FORUMMemory Error – MACS2 bdgdiff
ishtiaqueh asked 2 years ago


I have been trying to run macs2 bdgdiff to assess differential binding between two closely related transcription factors. I keep getting the following error:

-bash-4.2$ macs2 bdgdiff –t1 ZIC2_treat_pileup.bdg –c1 ZIC2_control_lambda.bdg –t2 ZIC3_treat_pileup.bdg –c2 ZIC3_control_lambda.bdg –d1 143285994 –d2 55920284 –o-prefix diff_c1_vs_c2
INFO  @ Fri, 24 Jan 2020 21:23:15: Read and build treatment 1 bedGraph…
INFO  @ Fri, 24 Jan 2020 21:26:44: Read and build control 1 bedGraph…
INFO  @ Fri, 24 Jan 2020 21:30:47: Read and build treatment 2 bedGraph…
INFO  @ Fri, 24 Jan 2020 21:32:13: Read and build control 2 bedGraph…
Traceback (most recent call last):
File “/cvmfs/soft.mugqic/CentOS6/software/MACS2/MACS2-”, line 4, in <module>
__import__(‘pkg_resources’).run_script(‘MACS2==’, ‘macs2’)
File “/cvmfs/soft.mugqic/CentOS6/software/python/Python-2.7.14/lib/python2.7/site-packages/pkg_resources/”, line 666, in run_script
self.require(requires)[0].run_script(script_name, ns)
File “/cvmfs/soft.mugqic/CentOS6/software/python/Python-2.7.14/lib/python2.7/site-packages/pkg_resources/”, line 1469, in run_script
exec(script_code, namespace, namespace)
File “/cvmfs/soft.mugqic/CentOS6/software/MACS2/MACS2-”, line 617, in <module>

File “/cvmfs/soft.mugqic/CentOS6/software/MACS2/MACS2-”, line 93, in main

Any help would be highly appreciated.

Thank you,

1 Answers
flefebvre Staff answered 2 years ago

Hi Ishtiaque, repeating your commands on your files (/home/ishtiaq/scratch/IH/ZIC_ChIP) returns “Disk quota exceeded”.
Please have a look at this page:
It provides a solution to change the group of your files and avoid the problem in the future. I believe you had a similar error before and had help from Hector at C3G.
Also, make sure you are submitting this as a proper job with enough memory and not just on the login node.
Let us know if the issue is not resolved after that. Ideally, you want to provide a complete description of all the steps and output you perform until the error message. The copy- paste above seems to be incomplete.
best regards,

ishtiaqueh replied 2 years ago

Thank you so much for getting back to me. I ran the task as a job script with more memory and that seem to have done the trick!