ERROR: macs2 peak calling was not successful

[aperreault]

Hello! I'm trying to test hichipper in my programming environment by running the following lines from the /tests/README.md:

hichipper call --out outputCallBAM --restriction-frags ../RestrictionFragmentFiles/hg19_MboI_resfrag.bed.gz --peaks chipseq/GM12878_SMC3_ChIPSeq_chr22.narrowPeak --skip-resfrag-pad --basic-qc --skip-diffloop --input-bam call_inputs/HiCUP_chr22.bam

hichipper --out combinedall --skip-diffloop yaml/example_COMBINED_ALL.yaml hichipper --out combinedself --skip-diffloop yaml/example_COMBINED_SELF.yaml

First error: [u'outputCallvi/userSuppliedPeaks.bed.tmp_pad.bed.tmp'] Not fully supported yet! What does this mean and what can I do to fix it?

Second error (applies to both the combined lines): AttributeError: 'Namespace' object has no attribute 'maxgap' ERROR: macs2 peak calling was not successful; make sure macs2 is in the environment and that *Pairs files exist for samples. Finally, note that only the narrowPeak file is being considered here, which may be a problem if you tried to do broad peak calling. MACS2 is in my PATH so I'm not sure how to fix this one either.

I appreciate any help I can get! -Andrea

[caleblareau]

Hi Andrea,

call mode is still under development and not fully supported. I’m hoping to finish it soon!

On Jul 2, 2018, at 6:30 PM, Andrea notifications@github.com wrote:

Hello! I'm trying to test hichipper in my programming environment by running the following lines from the /tests/README.md:

hichipper call --out outputCallBAM --restriction-frags ../RestrictionFragmentFiles/hg19_MboI_resfrag.bed.gz --peaks chipseq/GM12878_SMC3_ChIPSeq_chr22.narrowPeak --skip-resfrag-pad --basic-qc --skip-diffloop --input-bam call_inputs/HiCUP_chr22.bam

hichipper --out combinedall --skip-diffloop yaml/example_COMBINED_ALL.yaml hichipper --out combinedself --skip-diffloop yaml/example_COMBINED_SELF.yaml

First error: [u'outputCallvi/userSuppliedPeaks.bed.tmp_pad.bed.tmp'] Not fully supported yet! What does this mean and what can I do to fix it?

Second error (applies to both the combined lines): AttributeError: 'Namespace' object has no attribute 'maxgap' ERROR: macs2 peak calling was not successful; make sure macs2 is in the environment and that *Pairs files exist for samples. Finally, note that only the narrowPeak file is being considered here, which may be a problem if you tried to do broad peak calling. MACS2 is in my PATH so I'm not sure how to fix this one either.

I appreciate any help I can get! -Andrea

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[aperreault]

Thanks for the quick response Caleb! Any insights to the second error message I was getting?

[caleblareau]

Yes, sorry overlooked that second half…

Can you run hichipper keeping temporary files and then send me an ls -lrth? The error message is fairly generic but that should help quite a bit.

On Jul 2, 2018, at 6:36 PM, Andrea notifications@github.com wrote:

Thanks for the quick response Caleb! Any insights to the second error message I was getting?

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[aperreault]

bryan@venters-server:~/hichipper-master/tests $ hichipper --out combinedall --keep-temp-files --skip-diffloop yaml/example_COMBINED_ALL.yaml Mon Jul 02 17:42:44 CDT 2018: Starting hichipper pipeline v0.7.3 Mon Jul 02 17:42:44 CDT 2018: Parsing user parameters Mon Jul 02 17:42:44 CDT 2018: .yaml file detected Traceback (most recent call last): File "/home/bryan/anaconda2/bin/macs2", line 617, in main() File "/home/bryan/anaconda2/bin/macs2", line 57, in main run( args ) File "/home/bryan/anaconda2/lib/python2.7/site-packages/MACS2-2.1.2.dev0-py2.7-linux-x86_64.egg/MACS2/callpeak_cmd.py", line 56, in run options = opt_validate( args ) File "/home/bryan/anaconda2/lib/python2.7/site-packages/MACS2-2.1.2.dev0-py2.7-linux-x86_64.egg/MACS2/OptValidator.py", line 193, in opt_validate options.argtxt += "# max. gap between significant sites = %d\n" % options.maxgap AttributeError: 'Namespace' object has no attribute 'maxgap' ERROR: macs2 peak calling was not successful; make sure macs2 is in the environment and that *Pairs files exist for samples. Finally, note that only the narrowPeak file is being considered here, which may be a problem if you tried to do broad peak calling.

