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Terim1 / zinba

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Error in run.zinba #11

Closed GoogleCodeExporter closed 8 years ago

GoogleCodeExporter commented 8 years ago 
1) OpenSUSE 12.1 x64

2) Error in run.zinba(align = align, numProc = numProc, seq = seq, input = 
input,  : 
  File list  /mnt/sf_G_DRIVE/FASTQ-DATA/CD4-DNASE/SRR097566_files/SRR097566.list  does not exist, check whether your reads have been formatted properly

3) script section

4) output section

-----------------------SCRIPT-----------------------------------
#generateAlignability(
# mapdir='/mnt/sf_G_DRIVE/FASTQ-DATA/CD4-DNASE/map36/',
# outdir='/mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/output_200/',
# athresh=1,
# extension=200,
# twoBitFile='/mnt/sf_G_DRIVE/FASTQ-DATA/b_indexes/hg19.2bit');

#basealigncount(inputfile='/mnt/sf_G_DRIVE/FASTQ-DATA/CD4-DNASE/SRR097566.hits',
#  outputfile='/mnt/sf_G_DRIVE/FASTQ-DATA/CD4-DNASE/SRR097566.basecount',
#  extension=200,
#  filetype='bowtie',
#  twoBitFile='/mnt/sf_G_DRIVE/FASTQ-DATA/b_indexes/hg19.2bit' );

zinba(
  align='/mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/output_200/',
  numProc=4,
  seq='/mnt/sf_G_DRIVE/FASTQ-DATA/CD4-DNASE/SRR097566.hits',
  basecountfile='/mnt/sf_G_DRIVE/FASTQ-DATA/CD4-DNASE/SRR097566.basecount',
  filetype='bowtie',
  outfile='/mnt/sf_G_DRIVE/FASTQ-DATA/CD4-DNASE/SRR097566',
  twoBit='/mnt/sf_G_DRIVE/FASTQ-DATA/b_indexes/hg19.2bit',
  extension=200,
  printFullOut=1,
  refinepeaks=1,
  broad=F,
  input='/mnt/sf_G_DRIVE/FASTQ-DATA/CD4-DNASE/SRR097566.hits'
)

-----------------------OUTPUT-----------------------------------
> source("./ZINBA/com.R")
[1] "parameters in effect:"
$filelist
NULL

$formula
NULL

$formulaE
NULL

$formulaZ
NULL

$outfile
[1] "/mnt/sf_G_DRIVE/FASTQ-DATA/CD4-DNASE/SRR097566"

$seq
[1] "/mnt/sf_G_DRIVE/FASTQ-DATA/CD4-DNASE/SRR097566.hits"

$align
[1] "/mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/output_200/"

$input
[1] "/mnt/sf_G_DRIVE/FASTQ-DATA/CD4-DNASE/SRR097566.hits"

$twoBit
[1] "/mnt/sf_G_DRIVE/FASTQ-DATA/b_indexes/hg19.2bit"

$winSize
[1] 250

$offset
[1] 125

$cnvWinSize
[1] 1e+05

$cnvOffset
[1] 2500

$basecountfile
NULL

$threshold
[1] 0.05

$peakconfidence
[1] 0.95

$tol
[1] 1e-05

$numProc
[1] 4

$buildwin
[1] 1

$winGap
[1] 0

$pWinSize
[1] 200

$pquant
[1] 1

$refinepeaks
[1] 0

$printFullOut
[1] 1

$method
[1] "mixture"

$initmethod
[1] "count"

$diff
[1] 0

$filetype
[1] "bowtie"

$extension
[1] 200

$cleanup
[1] FALSE

$selectmodel
[1] TRUE

$selectchr
[1] "chr22"

$selecttype
[1] "complete"

$selectcovs
[1] "input_count"

$FDR
[1] TRUE

$interaction
[1] TRUE

Loading required package: multicore
Loading required package: doMC
Loading required package: foreach
Loading required package: iterators
Loading required package: codetools
foreach: simple, scalable parallel programming from Revolution Analytics
Use Revolution R for scalability, fault tolerance and more.
http://www.revolutionanalytics.com
Loading required package: R.oo
Loading required package: R.methodsS3
R.methodsS3 v1.2.1 (2010-09-18) successfully loaded. See ?R.methodsS3 for help.
R.oo v1.8.3 (2011-11-01) successfully loaded. See ?R.oo for help.

Attaching package: ‘R.oo’

The following object(s) are masked from ‘package:R.methodsS3’:

    throw.default

The following object(s) are masked from ‘package:methods’:

    getClass, getClasses, getMethods

The following object(s) are masked from ‘package:base’:

    attach, detach, environment, gc, load, save

R.utils v1.9.11 (2012-01-17) successfully loaded. See ?R.utils for help.

Attaching package: ‘R.utils’

The following object(s) are masked from ‘package:multicore’:

    exit

The following object(s) are masked from ‘package:utils’:

    timestamp

The following object(s) are masked from ‘package:base’:

    cat, commandArgs, getOption, inherits, isOpen, lapply, parse,
    remove, warnings

Overwriting previously existing directory 
/mnt/sf_G_DRIVE/FASTQ-DATA/CD4-DNASE/SRR097566_files/

