MACS2 fails to create *_treat_pvalue.bdg

[Artur Jaroszewicz]

Hi all,

Thanks in advance for any help. I'm currently using MACS2 and trying to generate p-value tracks for some ChIP seq data as compared to input data. I am running the command

macs2 callpeak -t H3K79me2_0min.unique.bedgraph -c Input.unique.bedgraph -f BED -n H3K79me2_0min -g 1.87e9 -p 1e-2 -B --nomodel --extsize 200

and it creates the following files:

-rw-r--r-- 1 arturj eeskin 3078594574 Jan 19 03:29 H3K79me2_0min_control_lambda.bdg
-rw-r--r-- 1 arturj eeskin 133197 Jan 19 03:29 H3K79me2_0min_peaks.narrowPeak
-rw-r--r-- 1 arturj eeskin 149351 Jan 19 03:29 H3K79me2_0min_peaks.xls
-rw-r--r-- 1 arturj eeskin 85919 Jan 19 03:29 H3K79me2_0min_summits.bed
-rw-r--r-- 1 arturj eeskin 2121745129 Jan 19 03:29 H3K79me2_0min_treat_pileup.bdg
-rw-r--r-- 1 arturj eeskin 1250893738 Jan 18 23:20 H3K79me2_0min.unique.bedgraph

but not H3K79me2_0min_treat_pvalue.bdg or H3K79me2_0min_treat_qvalue.bdg.

Any ideas as to why this could be? For reference, here is the (very limited) documentations for MACS2. https://pypi.python.org/pypi/MACS2

Thanks!
Artur