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polish_genome failed #128

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liuyca1 opened this issue Mar 15, 2024 · 1 comment
Open

polish_genome failed #128

liuyca1 opened this issue Mar 15, 2024 · 1 comment

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@liuyca1
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liuyca1 commented Mar 15, 2024

Describe the bug
When I used second-generation sequencing data (MGI_DNBSEQ platform) to optimize Nanopore assembly (using nextdenovo software) data, an error occurred. The running log is as follows:

run.cfg
[General]
job_type = local
job_prefix = nextPolish
task = best
rewrite = no
deltmp = yes
rerun = 3
parallel_jobs = 3
multithread_jobs = 10
genome = /public/home/user/Plant_genome/assembly/nextDenovo_output/03.ctg_graph/nd.asm.fasta
genome_size = 800Mb
workdir = ./01_rundir
polish_options = -p {multithread_jobs}

[sgs_option]
sgs_fofn = /public/home/user/Plant_genome/assembly/Nextdenove_NextPolish/sgs.fofn
sgs_options = -max_depth 100 -bwa

Error message
$cat log
[302167 INFO] 2024-03-15 09:01:07 NextPolish start...
[302167 INFO] 2024-03-15 09:01:07 version:1.4.1 logfile:pid302167.log.info
[302167 WARNING] 2024-03-15 09:01:07 Delete task: 5 due to missing lgs_fofn.
[302167 WARNING] 2024-03-15 09:01:07 Delete task: 5 due to missing lgs_fofn.
[302167 WARNING] 2024-03-15 09:01:07 Delete task: 6 due to missing hifi_fofn.
[302167 WARNING] 2024-03-15 09:01:07 Delete task: 6 due to missing hifi_fofn.
[302167 INFO] 2024-03-15 09:01:07 scheduled tasks:
[1, 2, 1, 2]
[302167 INFO] 2024-03-15 09:01:07 options:
[302167 INFO] 2024-03-15 09:01:07
rerun: 3
rewrite: 0
kill: None
cleantmp: 0
use_drmaa: 0
deltmp: True
submit: None
job_type: local
sgs_unpaired: 0
sgs_rm_nread: 1
lgs_read_type:
parallel_jobs: 3
check_alive: None
align_threads: 10
task: [1, 2, 1, 2]
job_id_regex: None
sgs_max_depth: 100
lgs_max_depth: 100
lgs_max_read_len: 0
hifi_max_depth: 100
multithread_jobs: 10
lgs_block_size: 500M
lgs_min_read_len: 1k
hifi_max_read_len: 0
polish_options: -p 10
hifi_block_size: 500M
hifi_min_read_len: 1k
job_prefix: nextPolish
genome_size: 800000000
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 10
sgs_fofn: /public/home/user/Plant_genome/assembly/Nextdenove_NextPolish/sgs.fofn
workdir: /public/home/user/Plant_genome/assembly/Nextdenove_NextPolish/./01_rundir
genome: /public/home/user/Plant_genome/assembly/nextDenovo_output/03.ctg_graph/nd.asm.fasta
snp_phase: /public/home/user/Plant_genome/assembly/Nextdenove_NextPolish/./01_rundir/%02d.snp_phase
snp_valid: /public/home/user/Plant_genome/assembly/Nextdenove_NextPolish/./01_rundir/%02d.snp_valid
lgs_polish: /public/home/user/Plant_genome/assembly/Nextdenove_NextPolish/./01_rundir/%02d.lgs_polish
kmer_count: /public/home/user/Plant_genome/assembly/Nextdenove_NextPolish/./01_rundir/%02d.kmer_count
hifi_polish: /public/home/user/Plant_genome/assembly/Nextdenove_NextPolish/./01_rundir/%02d.hifi_polish
score_chain: /public/home/user/Plant_genome/assembly/Nextdenove_NextPolish/./01_rundir/%02d.score_chain
[302167 INFO] 2024-03-15 09:01:07 step 0 and task 1 start:
[302167 INFO] 2024-03-15 09:01:12 Total jobs: 3
[302167 INFO] 2024-03-15 09:01:12 Submitted jobID:[302172] jobCmd:[/public/home/user/Plant_genome/assembly/Nextdenove_NextPolish/01_rundir/00.score_chain/01.db_split.sh.work/db_split1/nextPolish.sh] in the local_cycle.
[302167 INFO] 2024-03-15 09:01:13 Submitted jobID:[302188] jobCmd:[/public/home/user/Plant_genome/assembly/Nextdenove_NextPolish/01_rundir/00.score_chain/01.db_split.sh.work/db_split2/nextPolish.sh] in the local_cycle.
[302167 INFO] 2024-03-15 09:01:13 Submitted jobID:[302193] jobCmd:[/public/home/user/Plant_genome/assembly/Nextdenove_NextPolish/01_rundir/00.score_chain/01.db_split.sh.work/db_split3/nextPolish.sh] in the local_cycle.
