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SHZ66 / zinba

Automatically exported from code.google.com/p/zinba
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zinba.so crushed R #12

Closed GoogleCodeExporter closed 8 years ago

GoogleCodeExporter commented 8 years ago 
1) OpenSUSE 12.1 x64

2) *** glibc detected *** /usr/lib64/R/bin/exec/R: double free or corruption 
(out): 0x00007fff32499cb0 ***
======= Backtrace: =========
/lib64/libc.so.6(+0x74c06)[0x7f004fd73c06]
/usr/lib64/R/library/zinba/libs/zinba.so(+0x3af4a)[0x7f004c6c2f4a]

3) 
zinba(
  align='/mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/output_200/',
  numProc=4,
  seq='/mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/Naive-H3K4me3-Duplicate-236-8.hits',
  basecountfile='/mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/Naive-H3K4me3-Duplicate-236-8.basecount',
  filetype='bowtie',
  outfile='/mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/Naive-H3K4me3',
  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/ZINBA/Naive-H3K4me3-Duplicate-236-8.hits'
)

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

Not whole output are saved... I'll increase output buffer. Also the size of 
.hits file is 520MB(uncompressed) should I compressed and attach ?
________________________________________________________________________
    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 0 reads
    Imported 4811071 reads
    Sorting reads ...COMPLETE

Building window data

...

Original issue reported on code.google.com by por...@porter.st on 3 Feb 2012 at 3:26

GoogleCodeExporter commented 8 years ago 
Processing chr1
    Initializing to length 249250621
    Mapping reads to chromosome......
    Getting alignability info from:
        /mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/output_200/chr1.wig
    Getting sequence from .2bit file:
        /mnt/sf_G_DRIVE/FASTQ-DATA/b_indexes/hg19.2bit
    Getting counts for 100000bp windows..........
        Refining boundaries....
            Global variance is 3.73992e-06
            Refining 211 boundaries
    Loading reads from input file /mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/Naive-H3K4me3-Duplicate-236-8.hits.........
    Importing bowtie formatted reads
    Skipped 0 reads
        Imported 4811071 inpput reads
        Sorting reads ...COMPLETE
    Mapping input tags to the genome.........
    Getting counts for zinba windows..........
        Offset 0bp......
    Printed out data to /mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/Naive-H3K4me3_files/Naive-H3K4me3-Duplicate-236-8_chr1_win250bp_offset0bp.txt
        Offset 125bp......
    Printed out data to /mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/Naive-H3K4me3_files/Naive-H3K4me3-Duplicate-236-8_chr1_win250bp_offset125bp.txt

Processing chr2
    Initializing to length 243199373
    Mapping reads to chromosome......
    Getting alignability info from:
        /mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/output_200/chr2.wig
    Getting sequence from .2bit file:
        /mnt/sf_G_DRIVE/FASTQ-DATA/b_indexes/hg19.2bit
    Getting counts for 100000bp windows..........
        Refining boundaries....
            Global variance is 2.3066e-06
            Refining 230 boundaries
    Mapping input tags to the genome.........
    Getting counts for zinba windows..........
        Offset 0bp......
    Printed out data to /mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/Naive-H3K4me3_files/Naive-H3K4me3-Duplicate-236-8_chr2_win250bp_offset0bp.txt
        Offset 125bp......
    Printed out data to /mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/Naive-H3K4me3_files/Naive-H3K4me3-Duplicate-236-8_chr2_win250bp_offset125bp.txt

Processing chr3
    Initializing to length 198022430
    Mapping reads to chromosome......
    Getting alignability info from:
        /mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/output_200/chr3.wig
    Getting sequence from .2bit file:
        /mnt/sf_G_DRIVE/FASTQ-DATA/b_indexes/hg19.2bit
    Getting counts for 100000bp windows..........
        Refining boundaries....
            Global variance is 2.23328e-06
            Refining 201 boundaries
    Mapping input tags to the genome.........
    Getting counts for zinba windows..........
        Offset 0bp......
    Printed out data to /mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/Naive-H3K4me3_files/Naive-H3K4me3-Duplicate-236-8_chr3_win250bp_offset0bp.txt
        Offset 125bp......
    Printed out data to /mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/Naive-H3K4me3_files/Naive-H3K4me3-Duplicate-236-8_chr3_win250bp_offset125bp.txt

