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aryeelab / hichipper

A preprocessing and QC pipeline for HiChIP data
MIT License
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Data test exception #39

Open tiagochst opened 6 years ago

tiagochst commented 6 years ago

I'm trying to run the example data test. But I got the following problem.

screen shot 2018-05-14 at 10 30 37 pm

Which would be the problem ? Thanks in advance!

caleblareau commented 6 years ago

everything looks fine from my end

hichipper --out output1 yaml/one.yaml
Mon May 14 23:30:04 EDT 2018: Starting hichipper pipeline v0.7.2
Mon May 14 23:30:04 EDT 2018: Parsing user parameters
Mon May 14 23:30:04 EDT 2018: .yaml file detected
Anchors removed due to excessive size (likely at ends of chromosomes): 0 
Mon May 14 23:30:07 EDT 2018: Processing d1
Mon May 14 23:30:07 EDT 2018: Total_PETs=164332898
Mon May 14 23:30:10 EDT 2018: Mapped_unique_quality_pairs=1888170
Mon May 14 23:30:10 EDT 2018: Mapped_unique_quality_valid_pairs=627403
Mon May 14 23:30:10 EDT 2018: Intersecting PETs with anchors
Mon May 14 23:30:10 EDT 2018: Finished the anchor merging.

Can you verify that the files specified in the yaml file are actually there?

tiagochst commented 6 years ago

I found the problem, the variable script_dir was pointing to /usr/local/bin/Rscript, but my Rscript was in /usr/bin/Rscript.

screen shot 2018-05-15 at 8 38 57 am
caleblareau commented 6 years ago

Out of curiosity, what did you wind up doing to fix this?