Hi there, I am trying to use zinba, but the tools errors and exits when running
zinba(). The reason for this, i think, is the fact that the hg19.2bit file does
not contain extra "chromosomes" (e.g.chr6_ssto_hap7, chrUn* etc) while the
standard uscg.hg19.fasta does. Is there a way I can solve this in zinba?
1) What operating system are you using?
Linux .x86_64
2) What error message was displayed?
Processing chr6_ssto_hap7
Initializing to length 4928567
Mapping reads to chromosome......
Getting alignability info from:
/u/home/.../chr6_ssto_hap7.wig
Unable to open alignability file /u/home/.../chr6_ssto_hap7.wig
Error in buildwindowdata(seq = seq, align = align, input = input, twoBit =
twoBit, :
ERROR: building windows was unsuccssful
3) What was the exact command you used that resulted in the error?
generateAlignability(
mapdir='/u/home/.../files',
outdir='/u/home/...zinba_out',
athresh=1,
extension=200,
twoBitFile='/u/home/.../files/hg19.2bit'
)
basealigncount(
inputfile='/u/home/...file_mergeall.bed', #mapped sample reads
outputfile='/u/home/.../file_mergeall_zinba', # output path
extension=300, #average fragment library length
filetype='bed', #either "bed", "bowtie", or "tagAlign"
twoBitFile='/u/home/.../files/hg19.2bit', #path to downloaded genome build file in .2bit format
)
zinba(
refinepeaks=1, #refine peaks? 1 for yes, 0 for no
align='/u/home/...zinba_out',
seq='/u/home/...file_mergeall.bed', #path to mapped experimental reads
input="none", #path to mapped input reads if available (default is "none")
filetype='bed', #either 'bed', 'bowtie', or 'tagAlign'
threshold=0.2, #FDR threshold, default is 0.05
numProc=1, #number of CPUs to use, must be less than max available (default 1)
basecountfile='/u/home/.../file_mergeall_zinba',
twoBit='/u/home/.../files/hg19.2bit', #path to genome build in .2bit format
outfile='/u/home/.../file_mergeall_zinba_peak', #prefix for outputted files
extension=300, #average fragment library length (size selected)
broad=T
)
4) Please copy and paste any additional screen output that resulted from
running the command
> generateAlignability(
+ mapdir='/u/home/.../files',
+ outdir='/u/home/...zinba_out',
+ athresh=1,
+ extension=200,
+ twoBitFile='/u/home/.../files/hg19.2bit'
+ )
Overwriting existing directory at /u/home/.../
Starting generateAlignability
Processing chr10b.out .......
chr10 .......
Processing chr11b.out .......
chr11 .............
......
Processing chrYb.out .......
chrY .......
Loading align count data from /u/home/.../files/temp.wig
Processing chr10
Printing output to: /u/home/.../chr10.wig
Processing chr11
Printing output to: /u/home/.../chr11.wig
........
Processing chrY
Printing output to: /u/home/.../chrY.wig
Processing chrY
Printing output to: /u/home/.../chrY.wig
---------------- ALIGN ADJUST COMPLETED SUCCESSFULLY ----------------
> basealigncount(
+ inputfile='/u/home/...file_mergeall.bed', #mapped sample reads
+ outputfile='/u/home/.../file_mergeall_zinba', # output path
+ extension=300, #average fragment library length
+ filetype='bed', #either "bed", "bowtie", or "tagAlign"
+ twoBitFile='/u/home/.../files/hg19.2bit', #path to downloaded genome build
file in .2bit format
+ )
Importing reads from file /u/home/...file_mergeall.bed ....
Reads are formatted as bed ....
Extending reads by 300 bp....
For chr1 length is 249250621
For chr2 length is 243199373
.......
For chrUn_gl000226 length is 15008
For chr18_gl000207_random length is 4262
For chr18_gl000207_random length is 4262
Importing bed formatted reads
Skipped 0 reads
Loaded 62359102 reads
Sorting reads ...COMPLETE
Calculating counts at each base
Processing 62359102 reads
Processing chr1..........
Initializing length to 249250621
5110647 reads mapped to chr1
Printed results to /u/home/.../file_mergeall_zinba
..........
Processing chrM..........
Initializing length to 16571
287206 reads mapped to chrM
Printed results to /u/home/.../file_mergeall_zinba
Processing chrUn_gl000226..........
Initializing length to 15008
23440 reads mapped to chrUn_gl000226
Printed results to /u/home/.../file_mergeall_zinba
Processing chr18_gl000207_random..........