[302167 INFO] 2024-03-15 11:36:27 db_split done
[302167 INFO] 2024-03-15 11:36:32 Total jobs: 3
[302167 INFO] 2024-03-15 11:36:32 Submitted jobID:[398779] jobCmd:[/public/home/user/Plant_genome/assembly/Nextdenove_NextPolish/01_rundir/00.score_chain/02.map.ref.sh.work/map_genome1/nextPolish.sh] in the local_cycle.
[302167 INFO] 2024-03-15 11:36:33 Submitted jobID:[398782] jobCmd:[/public/home/user/Plant_genome/assembly/Nextdenove_NextPolish/01_rundir/00.score_chain/02.map.ref.sh.work/map_genome2/nextPolish.sh] in the local_cycle.
[302167 INFO] 2024-03-15 11:36:33 Submitted jobID:[398796] jobCmd:[/public/home/user/Plant_genome/assembly/Nextdenove_NextPolish/01_rundir/00.score_chain/02.map.ref.sh.work/map_genome3/nextPolish.sh] in the local_cycle.
[302167 INFO] 2024-03-15 14:06:27 align_genome done
[302167 INFO] 2024-03-15 14:06:33 Total jobs: 1
[302167 INFO] 2024-03-15 14:06:33 Submitted jobID:[47847] jobCmd:[/public/home/user/Plant_genome/assembly/Nextdenove_NextPolish/01_rundir/00.score_chain/03.merge.bam.sh.work/merge_bam1/nextPolish.sh] in the local_cycle.
[302167 INFO] 2024-03-15 15:03:05 merge_bam done
[302167 INFO] 2024-03-15 15:03:05 remove temporary result: /public/home/user/Plant_genome/assembly/Nextdenove_NextPolish/01_rundir/00.score_chain/02.map.ref.sh.work/map_genome1/sgs.part000.sort.bam
[302167 INFO] 2024-03-15 15:03:06 remove temporary result: /public/home/user/Plant_genome/assembly/Nextdenove_NextPolish/01_rundir/00.score_chain/02.map.ref.sh.work/map_genome2/sgs.part001.sort.bam
[302167 INFO] 2024-03-15 15:03:10 remove temporary result: /public/home/user/Plant_genome/assembly/Nextdenove_NextPolish/01_rundir/00.score_chain/02.map.ref.sh.work/map_genome3/sgs.part002.sort.bam
[302167 INFO] 2024-03-15 15:03:16 Total jobs: 3
[302167 INFO] 2024-03-15 15:03:16 Submitted jobID:[83886] jobCmd:[/public/home/user/Plant_genome/assembly/Nextdenove_NextPolish/01_rundir/00.score_chain/04.polish.ref.sh.work/polish_genome1/nextPolish.sh] in the local_cycle.
[302167 INFO] 2024-03-15 15:03:16 Submitted jobID:[83891] jobCmd:[/public/home/user/Plant_genome/assembly/Nextdenove_NextPolish/01_rundir/00.score_chain/04.polish.ref.sh.work/polish_genome2/nextPolish.sh] in the local_cycle.
[302167 INFO] 2024-03-15 15:03:17 Submitted jobID:[83897] jobCmd:[/public/home/user/Plant_genome/assembly/Nextdenove_NextPolish/01_rundir/00.score_chain/04.polish.ref.sh.work/polish_genome3/nextPolish.sh] in the local_cycle.
[83897 CRITICAL] 2024-03-15 15:03:19 Command '/bin/sh /public/home/user/Plant_genome/assembly/Nextdenove_NextPolish/01_rundir/00.score_chain/04.polish.ref.sh.work/polish_genome3/nextPolish.sh > /public/home/user/Plant_genome/assembly/Nextdenove_NextPolish/01_rundir/00.score_chain/04.polish.ref.sh.work/polish_genome3/nextPolish.sh.o 2> /public/home/user/Plant_genome/assembly/Nextdenove_NextPolish/01_rundir/00.score_chain/04.polish.ref.sh.work/polish_genome3/nextPolish.sh.e' returned non-zero exit status 1, error info: .
[83886 CRITICAL] 2024-03-15 15:03:19 Command '/bin/sh /public/home/user/Plant_genome/assembly/Nextdenove_NextPolish/01_rundir/00.score_chain/04.polish.ref.sh.work/polish_genome1/nextPolish.sh > /public/home/user/Plant_genome/assembly/Nextdenove_NextPolish/01_rundir/00.score_chain/04.polish.ref.sh.work/polish_genome1/nextPolish.sh.o 2> /public/home/user/Plant_genome/assembly/Nextdenove_NextPolish/01_rundir/00.score_chain/04.polish.ref.sh.work/polish_genome1/nextPolish.sh.e' returned non-zero exit status 1, error info: .
[83891 CRITICAL] 2024-03-15 15:03:19 Command '/bin/sh /public/home/user/Plant_genome/assembly/Nextdenove_NextPolish/01_rundir/00.score_chain/04.polish.ref.sh.work/polish_genome2/nextPolish.sh > /public/home/user/Plant_genome/assembly/Nextdenove_NextPolish/01_rundir/00.score_chain/04.polish.ref.sh.work/polish_genome2/nextPolish.sh.o 2> /public/home/user/Plant_genome/assembly/Nextdenove_NextPolish/01_rundir/00.score_chain/04.polish.ref.sh.work/polish_genome2/nextPolish.sh.e' returned non-zero exit status 1, error info: .