--------BEGIN BUILDING WINDOW DATA-------- 2012-01-30 20:48:14 

Importing reads from file /mnt/sf_G_DRIVE/FASTQ-DATA/CD4-DNASE/SRR097566.hits 
    Filetype is bowtie 
    Extension is 200 
        For chr1 length is 249250621
        For chr2 length is 243199373
        For chr3 length is 198022430
        For chr4 length is 191154276
        For chr5 length is 180915260
        For chr6 length is 171115067
        For chr7 length is 159138663
        For chrX length is 155270560
        For chr8 length is 146364022
        For chr9 length is 141213431
        For chr10 length is 135534747
        For chr11 length is 135006516
        For chr12 length is 133851895
        For chr13 length is 115169878
        For chr14 length is 107349540
        For chr15 length is 102531392
        For chr16 length is 90354753
        For chr17 length is 81195210
        For chr18 length is 78077248
        For chr20 length is 63025520
        For chrY length is 59373566
        For chr19 length is 59128983
        For chr22 length is 51304566
        For chr21 length is 48129895
        For chr6_ssto_hap7 length is 4928567
        For chr6_mcf_hap5 length is 4833398
        For chr6_cox_hap2 length is 4795371
        For chr6_mann_hap4 length is 4683263
        For chr6_apd_hap1 length is 4622290
        For chr6_qbl_hap6 length is 4611984
        For chr6_dbb_hap3 length is 4610396
        For chr17_ctg5_hap1 length is 1680828
        For chr4_ctg9_hap1 length is 590426
        For chr1_gl000192_random length is 547496
        For chrUn_gl000225 length is 211173
        For chr4_gl000194_random length is 191469
        For chr4_gl000193_random length is 189789
        For chr9_gl000200_random length is 187035
        For chrUn_gl000222 length is 186861
        For chrUn_gl000212 length is 186858
        For chr7_gl000195_random length is 182896
        For chrUn_gl000223 length is 180455
        For chrUn_gl000224 length is 179693
        For chrUn_gl000219 length is 179198
        For chr17_gl000205_random length is 174588
        For chrUn_gl000215 length is 172545
        For chrUn_gl000216 length is 172294
        For chrUn_gl000217 length is 172149
        For chr9_gl000199_random length is 169874
        For chrUn_gl000211 length is 166566
        For chrUn_gl000213 length is 164239
        For chrUn_gl000220 length is 161802
        For chrUn_gl000218 length is 161147
        For chr19_gl000209_random length is 159169
        For chrUn_gl000221 length is 155397
        For chrUn_gl000214 length is 137718
        For chrUn_gl000228 length is 129120
        For chrUn_gl000227 length is 128374
        For chr1_gl000191_random length is 106433
        For chr19_gl000208_random length is 92689
        For chr9_gl000198_random length is 90085
        For chr17_gl000204_random length is 81310
        For chrUn_gl000233 length is 45941
        For chrUn_gl000237 length is 45867
        For chrUn_gl000230 length is 43691
        For chrUn_gl000242 length is 43523
        For chrUn_gl000243 length is 43341
        For chrUn_gl000241 length is 42152
        For chrUn_gl000236 length is 41934
        For chrUn_gl000240 length is 41933
        For chr17_gl000206_random length is 41001
        For chrUn_gl000232 length is 40652
        For chrUn_gl000234 length is 40531
        For chr11_gl000202_random length is 40103
        For chrUn_gl000238 length is 39939
        For chrUn_gl000244 length is 39929
        For chrUn_gl000248 length is 39786
        For chr8_gl000196_random length is 38914
        For chrUn_gl000249 length is 38502
        For chrUn_gl000246 length is 38154
        For chr17_gl000203_random length is 37498
        For chr8_gl000197_random length is 37175
        For chrUn_gl000245 length is 36651
        For chrUn_gl000247 length is 36422
        For chr9_gl000201_random length is 36148
        For chrUn_gl000235 length is 34474
        For chrUn_gl000239 length is 33824
        For chr21_gl000210_random length is 27682
        For chrUn_gl000231 length is 27386
        For chrUn_gl000229 length is 19913
        For chrM length is 16571
        For chrUn_gl000226 length is 15008
        For chr18_gl000207_random length is 4262
        For chr18_gl000207_random length is 4262
    Importing bowtie formatted reads
    Skipped 27645394 reads
    Imported 1 reads
    Sorting reads ...COMPLETE

Building window data

Processing 30
    Initializing to length 0
    Mapping reads to chromosome......
    Getting alignability info from:
        /mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/output_200/30.wig
Unable to open alignability file 
/mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/output_200/30.wig
ERROR: building windows was unsuccssful

--------BUILD WINDOWS COMPLETE-------

Error in run.zinba(align = align, numProc = numProc, seq = seq, input = input,  
: 
  File list  /mnt/sf_G_DRIVE/FASTQ-DATA/CD4-DNASE/SRR097566_files/SRR097566.list  does not exist, check whether your reads have been formatted properly
>

Original issue reported on code.google.com by por...@porter.st on 31 Jan 2012 at 2:03

GoogleCodeExporter commented 8 years ago 
please use version 2.01 of zinba, as the version in the subversion trunk is 
experimental and not intended for installation.  The newest version is still 
being tested on our servers and will be released soon.  If you receive this 
error again, please post again.

Original comment by homer...@gmail.com on 31 Jan 2012 at 2:14

GoogleCodeExporter commented 8 years ago 
I've used subversion after got this error in stable release (2.01). So the 
error the same.

Original comment by por...@porter.st on 31 Jan 2012 at 2:47

GoogleCodeExporter commented 8 years ago 
It looks like there is a problem with the mappability files.  Can you please 
show the output from  the following:

ls -lt /mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/output_200/

in addition to the screen output from your generateAlignability command

Original comment by homer...@gmail.com on 31 Jan 2012 at 3:00

GoogleCodeExporter commented 8 years ago 
Thank you for immediate response.
It'll be done tomorrow morning. I'm sorry I'm not at experimental computer.

Original comment by por...@porter.st on 31 Jan 2012 at 3:21

GoogleCodeExporter commented 8 years ago 
P12-0709-1:...# ls -lt /mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/output_200/
total 6046284
-rw-rw-rw- 1 root root 118747132 Jan 30 20:01 chrY.wig
-rw-rw-rw- 1 root root 310541120 Jan 30 20:00 chrX.wig
-rw-rw-rw- 1 root root     33142 Jan 30 19:59 chrM.wig
-rw-rw-rw- 1 root root 282426862 Jan 30 19:59 chr9.wig
-rw-rw-rw- 1 root root 292728044 Jan 30 19:58 chr8.wig
-rw-rw-rw- 1 root root 318277326 Jan 30 19:57 chr7.wig
-rw-rw-rw- 1 root root 342230134 Jan 30 19:56 chr6.wig
-rw-rw-rw- 1 root root 361830520 Jan 30 19:55 chr5.wig
-rw-rw-rw- 1 root root 382308552 Jan 30 19:54 chr4.wig
-rw-rw-rw- 1 root root 396044860 Jan 30 19:52 chr3.wig
-rw-rw-rw- 1 root root 486398746 Jan 30 19:51 chr2.wig
-rw-rw-rw- 1 root root 102609132 Jan 30 19:49 chr22.wig
-rw-rw-rw- 1 root root  96259790 Jan 30 19:49 chr21.wig
-rw-rw-rw- 1 root root 126051040 Jan 30 19:48 chr20.wig
-rw-rw-rw- 1 root root 498501242 Jan 30 19:48 chr1.wig
-rw-rw-rw- 1 root root 118257966 Jan 30 19:46 chr19.wig
-rw-rw-rw- 1 root root 156154496 Jan 30 19:46 chr18.wig
-rw-rw-rw- 1 root root 162390420 Jan 30 19:45 chr17.wig
-rw-rw-rw- 1 root root 180709506 Jan 30 19:44 chr16.wig
-rw-rw-rw- 1 root root 205062784 Jan 30 19:44 chr15.wig
-rw-rw-rw- 1 root root 214699080 Jan 30 19:43 chr14.wig
-rw-rw-rw- 1 root root 230339756 Jan 30 19:42 chr13.wig
-rw-rw-rw- 1 root root 267703790 Jan 30 19:42 chr12.wig
-rw-rw-rw- 1 root root 270013032 Jan 30 19:41 chr11.wig
-rw-rw-rw- 1 root root 271069494 Jan 30 19:40 chr10.wig

Original comment by por...@porter.st on 31 Jan 2012 at 3:07

GoogleCodeExporter commented 8 years ago 
In your earlier output (which I believe is the output from the subversion 
version of zinba) the following file was trying to be accessed during the 
buildwindows process:  

/mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/output_200/30.wig

Could you send me the output from running your zinba() command on version 2.01 
just to confirm the issue?

Original comment by homer...@gmail.com on 31 Jan 2012 at 3:28

GoogleCodeExporter commented 8 years ago 
Yes I'll, at this moment I'm running generateAlignability command.

