danpos 2.2.2  version

command:
python /usr/local/apps/danpos/2.2.2/danpos.py dpos /usr/local/apps/danpos/2.2.2/testdata/nucleosome_sampleA_rep1.bowtie

Namespace(bg=None, clonalcut='0', command='dpos', count=None, distance=100, edge=0, exclude_high_percent=0, exclude_low_percent=0, extend=80, fdr=1, fs=None, gapfill=0, height=5, lmd=300, mafrsz=300, mifrsz=50, name='result', nonzero=0, nor='F', nor_region_file=None, paired=0, path='/usr/local/apps/danpos/2.2.2/testdata/nucleosome_sampleA_rep1.bowtie', pheight='0', position_reference=None, ratio=0.9, save=0, separator1=None, smooth_width=20, span=10, testcut='0', width=40)
rd 100 , step 10  fcut, 55.843533

parsing from bowtie file /usr/local/apps/danpos/2.2.2/testdata/nucleosome_sampleA_rep1.bowtie ...
1000000 reads parsed
2000000 reads parsed
3000000 reads parsed
4000000 reads parsed
5000000 reads parsed
6000000 reads parsed
7000000 reads parsed
8000000 reads parsed
9000000 reads parsed
10000000 reads parsed
11000000 reads parsed
12000000 reads parsed
13000000 reads parsed
14000000 reads parsed
15000000 reads parsed
16000000 reads parsed
17000000 reads parsed
parsing finished, 17423650 reads parsed
calculating fragment size ...
sizes distribution:
-------------------------------------- 50bp 37102512.0
------------------------------------ 60bp 34999182.0
----------------------------------- 70bp 34495980.0
------------------------------------- 80bp 35759703.0
---------------------------------------- 90bp 39411126.0
---------------------------------------------- 100bp 44682428.0
------------------------------------------------------ 110bp 52438164.0
----------------------------------------------------------------- 120bp 62648554.0
----------------------------------------------------------------------------- 130bp 74739039.0
----------------------------------------------------------------------------------------- 140bp 85972442.0
------------------------------------------------------------------------------------------------- 150bp 94356256.0
---------------------------------------------------------------------------------------------------- 160bp 96342968.0
------------------------------------------------------------------------------------------- 170bp 88481177.0
------------------------------------------------------------------------------ 180bp 75320635.0
----------------------------------------------------------------- 190bp 62706741.0
------------------------------------------------------ 200bp 52066264.0
--------------------------------------------- 210bp 44084782.0
---------------------------------------- 220bp 38911305.0
------------------------------------- 230bp 36026681.0
------------------------------------ 240bp 35105723.0
------------------------------------- 250bp 36020117.0
---------------------------------------- 260bp 38792646.0
-------------------------------------------- 270bp 43349597.0
--------------------------------------------------- 280bp 49523715.0
----------------------------------------------------------- 290bp 56903537.0
------------------------------------------------------------------ 300bp 64481060.0
potential size: 150 160 
calculated fragment size: 160
extend to 80
generating wig ...
time elapsed: 113.613048077 seconds

pooling group usr_local_apps_danpos_2.2.2_testdata_nucleosome_sampleA_rep1 ...
smooth width: 20
saving  to result/pooled/usr_local_apps_danpos_2.2.2_testdata_nucleosome_sampleA_rep1.smooth.wig
chrV
chrII
chrVI
chrIV
chrXIV
chrXVI
chrXI
chrX
chrXV
chrIX
chrIII
chrXII
chrXIII
chrM
chrVII
chrI
chrVIII
completed
time elapsed: 115.982922077 seconds

position calling for usr_local_apps_danpos_2.2.2_testdata_nucleosome_sampleA_rep1 ...
whole genome aveage value is 1034.10987069, use calling cutoff 5
calling summits ...
chrV
chrII
chrVI
chrXIV
chrXVI
chrXI
chrVII
chrX
chrXV
chrIX
chrI
chrXII
chrXIII
chrIII
chrIV
chrM
chrVIII
merging summits ...
chrV : 3634 summits, merging ...
3203 left
chrII : 38673 summits, merging ...
4522 left
chrVI : 12668 summits, merging ...
1478 left
chrIV : 71534 summits, merging ...
8384 left
chrXIV : 37194 summits, merging ...
4385 left
chrXVI : 44418 summits, merging ...
5174 left
chrXI : 32768 summits, merging ...
3832 left
chrX : 34395 summits, merging ...
3998 left
chrXV : 51932 summits, merging ...
6061 left
chrIX : 20544 summits, merging ...
2384 left
chrM : 2368 summits, merging ...
302 left
chrXII : 48916 summits, merging ...
5691 left
chrXIII : 44117 summits, merging ...
5127 left
chrIII : 14684 summits, merging ...
1714 left
chrVII : 51843 summits, merging ...
6034 left
chrI : 10138 summits, merging ...
1198 left
chrVIII : 25900 summits, merging ...
3034 left
calculating positioning score
chrV
571770 80 57185
571770 90 57185
571770 100 57185
chrII
813090 90 81318
813090 100 81318
chrVI
chrIV
1525490 90 152558
1525490 100 152558
chrXIV
chrXVI
946290 60 94635
946290 70 94635
946290 80 94635
946290 90 94635
946290 100 94635
chrXI
chrX
chrXV
1091230 60 109129
1091230 70 109129
1091230 80 109129
1091230 90 109129
1091230 100 109129
chrIX
chrM
85630 80 8571
85630 90 8571
85630 100 8571
chrXII
chrXIII
chrIII
chrVII
chrI
230160 60 23022
230160 70 23022
230160 80 23022
230160 90 23022
230160 100 23022
chrVIII
saving positions ...
chrV
chrII
chrVI
chrIV
chrXIV
chrXVI
chrXI
chrX
chrXV
chrIX
chrM
chrXII
chrXIII
chrIII
chrVII
chrI
chrVIII
time elapsed: 236.545619965 seconds
reading from result/pooled/usr_local_apps_danpos_2.2.2_testdata_nucleosome_sampleA_rep1.smooth.positions.xls ...
mering ...
chrV : 3203 summits, merging ...
3203 left
chrII : 4522 summits, merging ...
4522 left
chrVI : 1478 summits, merging ...
1478 left
chrXIV : 4385 summits, merging ...
4385 left
chrXVI : 5174 summits, merging ...
5174 left
chrXI : 3832 summits, merging ...
3832 left
chrVII : 6034 summits, merging ...
6034 left
chrX : 3998 summits, merging ...
3998 left
chrXV : 6061 summits, merging ...
6061 left
chrIX : 2384 summits, merging ...
2384 left
chrIII : 1714 summits, merging ...
1714 left
chrXII : 5691 summits, merging ...
5691 left
chrXIII : 5127 summits, merging ...
5127 left
chrM : 302 summits, merging ...
302 left
chrIV : 8384 summits, merging ...
8384 left
chrI : 1198 summits, merging ...
1198 left
chrVIII : 3034 summits, merging ...
3034 left

total time elapsed: 0 hours 3 minutes 56 seconds

job done, cheers!