Closed GoogleCodeExporter closed 8 years ago
Could you please paste the output after executing the following unix commands
in your shell (will also work on Macs):
head /home/darstr/ZINBA/my_chip.bed
head /home/darstr/ZINBA/my_input.bed
Most likely your bed file is not formatted exactly to what is required. I'll
update the wiki regardless to provide more guidance on this.
Original comment by homer...@gmail.com
on 29 Jul 2011 at 12:43
$ head /home/darstr/ZINBA/my_chip.bed
chr1 60 109 A209TTABXX:3:47:5455:102867#/1 255 -
chr1 129 178 A209TTABXX:3:48:3653:7844#/1 255 +
chr1 477 526 A209TTABXX:3:48:12276:2760#/1 255 -
chr1 509 558 A209TTABXX:3:65:1541:104391#/1 255 +
chr1 2917 2966 A209TTABXX:3:7:10924:152362#/1 255 -
chr1 3324 3373 A209TTABXX:3:41:4262:66897#/1 255 -
chr1 6104 6153 A209TTABXX:3:3:10620:171761#/1 255 -
chr1 6286 6335 A209TTABXX:3:2:20964:76076#/1 255 -
chr1 6295 6344 A209TTABXX:3:41:14578:194581#/1 255 -
chr1 6301 6350 A209TTABXX:3:21:4428:170903#/1 255 +
$ head /home/darstr/ZINBA/my_input.bed
chr1 247 283 GAPC:8:33:1535:1675#0/1 255 +
chr1 446 482 GAPC:8:70:204:737#0/1 255 -
chr1 601 637 GAPC:8:40:1558:1592#0/1 255 -
chr1 3181 3217 GAPC:8:96:1117:1829#0/1 255 +
chr1 4782 4818 GAPC:8:74:815:1829#0/1 255 -
chr1 6286 6322 GAPC:8:5:1699:554#0/1 255 -
chr1 6309 6345 GAPC:8:57:446:772#0/1 255 +
chr1 7339 7375 GAPC:8:50:623:2042#0/1 255 -
chr1 9102 9138 GAPC:8:64:676:631#0/1 255 -
chr1 38022 38058 GAPC:8:18:1558:1206#0/1 255 +
Original comment by dario.ga...@gmail.com
on 29 Jul 2011 at 1:16
If you could also attach the screen output from the buildwindows process, that
would also be helpful. After each chromosome during the buildwindows process, a
message regarding the number of reads that were skipped is printed if a
possible formatting issue exists (this message will be made more informative in
the next version).
Original comment by homer...@gmail.com
on 29 Jul 2011 at 1:25
Interesting. Seems that half way through, it starts generating empty files.
$ ls -l
total 643880
-rw-r--r-- 1 darstr darstr 3876 2011-07-28 17:06 chip.list
-rw-r--r-- 1 darstr darstr 0 2011-07-28 17:23 chip.model
-rw-r--r-- 1 darstr darstr 32839739 2011-07-28 16:52
my_chip_chr10_win250bp_offset0bp.txt
-rw-r--r-- 1 darstr darstr 32839709 2011-07-28 16:52
my_chip_chr10_win250bp_offset125bp.txt
-rw-r--r-- 1 darstr darstr 32711718 2011-07-28 16:53
my_chip_chr11_win250bp_offset0bp.txt
-rw-r--r-- 1 darstr darstr 32711883 2011-07-28 16:53
my_chip_chr11_win250bp_offset125bp.txt
-rw-r--r-- 1 darstr darstr 32486578 2011-07-28 16:54
my_chip_chr12_win250bp_offset0bp.txt
-rw-r--r-- 1 darstr darstr 32486468 2011-07-28 16:54
my_chip_chr12_win250bp_offset125bp.txt
-rw-r--r-- 1 darstr darstr 23808613 2011-07-28 16:54
my_chip_chr13_win250bp_offset0bp.txt
-rw-r--r-- 1 darstr darstr 23808340 2011-07-28 16:54
my_chip_chr13_win250bp_offset125bp.txt
-rw-r--r-- 1 darstr darstr 21949140 2011-07-28 16:55
my_chip_chr14_win250bp_offset0bp.txt
-rw-r--r-- 1 darstr darstr 21949035 2011-07-28 16:55
my_chip_chr14_win250bp_offset125bp.txt
-rw-r--r-- 1 darstr darstr 20177275 2011-07-28 16:55
my_chip_chr15_win250bp_offset0bp.txt
-rw-r--r-- 1 darstr darstr 20177050 2011-07-28 16:55
my_chip_chr15_win250bp_offset125bp.txt
-rw-r--r-- 1 darstr darstr 19476667 2011-07-28 16:56
my_chip_chr16_win250bp_offset0bp.txt
-rw-r--r-- 1 darstr darstr 19476707 2011-07-28 16:56
my_chip_chr16_win250bp_offset125bp.txt
-rw-r--r-- 1 darstr darstr 19208748 2011-07-28 16:56
my_chip_chr17_win250bp_offset0bp.txt
-rw-r--r-- 1 darstr darstr 19208744 2011-07-28 16:56
my_chip_chr17_win250bp_offset125bp.txt
-rw-r--r-- 1 darstr darstr 18427074 2011-07-28 16:56
my_chip_chr18_win250bp_offset0bp.txt
-rw-r--r-- 1 darstr darstr 18427224 2011-07-28 16:56
my_chip_chr18_win250bp_offset125bp.txt
-rw-r--r-- 1 darstr darstr 13748549 2011-07-28 16:57
my_chip_chr19_win250bp_offset0bp.txt
-rw-r--r-- 1 darstr darstr 13748582 2011-07-28 16:57
my_chip_chr19_win250bp_offset125bp.txt
-rw-r--r-- 1 darstr darstr 55824015 2011-07-28 16:58
my_chip_chr1_win250bp_offset0bp.txt
-rw-r--r-- 1 darstr darstr 55823453 2011-07-28 16:58
my_chip_chr1_win250bp_offset125bp.txt
-rw-r--r-- 1 darstr darstr 14670334 2011-07-28 16:58
my_chip_chr20_win250bp_offset0bp.txt
-rw-r--r-- 1 darstr darstr 14670251 2011-07-28 16:58
my_chip_chr20_win250bp_offset125bp.txt
-rw-r--r-- 1 darstr darstr 8472774 2011-07-28 16:58
my_chip_chr21_win250bp_offset0bp.txt
-rw-r--r-- 1 darstr darstr 8472773 2011-07-28 16:58
my_chip_chr21_win250bp_offset125bp.txt
-rw-r--r-- 1 darstr darstr 8643924 2011-07-28 16:59
my_chip_chr22_win250bp_offset0bp.txt
-rw-r--r-- 1 darstr darstr 8643953 2011-07-28 16:59
my_chip_chr22_win250bp_offset125bp.txt
-rw-r--r-- 1 darstr darstr 13557760 2011-07-28 17:00
my_chip_chr2_win250bp_offset0bp.txt
-rw-r--r-- 1 darstr darstr 0 2011-07-28 17:00
my_chip_chr2_win250bp_offset125bp.txt
-rw-r--r-- 1 darstr darstr 0 2011-07-28 17:01
my_chip_chr3_win250bp_offset0bp.txt
-rw-r--r-- 1 darstr darstr 0 2011-07-28 17:01
my_chip_chr3_win250bp_offset125bp.txt
-rw-r--r-- 1 darstr darstr 0 2011-07-28 17:01
my_chip_chr4_win250bp_offset0bp.txt
-rw-r--r-- 1 darstr darstr 0 2011-07-28 17:01
my_chip_chr4_win250bp_offset125bp.txt
-rw-r--r-- 1 darstr darstr 0 2011-07-28 17:02
my_chip_chr5_win250bp_offset0bp.txt
-rw-r--r-- 1 darstr darstr 0 2011-07-28 17:02
my_chip_chr5_win250bp_offset125bp.txt
-rw-r--r-- 1 darstr darstr 0 2011-07-28 17:03
my_chip_chr6_win250bp_offset0bp.txt
-rw-r--r-- 1 darstr darstr 0 2011-07-28 17:03
my_chip_chr6_win250bp_offset125bp.txt
-rw-r--r-- 1 darstr darstr 0 2011-07-28 17:04
my_chip_chr7_win250bp_offset0bp.txt
-rw-r--r-- 1 darstr darstr 0 2011-07-28 17:04
my_chip_chr7_win250bp_offset125bp.txt
-rw-r--r-- 1 darstr darstr 0 2011-07-28 17:05
