Getting done without running processes

[vhfsantos]

Hi, Thank you for this amazing pipeline!

I tried to run the intire pipeline with the test dataset (-profile conda,test) and everything was ok.

However, when I try to run with my data, it gets done after running only the first three processes:

I tried to run with --onlyAsm option as well, but it gets done without running any process:

I also tested running with all different profiles and got the same error. Do you know what might be happening here?

Thanks in advance!

[rivera10]

Hello @vhfsantos,

Can you share the command used to start the pipeline? I see you are using conda, but I am not sure if it is with the TransPi environment (installed with the precheck) or with individual conda environments. Also, it looks that it could be an issue with the --reads option since it is starting but then stopping after the databases are created. Let me know.

Best, Ramon

P.S. I suggest pulling the repository again since I fixed some minor bugs.

[vhfsantos]

Hello @rivera10 , thank you for your reply.

Here is the command line:

$ ./nextflow run TransPi.nf --all -profile conda --maxReadLen 101 --k 25,41,53,61 --reads '/home/vinicius/raw/*fastq.gz' --outdir 2021_TRANSPI-RESULTS

I also tried with:

$ ./nextflow run TransPi.nf --all -profile conda --myConda --maxReadLen 101 --k 25,41,53,61 --reads '/home/vinicius/raw/*fastq.gz' --outdir 2021_TRANSPI-RESULTS

But I got the same result. I pulled the repo yesterday. Also, I am running everything inside the TransPi directory

Thanks, Vinícius

[rivera10]

It seems the issue is in the way the --reads parameter is interpreted by nextflow while creating the channels using fromFilePairs. It accepts R[1,2].fastq.gz and not *.fastq.gz.

Try like this

./nextflow run TransPi.nf --all -profile conda --myConda --maxReadLen 101 --k 25,41,53,61 --reads '/home/vinicius/raw/*R[1,2].fastq.gz' --outdir 2021_TRANSPI-RESULTS

Let me know if this works

Best, Ramon

[vhfsantos]

Oh, now it's running! :blush: Thank you for your help!

Best, Vinícius

[rivera10]

No worries. Anything let me know.