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Error "RuntimeError: close method on generator classes unimplemented" is reported when "--parallel" is used #1658
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Hi @kongxiangya I have
Could you share what steps you are exactly using to run the workflow? Both of the commands below work for me with your attached files. (venv) kinow@ranma:/tmp/cwl$ cwltool test.cwl
...
...
INFO [job cutadapt_v2] Max memory used: 0MiB
INFO [job cutadapt_v2] completed success
INFO [step cutadapt_v2] completed success
INFO [workflow cutadaptparallel_v2] completed success
INFO [step cutadaptparallel_v2] completed success
INFO [workflow ] completed success
{}
INFO Final process status is success (venv) kinow@ranma:/tmp/cwl$ cwltool --parallel test.cwl
...
...
INFO [job cutadapt_v2] Max memory used: 0MiB
INFO [job cutadapt_v2] completed success
INFO [step cutadapt_v2] completed success
INFO [workflow cutadaptparallel_v2] completed success
INFO [step cutadaptparallel_v2] completed success
INFO [workflow ] completed success
{}
INFO Final process status is success |
Hi @kinow I also tried using PIP to install CWLTOOL Now my problem should be that if I build the image using cwltool.Dockerfile, the error will occur my Dockerfile is:
Relevant files are downloaded from https://github.com/common-workflow-language/cwltool/releases/tag/3.1.20220406080846 My image by Dockerfile: cwltool:3.1.20220406080846 |
This might be a mypyc failure. Can you try again with |
Hi @mr-c |
Glad to hear it, @kongxiangya ; Did you build from the latest development code of cwltool (which uses mypy 0.950), or the latest cwltool pypi release (which uses mypy 0.942)? I'm curious if the latest version of mypy still have this issue. If so, I will stop publishing binary wheels of cwltool so that others don't have this problem. |
I was able to reproduce this problem using mypy 0.942 and with mypy 0.950 it is fixed; I'll make a new cwltool release so that others aren't affected. Thanks! |
I have tested version 3.1.20220502060230 and SET |
workflow:
If the image is created using "cwltool.Dockerfile", the following error message is displayed:
However, if use cwLTool installed directly by Conda, it will work without error
The file used for the test:
test.zip
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