Processing chr4
    Initializing to length 191154276
    Mapping reads to chromosome......
    Getting alignability info from:
        /mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/output_200/chr4.wig
    Getting sequence from .2bit file:
        /mnt/sf_G_DRIVE/FASTQ-DATA/b_indexes/hg19.2bit
    Getting counts for 100000bp windows..........
        Refining boundaries....
            Global variance is 1.40515e-06
            Refining 179 boundaries
    Mapping input tags to the genome.........
    Getting counts for zinba windows..........
        Offset 0bp......
    Printed out data to /mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/Naive-H3K4me3_files/Naive-H3K4me3-Duplicate-236-8_chr4_win250bp_offset0bp.txt
        Offset 125bp......
    Printed out data to /mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/Naive-H3K4me3_files/Naive-H3K4me3-Duplicate-236-8_chr4_win250bp_offset125bp.txt

Processing chr5
    Initializing to length 180915260
    Mapping reads to chromosome......
    Getting alignability info from:
        /mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/output_200/chr5.wig
    Getting sequence from .2bit file:
        /mnt/sf_G_DRIVE/FASTQ-DATA/b_indexes/hg19.2bit
    Getting counts for 100000bp windows..........
        Refining boundaries....
            Global variance is 2.67944e-06
            Refining 141 boundaries
    Mapping input tags to the genome.........
    Getting counts for zinba windows..........
        Offset 0bp......
    Printed out data to /mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/Naive-H3K4me3_files/Naive-H3K4me3-Duplicate-236-8_chr5_win250bp_offset0bp.txt
        Offset 125bp......
    Printed out data to /mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/Naive-H3K4me3_files/Naive-H3K4me3-Duplicate-236-8_chr5_win250bp_offset125bp.txt

Processing chr6
    Initializing to length 171115067
    Mapping reads to chromosome......
    Getting alignability info from:
        /mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/output_200/chr6.wig
    Getting sequence from .2bit file:
        /mnt/sf_G_DRIVE/FASTQ-DATA/b_indexes/hg19.2bit
    Getting counts for 100000bp windows..........
        Refining boundaries....
            Global variance is 3.34593e-06
            Refining 130 boundaries
    Mapping input tags to the genome.........
    Getting counts for zinba windows..........
        Offset 0bp......
    Printed out data to /mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/Naive-H3K4me3_files/Naive-H3K4me3-Duplicate-236-8_chr6_win250bp_offset0bp.txt
        Offset 125bp......
    Printed out data to /mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/Naive-H3K4me3_files/Naive-H3K4me3-Duplicate-236-8_chr6_win250bp_offset125bp.txt

Processing chr7
    Initializing to length 159138663
    Mapping reads to chromosome......
    Getting alignability info from:
        /mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/output_200/chr7.wig
    Getting sequence from .2bit file:
        /mnt/sf_G_DRIVE/FASTQ-DATA/b_indexes/hg19.2bit
    Getting counts for 100000bp windows..........
        Refining boundaries....
            Global variance is 2.36365e-06
            Refining 124 boundaries
    Mapping input tags to the genome.........
    Getting counts for zinba windows..........
        Offset 0bp......
    Printed out data to /mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/Naive-H3K4me3_files/Naive-H3K4me3-Duplicate-236-8_chr7_win250bp_offset0bp.txt
        Offset 125bp......
    Printed out data to /mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/Naive-H3K4me3_files/Naive-H3K4me3-Duplicate-236-8_chr7_win250bp_offset125bp.txt

Processing chrX
    Initializing to length 155270560
    Mapping reads to chromosome......
    Getting alignability info from:
        /mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/output_200/chrX.wig
    Getting sequence from .2bit file:
        /mnt/sf_G_DRIVE/FASTQ-DATA/b_indexes/hg19.2bit
    Getting counts for 100000bp windows..........
        Refining boundaries....
            Global variance is 6.45025e-07
            Refining 127 boundaries
    Mapping input tags to the genome.........
    Getting counts for zinba windows..........
        Offset 0bp......
    Printed out data to /mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/Naive-H3K4me3_files/Naive-H3K4me3-Duplicate-236-8_chrX_win250bp_offset0bp.txt
        Offset 125bp......
    Printed out data to /mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/Naive-H3K4me3_files/Naive-H3K4me3-Duplicate-236-8_chrX_win250bp_offset125bp.txt