Traceback (most recent call last):
Traceback (most recent call last):
Traceback (most recent call last):
File "/public/home/user/software/anaconda3/envs/nextpolish/bin/nextPolish", line 553, in
File "/public/home/user/software/anaconda3/envs/nextpolish/bin/nextPolish", line 553, in
File "/public/home/user/software/anaconda3/envs/nextpolish/bin/nextPolish", line 553, in
main(args)
main(args)
main(args)
File "/public/home/user/software/anaconda3/envs/nextpolish/bin/nextPolish", line 502, in main
File "/public/home/user/software/anaconda3/envs/nextpolish/bin/nextPolish", line 502, in main
File "/public/home/user/software/anaconda3/envs/nextpolish/bin/nextPolish", line 502, in main
task.run.start()
task.run.start()
File "/public/home/user/software/anaconda3/envs/nextpolish/lib/python3.11/site-packages/paralleltask/task_control.py", line 344, in start
File "/public/home/user/software/anaconda3/envs/nextpolish/lib/python3.11/site-packages/paralleltask/task_control.py", line 344, in start
task.run.start()
File "/public/home/user/software/anaconda3/envs/nextpolish/lib/python3.11/site-packages/paralleltask/task_control.py", line 344, in start
self._start()
self._start()
File "/public/home/user/software/anaconda3/envs/nextpolish/lib/python3.11/site-packages/paralleltask/task_control.py", line 368, in _start
File "/public/home/user/software/anaconda3/envs/nextpolish/lib/python3.11/site-packages/paralleltask/task_control.py", line 368, in _start
self._start()
File "/public/home/user/software/anaconda3/envs/nextpolish/lib/python3.11/site-packages/paralleltask/task_control.py", line 368, in _start
self.submit(job)
File "/public/home/user/software/anaconda3/envs/nextpolish/lib/python3.11/site-packages/paralleltask/task_control.py", line 252, in submit
self.submit(job)
File "/public/home/user/software/anaconda3/envs/nextpolish/lib/python3.11/site-packages/paralleltask/task_control.py", line 252, in submit
self.submit(job)
File "/public/home/user/software/anaconda3/envs/nextpolish/lib/python3.11/site-packages/paralleltask/task_control.py", line 252, in submit
_, stdout, _ = self.run(job.cmd)
_, stdout, _ = self.run(job.cmd)
^^^^^^^^^^^^^^^^^
File "/public/home/user/software/anaconda3/envs/nextpolish/lib/python3.11/site-packages/paralleltask/task_control.py", line 288, in run
^^^^^^^^^^^^^^^^^
File "/public/home/user/software/anaconda3/envs/nextpolish/lib/python3.11/site-packages/paralleltask/task_control.py", line 288, in run
_, stdout, _ = self.run(job.cmd)
^^^^^^^^^^^^^^^^^
File "/public/home/user/software/anaconda3/envs/nextpolish/lib/python3.11/site-packages/paralleltask/task_control.py", line 288, in run
log.critical("Command '%s' returned non-zero exit status %d, error info: %s." % (cmd, p.returncode, stderr))
log.critical("Command '%s' returned non-zero exit status %d, error info: %s." % (cmd, p.returncode, stderr))
File "/public/home/user/software/anaconda3/envs/nextpolish/lib/python3.11/logging/init.py", line 1536, in critical
File "/public/home/user/software/anaconda3/envs/nextpolish/lib/python3.11/logging/init.py", line 1536, in critical
log.critical("Command '%s' returned non-zero exit status %d, error info: %s." % (cmd, p.returncode, stderr))
File "/public/home/user/software/anaconda3/envs/nextpolish/lib/python3.11/logging/init.py", line 1536, in critical
self._log(CRITICAL, msg, args, **kwargs)
self._log(CRITICAL, msg, args, **kwargs)
File "/public/home/user/software/anaconda3/envs/nextpolish/lib/python3.11/logging/init.py", line 1634, in _log
File "/public/home/user/software/anaconda3/envs/nextpolish/lib/python3.11/logging/init.py", line 1634, in _log
self._log(CRITICAL, msg, args, **kwargs)
File "/public/home/user/software/anaconda3/envs/nextpolish/lib/python3.11/logging/init.py", line 1634, in _log
