Question: Running MACS locally
0
gravatar for leiah.luoma
3.4 years ago by
Canada
leiah.luoma0 wrote:

Hello,

I have downloaded my ChIP-seq data which I aligned to the human genome using Bowtie for Illumina on Galaxy, and have installed MACS on my computer (4Gb RAM) and gotten it running in CMD/DOS.  Unfortunately my data files appear too large to run locally (25Gb [90 000 000 lines] input control, 30Gb [120 000 000 lines] ChIP). When I run MACS14 it returns:

Traceback (most recent call last):

File "macs14.py", line 366, in ,module.

main()

File "macs14.py", liine 60, in main

(treat, control) = load_tag_files_options (options)

File "macs14.py", line 355, in load_tag_files_options

ttsize = tp.size()

File "C:\Python27\Lib\site-packages\MACS14\Parser.py", line 759, in tsize for x in rage(nc):

MemoryError

Is there any way for me to run this analysis (peak finding) on my computer? I can gain access to a 12Gb RAM computer, I just need to move my data files. Would that work, or do I need to look at running the analysis on a server? I don't have access to a server so I think I am stuck at this point.

Thanks for your help.

Leiah Luoma

macs chip-seq • 888 views
ADD COMMENTlink modified 3.4 years ago by Jennifer Hillman Jackson25k • written 3.4 years ago by leiah.luoma0
0
gravatar for Jennifer Hillman Jackson
3.4 years ago by
United States
Jennifer Hillman Jackson25k wrote:

Hello,

If there is a computer with more resource available, then it seems worth trying that first. It does mean starting over from install. A Cloud Galaxy is another choice. AWS offers grants for research projects.

Best, Jen, Galaxy team

ADD COMMENTlink written 3.4 years ago by Jennifer Hillman Jackson25k
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