Closed shenwei356 closed 2 years ago
Hi @shenwei356,
The pipeline was designed to process only input fasta at the time, but you should be able to run as many instances if VIRify as you want.
That error you are getting is related to Nextflow, not VIRIfy (as far as I can tell). Things you could try:
rm -r /home/shenwei/.nextflow/assets/EBI-Metagenomics/emg-viral-pipeline
and nextflow pull EBI-Metagenomics/emg-viral-pipeline
(similar to https://github.com/nf-core/ampliseq/issues/160)Cheers
Hi Martín, thanks for your rapid reply.
I've tried to clean and re-pull the pipeline, but the same error occurred. Besides, after trying with multiple instances, it would be failed to run with one instance. So I have to re-pull again to run with one instance.
Not sure if related, but check that each instance of VIRify is using a different work directory
Confirmed.
BTW the server has an old java:
NOTE: Nextflow is not tested with Java 1.8.0_332 -- It's recommended the use of version 11 up to 18
Hey @shenwei356 thanks for your interest in the pipeline! I'm not sure if I fully get what you are trying to do. But just in general and as also mentioned by @mberacochea:
.nextflow.log
file and therefore starting multiple nextflow commands from the same directory will cause errors.I'm not sure if the old JAVA might also cause issues.
you can only start one nextflow pipeline from the same directory simultaneously. Nextflow is writing a hidden .nextflow.log file and therefore starting multiple nextflow commands from the same directory will cause errors.
I see, but I specify the --workdir which point different places (where the inputs are). If it's true, the right way should be changing directory to where the input file is before running the pipline.
you can only start one nextflow pipeline from the same directory simultaneously. Nextflow is writing a hidden .nextflow.log file and therefore starting multiple nextflow commands from the same directory will cause errors.
I see, but I specify the --workdir which point different places (where the inputs are). If it's true, the right way should be changing directory to where the input file is before running the pipline.
Yeah --workdir
or in short -w
will not help you. This just changes where to working directories are written when running processes in the pipeline. Still there will be the hidden .nextflow.log
file written to the directory from which you start the pipeline. No other pipeline can then be started from the same folder while the other one is still running and locks the .nextflow.log
file - at least as far as I know. So yes, what you would need to do is: create a directory for each run, cd
into that dir and then execute nextflow.
Thank you all!
Hi team, it's thrilling to have successfully run VIRify for the first time!
I found the CPU usage is low when running
hmmsearch
, so I'd like to execute multiple VIRfy processes in parallel. However, an error occurred:Then I have to process all samples one by one, no error by now.
Does VIRfy (nextflow) support processing multiple inputs in parallel? I think it does cause there's an option
--cores
:Wei
Command: