Fail to create conda environment and fail to process QC run

[gghyl]

Hi,

I have installed the NanoCLUST, but errors occur when running the commands. When we tested the command line with our sample fastq file, error message was given that the path to some libgcc-ng packages could not be found. Also, it could not pass the QC(1). The problem could not be solved after the update of the package.

I have attached the error message for your reference.

[Thomieh73]

If you have the option to install docker on your system, than I recommend running this pipeline with that option instead of conda.

[ke-shin]

I also have the same issue of not being able to pass the QC step. I get a message saying "Process QC (1) terminated with an error exit status (126)". How can I get past this? Thank you.

[Thomieh73]

Can you look up the file .command.log in your work folder: /f6/45d12d... That should give the complete output of the error. If you post that here, we can take a look at what is wrong.

You can also check the other files named .command.err and .command.out to see what those say.

[DanBeaton]

I have a similar issue. the message is: .command.sh: line 3: fastp: command not found

when running as conda, I notice that a new conda environment has been created with the version of fastp listed in environment.yml.

[Thomieh73]

One way to test if the environment is okay, is to load it and then try to run the tool. If that does not work, than remove the environment, and try running the pipeline again. That should install a new conda environment

[caolijia]

I also had the same error message, but I cannot check the log file as the work directory is empty...

[Thomieh73]

What is the error that you get:?

The working directory is usually not empty, but the nextflow command files are hidden. Use the command : ls -la

[Claudia-Barrera]

Hi!

I'm facing the same problem but I'm not able to use docker. When I check the .command.log file this is the content: File "/dss/dsshome1/0F/ge53xen2/scripts/NanoCLUST/bin/markdown_to_html.py", line 4, in import markdown ModuleNotFoundError: No module named 'markdown'

But the markdown file is there. Does someone have any idea how to fix it? I really appreciate your suggestions.

Thanks!

[jennyfothergill]

@gghyl If running conda info -e does not show that the environments have been created, check your nextflow.config to see if conda.enabled = true is in your conda profile. I had this same issue, and adding this line was my fix.

[timyerg]

@jennyfothergill Thank you for sharing your solution. Worked for me!