my_chip_chr8_win250bp_offset0bp.txt
-rw-r--r-- 1 darstr darstr 0 2011-07-28 17:05
my_chip_chr8_win250bp_offset125bp.txt
-rw-r--r-- 1 darstr darstr 0 2011-07-28 17:05
my_chip_chr9_win250bp_offset0bp.txt
-rw-r--r-- 1 darstr darstr 0 2011-07-28 17:05
my_chip_chr9_win250bp_offset125bp.txt
-rw-r--r-- 1 darstr darstr 0 2011-07-28 17:05
my_chip_chrM_win250bp_offset0bp.txt
-rw-r--r-- 1 darstr darstr 0 2011-07-28 17:05
my_chip_chrM_win250bp_offset125bp.txt
-rw-r--r-- 1 darstr darstr 0 2011-07-28 17:06
my_chip_chrX_win250bp_offset0bp.txt
-rw-r--r-- 1 darstr darstr 0 2011-07-28 17:06
my_chip_chrX_win250bp_offset125bp.txt
-rw-r--r-- 1 darstr darstr 0 2011-07-28 17:06
my_chip_chrY_win250bp_offset0bp.txt
-rw-r--r-- 1 darstr darstr 0 2011-07-28 17:06
my_chip_chrY_win250bp_offset125bp.txt
But looking at the build windows output of chr2, its output doesn't look any
different to any of the other chromosomes.
Processing chr2
Initializing to length 242951149
Mapping reads to chromosome......
Getting alignability info from:
/home/darstr/ZINBA/results/chr2.wig
Getting sequence from .2bit file:
/home/aarsta/data/genome/hg18/hg18.2bit
WARNING: ignoring environment value of R_HOME
Getting counts for 100000bp windows..........
Refining boundaries....
Global variance is 3.90753e-07
Refining 108 boundaries
Mapping input tags to the genome.........
Getting counts for zinba windows..........
Offset 0bp......
Printed out data to /home/darstr/ZINBA/results/CTCF_files/PrEC_CTCF_chr2_win250bp_offset0bp.txt
Offset 125bp......
Printed out data to /home/darstr/ZINBA/results/CTCF_files/PrEC_CTCF_chr2_win250bp_offset125bp.txt
Original comment by dario.ga...@gmail.com
on 29 Jul 2011 at 1:45
"WARNING: ignoring environment value of R_HOME"
This is not part of the typical output, and may be pointing towards a
system-specific issue. What operating system are you using currently? Are you
currently submitting your jobs on a high performance computing cluster?
Original comment by homer...@gmail.com
on 29 Jul 2011 at 1:57
I'm using Ubuntu 10.10 and R version 2.13.1 (2011-07-08). That particular
environment variable is empty, as I see when I do echo $R_HOME at the terminal.
Original comment by dario.ga...@gmail.com
on 29 Jul 2011 at 2:30
I used an older version of R, 2.13.0 and the WARNING disappeared, but I'm still
getting the same empty model files. Any other ideas ?
Original comment by dario.ga...@gmail.com
on 29 Jul 2011 at 2:45
It also appears that the last printed chromosome (chr2) offset is much smaller
than it should be, almost as large as the chr22 file:
-rw-r--r-- 1 darstr darstr 13557760 2011-07-28 17:00
my_chip_chr2_win250bp_offset0bp.txt
Could it be possible that you might be running low on disk space? This may
explain the abrupt truncation of the printing of the first chr2 offset and the
following empty files.
