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Error After Model Building #1

Closed GoogleCodeExporter closed 8 years ago

GoogleCodeExporter commented 8 years ago 
Hello,

I was using the zinba() function, and I got the error

model  8  completed out of  8   Error in read.table(loc, header = T, sep = 
"\t") : 
  no lines available in input

My call was

zinba(
  refinepeaks=1,
  seq="/home/darstr/ZINBA/my_chip.bed",
  input="/home/darstr/ZINBA/my_input.bed",
  filetype="bed",
  align="/home/darstr/ZINBA/results",
  numProc=4,
  twoBit="/home/aarsta/data/genome/hg18/hg18.2bit",
  outfile="/home/darstr/ZINBA/results/x",
  extension=300,
  basecountfile="/home/darstr/ZINBA/results/my_counts"
)

Indeed, looking at the temporary files, it seems the model file is empty.

-rw-r--r-- 1 darstr darstr 0 2011-07-28 17:23 
/home/darstr/ZINBA/results/x_files/x.model

Original issue reported on code.google.com by dario.ga...@gmail.com on 29 Jul 2011 at 12:00

GoogleCodeExporter commented 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

GoogleCodeExporter commented 8 years ago 
$ 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

GoogleCodeExporter commented 8 years ago 
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

GoogleCodeExporter commented 8 years ago 
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

GoogleCodeExporter commented 8 years ago 
"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

GoogleCodeExporter commented 8 years ago 
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

GoogleCodeExporter commented 8 years ago 
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

GoogleCodeExporter commented 8 years ago 
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

GoogleCodeExporter commented 8 years ago 
$ 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

GoogleCodeExporter commented 8 years ago 
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

GoogleCodeExporter commented 8 years ago 
Great, I will mark this issue as closed.

Original comment by homer...@gmail.com on 29 Jul 2011 at 12:51