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databio / bedboss

Python pipeline for processing BED files for BEDbase
https://docs.bedbase.org
BSD 2-Clause "Simplified" License
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R 'caught an error!' message #13

Closed nsheff closed 7 months ago

nsheff commented 1 year ago

I'm seeing this in a bedboss run.

Caught an error!
<simpleError in getReferenceData(refAssembly, tagline = "TSS_"): TSS_hg38 not available in GenomicDistributions and GenomicDistributionsData packages>
[1] "Plotting: /home/nsheff/garage/bedbase_tutorial/out2023/output/bedstat_output/78c0e4753d04b238fc07e4ebe5a02984/GSE105587_ENCFF018NNF_conservative_idr_thresholded_peaks_GRCh38_chrombins"
Caught an error!
<simpleError in getReferenceData(refAssembly, tagline = "chromSizes_"): chromSizes_hg38 not available in GenomicDistributions and GenomicDistributionsData packages>

The pipeline then completes successfully... so, not sure what this means.

khoroshevskyi commented 1 year ago

This is R script error, it couldn't generate one plot, so it skipped it. (It's my assumption)

khoroshevskyi commented 11 months ago

Error messages were improved in bedboss version: 0.1.0a6