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cutadapt error for methylpy v 1.4.6 #69
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I think I figured out the issue -f parameter is deprecated in cutadapt v3.1+ |
Cool. Do you need any help with this? Downgrading cutadapt to the version methylpy supported is one option. Alternatively, we can run cutadapt manually and then run methylpy with trimming step turned off. |
FYI - success here with downgrade to 2.10 eg after building the env I forced the cutadapt version down to 2.x
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Hi Yupeng,
I am getting some strange error for cutadapt (3.4) after upgrading methylpy from 1.4.2 to 1.4.6. Here is the error message:
And this is reported for all split files. here is the rest of the error log:
Below is my code for methylpy (which worked fine for cutadapt 2.10, methylpy 1.4.2)
Could you help me to figure out how to fix this? thanks.
Update:
Just to clarify - I saw that the split files are generated in my home directory initially. After the run is aborted due to the above errors, the temporary files are gone. I also tried running the command by specifying the path to output, it still showed me errors for split file not found.
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