self.handle(record)
File "/public/home/user/software/anaconda3/envs/nextpolish/lib/python3.11/logging/init.py", line 1644, in handle
self.handle(record)
File "/public/home/user/software/anaconda3/envs/nextpolish/lib/python3.11/logging/init.py", line 1644, in handle
self.handle(record)
File "/public/home/user/software/anaconda3/envs/nextpolish/lib/python3.11/logging/init.py", line 1644, in handle
self.callHandlers(record)
File "/public/home/user/software/anaconda3/envs/nextpolish/lib/python3.11/logging/init.py", line 1706, in callHandlers
self.callHandlers(record)
File "/public/home/user/software/anaconda3/envs/nextpolish/lib/python3.11/logging/init.py", line 1706, in callHandlers
self.callHandlers(record)
File "/public/home/user/software/anaconda3/envs/nextpolish/lib/python3.11/logging/init.py", line 1706, in callHandlers
hdlr.handle(record)
File "/public/home/user/software/anaconda3/envs/nextpolish/lib/python3.11/logging/init.py", line 978, in handle
hdlr.handle(record)
File "/public/home/user/software/anaconda3/envs/nextpolish/lib/python3.11/logging/init.py", line 978, in handle
hdlr.handle(record)
File "/public/home/user/software/anaconda3/envs/nextpolish/lib/python3.11/logging/init.py", line 978, in handle
self.emit(record)
File "/public/home/user/software/anaconda3/envs/nextpolish/lib/python3.11/site-packages/paralleltask/kit.py", line 42, in emit
self.emit(record)
File "/public/home/user/software/anaconda3/envs/nextpolish/lib/python3.11/site-packages/paralleltask/kit.py", line 42, in emit
self.emit(record)
File "/public/home/user/software/anaconda3/envs/nextpolish/lib/python3.11/site-packages/paralleltask/kit.py", line 42, in emit
raise Exception(record.msg)
raise Exception(record.msg)
Exception: Command '/bin/sh /public/home/user/Plant_genome/assembly/Nextdenove_NextPolish/01_rundir/00.score_chain/04.polish.ref.sh.work/polish_genome2/nextPolish.sh > /public/home/user/Plant_genome/assembly/Nextdenove_NextPolish/01_rundir/00.score_chain/04.polish.ref.sh.work/polish_genome2/nextPolish.sh.o 2> /public/home/user/Plant_genome/assembly/Nextdenove_NextPolish/01_rundir/00.score_chain/04.polish.ref.sh.work/polish_genome2/nextPolish.sh.e' returned non-zero exit status 1, error info: .
Exception: Command '/bin/sh /public/home/user/Plant_genome/assembly/Nextdenove_NextPolish/01_rundir/00.score_chain/04.polish.ref.sh.work/polish_genome1/nextPolish.sh > /public/home/user/Plant_genome/assembly/Nextdenove_NextPolish/01_rundir/00.score_chain/04.polish.ref.sh.work/polish_genome1/nextPolish.sh.o 2> /public/home/user/Plant_genome/assembly/Nextdenove_NextPolish/01_rundir/00.score_chain/04.polish.ref.sh.work/polish_genome1/nextPolish.sh.e' returned non-zero exit status 1, error info: .
raise Exception(record.msg)
Exception: Command '/bin/sh /public/home/user/Plant_genome/assembly/Nextdenove_NextPolish/01_rundir/00.score_chain/04.polish.ref.sh.work/polish_genome3/nextPolish.sh > /public/home/user/Plant_genome/assembly/Nextdenove_NextPolish/01_rundir/00.score_chain/04.polish.ref.sh.work/polish_genome3/nextPolish.sh.o 2> /public/home/user/Plant_genome/assembly/Nextdenove_NextPolish/01_rundir/00.score_chain/04.polish.ref.sh.work/polish_genome3/nextPolish.sh.e' returned non-zero exit status 1, error info: .
[302167 ERROR] 2024-03-15 15:03:26 polish_genome failed: please check the following logs:
[302167 ERROR] 2024-03-15 15:03:26 /public/home/user/Plant_genome/assembly/Nextdenove_NextPolish/01_rundir/00.score_chain/04.polish.ref.sh.work/polish_genome1/nextPolish.sh.e
[302167 ERROR] 2024-03-15 15:03:26 /public/home/user/Plant_genome/assembly/Nextdenove_NextPolish/01_rundir/00.score_chain/04.polish.ref.sh.work/polish_genome2/nextPolish.sh.e
[302167 ERROR] 2024-03-15 15:03:26 /public/home/user/Plant_genome/assembly/Nextdenove_NextPolish/01_rundir/00.score_chain/04.polish.ref.sh.work/polish_genome3/nextPolish.sh.e

