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Error using zarp-cli #167
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Thanks a lot for your interest in using ZARP/HTSinfer and taking the time to report the issue you are facing, @MSaadfarooq. It looks like you are experiencing a problem when Snakemake tries to set up the HTSinfer Conda environment during the step where ZARP-cli tries to infer the metadata for your samples through running the HTSinfer accessory workflow available in the ZARP repository. To be honest, I don't quite understand where it's coming from. My efforts towards trying to reproduce your errorThe Conda recipe file being used to install HTSinfer contains the following: ---
channels:
- bioconda
dependencies:
- htsinfer=0.11.0
... This amounts to Snakemake running, more or less, the following command (in a fresh Conda environment): mamba install -c bioconda htsinfer=0.11.0 This works fine in my case (Ubuntu 20.04), i.e., HTSinfer install fine and is usable. For example, this command does not raise an error on my Ubuntu 20.04 machine, using the htsinfer synthetic_split_lane1.mate_1.fastq.gz Likewise, I cannot reproduce the error you received when installing ZARP-cli following the installation instructions, after initializing with zarp synthetic_split_lane1.mate_1.fastq.gz Again, this works as expected, up until and including the full execution of the ZARP pipeline. In other words, with the information I currently have, I am unable to reproduce the issue you are facing. Additional information to debug the problemI am afraid that we will need additional information to get to the root of the problem, and we hope that you can kindly assist us with that.
Again, thanks a lot for reporting, and we hope that we can identify the culprit with this additional information. |
Hi I installed zarp-cli when when ran on the paired-end fastq files, it initialized but then got the error on htsinfer.
Input command
zarp ER14_1.fastq,ER14_2.fastq
output error is attached:
![Screenshot 2024-05-31 123606](https://private-user-images.githubusercontent.com/154872971/335489003-238ac8c4-632f-4dee-9cdf-4363f6aeadd3.png?jwt=eyJhbGciOiJIUzI1NiIsInR5cCI6IkpXVCJ9.eyJpc3MiOiJnaXRodWIuY29tIiwiYXVkIjoicmF3LmdpdGh1YnVzZXJjb250ZW50LmNvbSIsImtleSI6ImtleTUiLCJleHAiOjE3MjQxOTA5MTAsIm5iZiI6MTcyNDE5MDYxMCwicGF0aCI6Ii8xNTQ4NzI5NzEvMzM1NDg5MDAzLTIzOGFjOGM0LTYzMmYtNGRlZS05Y2RmLTQzNjNmNmFlYWRkMy5wbmc_WC1BbXotQWxnb3JpdGhtPUFXUzQtSE1BQy1TSEEyNTYmWC1BbXotQ3JlZGVudGlhbD1BS0lBVkNPRFlMU0E1M1BRSzRaQSUyRjIwMjQwODIwJTJGdXMtZWFzdC0xJTJGczMlMkZhd3M0X3JlcXVlc3QmWC1BbXotRGF0ZT0yMDI0MDgyMFQyMTUwMTBaJlgtQW16LUV4cGlyZXM9MzAwJlgtQW16LVNpZ25hdHVyZT04Y2JjMzc5ZDU1NTE3NWM5OGJmYmZmZmI0NDZkY2UwMWIwMzg2YjFiZDkxMjBkMDFlMzI1NmZjN2U2ZThhNzY1JlgtQW16LVNpZ25lZEhlYWRlcnM9aG9zdCZhY3Rvcl9pZD0wJmtleV9pZD0wJnJlcG9faWQ9MCJ9.3bd-jspEBgVZxMq3kbxjxFJojcmGp9WIQN-l5OM5KA8)
thanks in advance.
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