Original comment by por...@porter.st on 31 Jan 2012 at 3:31

GoogleCodeExporter commented 8 years ago 
> generateAlignability(
+  mapdir='/mnt/sf_G_DRIVE/FASTQ-DATA/CD4-DNASE/map36/',
+  outdir='/mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/output_200/',
+  athresh=1,
+  extension=200,
+  twoBitFile='/mnt/sf_G_DRIVE/FASTQ-DATA/b_indexes/hg19.2bit');

Processing chr10b.out .......
    chr10 .......

Processing chr11b.out .......
    chr11 .......

Processing chr12b.out .......
    chr12 .......

Processing chr13b.out .......
    chr13 .......

Processing chr14b.out .......
    chr14 .......

Processing chr15b.out .......
    chr15 .......

Processing chr16b.out .......
    chr16 .......

Processing chr17b.out .......
    chr17 .......

Processing chr18b.out .......
    chr18 .......

Processing chr19b.out .......
    chr19 .......

Processing chr1b.out .......
    chr1 .......

Processing chr20b.out .......
    chr20 .......

Processing chr21b.out .......
    chr21 .......

Processing chr22b.out .......
    chr22 .......

Processing chr2b.out .......
    chr2 .......

Processing chr3b.out .......
    chr3 .......

Processing chr4b.out .......
    chr4 .......

Processing chr5b.out .......
    chr5 .......

Processing chr6b.out .......
    chr6 .......

Processing chr7b.out .......
    chr7 .......

Processing chr8b.out .......
    chr8 .......

Processing chr9b.out .......
    chr9 .......

Processing chrMb.out .......
    chrM .......

Processing chrXb.out .......
    chrX .......

Processing chrYb.out .......
    chrY .......

Processing chrYb.out .......
    chrY .......
Loading align count data from 
/mnt/sf_G_DRIVE/FASTQ-DATA/CD4-DNASE/map36/temp.wig
    Processing chr10
        Printing output to: /mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/output_200/chr10.wig
    Processing chr11
        Printing output to: /mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/output_200/chr11.wig
    Processing chr12
        Printing output to: /mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/output_200/chr12.wig
    Processing chr13
        Printing output to: /mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/output_200/chr13.wig
    Processing chr14
        Printing output to: /mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/output_200/chr14.wig
    Processing chr15
        Printing output to: /mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/output_200/chr15.wig
    Processing chr16
        Printing output to: /mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/output_200/chr16.wig
    Processing chr17
        Printing output to: /mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/output_200/chr17.wig
    Processing chr18
        Printing output to: /mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/output_200/chr18.wig
    Processing chr19
        Printing output to: /mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/output_200/chr19.wig
    Processing chr1
        Printing output to: /mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/output_200/chr1.wig
    Processing chr20
        Printing output to: /mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/output_200/chr20.wig
    Processing chr21
        Printing output to: /mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/output_200/chr21.wig
    Processing chr22
        Printing output to: /mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/output_200/chr22.wig
    Processing chr2
        Printing output to: /mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/output_200/chr2.wig
    Processing chr3
        Printing output to: /mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/output_200/chr3.wig
    Processing chr4
        Printing output to: /mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/output_200/chr4.wig
    Processing chr5
        Printing output to: /mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/output_200/chr5.wig
    Processing chr6
        Printing output to: /mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/output_200/chr6.wig
    Processing chr7
        Printing output to: /mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/output_200/chr7.wig
    Processing chr8
        Printing output to: /mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/output_200/chr8.wig
    Processing chr9
        Printing output to: /mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/output_200/chr9.wig
    Processing chrM
        Printing output to: /mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/output_200/chrM.wig
    Processing chrX
        Printing output to: /mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/output_200/chrX.wig
    Processing chrY
        Printing output to: /mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/output_200/chrY.wig
    Processing chrY
        Printing output to: /mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/output_200/chrY.wig

---------------- ALIGN ADJUST COMPLETED SUCCESSFULLY ----------------
>

Original comment by por...@porter.st on 31 Jan 2012 at 3:51

GoogleCodeExporter commented 8 years ago 
If you can send the output from the zinba() function (using version 2.01) you 
ran utilizing this alignability directory than that should be sufficient for 
now. The previous output from the zinba() command showed that it was trying to 
access an alignability file that didnt exist.

Original comment by homer...@gmail.com on 31 Jan 2012 at 4:04

GoogleCodeExporter commented 8 years ago 
All steps, from the beginning to end:

> library(zinba)
> generateAlignability(
+  mapdir='/mnt/sf_G_DRIVE/FASTQ-DATA/CD4-DNASE/map36/',
+  outdir='/mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/output_200/',
+  athresh=1,
+  extension=200,
+  twoBitFile='/mnt/sf_G_DRIVE/FASTQ-DATA/b_indexes/hg19.2bit');

Processing chr10b.out .......
    chr10 .......

Processing chr11b.out .......
    chr11 .......

Processing chr12b.out .......
    chr12 .......

Processing chr13b.out .......
    chr13 .......

Processing chr14b.out .......
    chr14 .......

Processing chr15b.out .......
    chr15 .......

Processing chr16b.out .......
    chr16 .......

Processing chr17b.out .......
    chr17 .......

Processing chr18b.out .......
    chr18 .......

Processing chr19b.out .......
    chr19 .......

Processing chr1b.out .......
    chr1 .......

Processing chr20b.out .......
    chr20 .......

Processing chr21b.out .......
    chr21 .......

Processing chr22b.out .......
    chr22 .......

Processing chr2b.out .......
    chr2 .......

Processing chr3b.out .......
    chr3 .......

Processing chr4b.out .......
    chr4 .......

Processing chr5b.out .......
    chr5 .......

Processing chr6b.out .......
    chr6 .......

Processing chr7b.out .......
    chr7 .......

Processing chr8b.out .......
    chr8 .......

Processing chr9b.out .......
    chr9 .......

Processing chrMb.out .......
    chrM .......

Processing chrXb.out .......
    chrX .......

Processing chrYb.out .......
    chrY .......

Processing chrYb.out .......
    chrY .......
Loading align count data from 
/mnt/sf_G_DRIVE/FASTQ-DATA/CD4-DNASE/map36/temp.wig
    Processing chr10
        Printing output to: /mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/output_200/chr10.wig
    Processing chr11
        Printing output to: /mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/output_200/chr11.wig
    Processing chr12
        Printing output to: /mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/output_200/chr12.wig
    Processing chr13
        Printing output to: /mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/output_200/chr13.wig
    Processing chr14
        Printing output to: /mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/output_200/chr14.wig
    Processing chr15
        Printing output to: /mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/output_200/chr15.wig
    Processing chr16
        Printing output to: /mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/output_200/chr16.wig
    Processing chr17
        Printing output to: /mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/output_200/chr17.wig
    Processing chr18
        Printing output to: /mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/output_200/chr18.wig
    Processing chr19
        Printing output to: /mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/output_200/chr19.wig
    Processing chr1
        Printing output to: /mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/output_200/chr1.wig
    Processing chr20
        Printing output to: /mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/output_200/chr20.wig
    Processing chr21
        Printing output to: /mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/output_200/chr21.wig
    Processing chr22
        Printing output to: /mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/output_200/chr22.wig
    Processing chr2
        Printing output to: /mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/output_200/chr2.wig
    Processing chr3
        Printing output to: /mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/output_200/chr3.wig
    Processing chr4
        Printing output to: /mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/output_200/chr4.wig
    Processing chr5
        Printing output to: /mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/output_200/chr5.wig
    Processing chr6
        Printing output to: /mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/output_200/chr6.wig
    Processing chr7
        Printing output to: /mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/output_200/chr7.wig
    Processing chr8
        Printing output to: /mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/output_200/chr8.wig
    Processing chr9
        Printing output to: /mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/output_200/chr9.wig
    Processing chrM
        Printing output to: /mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/output_200/chrM.wig
    Processing chrX
        Printing output to: /mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/output_200/chrX.wig
    Processing chrY
        Printing output to: /mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/output_200/chrY.wig
    Processing chrY
        Printing output to: /mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/output_200/chrY.wig