$more /public/home/user/Plant_genome/assembly/Nextdenove_NextPolish/01_rundir/00.score_chain/04.polish.ref.sh.work/polish_genome1/nextPolish.sh.e
hostname

  • hostname
    cd /public/home/user/Plant_genome/assembly/Nextdenove_NextPolish/01_rundir/00.score_chain/04.polish.ref.sh.work/polish_genome1
  • cd /public/home/user/Plant_genome/assembly/Nextdenove_NextPolish/01_rundir/00.score_chain/04.polish.ref.sh.work/polish_genome1
    time /public/home/user/software/anaconda3/envs/nextpolish/bin/python /public/home/user/software/anaconda3/envs/nextpolish/share/nextpolish-1.4.1/lib/nextpolish1.py -p 10 -g /p
    ublic/home/user/Plant_genome/assembly/Nextdenove_NextPolish/./01_rundir/00.score_chain/input.genome.fasta -b /public/home/user/Plant_genome/assembly/Nextdenove_NextPolish/./01
    _rundir/00.score_chain/input.genome.fasta.blc -i 0 -t 1 -s /public/home/user/Plant_genome/assembly/Nextdenove_NextPolish/./01_rundir/00.score_chain/sgs.sort.bam -l /public/home/liuyu
    anchao/Plant_genome/assembly/Nextdenove_NextPolish/./01_rundir/00.score_chain/lgs.sort.bam -o genome.nextpolish.part000.fasta
  • /public/home/user/software/anaconda3/envs/nextpolish/bin/python /public/home/user/software/anaconda3/envs/nextpolish/share/nextpolish-1.4.1/lib/nextpolish1.py -p 10 -g /publ
    ic/home/user/Plant_genome/assembly/Nextdenove_NextPolish/./01_rundir/00.score_chain/input.genome.fasta -b /public/home/user/Plant_genome/assembly/Nextdenove_NextPolish/./01_ru
    ndir/00.score_chain/input.genome.fasta.blc -i 0 -t 1 -s /public/home/user/Plant_genome/assembly/Nextdenove_NextPolish/./01_rundir/00.score_chain/sgs.sort.bam -l /public/home/liuyuanc
    hao/Plant_genome/assembly/Nextdenove_NextPolish/./01_rundir/00.score_chain/lgs.sort.bam -o genome.nextpolish.part000.fasta
    Traceback (most recent call last):
    File "/public/home/user/software/anaconda3/envs/nextpolish/share/nextpolish-1.4.1/lib/nextpolish1.py", line 84, in
    P = CDLL(os.path.dirname(os.path.realpath(file)) + '/' + "nextpolish1.so")
    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    File "/public/home/user/software/anaconda3/envs/nextpolish/lib/python3.11/ctypes/init.py", line 376, in init
    self._handle = _dlopen(self._name, mode)
    ^^^^^^^^^^^^^^^^^^^^^^^^^
    OSError: /public/home/user/software/anaconda3/envs/nextpolish/share/nextpolish-1.4.1/lib/nextpolish1.so: ELF load command address/offset not properly aligned

