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line, file, marcelm, cutadapt, sign, issue, error, retrogenomics, cores, commented, problem, navigation, pull, requests, actions, security, multicores, closed, python, command, rtrimmedfastqgz, rfastqgz, recent, optlocallibraryframeworkspythonframeworkversionslibpythonsitepackagescutadaptmainpy, optlocallibraryframeworkspythonframeworkversionslibpythonsitepackagescutadaptpipelinepy, optlocallibraryframeworkspythonframeworkversionslibpythonmultiprocessingcontextpy, popen, return, optlocallibraryframeworkspythonframeworkversionslibpythonmultiprocessingpopenspawnposixpy, init, pickle, working, version, owner, macos, wont, github, labels, projects, milestone, footer, skip, content, menu, product, solutions, resources, open, source, enterprise,

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/opt/local/library/frameworks/python 8/site-packages/cutadapt/__main__ 8/site-packages/cutadapt/pipeline personal information error future cutadapt releases marcelm closed comment metadata assignees 8/bin/cutadapt improving cutadapt macos-specific problem error cores=2 argument cutadapt python 3 issue recent call framework/versions/3 8/lib/python3 8/multiprocessing/context 8/multiprocessing/popen_spawn_posix 8/multiprocessing/popen_fork 8/multiprocessing/reduction pickle '_io bufferedwriter' object working smoothly working fine recent change automated tests quick answer great tool pickle outputfiles assigned labels labels projects projects milestone milestone relationships 8/multiprocessing/process previous version github cores=1 command line _popen = _popen problem macos command r2 main_cli sys run _start_workers

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DiscussionForumPosting:
      context:https://schema.org
      headline:error when using multicores
      articleBody:- Cutadapt 3.0, installed by pip; Python 3.8; pigz 2.4 Hi, Using the following command: ``` cutadapt \ --cores=2 \ --nextseq-trim=20 \ --minimum-length=36:189 \ --trim-n \ --discard-untrimmed \ --action=none \ -G a="^AAAAACTCCCTAACCCCTTA;e=0.15;o=5" \ -o "R1.trimmed.fastq.gz" \ -p "R2.trimmed.fastq.gz" \ R1.fastq.gz \ R2.fastq.gz ``` I got this type of error: ``` Traceback (most recent call last): File "/opt/local/Library/Frameworks/Python.framework/Versions/3.8/bin/cutadapt", line 8, in <module> sys.exit(main_cli()) File "/opt/local/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/cutadapt/__main__.py", line 825, in main_cli main(sys.argv[1:]) File "/opt/local/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/cutadapt/__main__.py", line 892, in main stats = r.run() File "/opt/local/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/cutadapt/pipeline.py", line 793, in run workers, connections = self._start_workers() File "/opt/local/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/cutadapt/pipeline.py", line 788, in _start_workers worker.start() File "/opt/local/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/multiprocessing/process.py", line 121, in start self._popen = self._Popen(self) File "/opt/local/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/multiprocessing/context.py", line 224, in _Popen return _default_context.get_context().Process._Popen(process_obj) File "/opt/local/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/multiprocessing/context.py", line 284, in _Popen return Popen(process_obj) File "/opt/local/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/multiprocessing/popen_spawn_posix.py", line 32, in __init__ super().__init__(process_obj) File "/opt/local/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/multiprocessing/popen_fork.py", line 19, in __init__ self._launch(process_obj) File "/opt/local/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/multiprocessing/popen_spawn_posix.py", line 47, in _launch reduction.dump(process_obj, fp) File "/opt/local/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/multiprocessing/reduction.py", line 60, in dump ForkingPickler(file, protocol).dump(obj) TypeError: cannot pickle '_io.BufferedWriter' object ``` However it is working smoothly if I remove the `--cores=2` argument. I used this command line before in a script which was working fine with a previous version of cutadapt. Thus, it could be related to a recent change. Unfortunately I did not record which version it was. Thanks for your help -Gael
      author:
         url:https://github.com/retrogenomics
         type:Person
         name:retrogenomics
      datePublished:2020-11-25T14:58:59.000Z
      interactionStatistic:
         type:InteractionCounter
         interactionType:https://schema.org/CommentAction
         userInteractionCount:3
      url:https://github.com/495/cutadapt/issues/495
      context:https://schema.org
      headline:error when using multicores
      articleBody:- Cutadapt 3.0, installed by pip; Python 3.8; pigz 2.4 Hi, Using the following command: ``` cutadapt \ --cores=2 \ --nextseq-trim=20 \ --minimum-length=36:189 \ --trim-n \ --discard-untrimmed \ --action=none \ -G a="^AAAAACTCCCTAACCCCTTA;e=0.15;o=5" \ -o "R1.trimmed.fastq.gz" \ -p "R2.trimmed.fastq.gz" \ R1.fastq.gz \ R2.fastq.gz ``` I got this type of error: ``` Traceback (most recent call last): File "/opt/local/Library/Frameworks/Python.framework/Versions/3.8/bin/cutadapt", line 8, in <module> sys.exit(main_cli()) File "/opt/local/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/cutadapt/__main__.py", line 825, in main_cli main(sys.argv[1:]) File "/opt/local/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/cutadapt/__main__.py", line 892, in main stats = r.run() File "/opt/local/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/cutadapt/pipeline.py", line 793, in run workers, connections = self._start_workers() File "/opt/local/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/cutadapt/pipeline.py", line 788, in _start_workers worker.start() File "/opt/local/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/multiprocessing/process.py", line 121, in start self._popen = self._Popen(self) File "/opt/local/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/multiprocessing/context.py", line 224, in _Popen return _default_context.get_context().Process._Popen(process_obj) File "/opt/local/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/multiprocessing/context.py", line 284, in _Popen return Popen(process_obj) File "/opt/local/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/multiprocessing/popen_spawn_posix.py", line 32, in __init__ super().__init__(process_obj) File "/opt/local/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/multiprocessing/popen_fork.py", line 19, in __init__ self._launch(process_obj) File "/opt/local/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/multiprocessing/popen_spawn_posix.py", line 47, in _launch reduction.dump(process_obj, fp) File "/opt/local/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/multiprocessing/reduction.py", line 60, in dump ForkingPickler(file, protocol).dump(obj) TypeError: cannot pickle '_io.BufferedWriter' object ``` However it is working smoothly if I remove the `--cores=2` argument. I used this command line before in a script which was working fine with a previous version of cutadapt. Thus, it could be related to a recent change. Unfortunately I did not record which version it was. Thanks for your help -Gael
      author:
         url:https://github.com/retrogenomics
         type:Person
         name:retrogenomics
      datePublished:2020-11-25T14:58:59.000Z
      interactionStatistic:
         type:InteractionCounter
         interactionType:https://schema.org/CommentAction
         userInteractionCount:3
      url:https://github.com/495/cutadapt/issues/495
Person:
      url:https://github.com/retrogenomics
      name:retrogenomics
      url:https://github.com/retrogenomics
      name:retrogenomics
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      interactionType:https://schema.org/CommentAction
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