---------------- ALIGN ADJUST COMPLETED SUCCESSFULLY ----------------
>basealigncount(inputfile='/mnt/sf_G_DRIVE/FASTQ-DATA/CD4-DNASE/SRR097566.hits',
+   outputfile='/mnt/sf_G_DRIVE/FASTQ-DATA/CD4-DNASE/SRR097566.basecount',
+   extension=200,
+   filetype='bowtie',
+   twoBitFile='/mnt/sf_G_DRIVE/FASTQ-DATA/b_indexes/hg19.2bit' );

Importing reads from file /mnt/sf_G_DRIVE/FASTQ-DATA/CD4-DNASE/SRR097566.hits 
....
    Reads are formatted as bowtie ....
    Extending reads by 200 bp....
    Getting chromosome lengths from .2bit file: /mnt/sf_G_DRIVE/FASTQ-DATA/b_indexes/hg19.2bit
        For chr1 length is 249250621
        For chr2 length is 243199373
        For chr3 length is 198022430
        For chr4 length is 191154276
        For chr5 length is 180915260
        For chr6 length is 171115067
        For chr7 length is 159138663
        For chrX length is 155270560
        For chr8 length is 146364022
        For chr9 length is 141213431
        For chr10 length is 135534747
        For chr11 length is 135006516
        For chr12 length is 133851895
        For chr13 length is 115169878
        For chr14 length is 107349540
        For chr15 length is 102531392
        For chr16 length is 90354753
        For chr17 length is 81195210
        For chr18 length is 78077248
        For chr20 length is 63025520
        For chrY length is 59373566
        For chr19 length is 59128983
        For chr22 length is 51304566
        For chr21 length is 48129895
        For chr6_ssto_hap7 length is 4928567
        For chr6_mcf_hap5 length is 4833398
        For chr6_cox_hap2 length is 4795371
        For chr6_mann_hap4 length is 4683263
        For chr6_apd_hap1 length is 4622290
        For chr6_qbl_hap6 length is 4611984
        For chr6_dbb_hap3 length is 4610396
        For chr17_ctg5_hap1 length is 1680828
        For chr4_ctg9_hap1 length is 590426
        For chr1_gl000192_random length is 547496
        For chrUn_gl000225 length is 211173
        For chr4_gl000194_random length is 191469
        For chr4_gl000193_random length is 189789
        For chr9_gl000200_random length is 187035
        For chrUn_gl000222 length is 186861
        For chrUn_gl000212 length is 186858
        For chr7_gl000195_random length is 182896
        For chrUn_gl000223 length is 180455
        For chrUn_gl000224 length is 179693
        For chrUn_gl000219 length is 179198
        For chr17_gl000205_random length is 174588
        For chrUn_gl000215 length is 172545
        For chrUn_gl000216 length is 172294
        For chrUn_gl000217 length is 172149
        For chr9_gl000199_random length is 169874
        For chrUn_gl000211 length is 166566
        For chrUn_gl000213 length is 164239
        For chrUn_gl000220 length is 161802
        For chrUn_gl000218 length is 161147
        For chr19_gl000209_random length is 159169
        For chrUn_gl000221 length is 155397
        For chrUn_gl000214 length is 137718
        For chrUn_gl000228 length is 129120
        For chrUn_gl000227 length is 128374
        For chr1_gl000191_random length is 106433
        For chr19_gl000208_random length is 92689
        For chr9_gl000198_random length is 90085
        For chr17_gl000204_random length is 81310
        For chrUn_gl000233 length is 45941
        For chrUn_gl000237 length is 45867
        For chrUn_gl000230 length is 43691
        For chrUn_gl000242 length is 43523
        For chrUn_gl000243 length is 43341
        For chrUn_gl000241 length is 42152
        For chrUn_gl000236 length is 41934
        For chrUn_gl000240 length is 41933
        For chr17_gl000206_random length is 41001
        For chrUn_gl000232 length is 40652
        For chrUn_gl000234 length is 40531
        For chr11_gl000202_random length is 40103
        For chrUn_gl000238 length is 39939
        For chrUn_gl000244 length is 39929
        For chrUn_gl000248 length is 39786
        For chr8_gl000196_random length is 38914
        For chrUn_gl000249 length is 38502
        For chrUn_gl000246 length is 38154
        For chr17_gl000203_random length is 37498
        For chr8_gl000197_random length is 37175
        For chrUn_gl000245 length is 36651
        For chrUn_gl000247 length is 36422
        For chr9_gl000201_random length is 36148
        For chrUn_gl000235 length is 34474
        For chrUn_gl000239 length is 33824
        For chr21_gl000210_random length is 27682
        For chrUn_gl000231 length is 27386
        For chrUn_gl000229 length is 19913
        For chrM length is 16571
        For chrUn_gl000226 length is 15008
        For chr18_gl000207_random length is 4262
        For chr18_gl000207_random length is 4262

Loading bowtie formatted reads
    Skipped 27645394 reads
    Loaded 1 reads
    Sorting reads ...COMPLETE

Calculating counts at each base
Processing 1 reads
    Processing 30..........
        Initializing length to 0
        1 reads mapped to 30
        Printed results to /mnt/sf_G_DRIVE/FASTQ-DATA/CD4-DNASE/SRR097566.basecount
-------- BASE ALIGN COUNTS COMPLETE SUCCESSFULLY --------
> zinba(
+   align='/mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/output_200/',
+   numProc=4,
+   seq='/mnt/sf_G_DRIVE/FASTQ-DATA/CD4-DNASE/SRR097566.hits',
+   basecountfile='/mnt/sf_G_DRIVE/FASTQ-DATA/CD4-DNASE/SRR097566.basecount',
+   filetype='bowtie',
+   outfile='/mnt/sf_G_DRIVE/FASTQ-DATA/CD4-DNASE/SRR097566',
+   twoBit='/mnt/sf_G_DRIVE/FASTQ-DATA/b_indexes/hg19.2bit',
+   extension=200,
+   printFullOut=1,
+   refinepeaks=1,
+   broad=F,
+   input='/mnt/sf_G_DRIVE/FASTQ-DATA/CD4-DNASE/SRR097566.hits'
+ )
[1] "parameters in effect:"
$filelist
NULL

$formula
NULL

$formulaE
NULL

$formulaZ
NULL

$outfile
[1] "/mnt/sf_G_DRIVE/FASTQ-DATA/CD4-DNASE/SRR097566"