Processing chr8
    Initializing to length 146364022
    Mapping reads to chromosome......
    Getting alignability info from:
        /mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/output_200/chr8.wig
    Getting sequence from .2bit file:
        /mnt/sf_G_DRIVE/FASTQ-DATA/b_indexes/hg19.2bit
    Getting counts for 100000bp windows..........
        Refining boundaries....
            Global variance is 1.60753e-06
            Refining 133 boundaries
    Mapping input tags to the genome.........
    Getting counts for zinba windows..........
        Offset 0bp......
    Printed out data to /mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/Naive-H3K4me3_files/Naive-H3K4me3-Duplicate-236-8_chr8_win250bp_offset0bp.txt
        Offset 125bp......
    Printed out data to /mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/Naive-H3K4me3_files/Naive-H3K4me3-Duplicate-236-8_chr8_win250bp_offset125bp.txt

Processing chr9
    Initializing to length 141213431
    Mapping reads to chromosome......
    Getting alignability info from:
        /mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/output_200/chr9.wig
    Getting sequence from .2bit file:
        /mnt/sf_G_DRIVE/FASTQ-DATA/b_indexes/hg19.2bit
    Getting counts for 100000bp windows..........
        Refining boundaries....
            Global variance is 2.32899e-06
            Refining 114 boundaries
    Mapping input tags to the genome.........
    Getting counts for zinba windows..........
        Offset 0bp......
    Printed out data to /mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/Naive-H3K4me3_files/Naive-H3K4me3-Duplicate-236-8_chr9_win250bp_offset0bp.txt
        Offset 125bp......
    Printed out data to /mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/Naive-H3K4me3_files/Naive-H3K4me3-Duplicate-236-8_chr9_win250bp_offset125bp.txt

Processing chr10
    Initializing to length 135534747
    Mapping reads to chromosome......
    Getting alignability info from:
        /mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/output_200/chr10.wig
    Getting sequence from .2bit file:
        /mnt/sf_G_DRIVE/FASTQ-DATA/b_indexes/hg19.2bit
    Getting counts for 100000bp windows..........
        Refining boundaries....
            Global variance is 2.12094e-06
            Refining 134 boundaries
    Mapping input tags to the genome.........
    Getting counts for zinba windows..........
        Offset 0bp......
    Printed out data to /mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/Naive-H3K4me3_files/Naive-H3K4me3-Duplicate-236-8_chr10_win250bp_offset0bp.txt
        Offset 125bp......
    Printed out data to /mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/Naive-H3K4me3_files/Naive-H3K4me3-Duplicate-236-8_chr10_win250bp_offset125bp.txt

Processing chr11
    Initializing to length 135006516
    Mapping reads to chromosome......
    Getting alignability info from:
        /mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/output_200/chr11.wig
    Getting sequence from .2bit file:
        /mnt/sf_G_DRIVE/FASTQ-DATA/b_indexes/hg19.2bit
    Getting counts for 100000bp windows..........
        Refining boundaries....
            Global variance is 4.2534e-06
            Refining 95 boundaries
    Mapping input tags to the genome.........
    Getting counts for zinba windows..........
        Offset 0bp......
    Printed out data to /mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/Naive-H3K4me3_files/Naive-H3K4me3-Duplicate-236-8_chr11_win250bp_offset0bp.txt
        Offset 125bp......
    Printed out data to /mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/Naive-H3K4me3_files/Naive-H3K4me3-Duplicate-236-8_chr11_win250bp_offset125bp.txt

Processing chr12
    Initializing to length 133851895
    Mapping reads to chromosome......
    Getting alignability info from:
        /mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/output_200/chr12.wig
    Getting sequence from .2bit file:
        /mnt/sf_G_DRIVE/FASTQ-DATA/b_indexes/hg19.2bit
    Getting counts for 100000bp windows..........
        Refining boundaries....
            Global variance is 3.27651e-06
            Refining 112 boundaries
    Mapping input tags to the genome.........
    Getting counts for zinba windows..........
        Offset 0bp......
    Printed out data to /mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/Naive-H3K4me3_files/Naive-H3K4me3-Duplicate-236-8_chr12_win250bp_offset0bp.txt
        Offset 125bp......
    Printed out data to /mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/Naive-H3K4me3_files/Naive-H3K4me3-Duplicate-236-8_chr12_win250bp_offset125bp.txt

