rresendepinto

Thank you for the quick answer! What if the HPC doesnt run SLURM, but SGE instead?

If you could do that, it would help me a lot. Thank you!

Hi! I tried the new version but I think there was a conflict with SGE. ``` Error executing process > 'check_fasta_format (1)' Caused by: Failed to submit process to grid...

It just hangs indefinitely in the clusters head node. I can't figure out why.

Command: `NXF_JAVA_HOME=/home/rpinto/Documents/bin/jre1.8.0_321 NXF_VER=20.09.0-edge nextflow run hoelzer/poseidon -r sge_profile --fasta poseidon/test_data/bats_mx1_small.fasta --cores 4 -profile sge,singularity >> qsub2.out &` Nextflow log file [nextflow_0703.log](https://github.com/hoelzer/poseidon/files/8198615/nextflow_0703.log) This is the output: Tree root species: NA Reference...

This is the first nextflow pipeline I am trying to run on this cluster. The qsub file only presents what I reported before as output. The same thing happens with...

The hello program works. The HPC runs bash as default. The pipeline doesn't hang anymore but throws a different error related to the job scheduler: [qsub4.out.txt](https://github.com/hoelzer/poseidon/files/8207072/qsub4.out.txt)

I think it uses mpi. Where is the pipeline code stored?

I changed to mpi but it won't run because it has uncommited changes.

I ran the pipeline from the local directory and it seems to have solved the issues with the job scheduler. However, it threw an error on the "gard_detect" step. The...