To help narrow down the possible sources of the problem, I'll need a little
more info
1) head -25 chip.list
2) tail my_chip_chr2_win250bp_offset0bp.txt
3) head my_chip_chr22_win250bp_offset0bp.txt
Original comment by homer...@gmail.com
on 29 Jul 2011 at 2:54
$ head -25 chip.list
/home/darstr/ZINBA/results/chip_files/my_chip_chr10_win250bp_offset0bp.txt;/home
/darstr/ZINBA/results/chip_files/my_chip_chr10_win250bp_offset125bp.txt
/home/darstr/ZINBA/results/chip_files/my_chip_chr11_win250bp_offset0bp.txt;/home
/darstr/ZINBA/results/chip_files/my_chip_chr11_win250bp_offset125bp.txt
/home/darstr/ZINBA/results/chip_files/my_chip_chr12_win250bp_offset0bp.txt;/home
/darstr/ZINBA/results/chip_files/my_chip_chr12_win250bp_offset125bp.txt
/home/darstr/ZINBA/results/chip_files/my_chip_chr13_win250bp_offset0bp.txt;/home
/darstr/ZINBA/results/chip_files/my_chip_chr13_win250bp_offset125bp.txt
/home/darstr/ZINBA/results/chip_files/my_chip_chr14_win250bp_offset0bp.txt;/home
/darstr/ZINBA/results/chip_files/my_chip_chr14_win250bp_offset125bp.txt
/home/darstr/ZINBA/results/chip_files/my_chip_chr15_win250bp_offset0bp.txt;/home
/darstr/ZINBA/results/chip_files/my_chip_chr15_win250bp_offset125bp.txt
/home/darstr/ZINBA/results/chip_files/my_chip_chr16_win250bp_offset0bp.txt;/home
/darstr/ZINBA/results/chip_files/my_chip_chr16_win250bp_offset125bp.txt
/home/darstr/ZINBA/results/chip_files/my_chip_chr17_win250bp_offset0bp.txt;/home
/darstr/ZINBA/results/chip_files/my_chip_chr17_win250bp_offset125bp.txt
/home/darstr/ZINBA/results/chip_files/my_chip_chr18_win250bp_offset0bp.txt;/home
/darstr/ZINBA/results/chip_files/my_chip_chr18_win250bp_offset125bp.txt
/home/darstr/ZINBA/results/chip_files/my_chip_chr19_win250bp_offset0bp.txt;/home
/darstr/ZINBA/results/chip_files/my_chip_chr19_win250bp_offset125bp.txt
/home/darstr/ZINBA/results/chip_files/my_chip_chr1_win250bp_offset0bp.txt;/home/
darstr/ZINBA/results/chip_files/my_chip_chr1_win250bp_offset125bp.txt
/home/darstr/ZINBA/results/chip_files/my_chip_chr20_win250bp_offset0bp.txt;/home
/darstr/ZINBA/results/chip_files/my_chip_chr20_win250bp_offset125bp.txt
/home/darstr/ZINBA/results/chip_files/my_chip_chr21_win250bp_offset0bp.txt;/home
/darstr/ZINBA/results/chip_files/my_chip_chr21_win250bp_offset125bp.txt
/home/darstr/ZINBA/results/chip_files/my_chip_chr22_win250bp_offset0bp.txt;/home
/darstr/ZINBA/results/chip_files/my_chip_chr22_win250bp_offset125bp.txt
/home/darstr/ZINBA/results/chip_files/my_chip_chr2_win250bp_offset0bp.txt;/home/
darstr/ZINBA/results/chip_files/my_chip_chr2_win250bp_offset125bp.txt
/home/darstr/ZINBA/results/chip_files/my_chip_chr3_win250bp_offset0bp.txt;/home/
darstr/ZINBA/results/chip_files/my_chip_chr3_win250bp_offset125bp.txt
/home/darstr/ZINBA/results/chip_files/my_chip_chr4_win250bp_offset0bp.txt;/home/
darstr/ZINBA/results/chip_files/my_chip_chr4_win250bp_offset125bp.txt