(base) Fri Mar 15 16:48:41 [user@node5 /public/home/user/Plant_genome/assembly/Nextdenove_NextPolish]
$more /public/home/user/Plant_genome/assembly/Nextdenove_NextPolish/01_rundir/00.score_chain/04.polish.ref.sh.work/polish_genome2/nextPolish.sh.e
hostname

  • hostname
    cd /public/home/user/Plant_genome/assembly/Nextdenove_NextPolish/01_rundir/00.score_chain/04.polish.ref.sh.work/polish_genome2
  • cd /public/home/user/Plant_genome/assembly/Nextdenove_NextPolish/01_rundir/00.score_chain/04.polish.ref.sh.work/polish_genome2
    time /public/home/user/software/anaconda3/envs/nextpolish/bin/python /public/home/user/software/anaconda3/envs/nextpolish/share/nextpolish-1.4.1/lib/nextpolish1.py -p 10 -g /p
    ublic/home/user/Plant_genome/assembly/Nextdenove_NextPolish/./01_rundir/00.score_chain/input.genome.fasta -b /public/home/user/Plant_genome/assembly/Nextdenove_NextPolish/./01
    _rundir/00.score_chain/input.genome.fasta.blc -i 1 -t 1 -s /public/home/user/Plant_genome/assembly/Nextdenove_NextPolish/./01_rundir/00.score_chain/sgs.sort.bam -l /public/home/liuyu
    anchao/Plant_genome/assembly/Nextdenove_NextPolish/./01_rundir/00.score_chain/lgs.sort.bam -o genome.nextpolish.part001.fasta
  • /public/home/user/software/anaconda3/envs/nextpolish/bin/python /public/home/user/software/anaconda3/envs/nextpolish/share/nextpolish-1.4.1/lib/nextpolish1.py -p 10 -g /publ
    ic/home/user/Plant_genome/assembly/Nextdenove_NextPolish/./01_rundir/00.score_chain/input.genome.fasta -b /public/home/user/Plant_genome/assembly/Nextdenove_NextPolish/./01_ru
    ndir/00.score_chain/input.genome.fasta.blc -i 1 -t 1 -s /public/home/user/Plant_genome/assembly/Nextdenove_NextPolish/./01_rundir/00.score_chain/sgs.sort.bam -l /public/home/liuyuanc
    hao/Plant_genome/assembly/Nextdenove_NextPolish/./01_rundir/00.score_chain/lgs.sort.bam -o genome.nextpolish.part001.fasta
    Traceback (most recent call last):
    File "/public/home/user/software/anaconda3/envs/nextpolish/share/nextpolish-1.4.1/lib/nextpolish1.py", line 84, in
    P = CDLL(os.path.dirname(os.path.realpath(file)) + '/' + "nextpolish1.so")
    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    File "/public/home/user/software/anaconda3/envs/nextpolish/lib/python3.11/ctypes/init.py", line 376, in init
    self._handle = _dlopen(self._name, mode)
    ^^^^^^^^^^^^^^^^^^^^^^^^^
    OSError: /public/home/user/software/anaconda3/envs/nextpolish/share/nextpolish-1.4.1/lib/nextpolish1.so: ELF load command address/offset not properly aligned