Initializing length to 4262
81 reads mapped to chr18_gl000207_random
Printed results to /u/home/.../file_mergeall_zinba
-------- BASE ALIGN COUNTS COMPLETE SUCCESSFULLY --------
> zinba(
+ refinepeaks=1, #refine peaks? 1 for yes, 0 for no
+ align='/u/home/...zinba_out',
+ seq='/u/home/...file_mergeall.bed', #path to mapped experimental reads
+ input="none", #path to mapped input reads if available (default is "none")
+ filetype='bed', #either 'bed', 'bowtie', or 'tagAlign'
+ threshold=0.2, #FDR threshold, default is 0.05
+ numProc=1, #number of CPUs to use, must be less than max available
(default 1)
+ basecountfile='/u/home/.../file_mergeall_zinba',
+ twoBit='/u/home/.../files/hg19.2bit', #path to genome build in .2bit format
+ outfile='/u/home/.../file_mergeall_zinba_peak', #prefix for outputted files
+ extension=300, #average fragment library length (size selected)
+ broad=T
+ )
[1] "parameters in effect:"
$filelist
NULL
$formula
NULL
$formulaE
NULL
$formulaZ
NULL
$outfile
[1] "/u/home/.../file_mergeall_zinba_peak"
$seq
[1] "/u/home/...file_mergeall.bed"
$align
[1] "/u/home/...zinba_out"
$input
[1] "none"
$twoBit
[1] "/u/home/.../files/hg19.2bit"
$winSize
[1] 250
$offset
[1] 125
$cnvWinSize
[1] 1e+05
$cnvOffset
[1] 2500
$basecountfile
[1] "/u/home/.../file_mergeall_zinba"
$threshold
[1] 0.2
$peakconfidence
[1] 0.8
$tol
[1] 1e-05
$numProc
[1] 1
$buildwin
[1] 1
$winGap
[1] 5000
$pWinSize
[1] 200
$pquant
[1] 1
$refinepeaks
[1] 1
$printFullOut
[1] 1
$method
[1] "mixture"
$initmethod
[1] "count"
$diff
[1] 0
$filetype
[1] "bed"
$extension
[1] 300
$cleanup
[1] FALSE
$selectmodel
[1] TRUE
$selectchr
[1] "chr22"
$selecttype
[1] "dirty"
$selectcovs
[1] "gcPerc" "align_perc"
$FDR
[1] TRUE
$interaction
[1] TRUE
Loading required package: doMC
--------BEGIN BUILDING WINDOW DATA-------- 2014-05-13 14:29:36
Importing reads from file /u/home/...file_mergeall.bed
Filetype is bed
Extension is 300
Importing bed formatted reads
Skipped 0 reads
Imported 62359102 reads
Sorting reads ...COMPLETE
Building window data
Processing chr1
Initializing to length 249250621
Mapping reads to chromosome......
Getting alignability info from:
/u/home/.../chr1.wig
Getting sequence from .2bit file:
/u/home/.../files/hg19.2bit
Getting counts for 100000bp windows..........
Refining boundaries....
Global variance is 0.00103839
Refining 6 boundaries
Getting counts for zinba windows..........
Offset 0bp......
Printed out data to /u/home/.../file_mergeall_zinba_peak_files/file_mergeall_chr1_win250bp_offset0bp.txt
Offset 125bp......
Printed out data to /u/home/.../file_mergeall_zinba_peak_files/file_mergeall_chr1_win250bp_offset125bp.txt
Processing chr21
Initializing to length 48129895
Mapping reads to chromosome......
Getting alignability info from:
/u/home/.../chr21.wig
Getting sequence from .2bit file:
/u/home/.../files/hg19.2bit
Getting counts for 100000bp windows..........
Refining boundaries....
Global variance is 1.32689e-05
Refining 14 boundaries
Getting counts for zinba windows..........
Offset 0bp......
Printed out data to /u/home/.../file_mergeall_zinba_peak_files/file_mergeall_chr21_win250bp_offset0bp.txt
Offset 125bp......
Printed out data to /u/home/.../file_mergeall_zinba_peak_files/file_mergeall_chr21_win250bp_offset125bp.txt
Processing chr6_ssto_hap7
Initializing to length 4928567
Mapping reads to chromosome......
Getting alignability info from:
/u/home/.../chr6_ssto_hap7.wig
Unable to open alignability file /u/home/.../chr6_ssto_hap7.wig
Error in buildwindowdata(seq = seq, align = align, input = input, twoBit =
twoBit, :
ERROR: building windows was unsuccssful
In addition: Warning message:
In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return =
TRUE, :
there is no package called ‘doMC’
Original issue reported on code.google.com by l77ago...@gmail.com on 13 May 2014 at 10:45
Original issue reported on code.google.com by
l77ago...@gmail.comon 13 May 2014 at 10:45