Processing chr13
    Initializing to length 115169878
    Mapping reads to chromosome......
    Getting alignability info from:
        /mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/output_200/chr13.wig
    Getting sequence from .2bit file:
        /mnt/sf_G_DRIVE/FASTQ-DATA/b_indexes/hg19.2bit
    Getting counts for 100000bp windows..........
        Refining boundaries....
            Global variance is 1.44439e-06
            Refining 90 boundaries
    Mapping input tags to the genome.........
    Getting counts for zinba windows..........
        Offset 0bp......
    Printed out data to /mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/Naive-H3K4me3_files/Naive-H3K4me3-Duplicate-236-8_chr13_win250bp_offset0bp.txt
        Offset 125bp......
    Printed out data to /mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/Naive-H3K4me3_files/Naive-H3K4me3-Duplicate-236-8_chr13_win250bp_offset125bp.txt

Processing chr14
    Initializing to length 107349540
    Mapping reads to chromosome......
    Getting alignability info from:
        /mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/output_200/chr14.wig
    Getting sequence from .2bit file:
        /mnt/sf_G_DRIVE/FASTQ-DATA/b_indexes/hg19.2bit
    Getting counts for 100000bp windows..........
        Refining boundaries....
            Global variance is 3.28852e-06
            Refining 78 boundaries
    Mapping input tags to the genome.........
    Getting counts for zinba windows..........
        Offset 0bp......
    Printed out data to /mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/Naive-H3K4me3_files/Naive-H3K4me3-Duplicate-236-8_chr14_win250bp_offset0bp.txt
        Offset 125bp......
    Printed out data to /mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/Naive-H3K4me3_files/Naive-H3K4me3-Duplicate-236-8_chr14_win250bp_offset125bp.txt

Processing chr15
    Initializing to length 102531392
    Mapping reads to chromosome......
    Getting alignability info from:
        /mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/output_200/chr15.wig
    Getting sequence from .2bit file:
        /mnt/sf_G_DRIVE/FASTQ-DATA/b_indexes/hg19.2bit
    Getting counts for 100000bp windows..........
        Refining boundaries....
            Global variance is 2.67231e-06
            Refining 94 boundaries
    Mapping input tags to the genome.........
    Getting counts for zinba windows..........
        Offset 0bp......
    Printed out data to /mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/Naive-H3K4me3_files/Naive-H3K4me3-Duplicate-236-8_chr15_win250bp_offset0bp.txt
        Offset 125bp......
    Printed out data to /mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/Naive-H3K4me3_files/Naive-H3K4me3-Duplicate-236-8_chr15_win250bp_offset125bp.txt

Processing chr16
    Initializing to length 90354753
    Mapping reads to chromosome......
    Getting alignability info from:
        /mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/output_200/chr16.wig
    Getting sequence from .2bit file:
        /mnt/sf_G_DRIVE/FASTQ-DATA/b_indexes/hg19.2bit
    Getting counts for 100000bp windows..........
        Refining boundaries....
            Global variance is 4.05903e-06
            Refining 65 boundaries
    Mapping input tags to the genome.........
    Getting counts for zinba windows..........
        Offset 0bp......
    Printed out data to /mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/Naive-H3K4me3_files/Naive-H3K4me3-Duplicate-236-8_chr16_win250bp_offset0bp.txt
        Offset 125bp......
    Printed out data to /mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/Naive-H3K4me3_files/Naive-H3K4me3-Duplicate-236-8_chr16_win250bp_offset125bp.txt

Processing chr17
    Initializing to length 81195210
    Mapping reads to chromosome......
    Getting alignability info from:
        /mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/output_200/chr17.wig
    Getting sequence from .2bit file:
        /mnt/sf_G_DRIVE/FASTQ-DATA/b_indexes/hg19.2bit
    Getting counts for 100000bp windows..........
        Refining boundaries....
            Global variance is 5.21264e-06
            Refining 68 boundaries
    Mapping input tags to the genome.........
    Getting counts for zinba windows..........
        Offset 0bp......
    Printed out data to /mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/Naive-H3K4me3_files/Naive-H3K4me3-Duplicate-236-8_chr17_win250bp_offset0bp.txt
        Offset 125bp......
    Printed out data to /mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/Naive-H3K4me3_files/Naive-H3K4me3-Duplicate-236-8_chr17_win250bp_offset125bp.txt

