Issue with MACS Output

[jlpulice]

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]

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

…

On Aug 13, 2019, at 4:35 PM, jlpulice ***@***.***> 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!! — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#75?email_source=notifications&email_token=AD32FYIAIMNUGEW4N3DG3F3QEMLHNA5CNFSM4ILORE42YY3PNVWWK3TUL52HS4DFUVEXG43VMWVGG33NNVSW45C7NFSM4HFBUXJA>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AD32FYIFEQWFK7OAYW4EFZ3QEMLHNANCNFSM4ILORE4Q>.

[jlpulice]

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]

What are the contents of all.yaml?

…

On Aug 13, 2019, at 7:36 PM, jlpulice ***@***.***> 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. — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#75?email_source=notifications&email_token=AD32FYJ2AEN3G2X6S2GPBCDQENAQVA5CNFSM4ILORE42YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD4HJACI#issuecomment-521048073>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AD32FYKQ3NIHWBYFGCTJWGLQENAQVANCNFSM4ILORE4Q>.

[jlpulice]

all.yaml content:
peaks:

• EACH,ALL
  resfrags:
• hg19_MboI_resfrag.bed
  hicpro_output:
• hicpro_runall_080519

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

[caleblareau]

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

[caleblareau]

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

[jlpulice]

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]

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

[emilyklo]

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

[shanwai1234]

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