Trouble to run the example execution - Error executing process > detect:pprmeta (1)

[krluka]

Dear,

When I try to run the example execution with -profile local,singularity I get the following error message:

ERROR:

ERROR ~ Error executing process > 'detect:pprmeta (1)'

Caused by:
  Process `detect:pprmeta (1)` terminated with an error exit status (255)

Command executed:

  [ -d "pprmeta" ] && cp pprmeta/* .
  ./PPR_Meta assembly_renamed_filt1500bp.fasta assembly_pprmeta.csv

Command exit status:
  255

Command output:
  (empty)

Command error:
  INFO:    Environment variable SINGULARITYENV_NXF_TASK_WORKDIR is set, but APPTAINERENV_NXF_TASK_WORKDIR is preferred
  Could not access the MATLAB Runtime component cache. Details: fl:filesystem:SystemError; component cache root:; componentname: PPR_Meta

Work dir:
  /scratch/lukak/virify/89/da5d86a7234aabd05dfd7b618633e0

I don't have many experience with singularity/apptainer so any kind of help would be much appreciated.

Best regards,

Luka

[mberacochea]

Hey @krluka

Apologies for a very delayed response.

That looks like a there are issues with permissions on the directory the task is being executed. Do you have write/read/execute permissions on /scratch/lukak/virify/89/da5d86a7234aabd05dfd7b618633e0? I'm not very familiar with the MATLAB runtime, and I have never bumped into this problem.

If you are running this on an HPC cluster, could you contact your support team? They may be able to provide some guidance.

Cheers

[krluka]

Hey @mberacochea

Thank you for your reply.

I checked with local support and it seems that necessary permissions are in place.

Best,

Luka

[mberacochea]

Hey @krluka

Can you share the whole .nextflow.log file for the run please?. I'm not sure what is going one, and that log file may have some clues.

Cheers

[krluka]

Hey @mberacochea

Sure, I'm attaching it to this post.

Best,

Luka

nextflow.log

[dbespiatykh]

Hey @krluka,

I had the same issue on HPC without admin rights, and I was able to fix it by setting up the MCR_CACHE_ROOT=</writable/dir> environment variable with writable directory.

[mberacochea]

@dbespiatykh Can you try @dbespiatykh suggestion?

Thanks @dbespiatykh I will add this to the documentation

[krluka]

Hey @dbespiatykh,

Thank you for the suggestion - I will try that the first chance I get.

@mberacochea I'll post the outcome as soon I have it.

[egenomics]

I have the same error:
ERROR ~ Error executing process > 'detect:pprmeta (1)'

Caused by:
Process detect:pprmeta (1) terminated with an error exit status (255)

Command executed:

[ -d "pprmeta" ] && cp pprmeta/* .
./PPR_Meta assembly_renamed_filt1500bp.fasta assembly_pprmeta.csv

Command exit status:
255

Command output:
(empty)

Command error:
Could not access the MATLAB Runtime component cache. Details: fl:filesystem:SystemError; component cache root:; componentname: PPR_Meta

Work dir:
/soft/test_viral./work/e1/ba3c3cf6378ba3500b2882c1391883

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

In an installation from scratch.

[mberacochea]

Hi @egenomics

Did you try @dbespiatykh suggestion?

I had the same issue on HPC without admin rights, and I was able to fix it by setting up the MCR_CACHE_ROOT=</writable/dir> environment variable with writable directory.

Cheers

[egenomics]

I am in a local machine (testing it). When I use your suggestion about setting upthe MCR_CACHE_ROOT I get a similar error:
ERROR ~ Error executing process > 'detect:pprmeta (1)'

Caused by:
Process detect:pprmeta (1) terminated with an error exit status (255)

Command executed:

[ -d "pprmeta" ] && cp pprmeta/* .
./PPR_Meta assembly_renamed_filt1500bp.fasta assembly_pprmeta.csv

Command exit status:
255

Command output:
(empty)

Command error:

Could not access the MATLAB Runtime component cache. Details: fl:filesystem:SystemError; component cache root:; componentname: PPR_Meta

Work dir:
/soft/test_viral./work/ae/9ed47b42f085011346e1ceff79c36e

Tip: when you have fixed the problem you can continue the execution adding the option -resume to the run command line

-- Check '.nextflow.log' file for details

[dbespiatykh]

Hey @egenomics,

Try doing this:

• 1. Inside the VIRify database directory, locate the /pprmeta directory, and rename file PPR_Meta to something like PPR_Meta_w
• 2. Create file named PPR_Meta and paste the following code in it:

export MCR_CACHE_ROOT=/your/writable/directory

./PPR_Meta_w "$@"

• 3. Run chmod +x PPR_Meta

And try running the pipeline again

[egenomics]

Hi,
I did it and it works with the test!

thanks

[mberacochea]

Hey @egenomics,

Try doing this:

* 1. Inside the VIRify database directory, locate the `/pprmeta` directory, and rename file `PPR_Meta` to something like `PPR_Meta_w`

* 2. Create file named `PPR_Meta` and paste the following code in it:

export MCR_CACHE_ROOT=/your/writable/directory

./PPR_Meta_w "$@"

* 3. Run `chmod +x PPR_Meta`

And try running the pipeline again

Brilliant, and validated by @egenomics. I'll add this to the README.

Thank you @dbespiatykh

[corvinux]

export MCR_CACHE_ROOT doesn't work on nfs shares. I had to set it on local filesystem.