$seq
[1] "/mnt/sf_G_DRIVE/FASTQ-DATA/CD4-DNASE/SRR097566.hits"

$align
[1] "/mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/output_200/"

$input
[1] "/mnt/sf_G_DRIVE/FASTQ-DATA/CD4-DNASE/SRR097566.hits"

$twoBit
[1] "/mnt/sf_G_DRIVE/FASTQ-DATA/b_indexes/hg19.2bit"

$winSize
[1] 250

$offset
[1] 125

$cnvWinSize
[1] 1e+05

$cnvOffset
[1] 2500

$basecountfile
[1] "/mnt/sf_G_DRIVE/FASTQ-DATA/CD4-DNASE/SRR097566.basecount"

$threshold
[1] 0.05

$peakconfidence
[1] 0.95

$tol
[1] 1e-05

$numProc
[1] 4

$buildwin
[1] 1

$winGap
[1] 0

$pWinSize
[1] 200

$pquant
[1] 1

$refinepeaks
[1] 1

$printFullOut
[1] 1

$method
[1] "mixture"

$initmethod
[1] "count"

$diff
[1] 0

$filetype
[1] "bowtie"

$extension
[1] 200

$cleanup
[1] FALSE

$selectmodel
[1] TRUE

$selectchr
[1] "chr22"

$selecttype
[1] "complete"

$selectcovs
[1] "input_count"

$FDR
[1] TRUE

Loading required package: multicore

Attaching package: ‘multicore’

The following object(s) are masked from ‘package:R.utils’:

    exit

Loading required package: doMC
Loading required package: foreach
Loading required package: iterators
Loading required package: codetools
foreach: simple, scalable parallel programming from Revolution Analytics
Use Revolution R for scalability, fault tolerance and more.
http://www.revolutionanalytics.com

Overwriting previously existing directory 
/mnt/sf_G_DRIVE/FASTQ-DATA/CD4-DNASE/SRR097566_files/

--------BEGIN BUILDING WINDOW DATA-------- 2012-01-31 11:40:56 

Importing reads from file /mnt/sf_G_DRIVE/FASTQ-DATA/CD4-DNASE/SRR097566.hits 
    Filetype is bowtie 
    Extension is 200 
    Getting chromosome lengths from .2bit file: /mnt/sf_G_DRIVE/FASTQ-DATA/b_indexes/hg19.2bit
        For chr1 length is 249250621
        For chr2 length is 243199373
        For chr3 length is 198022430
        For chr4 length is 191154276
        For chr5 length is 180915260
        For chr6 length is 171115067
        For chr7 length is 159138663
        For chrX length is 155270560
        For chr8 length is 146364022
        For chr9 length is 141213431
        For chr10 length is 135534747
        For chr11 length is 135006516
        For chr12 length is 133851895
        For chr13 length is 115169878
        For chr14 length is 107349540
        For chr15 length is 102531392
        For chr16 length is 90354753
        For chr17 length is 81195210
        For chr18 length is 78077248
        For chr20 length is 63025520
        For chrY length is 59373566
        For chr19 length is 59128983
        For chr22 length is 51304566
        For chr21 length is 48129895
        For chr6_ssto_hap7 length is 4928567
        For chr6_mcf_hap5 length is 4833398
        For chr6_cox_hap2 length is 4795371
        For chr6_mann_hap4 length is 4683263
        For chr6_apd_hap1 length is 4622290
        For chr6_qbl_hap6 length is 4611984
        For chr6_dbb_hap3 length is 4610396
        For chr17_ctg5_hap1 length is 1680828
        For chr4_ctg9_hap1 length is 590426
        For chr1_gl000192_random length is 547496
        For chrUn_gl000225 length is 211173
        For chr4_gl000194_random length is 191469
        For chr4_gl000193_random length is 189789
        For chr9_gl000200_random length is 187035
        For chrUn_gl000222 length is 186861
        For chrUn_gl000212 length is 186858
        For chr7_gl000195_random length is 182896
        For chrUn_gl000223 length is 180455
        For chrUn_gl000224 length is 179693
        For chrUn_gl000219 length is 179198
        For chr17_gl000205_random length is 174588
        For chrUn_gl000215 length is 172545
        For chrUn_gl000216 length is 172294
        For chrUn_gl000217 length is 172149
        For chr9_gl000199_random length is 169874
        For chrUn_gl000211 length is 166566
        For chrUn_gl000213 length is 164239
        For chrUn_gl000220 length is 161802
        For chrUn_gl000218 length is 161147
        For chr19_gl000209_random length is 159169
        For chrUn_gl000221 length is 155397
        For chrUn_gl000214 length is 137718
        For chrUn_gl000228 length is 129120
        For chrUn_gl000227 length is 128374
        For chr1_gl000191_random length is 106433
        For chr19_gl000208_random length is 92689
        For chr9_gl000198_random length is 90085
        For chr17_gl000204_random length is 81310
        For chrUn_gl000233 length is 45941
        For chrUn_gl000237 length is 45867
        For chrUn_gl000230 length is 43691
        For chrUn_gl000242 length is 43523
        For chrUn_gl000243 length is 43341
        For chrUn_gl000241 length is 42152
        For chrUn_gl000236 length is 41934
        For chrUn_gl000240 length is 41933
        For chr17_gl000206_random length is 41001
        For chrUn_gl000232 length is 40652
        For chrUn_gl000234 length is 40531
        For chr11_gl000202_random length is 40103
        For chrUn_gl000238 length is 39939
        For chrUn_gl000244 length is 39929
        For chrUn_gl000248 length is 39786
        For chr8_gl000196_random length is 38914
        For chrUn_gl000249 length is 38502
        For chrUn_gl000246 length is 38154
        For chr17_gl000203_random length is 37498
        For chr8_gl000197_random length is 37175
        For chrUn_gl000245 length is 36651
        For chrUn_gl000247 length is 36422
        For chr9_gl000201_random length is 36148
        For chrUn_gl000235 length is 34474
        For chrUn_gl000239 length is 33824
        For chr21_gl000210_random length is 27682
        For chrUn_gl000231 length is 27386
        For chrUn_gl000229 length is 19913
        For chrM length is 16571
        For chrUn_gl000226 length is 15008
        For chr18_gl000207_random length is 4262
        For chr18_gl000207_random length is 4262
    Importing bowtie formatted reads
    Skipped 27645394 reads
    Imported 1 reads
    Sorting reads ...COMPLETE

Building window data

Processing 30
    Initializing to length 0
    Mapping reads to chromosome......
    Getting alignability info from:
        /mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/output_200/30.wig
Unable to open alignability file 
/mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/output_200/30.wig
ERROR: building windows was unsuccssful

--------BUILD WINDOWS COMPLETE-------

Error in file(file, "r") : cannot open the connection
In addition: Warning message:
In file(file, "r") :
  cannot open file '/mnt/sf_G_DRIVE/FASTQ-DATA/CD4-DNASE/SRR097566_files/SRR097566.list': No such file or directory
>

Original comment by por...@porter.st on 31 Jan 2012 at 4:47

GoogleCodeExporter commented 8 years ago 
Here is the issue:  

Loading bowtie formatted reads
       Skipped 27645394 reads
       Loaded 1 reads
       Sorting reads ...COMPLETE

The formatting for your reads is probably not correct.  See the input formats 
section on the Using ZINBA wiki for bowtie.  Version 2.01 only accepts seven 
columns for the bowtie output file and assumes there is not extra column 
pertaining to a comma-separated list of mismatch descriptors if mismatches are 
detected.  In the next version we will allow some flexibility for this mismatch 
column to be present when reading the mapped reads.

