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Error in covariateselect #41

Open GoogleCodeExporter opened 8 years ago

GoogleCodeExporter commented 8 years ago 
1) What operating system are you using?

Ubuntu 12.04.1 LTS (GNU/Linux 3.2.0-32-generic x86_64)

2) What error message was displayed?

Error in covariateselect(file = data, selection = selecttype, loc = 
paste(outfile_subpath,  : covselect.R:  all models failed after model selection 
final step

3) What was the exact command you used that resulted in the error?

> zinba(
+ refinepeaks = 1,
+ seq = 'bowtie_8790.bed',
+ input = 'bowtie_8789.bed',
+ filetype = 'bed',
+ threshold = 0.05,
+ align = 'align_athresh2_extension250/',
+ numProc = 2,
+ twoBit = 'mm9.2bit',
+ outfile = '8790',
+ extension = 250,
+ basecountfile = 'bowtie_8790.basecount')

4) Please copy and paste any additional screen output that resulted from
running the command

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

--------BEGIN BUILDING WINDOW DATA-------- 2013-02-09 07:49:16 

Importing reads from file bowtie_8790.bed 
    Filetype is bed 
    Extension is 250 
    Importing bed formatted reads
    Skipped 0 reads
    Imported 12826524 reads
    Sorting reads ...COMPLETE

Building window data

Processing chr1
    Initializing to length 197195432
    Mapping reads to chromosome......
    Getting alignability info from:
        align_athresh2_extension250/chr1.wig
    Getting sequence from .2bit file:
        mm9.2bit
    Getting counts for 100000bp windows..........
        Refining boundaries....
            Global variance is 6.54869e-07
            Refining 15 boundaries
    Loading reads from input file bowtie_8789.bed.........
    Importing bed formatted reads
    Skipped 0 reads
        Imported 12222854 inpput reads
        Sorting reads ...COMPLETE
    Mapping input tags to the genome.........
    Getting counts for zinba windows..........
        Offset 0bp......
    Printed out data to 8790_files/bowtie_8790_chr1_win250bp_offset0bp.txt
        Offset 125bp......
    Printed out data to 8790_files/bowtie_8790_chr1_win250bp_offset125bp.txt

Processing chr2
    Initializing to length 181748087
    Mapping reads to chromosome......
    Getting alignability info from:
        align_athresh2_extension250/chr2.wig
    Getting sequence from .2bit file:
        mm9.2bit
    Getting counts for 100000bp windows..........
        Refining boundaries....
            Global variance is 0.00200199
            Refining 0 boundaries
    Mapping input tags to the genome.........
    Getting counts for zinba windows..........
        Offset 0bp......
    Printed out data to 8790_files/bowtie_8790_chr2_win250bp_offset0bp.txt
        Offset 125bp......
    Printed out data to 8790_files/bowtie_8790_chr2_win250bp_offset125bp.txt

Processing chr3
    Initializing to length 159599783
    Mapping reads to chromosome......
    Getting alignability info from:
        align_athresh2_extension250/chr3.wig
    Getting sequence from .2bit file:
        mm9.2bit
    Getting counts for 100000bp windows..........
        Refining boundaries....
            Global variance is 3.66645e-07
            Refining 43 boundaries
    Mapping input tags to the genome.........
    Getting counts for zinba windows..........
        Offset 0bp......
    Printed out data to 8790_files/bowtie_8790_chr3_win250bp_offset0bp.txt
        Offset 125bp......
    Printed out data to 8790_files/bowtie_8790_chr3_win250bp_offset125bp.txt

Processing chr4
    Initializing to length 155630120
    Mapping reads to chromosome......
    Getting alignability info from:
        align_athresh2_extension250/chr4.wig
    Getting sequence from .2bit file:
        mm9.2bit
    Getting counts for 100000bp windows..........
        Refining boundaries....
            Global variance is 1.23984e-06
            Refining 15 boundaries
    Mapping input tags to the genome.........
    Getting counts for zinba windows..........
        Offset 0bp......
    Printed out data to 8790_files/bowtie_8790_chr4_win250bp_offset0bp.txt
        Offset 125bp......
    Printed out data to 8790_files/bowtie_8790_chr4_win250bp_offset125bp.txt

Processing chr5
    Initializing to length 152537259
    Mapping reads to chromosome......
    Getting alignability info from:
        align_athresh2_extension250/chr5.wig
    Getting sequence from .2bit file:
        mm9.2bit
    Getting counts for 100000bp windows..........
        Refining boundaries....
            Global variance is 6.02429e-06
            Refining 14 boundaries
    Mapping input tags to the genome.........
    Getting counts for zinba windows..........
        Offset 0bp......
    Printed out data to 8790_files/bowtie_8790_chr5_win250bp_offset0bp.txt
        Offset 125bp......
    Printed out data to 8790_files/bowtie_8790_chr5_win250bp_offset125bp.txt

Processing chr6
    Initializing to length 149517037
    Mapping reads to chromosome......
    Getting alignability info from:
        align_athresh2_extension250/chr6.wig
    Getting sequence from .2bit file:
        mm9.2bit
    Getting counts for 100000bp windows..........
        Refining boundaries....
            Global variance is 6.82558e-07
            Refining 30 boundaries
    Mapping input tags to the genome.........
    Getting counts for zinba windows..........
        Offset 0bp......
    Printed out data to 8790_files/bowtie_8790_chr6_win250bp_offset0bp.txt
        Offset 125bp......
    Printed out data to 8790_files/bowtie_8790_chr6_win250bp_offset125bp.txt

Processing chr7
    Initializing to length 152524553
    Mapping reads to chromosome......
    Getting alignability info from:
        align_athresh2_extension250/chr7.wig
    Getting sequence from .2bit file:
        mm9.2bit
    Getting counts for 100000bp windows..........
        Refining boundaries....
            Global variance is 8.95374e-07
            Refining 10 boundaries
    Mapping input tags to the genome.........
    Getting counts for zinba windows..........
        Offset 0bp......
    Printed out data to 8790_files/bowtie_8790_chr7_win250bp_offset0bp.txt
        Offset 125bp......
    Printed out data to 8790_files/bowtie_8790_chr7_win250bp_offset125bp.txt

Processing chr8
    Initializing to length 131738871
    Mapping reads to chromosome......
    Getting alignability info from:
        align_athresh2_extension250/chr8.wig
    Getting sequence from .2bit file:
        mm9.2bit
    Getting counts for 100000bp windows..........
        Refining boundaries....
            Global variance is 5.60723e-07
            Refining 23 boundaries
    Mapping input tags to the genome.........
    Getting counts for zinba windows..........
        Offset 0bp......
    Printed out data to 8790_files/bowtie_8790_chr8_win250bp_offset0bp.txt
        Offset 125bp......
    Printed out data to 8790_files/bowtie_8790_chr8_win250bp_offset125bp.txt

Processing chr9
    Initializing to length 124076172
    Mapping reads to chromosome......
    Getting alignability info from:
        align_athresh2_extension250/chr9.wig
    Getting sequence from .2bit file:
        mm9.2bit
    Getting counts for 100000bp windows..........
        Refining boundaries....
            Global variance is 3.37966e-05
            Refining 1 boundaries
    Mapping input tags to the genome.........
    Getting counts for zinba windows..........
        Offset 0bp......
    Printed out data to 8790_files/bowtie_8790_chr9_win250bp_offset0bp.txt
        Offset 125bp......
    Printed out data to 8790_files/bowtie_8790_chr9_win250bp_offset125bp.txt

Processing chr10
    Initializing to length 129993255
    Mapping reads to chromosome......
    Getting alignability info from:
        align_athresh2_extension250/chr10.wig
    Getting sequence from .2bit file:
        mm9.2bit
    Getting counts for 100000bp windows..........
        Refining boundaries....
            Global variance is 4.13887e-05
            Refining 11 boundaries
    Mapping input tags to the genome.........
    Getting counts for zinba windows..........
        Offset 0bp......
    Printed out data to 8790_files/bowtie_8790_chr10_win250bp_offset0bp.txt
        Offset 125bp......
    Printed out data to 8790_files/bowtie_8790_chr10_win250bp_offset125bp.txt

Processing chr11
    Initializing to length 121843856
    Mapping reads to chromosome......
    Getting alignability info from:
        align_athresh2_extension250/chr11.wig
    Getting sequence from .2bit file:
        mm9.2bit
    Getting counts for 100000bp windows..........
        Refining boundaries....
            Global variance is 4.15339e-06
            Refining 3 boundaries
    Mapping input tags to the genome.........
    Getting counts for zinba windows..........
        Offset 0bp......
    Printed out data to 8790_files/bowtie_8790_chr11_win250bp_offset0bp.txt
        Offset 125bp......
    Printed out data to 8790_files/bowtie_8790_chr11_win250bp_offset125bp.txt

