Emily Wissel

When I look at the jobs running on the server, this metaspades job is no longer running. I accidentally recreated this with 100 samples (my check at the end of...

Hey @proteinosome, yes I ran the same command but with different samples and additional flags (database paths, cpu usage, etc). I just reran the test data included in the tutorial...

Forgot the last part of your response - when I go to `$HOME/nf_conda` and run `bash .command.run`, I get the error message: >bash: .command.run: No such file or directory so...

Ah thank you for the correction. ``` cd /ceph/.../all_raw_fqs/work/85/3a3d48e4f5f3e45d5fe4deb0ae1aee conda activate $HOME/nf_conda/*qiime* bash .command.run ``` outputs the following: > > Loading required package: Rcpp > Warning messages: > 1: package...

sorry about that - I caught an issue in the path name that led to the `ls cannot access` error, but then fixed that, reran the test and all of...

so `for f in $(readlink -f /ceph/.../all_raw_fqs/work/85/3a3d48e4f5f3e45d5fe4deb0ae1aee/*); do ls -l ${f}; done` (removed >dev/null/) outputs > > -rw-rw-r-- 1 ewissel IBMS-PHLab 5693 Apr 18 00:58 /ceph/../all_raw_fqs/scripts/dada2_assign_tax.R > -rw-r--r-- 1 ewissel...

OK i will re-try with fresh directory/install and let you know how that goes

OK I went ahead and started with a fresh install on /ceph/ with the following ``` conda activate nf ## contains the version of nextflow used in the development of...

I'm getting a similar issue with an nf-core pipeline, so I suspect it may be a server issue on my end. I'll contact our server admin team and update later.

So this was a weird issue with file permissions across nodes on my HPC. The solution was to re-install nextflow and this repo on a different node (`/ceph/`) than `/home/$USER/`...