Original comment by homer...@gmail.com on 31 Jan 2012 at 4:54

GoogleCodeExporter commented 8 years ago 
Maybe this info will be helpful 

> R.version
               _                            
platform       x86_64-suse-linux-gnu        
arch           x86_64                       
os             linux-gnu                    
system         x86_64, linux-gnu            
status                                      
major          2                            
minor          14.1                         
year           2011                         
month          12                           
day            22                           
svn rev        57956                        
language       R                            
version.string R version 2.14.1 (2011-12-22)
>

Original comment by por...@porter.st on 31 Jan 2012 at 4:54

GoogleCodeExporter commented 8 years ago 
Ah, Ok, I'll check this!

Original comment by por...@porter.st on 31 Jan 2012 at 4:55

GoogleCodeExporter commented 8 years ago 
I'm grateful for deliberate explanation. I missed that fact. I appreciate your 
participation.

Original comment by por...@porter.st on 31 Jan 2012 at 5:11

GoogleCodeExporter commented 8 years ago 
No problem.  If you have any feedback about your results we would be happy to 
know, and please cite our work if you find our software is useful!

Original comment by homer...@gmail.com on 31 Jan 2012 at 5:34

GoogleCodeExporter commented 8 years ago 
I'm really sorry, but the problem still persist.

Part of the SRR097566.hits file, now without 8th column

SRR097566.sra.2 SOLEXA-1GA-2_0061_FC62988:7:1:3217:1128 length=36       -       
chr12   26720177        AGCACCTCTGTTATNAACAATGCAGCCTTTTTATTA    
GHHFEHDDDDDDDE%DHGHHHHHHHHGDFFGGEHGH    0
SRR097566.sra.1 SOLEXA-1GA-2_0061_FC62988:7:1:2074:1128 length=36       +       
chr6    140993970       TATAAATCCAAATGAATTCCANTTAATATCTCCACA    
=E=E=E?EBBGB@G=GGDG@C%ABB@@@@@DEDDGG    0
SRR097566.sra.5 SOLEXA-1GA-2_0061_FC62988:7:1:4921:1129 length=36       -       
chrM    6338    AACCATCTTCTCCTNACACCTAGCAGGTGTCTCCTC    
D@GG@GDDBD?@@8%5GCGGGHHHHHHGHGHHHHHH    0
SRR097566.sra.6 SOLEXA-1GA-2_0061_FC62988:7:1:5978:1128 length=36       +       
chr4    127316210       TACCTCCTCTTTAAGGTCAATNATTCTTAGATTGGT    
HHHHBHHHHHGHEHBG<GGDB%=BB>@@7=@GGGGH    0
SRR097566.sra.10 SOLEXA-1GA-2_0061_FC62988:7:1:8681:1129 length=36      -       
chr15   34058689        GGAAACAGTGAGTANAGTGAGATATTCAGATAATCC    
EGGDGGBBBBB@@A%@FDDEDEGGDG?FFFDCAA??    0
SRR097566.sra.3 SOLEXA-1GA-2_0061_FC62988:7:1:3554:1128 length=36       +       
chr10   64880102        TGTAGGTGCTATGGATTGAATNTGTCCCCCAAAAAG    
EGG?GGDGGGGGGGGGGGGGA%ABADEEDD@GGDGG    0
SRR097566.sra.12 SOLEXA-1GA-2_0061_FC62988:7:1:8975:1127 length=36      +       
chr22   30685123        CCATTTGACACTACTGAGTTANGCATTGCCCATCCC    
IIIHIIIIIIIIIIIIIIIIG%GGGEECFFIIIIII    0
SRR097566.sra.16 SOLEXA-1GA-2_0061_FC62988:7:1:12224:1129 length=36     -       
chr9    35167535        TTTTCTTTTCACTANTACAAACAGTGCTACAATGAA    
@9983@575547<7%57==<=BBB?8D?D=?EEG@@    0
SRR097566.sra.17 SOLEXA-1GA-2_0061_FC62988:7:1:12284:1129 length=36     -       
chrM    2395    AACCAACAAGTCATNATTACCCTCACTGTCAACCCA    
IIIIIIGGGGGEED%EGGFGGIIIIIIIIIIIIIII    0
SRR097566.sra.18 SOLEXA-1GA-2_0061_FC62988:7:1:13050:1128 length=36     -       
chr11   110004992       CGCACTTAAGTCCCNGTCTCTTTTATAGGCTTTTGT    
GGIGIIFFFFEFFF%FHGGIIIIIIIIIIIIIIIII    0
SRR097566.sra.19 SOLEXA-1GA-2_0061_FC62988:7:1:13330:1129 length=36     -       
chr3    38177592        CCCTAAATCCCTCANACCTTGATTCAATACAGCACA    
IIIIGIFEFFFEFF%BIIIIIIIIIIIIIIIIIIHI    0
SRR097566.sra.20 SOLEXA-1GA-2_0061_FC62988:7:1:13381:1128 length=36     +       
chr11   86973706        GCCAATTATCTGGCCAGCTCTNTTTCATGCTGCAGG    
GGGDGDHHHHGHHHHGEGGGB%?BBBB?BBGGG@GH    0
SRR097566.sra.14 SOLEXA-1GA-2_0061_FC62988:7:1:12028:1127 length=36     -       
chr16   88840523        TGGGCGTGGCCTGANCTTCTAAGCGCATGAGTGTCA    
HHHHGHGGGGGFEF%FHHHHHHHHHHHHGHHHHHHH    0
SRR097566.sra.21 SOLEXA-1GA-2_0061_FC62988:7:1:14630:1128 length=36     +       
chr3    86865877        CTTAGACCTTAGAAAGTCTGCNCAGAAGAAAGGCTC    
IIIIIIIIIIIIIIIIIIIIG%GGGFFFEFHIIIII    0
SRR097566.sra.22 SOLEXA-1GA-2_0061_FC62988:7:1:14905:1128 length=36     +       
chr6    118081724       GCATCAGCCCTGTTAAAACATNCAGAAAAGAGCTTT    
IIIIIIIIIIIIIIIIIIIH@%FFFFFF@@IIIHII    0
SRR097566.sra.23 SOLEXA-1GA-2_0061_FC62988:7:1:14952:1127 length=36     +       
chr6    26189090        TGACAGCATCGCGGATTACATNTTCCAGGAAAACTT    
GHBHEHHGHHHHHHFDHEHHE%DDDFFFFEHHGHHH    0

Original comment by por...@porter.st on 31 Jan 2012 at 5:54

GoogleCodeExporter commented 8 years ago 
> source("./ZINBA/com.R")