Processing chr12
    Initializing to length 121257530
    Mapping reads to chromosome......
    Getting alignability info from:
        align_athresh2_extension250/chr12.wig
    Getting sequence from .2bit file:
        mm9.2bit
    Getting counts for 100000bp windows..........
        Refining boundaries....
            Global variance is 2.04458e-06
            Refining 5 boundaries
    Mapping input tags to the genome.........
    Getting counts for zinba windows..........
        Offset 0bp......
    Printed out data to 8790_files/bowtie_8790_chr12_win250bp_offset0bp.txt
        Offset 125bp......
    Printed out data to 8790_files/bowtie_8790_chr12_win250bp_offset125bp.txt

Processing chr13
    Initializing to length 120284312
    Mapping reads to chromosome......
    Getting alignability info from:
        align_athresh2_extension250/chr13.wig
    Getting sequence from .2bit file:
        mm9.2bit
    Getting counts for 100000bp windows..........
        Refining boundaries....
            Global variance is 3.8046e-07
            Refining 29 boundaries
    Mapping input tags to the genome.........
    Getting counts for zinba windows..........
        Offset 0bp......
    Printed out data to 8790_files/bowtie_8790_chr13_win250bp_offset0bp.txt
        Offset 125bp......
    Printed out data to 8790_files/bowtie_8790_chr13_win250bp_offset125bp.txt

Processing chr14
    Initializing to length 125194864
    Mapping reads to chromosome......
    Getting alignability info from:
        align_athresh2_extension250/chr14.wig
    Getting sequence from .2bit file:
        mm9.2bit
    Getting counts for 100000bp windows..........
        Refining boundaries....
            Global variance is 8.73688e-07
            Refining 22 boundaries
    Mapping input tags to the genome.........
    Getting counts for zinba windows..........
        Offset 0bp......
    Printed out data to 8790_files/bowtie_8790_chr14_win250bp_offset0bp.txt
        Offset 125bp......
    Printed out data to 8790_files/bowtie_8790_chr14_win250bp_offset125bp.txt

Processing chr15
    Initializing to length 103494974
    Mapping reads to chromosome......
    Getting alignability info from:
        align_athresh2_extension250/chr15.wig
    Getting sequence from .2bit file:
        mm9.2bit
    Getting counts for 100000bp windows..........
        Refining boundaries....
            Global variance is 1.18667e-06
            Refining 13 boundaries
    Mapping input tags to the genome.........
    Getting counts for zinba windows..........
        Offset 0bp......
    Printed out data to 8790_files/bowtie_8790_chr15_win250bp_offset0bp.txt
        Offset 125bp......
    Printed out data to 8790_files/bowtie_8790_chr15_win250bp_offset125bp.txt

Processing chr16
    Initializing to length 98319150
    Mapping reads to chromosome......
    Getting alignability info from:
        align_athresh2_extension250/chr16.wig
    Getting sequence from .2bit file:
        mm9.2bit
    Getting counts for 100000bp windows..........
        Refining boundaries....
            Global variance is 4.57126e-07
            Refining 13 boundaries
    Mapping input tags to the genome.........
    Getting counts for zinba windows..........
        Offset 0bp......
    Printed out data to 8790_files/bowtie_8790_chr16_win250bp_offset0bp.txt
        Offset 125bp......
    Printed out data to 8790_files/bowtie_8790_chr16_win250bp_offset125bp.txt

Processing chr17
    Initializing to length 95272651
    Mapping reads to chromosome......
    Getting alignability info from:
        align_athresh2_extension250/chr17.wig
    Getting sequence from .2bit file:
        mm9.2bit
    Getting counts for 100000bp windows..........
        Refining boundaries....
            Global variance is 3.37504e-06
            Refining 3 boundaries
    Mapping input tags to the genome.........
    Getting counts for zinba windows..........
        Offset 0bp......
    Printed out data to 8790_files/bowtie_8790_chr17_win250bp_offset0bp.txt
        Offset 125bp......
    Printed out data to 8790_files/bowtie_8790_chr17_win250bp_offset125bp.txt

