Error using zarp-cli

[MSaadfarooq]

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:

thanks in advance.

• OS: [ubuntu 20.04, remote server]
• working in zarp env

[uniqueg]

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 error

The 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 tests/input_files/pe_lane1/synthetic_split_lane1.mate_1.fastq.gz test file in the ZARP repository (you can find it here):

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 --init (basically just accepting the defaults) and running:

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 problem

I 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.

1. Could you kindly let us know the exact commands that you used to install ZARP-cli? Did you follow the instructions at https://zavolanlab.github.io/zarp-cli/guides/installation?

2. Also, perhaps there is an issue with the Conda or Mamba version. Could you please run mamba --version? For example, in my case, this gave:

   mamba 1.4.2
   conda 23.3.1

3. Finally, it would greatly help us to pinpoint the exact issue if you

   • re-run the same command that gave you the error with the additional option --verbosity=DEBUG, i.e.:

   zarp --verbosity=DEBUG ER14_1.fastq,ER14_2.fastq

   • copy the entire screen output into a text file
   • send it to [email protected] (you could also attach it here, but it will contain information about the structure of your file system paths, which people may consider potentially sensitive information; to avoid disclosing any potentially sensitive info, you could also replace the file system specific information with some dummy value, e.g., replace all occurences of something like /home/myactualusername/myworkfolder/ to something like /dummy/path/ after you have copied the screen output into a text file)

Again, thanks a lot for reporting, and we hope that we can identify the culprit with this additional information.