPolish.sh.e to here?

ian-ariel commented 5 months ago

Could you paste the content of file /home/xly/work8/313/finalfasta/rundir/00.score_chain/01.db_split.sh.work/db_split1/nextPolish.sh.e to here?

take a look at mine, please. Had the same issue. My system is in portuguese, though

hostname

real 0m0,001s user 0m0,001s sys 0m0,000s