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aryeelab / hichipper

A preprocessing and QC pipeline for HiChIP data
MIT License
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Error determining peaks for anchor inference #89

Open AnaAzambuja opened 3 years ago

AnaAzambuja commented 3 years ago

Hi, I am trying to run hichipper in python 2.7 and I getting the error bellow. All R dependencies were re-installed. Any idea of what might be happening? Thanks, Ana

Error: The requested file (hichipper_output_ES_r1/allSamples_temporary_hichipperPeaks.bed_pad.bed.tmprf.tmp) could not be opened. Error message: (No such file or directory). Exiting! Wed Feb 3 10:02:36 EST 2021: Finished the anchor merging. /home/aa733/miniconda3/envs/py27/lib/python2.7/site-packages/hichipper/interactionsCall.sh: line 43: --keep-temp-files: command not found Wed Feb 3 10:02:36 EST 2021: 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

log file: Wed Feb 03 09:44:39 EST 2021: Starting hichipper pipeline v0.7.7 Wed Feb 03 09:44:39 EST 2021: Executed from: /data/Ana/ESInduction/ES_r1 Wed Feb 03 09:44:39 EST 2021: Output folder: /data/Ana/ESInduction/ES_r1/hichipper_output_ES_r1 Wed Feb 03 09:44:39 EST 2021: Parsed manifest as follows: {'peaks': ['COMBINED,ALL'], 'hicpro_output': ['hicpro_output_ES_r1'], 'resfrags': ['hg38_MboI_resfrag.bed']} Wed Feb 03 09:44:39 EST 2021: Determined that the following samples are good to go: ['ES_r1'] Wed Feb 03 09:44:39 EST 2021: User defined peaks specification: COMBINED,ALL Wed Feb 03 09:44:39 EST 2021: Calling one set of peaks from all HiChIP reads across all samples. Wed Feb 03 09:46:53 EST 2021: macs2 command: macs2 callpeak -t hichipper_output_ES_r1/allpairs.bed.tmp --keep-dup all -q 0.01 --extsize 147 --nomodel -g hs -B -f BED --verbose 0 -n hichipper_output_ES_r1/allSamples_temporary Wed Feb 03 10:02:19 EST 2021: Performing restriction fragment-aware padding Wed Feb 3 10:02:33 EST 2021: Processing ES_r1 Wed Feb 3 10:02:33 EST 2021: Total_PETs=49785694 Wed Feb 3 10:02:35 EST 2021: Mapped_unique_quality_pairs=50891511 Wed Feb 3 10:02:36 EST 2021: Mapped_unique_quality_valid_pairs=19658981 Wed Feb 3 10:02:36 EST 2021: Intersecting PETs with anchors Wed Feb 3 10:02:36 EST 2021: Finished the anchor merging. Wed Feb 3 10:02:36 EST 2021: Something went wrong in determining peaks for anchor inference; rerun with the flag to debug.

maharshi14 commented 3 years ago

I'm having the same problem! Any help would be greatly appreciated.

Gemma-Zhang-326 commented 3 years ago

same error looking forward help!