MACS2 no output. Fails to read Input

[Jsmith41]

Hi having used MACS to call peaks previously, using the same scripts but with new mapped data the following error keeps happening. Any suggestion as to why the input tags are no longer read? I have tried re-aligning, sorting and indexing the files but this happens each time, but does not happen on the older files.





INFO @ Tue, 29 Mar 2016 10:16:12: #1 read tag files...
INFO @ Tue, 29 Mar 2016 10:16:12: #1 read treatment tags...
INFO @ Tue, 29 Mar 2016 10:16:42: 1000000
INFO @ Tue, 29 Mar 2016 10:16:48: 2000000
INFO @ Tue, 29 Mar 2016 10:16:54: 3000000
INFO @ Tue, 29 Mar 2016 10:16:59: 4000000
INFO @ Tue, 29 Mar 2016 10:17:05: 5000000
INFO @ Tue, 29 Mar 2016 10:17:11: 6000000
INFO @ Tue, 29 Mar 2016 10:17:16: 7000000
INFO @ Tue, 29 Mar 2016 10:17:22: 8000000
INFO @ Tue, 29 Mar 2016 10:17:28: 9000000
INFO @ Tue, 29 Mar 2016 10:17:33: 10000000
INFO @ Tue, 29 Mar 2016 10:17:39: 11000000
INFO @ Tue, 29 Mar 2016 10:17:45: 12000000
INFO @ Tue, 29 Mar 2016 10:17:50: 13000000
INFO @ Tue, 29 Mar 2016 10:17:56: 14000000
INFO @ Tue, 29 Mar 2016 10:18:02: 15000000
INFO @ Tue, 29 Mar 2016 10:18:08: 16000000
INFO @ Tue, 29 Mar 2016 10:18:13: 17000000
INFO @ Tue, 29 Mar 2016 10:18:19: 18000000
INFO @ Tue, 29 Mar 2016 10:18:24: 19000000
INFO @ Tue, 29 Mar 2016 10:18:30: 20000000
INFO @ Tue, 29 Mar 2016 10:18:36: 21000000
INFO @ Tue, 29 Mar 2016 10:18:42: 22000000
INFO @ Tue, 29 Mar 2016 10:18:47: 23000000
INFO @ Tue, 29 Mar 2016 10:18:53: 24000000
INFO @ Tue, 29 Mar 2016 10:18:59: 25000000
INFO @ Tue, 29 Mar 2016 10:19:04: 26000000
INFO @ Tue, 29 Mar 2016 10:19:10: 27000000
INFO @ Tue, 29 Mar 2016 10:19:16: 28000000
INFO @ Tue, 29 Mar 2016 10:19:21: 29000000
INFO @ Tue, 29 Mar 2016 10:19:27: 30000000
INFO @ Tue, 29 Mar 2016 10:19:33: 31000000
INFO @ Tue, 29 Mar 2016 10:19:39: 32000000
INFO @ Tue, 29 Mar 2016 10:19:44: 33000000
INFO @ Tue, 29 Mar 2016 10:19:50: 34000000
INFO @ Tue, 29 Mar 2016 10:19:56: 35000000
INFO @ Tue, 29 Mar 2016 10:20:01: 36000000
INFO @ Tue, 29 Mar 2016 10:20:07: 37000000
INFO @ Tue, 29 Mar 2016 10:20:13: 38000000
INFO @ Tue, 29 Mar 2016 10:20:18: 39000000
INFO @ Tue, 29 Mar 2016 10:20:24: 40000000
INFO @ Tue, 29 Mar 2016 10:20:25: #1.2 read input tags...
INFO @ Tue, 29 Mar 2016 10:21:00: 1000000
i: 0
self.buffer_size: 100000
strand: 0
loc len: 100000
Traceback (most recent call last):
File "/opt/gridware/pkg/el6/apps/macs/2.1.0.20150731/gcc-4.7.3+numpy-1.9.2/bin/macs2", line 4, in <module>
__import__('pkg_resources').run_script('MACS2==2.1.0.20150731', 'macs2')
File "build/bdist.linux-x86_64/egg/pkg_resources/__init__.py", line 723, in run_script
File "build/bdist.linux-x86_64/egg/pkg_resources/__init__.py", line 1643, in run_script
File "/opt/gridware/pkg/el6/apps/macs/2.1.0.20150731/gcc-4.7.3+numpy-1.9.2/python/lib/python2.7/site-packages/MACS2-2.1.0.20150731-py2.7-linux-x86_64.egg/EGG-INFO/scripts/macs2", line 614, in <module>

File "/opt/gridware/pkg/el6/apps/macs/2.1.0.20150731/gcc-4.7.3+numpy-1.9.2/python/lib/python2.7/site-packages/MACS2-2.1.0.20150731-py2.7-linux-x86_64.egg/EGG-INFO/scripts/macs2", line 56, in main

File "build/bdist.linux-x86_64/egg/MACS2/callpeak_cmd.py", line 70, in run
File "build/bdist.linux-x86_64/egg/MACS2/callpeak_cmd.py", line 408, in load_tag_files_options
File "MACS2/IO/Parser.pyx", line 805, in MACS2.IO.Parser.BAMParser.build_fwtrack (MACS2/IO/Parser.c:11368)
File "MACS2/IO/Parser.pyx", line 810, in MACS2.IO.Parser.BAMParser.build_fwtrack (MACS2/IO/Parser.c:11235)
File "MACS2/IO/Parser.pyx", line 884, in MACS2.IO.Parser.BAMParser.__build_fwtrack_wo_pysam (MACS2/IO/Parser.c:12574)
File "MACS2/IO/FixWidthTrack.pyx", line 130, in MACS2.IO.FixWidthTrack.FWTrack.add_loc (MACS2/IO/FixWidthTrack.c:3359)
File "MACS2/IO/FixWidthTrack.pyx", line 157, in MACS2.IO.FixWidthTrack.FWTrack.add_loc (MACS2/IO/FixWidthTrack.c:3234)
Exception: !!

[dariober]

On macs2 callapeak try to set the temporary directory via the --tempdir option. Currently --tmpdir option is available in the code from the source repository on github.

The problem could be that temp files by default are written to /tmp, which is usually not very large so you might be running out of space. I had this problem before but I can't remember what error message I was getting.

[Jsmith41]

Will changing the tempdir work if i am using MACS from a server cluster? I dont have access to change any of the source code.

[dariober]

You don't need to change the source code yourself, rather you download the repository version, install it and run this on the server. This procedure might be something on these lines:

* Download

git clone https://github.com/taoliu/MACS.git

Or download the zip archive from github and put it somewhere on the server, e.g. in a subdirectory in your home directory, and unzip it.

* Install

Go inside the unzipped archive and install. Use the option --user since probably you don't have permission to install for the whole system.

cd MACS ## Or inside unzipped archive

python setup.py install --user

* Execute macs using the newly installed version

/path/to/my/macs2 callpeak --tempdir ...

Where '/path/to/my/' might be somewhere like '~/.local/bin/'. Look at the logs from setup.py install to see where the executable went.