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aryeelab / hichipper

A preprocessing and QC pipeline for HiChIP data
MIT License
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Something went wrong in determining peaks for anchor inference #88

Open woshiyangsi opened 4 years ago

woshiyangsi commented 4 years ago

(py2.7) [YANGSIYU@fat01 tests]$ hichipper --out output yaml/one.yaml Sat Oct 17 12:47:04 CST 2020: Starting hichipper pipeline v0.7.7 Sat Oct 17 12:47:05 CST 2020: Parsing user parameters /home/YANGSIYU/miniconda3/envs/py2.7/lib/python2.7/site-packages/hichipper/hichipperHelp.py:98: YAMLLoadWarning: calling yaml.load() without Loader=... is deprecated, as the default Loader is unsafe. Please read https://msg.pyyaml.org/load for full details. m = yaml.load(f) Sat Oct 17 12:47:05 CST 2020: .yaml file detected Error in library(GenomicRanges) : there is no package called ‘GenomicRanges’ Calls: suppressMessages -> withCallingHandlers Execution halted Sat Oct 17 12:47:07 CST 2020: Processing d1 Sat Oct 17 12:47:07 CST 2020: Total_PETs=164332898 Sat Oct 17 12:47:08 CST 2020: Mapped_unique_quality_pairs=1888170 Sat Oct 17 12:47:08 CST 2020: Mapped_unique_quality_valid_pairs=627403 Sat Oct 17 12:47:08 CST 2020: Intersecting PETs with anchors Error: The requested file (output/userSuppliedPeaks.bed.tmp_pad.bed.tmprf.tmp) could not be opened. Error message: (No such file or directory). Exiting! Sat Oct 17 12:47:08 CST 2020: Finished the anchor merging. /home/YANGSIYU/miniconda3/envs/py2.7/lib/python2.7/site-packages/hichipper/interactionsCall.sh: line 43: --keep-temp-files: command not found Sat Oct 17 12:47:08 CST 2020: Something went wrong in determining peaks for anchor inference; rerun with the flag to debug. ERROR: something failed at the individual sample level; check the .log file for more info

I used the test data but i got the error. looking forward your reply.

Thanks Siyu.