Closed vhfsantos closed 3 years ago
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.
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
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
Oh, now it's running! :blush: Thank you for your help!
Best, Vinícius
No worries. Anything let me know.
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!