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aryeelab / hichipper

A preprocessing and QC pipeline for HiChIP data
MIT License
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Issue with MACS Output #75

Open jlpulice opened 5 years ago

jlpulice commented 5 years ago

Hi!

I am getting this issue when running hichipper:

Tue Aug 13 15:22:36 EDT 2019: .yaml file detected Tue Aug 13 15:39:59 EDT 2019: Performing hichipper-modified background peak calling Tue Aug 13 15:40:56 EDT 2019: Modified background signal; performing peak calling Tue Aug 13 15:40:56 EDT 2019: MACS2 TEXT OUTPUT INCOMING INFO @ Tue, 13 Aug 2019 15:40:56: Read and build treatment bedGraph... Traceback (most recent call last): File "/n/data1/dfci/medonc/meyerson/jpulice/software/HiC-Pro/dependencies/pythonlib/bin/macs2", line 614, in main() File "/n/data1/dfci/medonc/meyerson/jpulice/software/HiC-Pro/dependencies/pythonlib/bin/macs2", line 72, in main run( args ) File "/n/data1/dfci/medonc/meyerson/jpulice/software/HiC-Pro/dependencies/pythonlib/lib/python2.7/site-packages/MACS2/bdgcmp_cmd.py", line 40, in run tbtrack = tbio.build_bdgtrack() File "MACS2/IO/BedGraphIO.pyx", line 97, in MACS2.IO.BedGraphIO.bedGraphIO.build_bdgtrack (MACS2/IO/BedGraphIO.c:1079) IOError: [Errno 2] No such file or directory: 'hichipper_081319_test/adjustedTreatment.bdg.tmp' INFO @ Tue, 13 Aug 2019 15:40:57: Read and build bedGraph... Traceback (most recent call last): File "/n/data1/dfci/medonc/meyerson/jpulice/software/HiC-Pro/dependencies/pythonlib/bin/macs2", line 614, in main() File "/n/data1/dfci/medonc/meyerson/jpulice/software/HiC-Pro/dependencies/pythonlib/bin/macs2", line 64, in main run( args ) File "/n/data1/dfci/medonc/meyerson/jpulice/software/HiC-Pro/dependencies/pythonlib/lib/python2.7/site-packages/MACS2/bdgpeakcall_cmd.py", line 51, in run btrack = bio.build_bdgtrack(baseline_value=0) File "MACS2/IO/BedGraphIO.pyx", line 97, in MACS2.IO.BedGraphIO.bedGraphIO.build_bdgtrack (MACS2/IO/BedGraphIO.c:1079) IOError: [Errno 2] No such file or directory: 'hichipper_081319_test/hichipper_qvalue.bdg.tmp' mv: cannot stat ‘hichipper_081319_test/hichipper_peaks.bed’: No such file or directory

I have tabix and bgzip in the path and as far as I can tell I have all the R and python packages installed. Please suggest additional remedies! I am getting all the peak calls for each file as well as the bdg outputs for treatment and control, but that is it. Thanks!!

caleblareau commented 5 years ago

Can you send your execution command + the ls -lR of the execution directory?

On Aug 13, 2019, at 4:35 PM, jlpulice notifications@github.com wrote:

Hi!

I am getting this issue when running hichipper:

Tue Aug 13 15:22:36 EDT 2019: .yaml file detected Tue Aug 13 15:39:59 EDT 2019: Performing hichipper-modified background peak calling Tue Aug 13 15:40:56 EDT 2019: Modified background signal; performing peak calling Tue Aug 13 15:40:56 EDT 2019: MACS2 TEXT OUTPUT INCOMING INFO @ Tue, 13 Aug 2019 15:40:56: Read and build treatment bedGraph... Traceback (most recent call last): File "/n/data1/dfci/medonc/meyerson/jpulice/software/HiC-Pro/dependencies/pythonlib/bin/macs2", line 614, in main() File "/n/data1/dfci/medonc/meyerson/jpulice/software/HiC-Pro/dependencies/pythonlib/bin/macs2", line 72, in main run( args ) File "/n/data1/dfci/medonc/meyerson/jpulice/software/HiC-Pro/dependencies/pythonlib/lib/python2.7/site-packages/MACS2/bdgcmp_cmd.py", line 40, in run tbtrack = tbio.build_bdgtrack() File "MACS2/IO/BedGraphIO.pyx", line 97, in MACS2.IO.BedGraphIO.bedGraphIO.build_bdgtrack (MACS2/IO/BedGraphIO.c:1079) IOError: [Errno 2] No such file or directory: 'hichipper_081319_test/adjustedTreatment.bdg.tmp' INFO @ Tue, 13 Aug 2019 15:40:57: Read and build bedGraph... Traceback (most recent call last): File "/n/data1/dfci/medonc/meyerson/jpulice/software/HiC-Pro/dependencies/pythonlib/bin/macs2", line 614, in main() File "/n/data1/dfci/medonc/meyerson/jpulice/software/HiC-Pro/dependencies/pythonlib/bin/macs2", line 64, in main run( args ) File "/n/data1/dfci/medonc/meyerson/jpulice/software/HiC-Pro/dependencies/pythonlib/lib/python2.7/site-packages/MACS2/bdgpeakcall_cmd.py", line 51, in run btrack = bio.build_bdgtrack(baseline_value=0) File "MACS2/IO/BedGraphIO.pyx", line 97, in MACS2.IO.BedGraphIO.bedGraphIO.build_bdgtrack (MACS2/IO/BedGraphIO.c:1079) IOError: [Errno 2] No such file or directory: 'hichipper_081319_test/hichipper_qvalue.bdg.tmp' mv: cannot stat ‘hichipper_081319_test/hichipper_peaks.bed’: No such file or directory

