Error in rule Index

[chrisodhams]

Hi DROP Team,

I'm having issues running the Aberrant Expression module in the DROP pipeline. It's not obvious whether it's the same issue reported in #222, so I decided to make a new issue.

I get an Error in rule Index.

I've checked the required input files and they all seem to be present (attached). The output *_index.html and *_dep.svg files are not created.

I've attached the full stdout and stderr and the snakemake log run with: snakemake --cores 1 --verbose

I've tried multiple times to unlock the run directory with snakemake --unlock, which unlocks, but it seems it still can't get passed the Index stage.

Output from unlock:

WARNING: Less than 30 IDs in DROP_GROUP group1
check for missing R packages
AberrantSplicing has been turned off in the config file
MonoallelicExpression has been turned off in the config file
rnaVariantCalling has been turned off in the config file
Structuring dependencies...
Dependencies file generated at: /tmp/tmps9eoibkx
Unlocking working directory.

Note that the major results of the pipeline do successfully return from previous steps of the pipeline (OUTRIDER full results table, Fitted OUTRIDER dataset (ods) object etc) - it seems to get stuck at the Index rule.

Any help would be much appreciated.

Best,

Chris Odhams

2023-03-31T115634.009663.snakemake.log drop_87879.stderr.log drop_87879.stdout.log

[vyepez88]

Hi, can you execute the following? snakemake -n /pgen_int_work/BRS/consultancy/XX/YY/data/transcriptomics/DROP/drop_fpf/htmlOutput/Scripts_AberrantExpression_pipeline_Counting_Datasets.html and then snakemake -n /pgen_int_work/BRS/consultancy/XX/YY/data/transcriptomics/DROP/drop_fpf/htmlOutput/Scripts_AberrantExpression_pipeline_OUTRIDER_Datasets.html what do you obtain?

[chrisodhams]

Hi Vicente,

See the attached file. Seems like things are up to date.

Best, output.txt

[vyepez88]

Hi Christian, Great, now please execute: snakemake -n aberrantExpression

[chrisodhams]

Hi, Attached output again. Best, Chris output.txt

[vyepez88]

and finally: snakemake --cores 1 aberrantExpression

[chrisodhams]

Hi @vyepez88 , See attached - this threw an error - which was also the same after an --unlock attempt. Best, output.txt