bryan@venters-server:~/hichipper-master/tests $ ls -lrth total 64K -rw-rw-r-- 1 bryan bryan 1.1K Jun 9 20:16 verifyHCP.py -rw-rw-r-- 1 bryan bryan 652 Jun 9 20:16 test_cli.py drwxrwxr-x 2 bryan bryan 4.0K Jun 9 20:16 resfrag -rw-rw-r-- 1 bryan bryan 1.3K Jun 9 20:16 README.md -rw-rw-r-- 1 bryan bryan 1 Jun 9 20:16 init.py drwxrwxr-x 4 bryan bryan 4.0K Jun 9 20:16 hicpro_one drwxrwxr-x 4 bryan bryan 4.0K Jun 9 20:16 hicpro drwxrwxr-x 2 bryan bryan 4.0K Jun 9 20:16 correct_output drwxrwxr-x 2 bryan bryan 4.0K Jun 9 20:16 chipseq drwxrwxr-x 2 bryan bryan 4.0K Jun 9 20:16 call_inputs drwxrwxr-x 2 bryan bryan 4.0K Jul 2 17:02 output1 drwxrwxr-x 2 bryan bryan 4.0K Jul 2 17:08 yaml drwxrwxr-x 2 bryan bryan 4.0K Jul 2 17:09 output1.1 drwxrwxr-x 2 bryan bryan 4.0K Jul 2 17:11 outputCallBAM drwxrwxr-x 2 bryan bryan 4.0K Jul 2 17:12 outputCallvi drwxrwxr-x 2 bryan bryan 4.0K Jul 2 17:42 combinedall

[aperreault]

Caleb,

Wanted to check back in to see if you had any insights to the MACS2 error I described above.

Thanks! -Andrea

[caleblareau]

Sorry this got away from me... I actually need to see the files output directory (hard to know which one this is from this list?)

[aperreault]

Quite alright! I've been working on some other files, so here's a recap on commands and errors: $ time hichipper --out output5 yaml/Mumbach_eachAll.yaml Traceback (most recent call last): File "/home/bryan/anaconda2/bin/macs2", line 617, in main() File "/home/bryan/anaconda2/bin/macs2", line 57, in main run( args ) File "/home/bryan/anaconda2/lib/python2.7/site-packages/MACS2-2.1.2.dev0-py2.7-linux-x86_64.egg/MACS2/callpeak_cmd.py", line 56, in run options = opt_validate( args ) File "/home/bryan/anaconda2/lib/python2.7/site-packages/MACS2-2.1.2.dev0-py2.7-linux-x86_64.egg/MACS2/OptValidator.py", line 193, in opt_validate options.argtxt += "# max. gap between significant sites = %d\n" % options.maxgap AttributeError: 'Namespace' object has no attribute 'maxgap' ERROR: macs2 peak calling was not successful; make sure macs2 is in the environment and that *Pairs files exist for samples. Finally, note that only the narrowPeak file is being considered here, which may be a problem if you tried to do broad peak calling.

Here's the directory info: bryan@venters-server:/media/bryan/2Tb_Workspace/AP/HiChIP/hichipper/Mumbach-hichipper $ ls -lrth total 16K drwxrwxr-x 4 bryan bryan 4.0K Oct 3 09:43 hicpro drwxrwxr-x 2 bryan bryan 4.0K Oct 3 09:50 yaml drwxrwxr-x 2 bryan bryan 4.0K Oct 3 10:28 output5 drwxrwxr-x 6 bryan bryan 4.0K Oct 3 10:42 z-archive

bryan@venters-server:/media/bryan/2Tb_Workspace/AP/HiChIP/hichipper/Mumbach-hichipper $ cd output5/

bryan@venters-server:/media/bryan/2Tb_Workspace/AP/HiChIP/hichipper/Mumbach-hichipper/output5 $ ls -lrth total 8.5G -rw-rw-r-- 1 bryan bryan 5.7G Oct 3 10:28 Rep2.all.Pairs.tmp -rw-rw-r-- 1 bryan bryan 2.9G Oct 3 10:29 Rep2.all.Pairs.bed.tmp -rw-rw-r-- 1 bryan bryan 1019 Oct 3 10:29 output5.hichipper.log

Let me know if you need any other info! -Andrea

[caleblareau]

As far as I can tell, everything in hichipper is working just fine. I’d recommend upgrading macs2?

On Oct 3, 2018, at 11:48 AM, Andrea notifications@github.com wrote:

Quite alright! I've been working on some other files, so here's a recap on commands and errors: $ time hichipper --out output5 yaml/Mumbach_eachAll.yaml Traceback (most recent call last): File "/home/bryan/anaconda2/bin/macs2", line 617, in main() File "/home/bryan/anaconda2/bin/macs2", line 57, in main run( args ) File "/home/bryan/anaconda2/lib/python2.7/site-packages/MACS2-2.1.2.dev0-py2.7-linux-x86_64.egg/MACS2/callpeak_cmd.py", line 56, in run options = opt_validate( args ) File "/home/bryan/anaconda2/lib/python2.7/site-packages/MACS2-2.1.2.dev0-py2.7-linux-x86_64.egg/MACS2/OptValidator.py", line 193, in opt_validate options.argtxt += "# max. gap between significant sites = %d\n" % options.maxgap AttributeError: 'Namespace' object has no attribute 'maxgap' ERROR: macs2 peak calling was not successful; make sure macs2 is in the environment and that *Pairs files exist for samples. Finally, note that only the narrowPeak file is being considered here, which may be a problem if you tried to do broad peak calling.

