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aertslab / SCENIC

SCENIC is an R package to infer Gene Regulatory Networks and cell types from single-cell RNA-seq data.
http://scenic.aertslab.org
GNU General Public License v3.0
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Error message when running the first tutorial notebook #207

Closed dyXDDD closed 2 years ago

dyXDDD commented 3 years ago

Hello,

I had an issue when running the tutorial notebook SCENIC_tutorial_1-RunningVSN.ipynb. When I was running the last step for the entire pipeline, which was commented in the notebook, it gave the error message pasted at the end. It says the directory /ddn1/vol1/staging/leuven/stg_00002/lcb/cflerin/resources does not exist. Is it a directory in the container, or should I change it to a directory in my system?

In the previous preprocessing and filtering steps, I met similar issues, but solved this by changing the path in singularity.runOptions to directory in my system. But I don't know how to fix this in the entire pipeline. I have attached the config file. Could you please help me check what's wrong?

Thank you.

I changed the config file to .txt since GitHub doesn't support .config attachments. pbmc10k.vsn-pipelines.complete.txt

Error message:

executor > local (12) ...... Error executing process > 'single_sample_scenic:SCENIC_APPEND:scenic:ARBORETO_WITH_MULTIPROCESSING (1)'

Caused by: Process single_sample_scenic:SCENIC_APPEND:scenic:ARBORETO_WITH_MULTIPROCESSING (1) terminated with an error exit status (255)

executor > local (12) ...... [89/0c2612] process > single_sample_scenic:SCENIC_APPEND:scenic:ARBORETO_WITH_MULTIPROCESSING (1) [100%] 1 of 1, failed: 1 ✘ ...... Error executing process > 'single_sample_scenic:SCENIC_APPEND:scenic:ARBORETO_WITH_MULTIPROCESSING (1)'

Caused by: Process single_sample_scenic:SCENIC_APPEND:scenic:ARBORETO_WITH_MULTIPROCESSING (1) terminated with an error exit status (255)

Command executed:

arboreto_with_multiprocessing.py pbmc10k_data.filtered.loom allTFs_hg38.txt --output pbmc10k_data__adj.tsv.gz --num_workers 4 --cell_id_attribute CellID --gene_attribute Gene --method grnboost2 --seed 250

Command exit status: 255

Command output: (empty)

Command error: WARNING: skipping mount of /ddn1/vol1/staging/leuven/stg_00002/lcb/cflerin/resources: stat /ddn1/vol1/staging/leuven/stg_00002/lcb/cflerin/resources: no such file or directory FATAL: container creation failed: mount /ddn1/vol1/staging/leuven/stg_00002/lcb/cflerin/resources->/ddn1/vol1/staging/leuven/stg_00002/lcb/cflerin/resources error: while mounting /ddn1/vol1/staging/leuven/stg_00002/lcb/cflerin/resources: mount source /ddn1/vol1/staging/leuven/stg_00002/lcb/cflerin/resources doesn't exist

Work dir: /gpfs/slayman/pi/gerstein/yd283/tutorials/SCENIC_pbmc/work/89/0c26127c8bdaf6de46c7ce5004fc36

gianfilippo commented 2 years ago

same here using nextflow

KrisDavie commented 2 years ago

This error message is because you have not changed the paths to the one/all of following parameters:

You will need to have these files available in your local computing platform and put the correct paths in these config parameters.