I have tabix and bgzip in the path and as far as I can tell I have all the R and python packages installed. Please suggest additional remedies! I am getting all the peak calls for each file as well as the bdg outputs for treatment and control, but that is it. Thanks!!

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jlpulice commented 5 years ago

I'm running this with hichipper --out hichipper_081319_test all.yaml

For every HiC-Pro it's generating these seven files: -rw-rw-r-- 1 jlp52 jlp52 4028159097 Aug 11 20:10 AGS.all.Pairs.bed.tmp -rw-rw-r-- 1 jlp52 jlp52 11036152258 Aug 11 20:06 AGS.all.Pairs.tmp -rw-rw-r-- 1 jlp52 jlp52 2574487508 Aug 11 20:29 AGS_temporary_control_lambda.bdg -rw-rw-r-- 1 jlp52 jlp52 23770936 Aug 11 20:29 AGS_temporary_peaks.narrowPeak -rw-rw-r-- 1 jlp52 jlp52 26002529 Aug 11 20:29 AGS_temporary_peaks.xls -rw-rw-r-- 1 jlp52 jlp52 18006622 Aug 11 20:29 AGS_temporary_summits.bed -rw-rw-r-- 1 jlp52 jlp52 4178289458 Aug 11 20:29 AGS_temporary_treat_pileup.bdg There's ~50 files so I won't send all of these but an example. Only these and the logs are generating. It seems it's stopping for each file before it generates the AGS_temporary_hichipperPeaks.bed file.

caleblareau commented 5 years ago

What are the contents of all.yaml?

On Aug 13, 2019, at 7:36 PM, jlpulice notifications@github.com wrote:

I'm running this with hichipper --out hichipper_081319_test all.yaml

For every HiC-Pro it's generating these seven files: -rw-rw-r-- 1 jlp52 jlp52 4028159097 Aug 11 20:10 AGS.all.Pairs.bed.tmp -rw-rw-r-- 1 jlp52 jlp52 11036152258 Aug 11 20:06 AGS.all.Pairs.tmp -rw-rw-r-- 1 jlp52 jlp52 2574487508 Aug 11 20:29 AGS_temporary_control_lambda.bdg -rw-rw-r-- 1 jlp52 jlp52 23770936 Aug 11 20:29 AGS_temporary_peaks.narrowPeak -rw-rw-r-- 1 jlp52 jlp52 26002529 Aug 11 20:29 AGS_temporary_peaks.xls -rw-rw-r-- 1 jlp52 jlp52 18006622 Aug 11 20:29 AGS_temporary_summits.bed -rw-rw-r-- 1 jlp52 jlp52 4178289458 Aug 11 20:29 AGS_temporary_treat_pileup.bdg There's ~50 files so I won't send all of these but an example. Only these and the logs are generating. It seems it's stopping for each file before it generates the AGS_temporary_hichipperPeaks.bed file.

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jlpulice commented 5 years ago

all.yaml content: peaks:

The HiC-Pro directory has all the required files in it.

caleblareau commented 5 years ago

is hg19_MboI_resfrag.bed in your directory from execution? The process is failing when trying to compute the new hichipper-adjusted peaks.

caleblareau commented 5 years ago

if not, try maybe specifying it as an absolute file path?

jlpulice commented 5 years ago

It's in the root directory of both hicpro_runall_080519 as well as where the output hichipper_081319_test will go. I can change that to an absolute file path and see if that works!

jlpulice commented 5 years ago

Rerunning with it specified as an absolute path didn't work. Still getting the same error. Any recommendations to check?

emilyklo commented 4 years ago

Do you have htslib installed? I was having the same issue but installing htslib seemed to do the trick.

shanwai1234 commented 4 years ago

I also have the same error reported, has this issue been resolved?