$more /public/home/user/Plant_genome/assembly/Nextdenove_NextPolish/01_rundir/00.score_chain/04.polish.ref.sh.work/polish_genome2/nextPolish.sh.e
hostname

  • hostname
    cd /public/home/user/Plant_genome/assembly/Nextdenove_NextPolish/01_rundir/00.score_chain/04.polish.ref.sh.work/polish_genome2
  • cd /public/home/user/Plant_genome/assembly/Nextdenove_NextPolish/01_rundir/00.score_chain/04.polish.ref.sh.work/polish_genome2
    time /public/home/user/software/anaconda3/envs/nextpolish/bin/python /public/home/user/software/anaconda3/envs/nextpolish/share/nextpolish-1.4.1/lib/nextpolish1.py -p 10 -g /p
    ublic/home/user/Plant_genome/assembly/Nextdenove_NextPolish/./01_rundir/00.score_chain/input.genome.fasta -b /public/home/user/Plant_genome/assembly/Nextdenove_NextPolish/./01
    _rundir/00.score_chain/input.genome.fasta.blc -i 1 -t 1 -s /public/home/user/Plant_genome/assembly/Nextdenove_NextPolish/./01_rundir/00.score_chain/sgs.sort.bam -l /public/home/liuyu
    anchao/Plant_genome/assembly/Nextdenove_NextPolish/./01_rundir/00.score_chain/lgs.sort.bam -o genome.nextpolish.part001.fasta
  • /public/home/user/software/anaconda3/envs/nextpolish/bin/python /public/home/user/software/anaconda3/envs/nextpolish/share/nextpolish-1.4.1/lib/nextpolish1.py -p 10 -g /publ
    ic/home/user/Plant_genome/assembly/Nextdenove_NextPolish/./01_rundir/00.score_chain/input.genome.fasta -b /public/home/user/Plant_genome/assembly/Nextdenove_NextPolish/./01_ru
    ndir/00.score_chain/input.genome.fasta.blc -i 1 -t 1 -s /public/home/user/Plant_genome/assembly/Nextdenove_NextPolish/./01_rundir/00.score_chain/sgs.sort.bam -l /public/home/liuyuanc
    hao/Plant_genome/assembly/Nextdenove_NextPolish/./01_rundir/00.score_chain/lgs.sort.bam -o genome.nextpolish.part001.fasta
    Traceback (most recent call last):
    File "/public/home/user/software/anaconda3/envs/nextpolish/share/nextpolish-1.4.1/lib/nextpolish1.py", line 84, in
    P = CDLL(os.path.dirname(os.path.realpath(file)) + '/' + "nextpolish1.so")
    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    File "/public/home/user/software/anaconda3/envs/nextpolish/lib/python3.11/ctypes/init.py", line 376, in init
    self._handle = _dlopen(self._name, mode)
    ^^^^^^^^^^^^^^^^^^^^^^^^^
    OSError: /public/home/user/software/anaconda3/envs/nextpolish/share/nextpolish-1.4.1/lib/nextpolish1.so: ELF load command address/offset not properly aligned
    (base) Fri Mar 15 16:50:26 [user@node5 /public/home/user/Plant_genome/assembly/Nextdenove_NextPolish]
    $more /public/home/user/Plant_genome/assembly/Nextdenove_NextPolish/01_rundir/00.score_chain/04.polish.ref.sh.work/polish_genome3/nextPolish.sh.e
    hostname
  • hostname
    cd /public/home/user/Plant_genome/assembly/Nextdenove_NextPolish/01_rundir/00.score_chain/04.polish.ref.sh.work/polish_genome3
  • cd /public/home/user/Plant_genome/assembly/Nextdenove_NextPolish/01_rundir/00.score_chain/04.polish.ref.sh.work/polish_genome3
