Example pipeline fails: error in rule predict_duplex

[hyphal-domenico]

Hi,

Thank you for making this available!

I run the pipeline a few months ago with no problems, however on a fresh installation I keep coming across this bug. I get this both on my local machine and a linux server.

The error is the predict_duplex step. In the ends 30 of 62 steps are completed, with only reference and some intermediate files generated.

Here is what I get from running the example pipeline:

Error in rule predict_duplex:
    jobid: 36
    output: pipeline_output/02_intermediate_files/07_predictions/chrII_predictions.csv
    conda-env: /datastore/home/username/smFISH/PaintSHOP_pipeline/shared_conda_envs/31c0d832b37db0c1b2b0f27d498a09b2

RuleException:
CalledProcessError in line 262 of /datastore/home/username/smFISH/PaintSHOP_pipeline/workflow/Snakefile:
Command 'source /datastore/home/username/miniconda3/bin/activate '/datastore/home/username/smFISH/PaintSHOP_pipeline/shared_conda_envs/31c0d832b37db0c1b2b0f27d498a09b2'; set -euo pipefail;  python /datastore/home/username/smFISH/PaintSHOP_pipeline/example_run/.snakemake/scripts/tmpg2o7_y0i.XGB_predict.py' returned non-zero exit status 1.
  File "/datastore/home/username/miniconda3/envs/paintshop_snakemake/lib/python3.8/site-packages/snakemake/executors/__init__.py", line 2168, in run_wrapper
  File "/datastore/home/username/smFISH/PaintSHOP_pipeline/workflow/Snakefile", line 262, in __rule_predict_duplex
  File "/datastore/home/username/miniconda3/envs/paintshop_snakemake/lib/python3.8/site-packages/snakemake/executors/__init__.py", line 529, in _callback
  File "/datastore/home/username/miniconda3/envs/paintshop_snakemake/lib/python3.8/concurrent/futures/thread.py", line 57, in run
  File "/datastore/home/username/miniconda3/envs/paintshop_snakemake/lib/python3.8/site-packages/snakemake/executors/__init__.py", line 515, in cached_or_run
  File "/datastore/home/username/miniconda3/envs/paintshop_snakemake/lib/python3.8/site-packages/snakemake/executors/__init__.py", line 2199, in run_wrapper

Thanks in advance for any help!

Best,
Domenico

[conorcamplisson]

Hi @hyphal-domenico,

Thanks for pointing this out. I think this is a result of incompatible package versions being installed with conda. I have updated the conda environment descriptions in order to lock down many more of the dependency versions.

If you pull the latest repo changes, remove any existing conda environments, and then re-try the example run, I believe it should work; I tested this on Linux and MacOS. Please let me know if you run into any issues!

Thanks,

Conor