caleblareau
commented
4 years ago Could you execute the command retaining intermediate files and then the ls -lRh of the directory?
Open AnaAzambuja opened 4 years ago
caleblareau
commented
4 years ago Could you execute the command retaining intermediate files and then the ls -lRh of the directory?
AnaAzambuja
commented
4 years ago Hi Caleb, thank you for your answer.
HEre it is.
Ana
(py27) aa733@ag-mbg-6003742:/data/Ana/ESInduction/D5_r1/hichipper_output_D5_r1$ ls -lRh
.:
total 88G
-rw-rw-r-- 1 aa733 aa733 19G Aug 21 17:28 allpairs.bed.tmp
-rw-rw-r-- 1 aa733 aa733 46G Aug 21 17:11 all.Pairs.tmp
-rw-rw-r-- 1 aa733 aa733 7.8G Aug 21 18:32 allSamples_temporary_control_lambda.bdg
-rw-rw-r-- 1 aa733 aa733 0 Aug 21 18:32 allSamples_temporary_hichipperPeaks.bed_pad.bed.tmp
-rw-rw-r-- 1 aa733 aa733 149M Aug 21 18:32 allSamples_temporary_peaks.narrowPeak
-rw-rw-r-- 1 aa733 aa733 163M Aug 21 18:32 allSamples_temporary_peaks.xls
-rw-rw-r-- 1 aa733 aa733 115M Aug 21 18:32 allSamples_temporary_summits.bed
-rw-rw-r-- 1 aa733 aa733 16G Aug 21 18:32 allSamples_temporary_treat_pileup.bdg
-rw-rw-r-- 1 aa733 aa733 0 Aug 21 18:33 D5_r1_temporary_peaks.merged.bed.tmp
-rw-rw-r-- 1 aa733 aa733 1.5K Aug 21 18:33 hichipper_output_D5_r1.hichipper.log
(py27) aa733@ag-mbg-6003742 :/data/Ana/ESInduction/D5_r1/hichipper_output_D5_r1$
On Mon, Aug 24, 2020 at 4:31 AM Caleb Lareau notifications@github.com wrote:
Could you execute the command retaining intermediate files and then the ls -lRh of the directory?
— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/aryeelab/hichipper/issues/84#issuecomment-678987509, or unsubscribe https://github.com/notifications/unsubscribe-auth/AMK23KXZIXLQZSYQWOYJFYLSCIQN3ANCNFSM4QGRTYQA .
Ana P. Azambuja
Postdoctoral Associate Simoes-Costa Lab Molecular Biology and Genetics - Cornell University
maharshi14
commented
3 years ago Has this bug been traced yet? Thanks!
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.