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haniffalab / webatlas-pipeline

A data pipeline built in Nextflow to process spatial and single-cell experiment data for visualisation in WebAtlas
MIT License
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Python scripts not executable #100

Closed davehorsfall closed 1 year ago

davehorsfall commented 1 year ago

[09/46fdcc] process > process_label (test-visium-label.zarr) [100%] 1 of 1, failed: 1 [84/5687b2] process > process_anndata (test-iss-anndata.zarr) [100%] 2 of 2, failed: 2 [- ] process > intersect_anndatas - [- ] process > ome_zarr_metadata (METADATA.ome.xml, raw) - [- ] process > Build_multimodal_config - ERROR ~ Error executing process > 'process_anndata (test-scrnaseq-anndata.zarr)'

Caused by: Process process_anndata (test-scrnaseq-anndata.zarr) terminated with an error exit status (126)

Command executed:

integrate_anndata.py reindex_and_concat --path test-scrnaseq-anndata.zarr --offset 2000000 --features celltype

Command exit status: 126

Command output: (empty)

Command error: .command.sh: line 2: /webatlas-pipeline/bin/integrate_anndata.py: Permission denied

Work dir: /webatlas-pipeline/work/1d/a5a50c277ca11e4b77c90858988b3e

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

BioinfoTongLI commented 1 year ago

I believe it's just that scirpt is executable and it's fixed now? Should we close this? @davehorsfall