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lehtiolab / proteogenomics-analysis-workflow

IPAW: a Nextflow workflow for proteogenomics
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ERROR ~ Error executing process > 'makeTargetSeqLookup (1)' #11

Open Jokendo-collab opened 4 years ago

Jokendo-collab commented 4 years ago

@yafeng , @glormph and @husensofteng I am getting the following error. I have followed the instruction on your README and when I run the job it fails. I am working on the with the LFQ raw files.

ERROR ~ Error executing process > 'makeTargetSeqLookup (1)'

glormph commented 4 years ago

If this is the same command not found error it is probably not running inside a container. Unfortunately we havent worked much on easy-to-use singularity automation, but in principle it would use the same container as for docker. You'd have to make singularity pull a docker container (it will automatically convert it). Our HPC is called UPPMAX, also runs singularity and we have a specific config profile for it (in conf/uppmax.config ). You can look at that profile and edit/delete the parts that dont fit your HPC (there is scratch disks, SLURM, etc in it), then run it with -profile uppmax.

IIRC we manually pulled the singularity container before running the pipeline. Something like the below, but you'd still have to make sure singularity can find it (correct path to dir), since the pulled container location is not specified in the pipeline. I cant remember exactly but I think there was some kind of cache for singularity where it stores its containers. Maybe it remembers the location from pulling. singularity pull --name glormph-ipaw-dev.img --dir /path/to/singularity_imgs/ docker://glormph/ipaw:dev

Jokendo-collab commented 4 years ago

Now I get the following error. N E X T F L O W ~ version 19.04.1 Launching main.nf [backstabbing_northcutt] - revision: 6ff5d47fa2 9 mzML files in analysis [warm up] executor > slurm WARN: Access to undefined parameter project -- Initialise it to a default value eg. params.project = some_value ERROR ~ Error executing process > 'makeTrypSeq'

Caused by: Failed to submit process to grid scheduler for execution

Command executed:

sbatch .command.run

Command exit status: 1

Command output: sbatch: error: slurm_persist_conn_open_without_init: failed to open persistent connection to localhost:6819: Connection refused sbatch: error: slurmdbd: Sending PersistInit msg: Connection refused sbatch: error: slurmdbd: Sending PersistInit msg: Connection refused sbatch: error: slurmdbd: DBD_GET_CLUSTERS failure: Connection refused sbatch: error: Problem talking to database sbatch: error: There is a problem talking to the database: Connection refused. Only local cluster communication is available, remove --cluster from your com mand line or contact your admin to resolve the problem.

Work dir: /scratch/oknjav001/proteogenomics/scripts/proteogenomics-analysis-workflow/work/a9/8deea53b8e18a7c7a6f83c76770e2e

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

-- Check '.nextflow.log' file for details [a9/8deea5] process > makeTrypSeq [ 0%] 1 of 0, failed: 1

yafeng commented 4 years ago

@javanOkendo An alternative is to use miniconda to download and install all required softwares. There are two conda environment files in the folder envs/.

glormph commented 4 years ago

The error implies some issue with SLURM, I don't know how the HPC is setup but it seems to refuse the --cluster parameter (as shown in the error). I am not sure where that comes from though, and dont know what config or params you're using. Is it in clusterOptions? That is what is typically passed to the executor (SLURM in this case).

Jokendo-collab commented 4 years ago

@glormph and @yafeng can this be attributed to the new version of nextflow?

Jokendo-collab commented 4 years ago

@glormph and @yafeng can this be attributed to the new version of nextflow?