Here's the directory info: bryan@venters-server:/media/bryan/2Tb_Workspace/AP/HiChIP/hichipper/Mumbach-hichipper $ ls -lrth total 16K drwxrwxr-x 4 bryan bryan 4.0K Oct 3 09:43 hicpro drwxrwxr-x 2 bryan bryan 4.0K Oct 3 09:50 yaml drwxrwxr-x 2 bryan bryan 4.0K Oct 3 10:28 output5 drwxrwxr-x 6 bryan bryan 4.0K Oct 3 10:42 z-archive

bryan@venters-server:/media/bryan/2Tb_Workspace/AP/HiChIP/hichipper/Mumbach-hichipper $ cd output5/

bryan@venters-server:/media/bryan/2Tb_Workspace/AP/HiChIP/hichipper/Mumbach-hichipper/output5 $ ls -lrth total 8.5G -rw-rw-r-- 1 bryan bryan 5.7G Oct 3 10:28 Rep2.all.Pairs.tmp -rw-rw-r-- 1 bryan bryan 2.9G Oct 3 10:29 Rep2.all.Pairs.bed.tmp -rw-rw-r-- 1 bryan bryan 1019 Oct 3 10:29 output5.hichipper.log

Let me know if you need any other info! -Andrea

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[aperreault]

Interesting. Which version of macs should I be running for hichipper? I'm currently running macs2 2.1.2_dev

[aperreault]

Caleb,

Another question for you- I tried rerunning the test files. Below is the command I used and the errors I got.

$ hichipper --out output1 yaml/one.yaml Wed Oct 10 10:07:31 CDT 2018: Starting hichipper pipeline v0.7.3 Wed Oct 10 10:07:31 CDT 2018: Parsing user parameters Wed Oct 10 10:07:31 CDT 2018: .yaml file detected Error: package ‘GenomeInfoDb’ could not be loaded Execution halted Wed Oct 10 10:07:32 CDT 2018: Processing d1 Wed Oct 10 10:07:32 CDT 2018: Total_PETs=164332898 Wed Oct 10 10:07:32 CDT 2018: Mapped_unique_quality_pairs=1888170 Wed Oct 10 10:07:32 CDT 2018: Mapped_unique_quality_valid_pairs=627403 Wed Oct 10 10:07:32 CDT 2018: Intersecting PETs with anchors Error: The requested file (output1/userSuppliedPeaks.bed.tmp_pad.bed.tmprf.tmp) could not be opened. Error message: (No such file or directory). Exiting! /home/bryan/anaconda2/lib/python2.7/site-packages/hichipper/interactionsCall.sh: line 36: --keep-temp-files: command not found Wed Oct 10 10:07:32 CDT 2018: 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

Any insights into what's going wrong? Thanks, -Andrea

[caleblareau]

Hmmm, looks like you are missing an R package in your system?

https://bioconductor.org/packages/release/bioc/html/GenomeInfoDb.html

On Oct 10, 2018, at 11:18 AM, Andrea notifications@github.com wrote:

Caleb,

Another question for you- I tried rerunning the test files. Below is the command I used and the errors I got.

$ hichipper --out output1 yaml/one.yaml Wed Oct 10 10:07:31 CDT 2018: Starting hichipper pipeline v0.7.3 Wed Oct 10 10:07:31 CDT 2018: Parsing user parameters Wed Oct 10 10:07:31 CDT 2018: .yaml file detected Error: package ‘GenomeInfoDb’ could not be loaded Execution halted Wed Oct 10 10:07:32 CDT 2018: Processing d1 Wed Oct 10 10:07:32 CDT 2018: Total_PETs=164332898 Wed Oct 10 10:07:32 CDT 2018: Mapped_unique_quality_pairs=1888170 Wed Oct 10 10:07:32 CDT 2018: Mapped_unique_quality_valid_pairs=627403 Wed Oct 10 10:07:32 CDT 2018: Intersecting PETs with anchors Error: The requested file (output1/userSuppliedPeaks.bed.tmp_pad.bed.tmprf.tmp) could not be opened. Error message: (No such file or directory). Exiting! /home/bryan/anaconda2/lib/python2.7/site-packages/hichipper/interactionsCall.sh: line 36: --keep-temp-files: command not found Wed Oct 10 10:07:32 CDT 2018: 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

Any insights into what's going wrong? Thanks, -Andrea

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[aperreault]

Okay, that's installed (I've never gotten that error when running the program)

Really what I think the issue is is the location of macs2. One error line says there's an error in bin/macs2 and the following line says there's an error in lib/python2.7/site-packages/MACS2. Do you know if the location of macs2 matters to hichipper? If so, how would I redirect the script to either of these locations?