After I run nextPolish run.cfg, the NextPolish vanished and generate a copy #135
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And the nextPolish.sh.e file shows like that:
real 0m0.001s but it was all good when I use the test data provided by the source. |
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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/task_control.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/task_control.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/task_control.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.
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