Importing reads from file /mnt/sf_G_DRIVE/FASTQ-DATA/CD4-DNASE/SRR097566.7.hits 
....
    Reads are formatted as bowtie ....
    Extending reads by 200 bp....
    Getting chromosome lengths from .2bit file: /mnt/sf_G_DRIVE/FASTQ-DATA/b_indexes/hg19.2bit
        For chr1 length is 249250621
        For chr2 length is 243199373
        For chr3 length is 198022430
        For chr4 length is 191154276
        For chr5 length is 180915260
        For chr6 length is 171115067
        For chr7 length is 159138663
        For chrX length is 155270560
        For chr8 length is 146364022
        For chr9 length is 141213431
        For chr10 length is 135534747
        For chr11 length is 135006516
        For chr12 length is 133851895
        For chr13 length is 115169878
        For chr14 length is 107349540
        For chr15 length is 102531392
        For chr16 length is 90354753
        For chr17 length is 81195210
        For chr18 length is 78077248
        For chr20 length is 63025520
        For chrY length is 59373566
        For chr19 length is 59128983
        For chr22 length is 51304566
        For chr21 length is 48129895
        For chr6_ssto_hap7 length is 4928567
        For chr6_mcf_hap5 length is 4833398
        For chr6_cox_hap2 length is 4795371
        For chr6_mann_hap4 length is 4683263
        For chr6_apd_hap1 length is 4622290
        For chr6_qbl_hap6 length is 4611984
        For chr6_dbb_hap3 length is 4610396
        For chr17_ctg5_hap1 length is 1680828
        For chr4_ctg9_hap1 length is 590426
        For chr1_gl000192_random length is 547496
        For chrUn_gl000225 length is 211173
        For chr4_gl000194_random length is 191469
        For chr4_gl000193_random length is 189789
        For chr9_gl000200_random length is 187035
        For chrUn_gl000222 length is 186861
        For chrUn_gl000212 length is 186858
        For chr7_gl000195_random length is 182896
        For chrUn_gl000223 length is 180455
        For chrUn_gl000224 length is 179693
        For chrUn_gl000219 length is 179198
        For chr17_gl000205_random length is 174588
        For chrUn_gl000215 length is 172545
        For chrUn_gl000216 length is 172294
        For chrUn_gl000217 length is 172149
        For chr9_gl000199_random length is 169874
        For chrUn_gl000211 length is 166566
        For chrUn_gl000213 length is 164239
        For chrUn_gl000220 length is 161802
        For chrUn_gl000218 length is 161147
        For chr19_gl000209_random length is 159169
        For chrUn_gl000221 length is 155397
        For chrUn_gl000214 length is 137718
        For chrUn_gl000228 length is 129120
        For chrUn_gl000227 length is 128374
        For chr1_gl000191_random length is 106433
        For chr19_gl000208_random length is 92689
        For chr9_gl000198_random length is 90085
        For chr17_gl000204_random length is 81310
        For chrUn_gl000233 length is 45941
        For chrUn_gl000237 length is 45867
        For chrUn_gl000230 length is 43691
        For chrUn_gl000242 length is 43523
        For chrUn_gl000243 length is 43341
        For chrUn_gl000241 length is 42152
        For chrUn_gl000236 length is 41934
        For chrUn_gl000240 length is 41933
        For chr17_gl000206_random length is 41001
        For chrUn_gl000232 length is 40652
        For chrUn_gl000234 length is 40531
        For chr11_gl000202_random length is 40103
        For chrUn_gl000238 length is 39939
        For chrUn_gl000244 length is 39929
        For chrUn_gl000248 length is 39786
        For chr8_gl000196_random length is 38914
        For chrUn_gl000249 length is 38502
        For chrUn_gl000246 length is 38154
        For chr17_gl000203_random length is 37498
        For chr8_gl000197_random length is 37175
        For chrUn_gl000245 length is 36651
        For chrUn_gl000247 length is 36422
        For chr9_gl000201_random length is 36148
        For chrUn_gl000235 length is 34474
        For chrUn_gl000239 length is 33824
        For chr21_gl000210_random length is 27682
        For chrUn_gl000231 length is 27386
        For chrUn_gl000229 length is 19913
        For chrM length is 16571
        For chrUn_gl000226 length is 15008
        For chr18_gl000207_random length is 4262
        For chr18_gl000207_random length is 4262

Loading bowtie formatted reads
    Skipped 27645394 reads
    Loaded 1 reads
    Sorting reads ...COMPLETE

Calculating counts at each base
Processing 1 reads
    Processing 30..........
        Initializing length to 0
        1 reads mapped to 30
        Printed results to /mnt/sf_G_DRIVE/FASTQ-DATA/CD4-DNASE/SRR097566.basecount
-------- BASE ALIGN COUNTS COMPLETE SUCCESSFULLY --------
[1] "parameters in effect:"
$filelist
NULL

$formula
NULL

$formulaE
NULL

$formulaZ
NULL

$outfile
[1] "/mnt/sf_G_DRIVE/FASTQ-DATA/CD4-DNASE/SRR097566"

$seq
[1] "/mnt/sf_G_DRIVE/FASTQ-DATA/CD4-DNASE/SRR097566.7.hits"

$align
[1] "/mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/output_200/"

$input
[1] "/mnt/sf_G_DRIVE/FASTQ-DATA/CD4-DNASE/SRR097566.hits"

$twoBit
[1] "/mnt/sf_G_DRIVE/FASTQ-DATA/b_indexes/hg19.2bit"

$winSize
[1] 250

$offset
[1] 125

$cnvWinSize
[1] 1e+05

$cnvOffset
[1] 2500

$basecountfile
[1] "/mnt/sf_G_DRIVE/FASTQ-DATA/CD4-DNASE/SRR097566.basecount"

$threshold
[1] 0.05

$peakconfidence
[1] 0.95

$tol
[1] 1e-05

$numProc
[1] 4

$buildwin
[1] 1

$winGap
[1] 0

$pWinSize
[1] 200

$pquant
[1] 1

$refinepeaks
[1] 1

$printFullOut
[1] 1

$method
[1] "mixture"

$initmethod
[1] "count"

$diff
[1] 0

$filetype
[1] "bowtie"

$extension
[1] 200

$cleanup
[1] FALSE

$selectmodel
[1] TRUE

$selectchr
[1] "chr22"

$selecttype
[1] "complete"

$selectcovs
[1] "input_count"

$FDR
[1] TRUE

Overwriting previously existing directory 
/mnt/sf_G_DRIVE/FASTQ-DATA/CD4-DNASE/SRR097566_files/

