8000 Error determining peaks for anchor inference · Issue #84 · aryeelab/hichipper · GitHub
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Error determining peaks for anchor inference #84

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AnaAzambuja opened this issue Aug 20, 2020 · 3 comments
8000 Open

Error determining peaks for anchor inference #84

AnaAzambuja opened this issue Aug 20, 2020 · 3 comments

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@AnaAzambuja
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Hi,
Running hichipper I got the following error:

Error: The requested file (hichipper_output_D3_r1/allSamples_temporary_hichipperPeaks.bed_pad.bed.tmprf.tmp) could not be opened. Error message: (No such file or directory). Exiting!

Any idea of what i can do to fix it?
Thanks,
Ana

Here is my log file:
Thu Aug 20 12:12:44 EDT 2020: Starting hichipper pipeline v0.7.7
Thu Aug 20 12:12:44 EDT 2020: Executed from: /data/Ana/ESInduction/D3_r1
Thu Aug 20 12:12:44 EDT 2020: Output folder: /data/Ana/ESInduction/D3_r1/hichipper_output_D3_r1
Thu Aug 20 12:12:44 EDT 2020: Parsed manifest as follows:
{'peaks': ['COMBINED,ALL'], 'hicpro_output': ['hicpro_output_D3_r1'], 'resfrags': ['hg38_MboI_resfrag.bed']}
Thu Aug 20 12:12:44 EDT 2020: Determined that the following samples are good to go:
['D3_r1']
Thu Aug 20 12:12:44 EDT 2020: User defined peaks specification: COMBINED,ALL
Thu Aug 20 12:12:44 EDT 2020: Calling one set of peaks from all HiChIP reads across all samples.
Thu Aug 20 12:31:38 EDT 2020: macs2 command: macs2 callpeak -t hichipper_output_D3_r1/allpairs.bed.tmp --keep-dup all -q 0.01 --extsize 147 --nomodel -g hs -B -f BED --verbose 0 -n hichipper_output_D3_r1/allSamples_temporary
Thu Aug 20 13:40:29 EDT 2020: Performing restriction fragment-aware padding
Thu Aug 20 13:40:30 EDT 2020: Processing D3_r1
Thu Aug 20 13:40:30 EDT 2020: Total_PETs=439212396
Thu Aug 20 13:41:02 EDT 2020: Mapped_unique_quality_pairs=456525244
Thu Aug 20 13:41:09 EDT 2020: Mapped_unique_quality_valid_pairs=164196962
Thu Aug 20 13:41:09 EDT 2020: Intersecting PETs with anchors
Thu Aug 20 13:41:09 EDT 2020: Finished the anchor merging.
Thu Aug 20 13:41:09 EDT 2020: Something went wrong in determining peaks for anchor inference; rerun with the flag to debug.
@caleblareau
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Could you execute the command retaining intermediate files and then the ls -lRh of the directory?

@AnaAzambuja
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AnaAzambuja commented Aug 24, 2020 via email

@maharshi14
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Has this bug been traced yet? Thanks!

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@caleblareau @maharshi14 @AnaAzambuja
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