Processing chr18
    Initializing to length 90772031
    Mapping reads to chromosome......
    Getting alignability info from:
        align_athresh2_extension250/chr18.wig
    Getting sequence from .2bit file:
        mm9.2bit
    Getting counts for 100000bp windows..........
        Refining boundaries....
            Global variance is 3.84077e-07
            Refining 21 boundaries
    Mapping input tags to the genome.........
    Getting counts for zinba windows..........
        Offset 0bp......
    Printed out data to 8790_files/bowtie_8790_chr18_win250bp_offset0bp.txt
        Offset 125bp......
    Printed out data to 8790_files/bowtie_8790_chr18_win250bp_offset125bp.txt

Processing chr19
    Initializing to length 61342430
    Mapping reads to chromosome......
    Getting alignability info from:
        align_athresh2_extension250/chr19.wig
    Getting sequence from .2bit file:
        mm9.2bit
    Getting counts for 100000bp windows..........
        Refining boundaries....
            Global variance is 1.0509e-06
            Refining 7 boundaries
    Mapping input tags to the genome.........
    Getting counts for zinba windows..........
        Offset 0bp......
    Printed out data to 8790_files/bowtie_8790_chr19_win250bp_offset0bp.txt
        Offset 125bp......
    Printed out data to 8790_files/bowtie_8790_chr19_win250bp_offset125bp.txt

Processing chrX
    Initializing to length 166650296
    Mapping reads to chromosome......
    Getting alignability info from:
        align_athresh2_extension250/chrX.wig
    Getting sequence from .2bit file:
        mm9.2bit
    Getting counts for 100000bp windows..........
        Refining boundaries....
            Global variance is 5.27737e-07
            Refining 34 boundaries
    Mapping input tags to the genome.........
    Getting counts for zinba windows..........
        Offset 0bp......
    Printed out data to 8790_files/bowtie_8790_chrX_win250bp_offset0bp.txt
        Offset 125bp......
    Printed out data to 8790_files/bowtie_8790_chrX_win250bp_offset125bp.txt

Processing chrY
    Initializing to length 15902555
    Mapping reads to chromosome......
    Getting alignability info from:
        align_athresh2_extension250/chrY.wig
    Getting sequence from .2bit file:
        mm9.2bit
    Getting counts for 100000bp windows..........
        Refining boundaries....
            Global variance is 4.09031e-06
            Refining 1 boundaries
    Mapping input tags to the genome.........
    Getting counts for zinba windows..........
        Offset 0bp......
    Printed out data to 8790_files/bowtie_8790_chrY_win250bp_offset0bp.txt
        Offset 125bp......
    Printed out data to 8790_files/bowtie_8790_chrY_win250bp_offset125bp.txt

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

--------STARTING MODEL SELECTION-------- 2013-02-09 07:57:11 

Specified chromosome not found or specified, using 
8790_files/bowtie_8790_chrY_win250bp_offset125bp.txt 
$`1`
exp_count ~ 1
<environment: 0x1ee7f38>

$`2`
exp_count ~ input_count + 1
<environment: 0x1ee7f38>

..
model  1  completed out of  8   
model  2  completed out of  8   ..
model  3  completed out of  8   
model  4  completed out of  8   
model  5  completed out of  8   
model  6  completed out of  8   .
model  7  completed out of  8   
model  8  completed out of  8   Error in covariateselect(file = data, selection 
= selecttype, loc = paste(outfile_subpath,  : 
  covselect.R:  all models failed after model selection final step
>

Original issue reported on code.google.com by ania_saw...@yahoo.com on 9 Feb 2013 at 7:18

GoogleCodeExporter commented 8 years ago 
The same error here

Original comment by zongzhi....@gmail.com on 20 May 2014 at 4:05

GoogleCodeExporter commented 8 years ago 
I'm having the same problem:
Error in covariateselect(file = data, selection = selecttype, loc = 
paste(outfile_subpath,  : 
  covselect.R:  all models failed after model selection intermediate step
Calls: zinba -> run.zinba -> covariateselect
Execution halted

Ubuntu 14.04 64 bits

sessionInfo()
R version 2.15.0 (2012-03-30)
Platform: x86_64-unknown-linux-gnu (64-bit)  

attached base packages:
[1] stats     graphics  grDevices utils     datasets  base     

other attached packages:
[1] zinba_2.02.03

Original comment by bionob...@gmail.com on 25 Sep 2014 at 9:30