--------BEGIN BUILDING WINDOW DATA-------- 2012-01-31 12:47:32 

Importing reads from file /mnt/sf_G_DRIVE/FASTQ-DATA/CD4-DNASE/SRR097566.7.hits 
    Filetype is bowtie 
    Extension is 200 
    Getting chromosome lengths from .2bit file: /mnt/sf_G_DRIVE/FASTQ-DATA/b_indexes/hg19.2bit
        For chr1 length is 249250621
        For chr2 length is 243199373
        For chr3 length is 198022430
        For chr4 length is 191154276
        For chr5 length is 180915260
        For chr6 length is 171115067
        For chr7 length is 159138663
        For chrX length is 155270560
        For chr8 length is 146364022
        For chr9 length is 141213431
        For chr10 length is 135534747
        For chr11 length is 135006516
        For chr12 length is 133851895
        For chr13 length is 115169878
        For chr14 length is 107349540
        For chr15 length is 102531392
        For chr16 length is 90354753
        For chr17 length is 81195210
        For chr18 length is 78077248
        For chr20 length is 63025520
        For chrY length is 59373566
        For chr19 length is 59128983
        For chr22 length is 51304566
        For chr21 length is 48129895
        For chr6_ssto_hap7 length is 4928567
        For chr6_mcf_hap5 length is 4833398
        For chr6_cox_hap2 length is 4795371
        For chr6_mann_hap4 length is 4683263
        For chr6_apd_hap1 length is 4622290
        For chr6_qbl_hap6 length is 4611984
        For chr6_dbb_hap3 length is 4610396
        For chr17_ctg5_hap1 length is 1680828
        For chr4_ctg9_hap1 length is 590426
        For chr1_gl000192_random length is 547496
        For chrUn_gl000225 length is 211173
        For chr4_gl000194_random length is 191469
        For chr4_gl000193_random length is 189789
        For chr9_gl000200_random length is 187035
        For chrUn_gl000222 length is 186861
        For chrUn_gl000212 length is 186858
        For chr7_gl000195_random length is 182896
        For chrUn_gl000223 length is 180455
        For chrUn_gl000224 length is 179693
        For chrUn_gl000219 length is 179198
        For chr17_gl000205_random length is 174588
        For chrUn_gl000215 length is 172545
        For chrUn_gl000216 length is 172294
        For chrUn_gl000217 length is 172149
        For chr9_gl000199_random length is 169874
        For chrUn_gl000211 length is 166566
        For chrUn_gl000213 length is 164239
        For chrUn_gl000220 length is 161802
        For chrUn_gl000218 length is 161147
        For chr19_gl000209_random length is 159169
        For chrUn_gl000221 length is 155397
        For chrUn_gl000214 length is 137718
        For chrUn_gl000228 length is 129120
        For chrUn_gl000227 length is 128374
        For chr1_gl000191_random length is 106433
        For chr19_gl000208_random length is 92689
        For chr9_gl000198_random length is 90085
        For chr17_gl000204_random length is 81310
        For chrUn_gl000233 length is 45941
        For chrUn_gl000237 length is 45867
        For chrUn_gl000230 length is 43691
        For chrUn_gl000242 length is 43523
        For chrUn_gl000243 length is 43341
        For chrUn_gl000241 length is 42152
        For chrUn_gl000236 length is 41934
        For chrUn_gl000240 length is 41933
        For chr17_gl000206_random length is 41001
        For chrUn_gl000232 length is 40652
        For chrUn_gl000234 length is 40531
        For chr11_gl000202_random length is 40103
        For chrUn_gl000238 length is 39939
        For chrUn_gl000244 length is 39929
        For chrUn_gl000248 length is 39786
        For chr8_gl000196_random length is 38914
        For chrUn_gl000249 length is 38502
        For chrUn_gl000246 length is 38154
        For chr17_gl000203_random length is 37498
        For chr8_gl000197_random length is 37175
        For chrUn_gl000245 length is 36651
        For chrUn_gl000247 length is 36422
        For chr9_gl000201_random length is 36148
        For chrUn_gl000235 length is 34474
        For chrUn_gl000239 length is 33824
        For chr21_gl000210_random length is 27682
        For chrUn_gl000231 length is 27386
        For chrUn_gl000229 length is 19913
        For chrM length is 16571
        For chrUn_gl000226 length is 15008
        For chr18_gl000207_random length is 4262
        For chr18_gl000207_random length is 4262
    Importing bowtie formatted reads
    Skipped 27645394 reads
    Imported 1 reads
    Sorting reads ...COMPLETE

Building window data

Processing 30
    Initializing to length 0
    Mapping reads to chromosome......
    Getting alignability info from:
        /mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/output_200/30.wig
Unable to open alignability file 
/mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/output_200/30.wig
ERROR: building windows was unsuccssful

--------BUILD WINDOWS COMPLETE-------

Error in file(file, "r") : cannot open the connection
In addition: Warning message:
In file(file, "r") :
  cannot open file '/mnt/sf_G_DRIVE/FASTQ-DATA/CD4-DNASE/SRR097566_files/SRR097566.list': No such file or directory
>

Original comment by por...@porter.st on 31 Jan 2012 at 5:55

GoogleCodeExporter commented 8 years ago 
basealigncount(inputfile='/mnt/sf_G_DRIVE/FASTQ-DATA/CD4-DNASE/SRR097566.hits',
  outputfile='/mnt/sf_G_DRIVE/FASTQ-DATA/CD4-DNASE/SRR097566.basecount',
  extension=200,
  filetype='bowtie',
  twoBitFile='/mnt/sf_G_DRIVE/FASTQ-DATA/b_indexes/hg19.2bit' );

zinba(
  align='/mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/output_200/',
  numProc=4,
  seq='/mnt/sf_G_DRIVE/FASTQ-DATA/CD4-DNASE/SRR097566.hits',
  basecountfile='/mnt/sf_G_DRIVE/FASTQ-DATA/CD4-DNASE/SRR097566.basecount',
  filetype='bowtie',
  outfile='/mnt/sf_G_DRIVE/FASTQ-DATA/CD4-DNASE/SRR097566',
  twoBit='/mnt/sf_G_DRIVE/FASTQ-DATA/b_indexes/hg19.2bit',
  extension=200,
  printFullOut=1,
  refinepeaks=1,
  broad=F,
  input='/mnt/sf_G_DRIVE/FASTQ-DATA/CD4-DNASE/SRR097566.hits'
)

Original comment by por...@porter.st on 31 Jan 2012 at 5:55

GoogleCodeExporter commented 8 years ago 
It looks like there is a remaining problem with the first column of the file 
(the read names).  The spaces in the name seem to be throwing off the code.  If 
you can remove the 

SOLEXA-1GA-2_0061_FC62988:7:1:3217:1128 length=36

from the first column of each row that will solve the problem.  I will have a 
new version of zinba by this saturday that will account for this issue.

Original comment by homer...@gmail.com on 31 Jan 2012 at 6:23

GoogleCodeExporter commented 8 years ago 
Finally, it looks like it start working. 

Loading bowtie formatted reads
    Skipped 0 reads
    Loaded 27645394 reads
    Sorting reads ...COMPLETE

Calculating counts at each base
Processing 27645394 reads
    Processing chr1..........
        Initializing length to 249250621
        2434477 reads mapped to chr1
        Printed results to /mnt/sf_G_DRIVE/FASTQ-DATA/CD4-DNASE/SRR097566.basecount
    Processing chr2..........
        Initializing length to 243199373
        2122618 reads mapped to chr2

Original comment by por...@porter.st on 31 Jan 2012 at 8:58

GoogleCodeExporter commented 8 years ago 
Great, I'll put this change on the agenda for this weekend.

Original comment by homer...@gmail.com on 31 Jan 2012 at 10:08