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BROOKELAB / Influenza-virus-DI-identification-pipeline

Influenza virus DVG detection tools
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"sbatch" error #2

Open katarinabraun opened 4 years ago

katarinabraun commented 4 years ago

Hi!

Thanks so much for putting together this repository -- I am excited to use it. I am hoping you can help me troubleshoot an error that is popping up. For a bit of background, I am working with paired-end Illumina fastqs (whole genome avian flu sequences). I am pretty sure I have all of the required dependencies and I have the config formatted correctly, but I when I run the exec command I am getting this error: 

Error executing process > 'bowtie2Index_genome (GD3_ferret1_day1.fasta)'

Caused by:
  Cannot run program "sbatch" (in directory "/Volumes/KMB_hard_drive_2/KMB_harddrive-2_to_coltrane/H7N9/DIPs/work/b9/c99314ab138b0ec19c6c23f5e4bbac"): error=2, No such file or directory

Command executed:

  sbatch .command.run

Command exit status:
  -

Command output:
  (empty)

Work dir:
  /Volumes/KMB_hard_drive_2/KMB_harddrive-2_to_coltrane/H7N9/DIPs/work/b9/c99314ab138b0ec19c6c23f5e4bbac

Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named `.command.sh

Please let me know if you have any suggestions for troubleshooting this. Thanks so much!

grendon commented 4 years ago

This pipeline runs with SLURM as the cluster (aka workload) manager. See documentation here: https://slurm.schedmd.com/ sbatch is one of the many tools in the SLURM toolkit.

In this particular case sbatch is trying to execute the process whose files are in that folder /long/path/work/b9/c99....

But it cannot do it because your computer does not understand that sbatch command. Very likely you do not have SLURM installed yet.

katarinabraun commented 4 years ago

Thanks @grendon for your quick response.

You were right -- I did not have SLURM installed.
I installed it using brew install slurm and it is now in my bin/ , but I am still getting the same error.
Can I run this pipeline on a personal mac? Or does this need to be submitted to a cluster? Thanks in advance for any additional suggestions you have.

grendon commented 4 years ago

The pipeline can be run on a laptop. Please contact the Nextflow developers to guide you through the process of configuring Nextflow properly in your particular case.

katarinabraun commented 4 years ago

Hi @grendon. Apologies, for bugging you but I am still having trouble figuring out this error. I did message with Nextflow people and Nextflow seems to be working just fine (eg I can run the simple nextflow run hello program without problems). I also have Slurm installed on my computer. I am still running into the same error stating that one "sbatch" cannot be run. I am not sure where to go from here.

katarinabraun commented 4 years ago

Hi @grendon. I have continued working on this and found in Slurm documentation that "Slurm has run on macOS in the past, but does not currently". Do I just need to find a different computer to run this on or are you aware of alternative work-arounds?

grendon commented 4 years ago

Katarina, I do not deal with these issues here in the lab. Anything related to SLURM installation, deployment, and troubleshooting is the purview of the cluster's system administrators. I already talked to them about it and they told me that the person that is in charge of these issues is out of the country at a conference and that he will be back in a week.

katarinabraun commented 4 years ago

Okay, thank you for the information. I'll reach out again in a week.