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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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After I run nextPolish run.cfg, the NextPolish vanished and generate a copy #135

Open SoSongzhi opened 2 months ago

SoSongzhi commented 2 months ago

Hi, I tried to polish a virus genome(hiv) with a single end long read file and a genome, the NextPolish folder only have one single file called 00.score_chain and It shows like that: (base) zhi@zhi-ThinkStation-P360-Tower:~/Desktop/NextPolish$ ./nextPolish run.cfg [77443 INFO] 2024-08-28 16:24:16 NextPolish start... [77443 INFO] 2024-08-28 16:24:16 version:v1.4.1 logfile:pid77443.log.info [77443 WARNING] 2024-08-28 16:24:16 Delete task: 5 due to missing lgs_fofn. [77443 WARNING] 2024-08-28 16:24:16 Delete task: 5 due to missing lgs_fofn. [77443 WARNING] 2024-08-28 16:24:16 Delete task: 6 due to missing hifi_fofn. [77443 WARNING] 2024-08-28 16:24:16 Delete task: 6 due to missing hifi_fofn. [77443 INFO] 2024-08-28 16:24:16 scheduled tasks: [1, 2, 1, 2] [77443 INFO] 2024-08-28 16:24:16 options: [77443 INFO] 2024-08-28 16:24:16 rerun: 3 rewrite: 0 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: 6 align_threads: 5 check_alive: None task: [1, 2, 1, 2] job_id_regex: None sgs_max_depth: 100 lgs_max_depth: 100 multithread_jobs: 5 genome_size: 492264 lgs_max_read_len: 0 hifi_max_depth: 100 lgs_block_size: 500M lgs_min_read_len: 1k hifi_max_read_len: 0 polish_options: -p 5 hifi_block_size: 500M hifi_min_read_len: 1k job_prefix: nextPolish sgs_block_size: 8204400.0 sgs_use_duplicate_reads: 0 lgs_minimap2_options: -x map-ont hifi_minimap2_options: -x map-pb sgs_align_options: bwa mem -p -t 5 workdir: /home/zhi/Desktop/NextPolish sgs_fofn: /home/zhi/Desktop/NextPolish/sgs.fofn genome: /home/zhi/Desktop/NextPolish/50x_6k_raw.fa snp_phase: /home/zhi/Desktop/NextPolish/%02d.snp_phase snp_valid: /home/zhi/Desktop/NextPolish/%02d.snp_valid lgs_polish: /home/zhi/Desktop/NextPolish/%02d.lgs_polish kmer_count: /home/zhi/Desktop/NextPolish/%02d.kmer_count hifi_polish: /home/zhi/Desktop/NextPolish/%02d.hifi_polish score_chain: /home/zhi/Desktop/NextPolish/%02d.score_chain [77443 WARNING] 2024-08-28 16:24:16 mv /home/zhi/Desktop/NextPolish to /home/zhi/Desktop/NextPolish.backup0 [77443 INFO] 2024-08-28 16:24:16 step 0 and task 1 start: [77443 INFO] 2024-08-28 16:24:21 Total jobs: 3 [77443 INFO] 2024-08-28 16:24:21 Submitted jobID:[77480] jobCmd:[/home/zhi/Desktop/NextPolish/00.score_chain/01.db_split.sh.work/db_split1/nextPolish.sh] in the local_cycle. [77480 CRITICAL] 2024-08-28 16:24:21 Command '/bin/bash /home/zhi/Desktop/NextPolish/00.score_chain/01.db_split.sh.work/db_split1/nextPolish.sh > /home/zhi/Desktop/NextPolish/00.score_chain/01.db_split.sh.work/db_split1/nextPolish.sh.o 2> /home/zhi/Desktop/NextPolish/00.score_chain/01.db_split.sh.work/db_split1/nextPolish.sh.e' returned non-zero exit status 127, error info: . Traceback (most recent call last): File "/home/zhi/Desktop/NextPolish/./nextPolish", line 553, in File "/home/zhi/Desktop/NextPolish/./nextPolish", line 403, in main File "/home/zhi/anaconda3/lib/python3.11/site-packages/paralleltask/task_control.py", line 350, in start self._start() File "/home/zhi/anaconda3/lib/python3.11/site-packages/paralleltask/task_control.py", line 376, in _start self.submit(job) File "/home/zhi/anaconda3/lib/python3.11/site-packages/paralleltask/taskcontrol.py", line 254, in submit , stdout, _ = self.run(job.cmd) ^^^^^^^^^^^^^^^^^ File "/home/zhi/anaconda3/lib/python3.11/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/zhi/anaconda3/lib/python3.11/logging/init.py", line 1536, in critical self._log(CRITICAL, msg, args, kwargs) File "/home/zhi/anaconda3/lib/python3.11/logging/init.py", line 1634, in _log self.handle(record) File "/home/zhi/anaconda3/lib/python3.11/logging/init.py", line 1644, in handle self.callHandlers(record) File "/home/zhi/anaconda3/lib/python3.11/logging/init.py", line 1706, in callHandlers hdlr.handle(record) File "/home/zhi/anaconda3/lib/python3.11/logging/init.py", line 978, in handle self.emit(record) File "/home/zhi/anaconda3/lib/python3.11/site-packages/paralleltask/kit.py", line 42, in emit raise Exception(record.msg) Exception: Command '/bin/bash /home/zhi/Desktop/NextPolish/00.score_chain/01.db_split.sh.work/db_split1/nextPolish.sh > /home/zhi/Desktop/NextPolish/00.score_chain/01.db_split.sh.work/db_split1/nextPolish.sh.o 2> /home/zhi/Desktop/NextPolish/00.score_chain/01.db_split.sh.work/db_split1/nextPolish.sh.e' returned non-zero exit status 127, error info: . [77443 INFO] 2024-08-28 16:24:22 Submitted jobID:[77487] jobCmd:[/home/zhi/Desktop/NextPolish/00.score_chain/01.db_split.sh.work/db_split2/nextPolish.sh] in the local_cycle. [77487 CRITICAL] 2024-08-28 16:24:22 Command '/bin/bash /home/zhi/Desktop/NextPolish/00.score_chain/01.db_split.sh.work/db_split2/nextPolish.sh > /home/zhi/Desktop/NextPolish/00.score_chain/01.db_split.sh.work/db_split2/nextPolish.sh.o 2> /home/zhi/Desktop/NextPolish/00.score_chain/01.db_split.sh.work/db_split2/nextPolish.sh.e' returned non-zero exit status 127, error info: . Traceback (most recent call last): File "/home/zhi/Desktop/NextPolish/./nextPolish", line 553, in File "/home/zhi/Desktop/NextPolish/./nextPolish", line 403, in main File "/home/zhi/anaconda3/lib/python3.11/site-packages/paralleltask/task_control.py", line 350, in start self._start() File "/home/zhi/anaconda3/lib/python3.11/site-packages/paralleltask/task_control.py", line 376, in _start self.submit(job) File "/home/zhi/anaconda3/lib/python3.11/site-packages/paralleltask/taskcontrol.py", line 254, in submit , stdout, _ = self.run(job.cmd) ^^^^^^^^^^^^^^^^^ File "/home/zhi/anaconda3/lib/python3.11/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/zhi/anaconda3/lib/python3.11/logging/init.py", line 1536, in critical self._log(CRITICAL, msg, args, kwargs) File "/home/zhi/anaconda3/lib/python3.11/logging/init.py", line 1634, in _log self.handle(record) File "/home/zhi/anaconda3/lib/python3.11/logging/init.py", line 1644, in handle self.callHandlers(record) File "/home/zhi/anaconda3/lib/python3.11/logging/init.py", line 1706, in callHandlers hdlr.handle(record) File "/home/zhi/anaconda3/lib/python3.11/logging/init.py", line 978, in handle self.emit(record) File "/home/zhi/anaconda3/lib/python3.11/site-packages/paralleltask/kit.py", line 42, in emit raise Exception(record.msg) Exception: Command '/bin/bash /home/zhi/Desktop/NextPolish/00.score_chain/01.db_split.sh.work/db_split2/nextPolish.sh > /home/zhi/Desktop/NextPolish/00.score_chain/01.db_split.sh.work/db_split2/nextPolish.sh.o 2> /home/zhi/Desktop/NextPolish/00.score_chain/01.db_split.sh.work/db_split2/nextPolish.sh.e' returned non-zero exit status 127, error info: . [77443 INFO] 2024-08-28 16:24:22 Submitted jobID:[77503] jobCmd:[/home/zhi/Desktop/NextPolish/00.score_chain/01.db_split.sh.work/db_split3/nextPolish.sh] in the local_cycle. [77503 CRITICAL] 2024-08-28 16:24:22 Command '/bin/bash /home/zhi/Desktop/NextPolish/00.score_chain/01.db_split.sh.work/db_split3/nextPolish.sh > /home/zhi/Desktop/NextPolish/00.score_chain/01.db_split.sh.work/db_split3/nextPolish.sh.o 2> /home/zhi/Desktop/NextPolish/00.score_chain/01.db_split.sh.work/db_split3/nextPolish.sh.e' returned non-zero exit status 127, error info: . Traceback (most recent call last): File "/home/zhi/Desktop/NextPolish/./nextPolish", line 553, in File "/home/zhi/Desktop/NextPolish/./nextPolish", line 403, in main File "/home/zhi/anaconda3/lib/python3.11/site-packages/paralleltask/task_control.py", line 350, in start self._start() File "/home/zhi/anaconda3/lib/python3.11/site-packages/paralleltask/task_control.py", line 376, in _start self.submit(job) File "/home/zhi/anaconda3/lib/python3.11/site-packages/paralleltask/taskcontrol.py", line 254, in submit , stdout, _ = self.run(job.cmd) ^^^^^^^^^^^^^^^^^ File "/home/zhi/anaconda3/lib/python3.11/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/zhi/anaconda3/lib/python3.11/logging/init.py", line 1536, in critical self._log(CRITICAL, msg, args, **kwargs) File "/home/zhi/anaconda3/lib/python3.11/logging/init.py", line 1634, in _log self.handle(record) File "/home/zhi/anaconda3/lib/python3.11/logging/init.py", line 1644, in handle self.callHandlers(record) File "/home/zhi/anaconda3/lib/python3.11/logging/init.py", line 1706, in callHandlers hdlr.handle(record) File "/home/zhi/anaconda3/lib/python3.11/logging/init.py", line 978, in handle self.emit(record) File "/home/zhi/anaconda3/lib/python3.11/site-packages/paralleltask/kit.py", line 42, in emit raise Exception(record.msg) Exception: Command '/bin/bash /home/zhi/Desktop/NextPolish/00.score_chain/01.db_split.sh.work/db_split3/nextPolish.sh > /home/zhi/Desktop/NextPolish/00.score_chain/01.db_split.sh.work/db_split3/nextPolish.sh.o 2> /home/zhi/Desktop/NextPolish/00.score_chain/01.db_split.sh.work/db_split3/nextPolish.sh.e' returned non-zero exit status 127, error info: . [77443 ERROR] 2024-08-28 16:24:29 db_split failed: please check the following logs: [77443 ERROR] 2024-08-28 16:24:29 /home/zhi/Desktop/NextPolish/00.score_chain/01.db_split.sh.work/db_split1/nextPolish.sh.e [77443 ERROR] 2024-08-28 16:24:29 /home/zhi/Desktop/NextPolish/00.score_chain/01.db_split.sh.work/db_split2/nextPolish.sh.e [77443 ERROR] 2024-08-28 16:24:29 /home/zhi/Desktop/NextPolish/00.score_chain/01.db_split.sh.work/db_split3/nextPolish.sh.e

Could you please help me to check where should I do to due with this problem. Thx.

SoSongzhi commented 2 months ago

And the nextPolish.sh.e file shows like that: hostname

real 0m0.001s user 0m0.001s sys 0m0.001s

but it was all good when I use the test data provided by the source.

moold commented 2 months ago

set rewrite=yes