NameError in line 134 of Skipper.py: name 'directory' is not defined File "Skipper.py", line 134, in <module>

[MSajek]

Hi, I try to run skipper on eCLIP data (not from ENCODE). I prepared proper environment with all dependencies, config file and manifest and when run: snakemake -ns ~/programs/skipper/Skipper.py -j 1 I have the following error: NameError in line 134 of Skipper.py: name 'directory' is not defined File "Skipper.py", line 134, in <module> It looks like directory() declaration is not recognized for some reasons. When I commented line 134 I have the next error: InputFunctionException in line 541 of Skipper.py: KeyError: '{experiment_label}' Wildcards: experiment_label={experiment_label} Any suggestions how to solve these issues will be helpful. I also suggest to add toy dataset to repo to make some tests before running on new data. Best, Marcin

[augustboyle]

Hi Marcin,

You can run the example on the GitHub repo to help troubleshoot: https://github.com/YeoLab/skipper/tree/main/example

The fastqs are available on SRA (it’s easiest to use SRA explorer to download all the files in my opinion): https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA882819

The enriched window output that you should get is available on GEO: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE213867

Skipper has a several dependencies (too many to download and install as part of a single container), which is probably the most time consuming part. We are working on a guide to make it easier to incorporate all the dependencies in the future.

Best, Evan

On Sep 12, 2023, at 8:53 PM, Marcin Sajek @.***> wrote:

Hi, I try to run skipper on eCLIP data (not from ENCODE). I prepared proper environment with all dependencies, config file and manifest and when run: snakemake -ns ~/programs/skipper/Skipper.py -j 1 I have the following error: NameError in line 134 of Skipper.py: name 'directory' is not defined File "Skipper.py", line 134, in It looks like directory() declaration is not recognized for some reasons. When I commented line 134 I have the next error: InputFunctionException in line 541 of Skipper.py: KeyError: '{experiment_label}' Wildcards: experiment_label={experiment_label} Any suggestions how to solve this issues will be helpful. I also suggest to add toy dataset to repo to make some tests before running on new data. Best, Marcin

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[MSajek]

Hi Evan, Thanks, I will download and try to run on suggested data. However errors themselves look like data independent. Any suggestions how to fix them? It can be helpful if you can post not only the list of required dependencies but also their versions. Best, Marcin

[augustboyle]

Most of the software versions are listed in the Key Resources Table in the publication. Snakemake got left out which could be related to the directory command problem.

We plan to include the versions in our guide.

It looks like there is an issue with the manifest so I would look closely at the example and make sure the experiment and replicate labels are filled in and don’t have any spaces or unexpected characters.

Best, Evan

On Sep 13, 2023, at 6:21 AM, Marcin Sajek @.***> wrote:

Hi Evan, Thanks, I will download and try to run on suggested data. However errors themselves look like data independent. Any suggestions how to fix them? It can be helpful if you can post not only the list of required dependencies but also their versions. Best, Marcin

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[MSajek]

Hi Evan, The same error: InputFunctionException in line 541 of Skipper.py: KeyError: '{experiment_label}' Wildcards: experiment_label={experiment_label} occurs with your manifest file, where I only replaced paths to files When I started to checking Skipper.py line by line everything was looking ok and I have no idea why I have this error.

[augustboyle]

Hi Marcin,Did you learn the source of this issue? I was busy for a while and couldn’t think of a way to troubleshoot immediately. I think perhaps writing some Snakemake test workflows and confirming you can access the config file would be appropriate Courtesy of my phoneOn Sep 16, 2023, at 10:28 PM, Marcin Sajek @.***> wrote: Hi Evan, The same error: InputFunctionException in line 541 of Skipper.py: KeyError: '{experiment_label}' Wildcards: experiment_label={experiment_label} occurs with your manifest file, where I only replaced paths to files

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[MSajek]

Unfortunately I don't. I tried a few things and nothing worked. I decided to run skipper script by script and then everything works fine.