    time /public/home/user/software/anaconda3/envs/nextpolish/bin/python /public/home/user/software/anaconda3/envs/nextpolish/share/nextpolish-1.4.1/lib/nextpolish1.py -p 10 -g /p
    ublic/home/user/Plant_genome/assembly/Nextdenove_NextPolish/./01_rundir/00.score_chain/input.genome.fasta -b /public/home/user/Plant_genome/assembly/Nextdenove_NextPolish/./01
    _rundir/00.score_chain/input.genome.fasta.blc -i 2 -t 1 -s /public/home/user/Plant_genome/assembly/Nextdenove_NextPolish/./01_rundir/00.score_chain/sgs.sort.bam -l /public/home/liuyu
    anchao/Plant_genome/assembly/Nextdenove_NextPolish/./01_rundir/00.score_chain/lgs.sort.bam -o genome.nextpolish.part002.fasta
  • /public/home/user/software/anaconda3/envs/nextpolish/bin/python /public/home/user/software/anaconda3/envs/nextpolish/share/nextpolish-1.4.1/lib/nextpolish1.py -p 10 -g /publ
    ic/home/user/Plant_genome/assembly/Nextdenove_NextPolish/./01_rundir/00.score_chain/input.genome.fasta -b /public/home/user/Plant_genome/assembly/Nextdenove_NextPolish/./01_ru
    ndir/00.score_chain/input.genome.fasta.blc -i 2 -t 1 -s /public/home/user/Plant_genome/assembly/Nextdenove_NextPolish/./01_rundir/00.score_chain/sgs.sort.bam -l /public/home/liuyuanc
    hao/Plant_genome/assembly/Nextdenove_NextPolish/./01_rundir/00.score_chain/lgs.sort.bam -o genome.nextpolish.part002.fasta
    Traceback (most recent call last):
    File "/public/home/user/software/anaconda3/envs/nextpolish/share/nextpolish-1.4.1/lib/nextpolish1.py", line 84, in
    P = CDLL(os.path.dirname(os.path.realpath(file)) + '/' + "nextpolish1.so")
    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    File "/public/home/user/software/anaconda3/envs/nextpolish/lib/python3.11/ctypes/init.py", line 376, in init
    self._handle = _dlopen(self._name, mode)
    ^^^^^^^^^^^^^^^^^^^^^^^^^
    OSError: /public/home/user/software/anaconda3/envs/nextpolish/share/nextpolish-1.4.1/lib/nextpolish1.so: ELF load command address/offset not properly aligned

Operating system
LSB Version: :core-4.1-amd64:core-4.1-noarch:cxx-4.1-amd64:cxx-4.1-noarch:desktop-4.1-amd64:desktop-4.1-noarch:languages-4.1-amd64:languages-4.1-noarch:printing-4.1-amd64:printing-4.1-noarch
Distributor ID: CentOS
Description: CentOS Linux release 7.6.1810 (Core)
Release: 7.6.1810
Codename: Core

GCC
$gcc -v
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 4.8.5-36) (GCC)

Python
Python 3.11.8

NextPolish
nextPolish 1.4.1

To Reproduce (Optional)
Steps to reproduce the behavior. Providing a minimal test dataset on which we can reproduce the behavior will generally lead to quicker turnaround time!

Additional context (Optional)
Add any other context about the problem here.
@moold
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moold commented Mar 18, 2024

Could you try this version.

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