Processing chr18
    Initializing to length 78077248
    Mapping reads to chromosome......
    Getting alignability info from:
        /mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/output_200/chr18.wig
    Getting sequence from .2bit file:
        /mnt/sf_G_DRIVE/FASTQ-DATA/b_indexes/hg19.2bit
    Getting counts for 100000bp windows..........
        Refining boundaries....
            Global variance is 1.31377e-06
            Refining 80 boundaries
    Mapping input tags to the genome.........
    Getting counts for zinba windows..........
        Offset 0bp......
    Printed out data to /mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/Naive-H3K4me3_files/Naive-H3K4me3-Duplicate-236-8_chr18_win250bp_offset0bp.txt
        Offset 125bp......
    Printed out data to /mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/Naive-H3K4me3_files/Naive-H3K4me3-Duplicate-236-8_chr18_win250bp_offset125bp.txt

Processing chr20
    Initializing to length 63025520
    Mapping reads to chromosome......
    Getting alignability info from:
        /mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/output_200/chr20.wig
    Getting sequence from .2bit file:
        /mnt/sf_G_DRIVE/FASTQ-DATA/b_indexes/hg19.2bit
    Getting counts for 100000bp windows..........
        Refining boundaries....
            Global variance is 2.36898e-06
            Refining 73 boundaries
    Mapping input tags to the genome.........
    Getting counts for zinba windows..........
        Offset 0bp......
    Printed out data to /mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/Naive-H3K4me3_files/Naive-H3K4me3-Duplicate-236-8_chr20_win250bp_offset0bp.txt
        Offset 125bp......
    Printed out data to /mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/Naive-H3K4me3_files/Naive-H3K4me3-Duplicate-236-8_chr20_win250bp_offset125bp.txt

Processing chrY
    Initializing to length 59373566
    Mapping reads to chromosome......
    Getting alignability info from:
        /mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/output_200/chrY.wig
    Getting sequence from .2bit file:
        /mnt/sf_G_DRIVE/FASTQ-DATA/b_indexes/hg19.2bit
    Getting counts for 100000bp windows..........
        Refining boundaries....
            Global variance is 2.68433e-07
            Refining 19 boundaries
    Mapping input tags to the genome.........
    Getting counts for zinba windows..........
        Offset 0bp......
    Printed out data to /mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/Naive-H3K4me3_files/Naive-H3K4me3-Duplicate-236-8_chrY_win250bp_offset0bp.txt
        Offset 125bp......
    Printed out data to /mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/Naive-H3K4me3_files/Naive-H3K4me3-Duplicate-236-8_chrY_win250bp_offset125bp.txt

Processing chr19
    Initializing to length 59128983
    Mapping reads to chromosome......
    Getting alignability info from:
        /mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/output_200/chr19.wig
    Getting sequence from .2bit file:
        /mnt/sf_G_DRIVE/FASTQ-DATA/b_indexes/hg19.2bit
    Getting counts for 100000bp windows..........
        Refining boundaries....
            Global variance is 6.56945e-06
            Refining 68 boundaries
    Mapping input tags to the genome.........
    Getting counts for zinba windows..........
        Offset 0bp......
    Printed out data to /mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/Naive-H3K4me3_files/Naive-H3K4me3-Duplicate-236-8_chr19_win250bp_offset0bp.txt
        Offset 125bp......
    Printed out data to /mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/Naive-H3K4me3_files/Naive-H3K4me3-Duplicate-236-8_chr19_win250bp_offset125bp.txt

Processing chr22
    Initializing to length 51304566
    Mapping reads to chromosome......
    Getting alignability info from:
        /mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/output_200/chr22.wig
    Getting sequence from .2bit file:
        /mnt/sf_G_DRIVE/FASTQ-DATA/b_indexes/hg19.2bit
    Getting counts for 100000bp windows..........
        Refining boundaries....
            Global variance is 3.49813e-06
            Refining 43 boundaries
    Mapping input tags to the genome.........
    Getting counts for zinba windows..........
        Offset 0bp......
    Printed out data to /mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/Naive-H3K4me3_files/Naive-H3K4me3-Duplicate-236-8_chr22_win250bp_offset0bp.txt
        Offset 125bp......
    Printed out data to /mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/Naive-H3K4me3_files/Naive-H3K4me3-Duplicate-236-8_chr22_win250bp_offset125bp.txt