/home/darstr/ZINBA/results/chip_files/my_chip_chr5_win250bp_offset0bp.txt;/home/
darstr/ZINBA/results/chip_files/my_chip_chr5_win250bp_offset125bp.txt
/home/darstr/ZINBA/results/chip_files/my_chip_chr6_win250bp_offset0bp.txt;/home/
darstr/ZINBA/results/chip_files/my_chip_chr6_win250bp_offset125bp.txt
/home/darstr/ZINBA/results/chip_files/my_chip_chr7_win250bp_offset0bp.txt;/home/
darstr/ZINBA/results/chip_files/my_chip_chr7_win250bp_offset125bp.txt
/home/darstr/ZINBA/results/chip_files/my_chip_chr8_win250bp_offset0bp.txt;/home/
darstr/ZINBA/results/chip_files/my_chip_chr8_win250bp_offset125bp.txt
/home/darstr/ZINBA/results/chip_files/my_chip_chr9_win250bp_offset0bp.txt;/home/
darstr/ZINBA/results/chip_files/my_chip_chr9_win250bp_offset125bp.txt
/home/darstr/ZINBA/results/chip_files/my_chip_chrM_win250bp_offset0bp.txt;/home/
darstr/ZINBA/results/chip_files/my_chip_chrM_win250bp_offset125bp.txt
/home/darstr/ZINBA/results/chip_files/my_chip_chrX_win250bp_offset0bp.txt;/home/
darstr/ZINBA/results/chip_files/my_chip_chrX_win250bp_offset125bp.txt
/home/darstr/ZINBA/results/chip_files/my_chip_chrY_win250bp_offset0bp.txt;/home/
darstr/ZINBA/results/chip_files/my_chip_chrY_win250bp_offset125bp.txt
2)
chr2 60310251 60310500 2 0.693147 0.476000
1.000000 0.879181
chr2 60310501 60310750 1 1.098612 0.408000
1.000000 0.879181
chr2 60310751 60311000 3 0.693147 0.436000
1.000000 0.879181
chr2 60311001 60311250 2 1.386294 0.388000
1.000000 0.879181
chr2 60311251 60311500 0 0.693147 0.408000
1.000000 0.879181
chr2 60311501 60311750 2 1.386294 0.376000
1.000000 0.879181
chr2 60311751 60312000 0 1.098612 0.396000
1.000000 0.879181
chr2 60312001 60312250 3 0.693147 0.308000
1.000000 0.879181
chr2 60312251 60312500 2 1.098612 0.288000
1.000000 0.879181
chr2 60312501 60312750 3 0.693147 0.268000
1.000000 0.880071
3)
chromosome start stop exp_count input_count gcPerc
align_perc exp_cnvwin_log
chr22 14430001 14430250 0 0.000000 0.472000
0.702000 0.467003
chr22 14430251 14430500 2 0.000000 0.324000
1.000000 0.467003
chr22 14430501 14430750 2 0.000000 0.448000
1.000000 0.467003
chr22 14430751 14431000 1 0.000000 0.476000
1.000000 0.467003
chr22 14431001 14431250 0 0.693147 0.388000
1.000000 0.467003
chr22 14431251 14431500 0 0.000000 0.380000
1.000000 0.467003
chr22 14431501 14431750 1 0.000000 0.408000
0.960000 0.467003
chr22 14431751 14432000 0 0.000000 0.488000
0.842000 0.467003
chr22 14432001 14432250 0 0.000000 0.424000
0.838000 0.467003
Original comment by dario.ga...@gmail.com
on 29 Jul 2011 at 3:00
Seems you're right, I checked disk usage, and I have run out of disk space.
Original comment by dario.ga...@gmail.com
on 29 Jul 2011 at 4:15
Great, I will mark this issue as closed.
Original comment by homer...@gmail.com
on 29 Jul 2011 at 12:51
Original issue reported on code.google.com by
dario.ga...@gmail.com
on 29 Jul 2011 at 12:00