Timeout waiting for connection from pool

[mazzalab]

Description of the bug

Hi,
I get the error in the title when I run the command line below.
The error is this one: https://www.biostars.org/p/9590721/ but related to circrna.

What's wrong?

thanks in advance

Command used and terminal output

./nextflow run nf-core/circrna -profile docker --genome GRCh38 --input samples.csv --tool 'ciriquant' --module 'circrna_discovery' --outdir ./results_single --tool_filter 1 -r dev

Relevant files

.nextflow.log

System information

N E X T F L O W ~ version 23.10.1
OS: Rocky Linux 8
Container: Docker
Version of nf-core/circrna: revision: c29124f [dev]

[nictru]

Hey, this seems to be a problem that is not really related to the pipeline, but a more general one. Since you provided the --genome parameter, nextflow tries to fetch reference genome data from an AWS S3 bucket. This is also what the people in the Biostars discussion figured out. I can only recommend to follow the same steps which were suggested there. If the problems persist, you might want to remove the genome parameter and instead download the fasta and gtf files of your genome manually and pass the downloaded versions to the pipeline using the --fastaand --gtf parameters, respectively.

Keep me posted!

[mazzalab]

Hi Nico, it should be a problem in amazon or whatnot. Setting static paths, it works. Thanks for the quick reply.