Processing chr21
    Initializing to length 48129895
    Mapping reads to chromosome......
    Getting alignability info from:
        /mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/output_200/chr21.wig
    Getting sequence from .2bit file:
        /mnt/sf_G_DRIVE/FASTQ-DATA/b_indexes/hg19.2bit
    Getting counts for 100000bp windows..........
        Refining boundaries....
            Global variance is 1.98445e-06
            Refining 34 boundaries
    Mapping input tags to the genome.........
    Getting counts for zinba windows..........
        Offset 0bp......
    Printed out data to /mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/Naive-H3K4me3_files/Naive-H3K4me3-Duplicate-236-8_chr21_win250bp_offset0bp.txt
        Offset 125bp......
    Printed out data to /mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/Naive-H3K4me3_files/Naive-H3K4me3-Duplicate-236-8_chr21_win250bp_offset125bp.txt

Processing chrM
    Initializing to length 16571
    Mapping reads to chromosome......
    Getting alignability info from:
        /mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/output_200/chrM.wig
    Getting sequence from .2bit file:
        /mnt/sf_G_DRIVE/FASTQ-DATA/b_indexes/hg19.2bit
    Getting counts for 100000bp windows..........
        Refining boundaries....
            Global variance is 1.68319e-06
            Refining 0 boundaries
    Mapping input tags to the genome.........
    Getting counts for zinba windows..........
        Offset 0bp......
    Printed out data to /mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/Naive-H3K4me3_files/Naive-H3K4me3-Duplicate-236-8_chrM_win250bp_offset0bp.txt
        Offset 125bp......
    Printed out data to /mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/Naive-H3K4me3_files/Naive-H3K4me3-Duplicate-236-8_chrM_win250bp_offset125bp.txt

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

Original comment by por...@porter.st on 3 Feb 2012 at 3:26

GoogleCodeExporter commented 8 years ago 
--------STARTING MODEL SELECTION-------- 2012-02-02 18:13:10 

$`1`
exp_count ~ 1
<environment: 0x399c688>

$`2`
exp_count ~ input_count + 1
<environment: 0x399c688>

...............................[1] "The estimated proportion of enrichment for  

/mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/Naive-H3K4me3_files/Naive-H3K4me3-Duplicate-236
-8_chr22_win250bp_offset0bp.txt  has exceeded 0.5, suggesting difficulty in 
estimating enrichment.  Switching to more conservative model"

model  3  completed out of  8   ............[1] "The estimated proportion of 
enrichment for   
/mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/Naive-H3K4me3_files/Naive-H3K4me3-Duplicate-236
-8_chr22_win250bp_offset0bp.txt  has exceeded 0.5, suggesting difficulty in 
estimating enrichment.  Switching to more conservative model"

model  4  completed out of  8   ...........................
model  2  completed out of  8 
    ...............................................................................
................................................................................
..............................................
model  6  completed out of  8   ........................
model  1  completed out of  8 
    ...............................................................................
................................................................................
.............................................
model  5  completed out of  8   ..
model  8  completed out of  8 
    ...............................................................................
......................................................
model  7  completed out of  8   Background formula is:
    exp_count ~ input_count + 1
<environment: 0x399c688>
Enrichment formula is:
    exp_count ~ 1
<environment: 0x399c688>
Zero-inflated formula is:
    exp_count ~ 1
<environment: 0x399c688>
--------MODEL SELECTION COMPLETE-------- 2012-02-02 18:56:51 

--------GETTING ENRICHED WINDOWS-------- 2012-02-02 18:56:51 

.......................................................
Processed 
/mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/Naive-H3K4me3_files/Naive-H3K4me3-Duplicate-236
-8_chr4_win250bp_offset0bp.txt
    Selected number of peaks: 0
    2012-02-02 19:44:02 ..
Processed 
/mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/Naive-H3K4me3_files/Naive-H3K4me3-Duplicate-236
-8_chr3_win250bp_offset0bp.txt
    Selected number of peaks: 0
    2012-02-02 19:45:26 ...
Processed 
/mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/Naive-H3K4me3_files/Naive-H3K4me3-Duplicate-236
-8_chr1_win250bp_offset0bp.txt
    Selected number of peaks: 0
    2012-02-02 19:48:09 .......
Processed 
/mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/Naive-H3K4me3_files/Naive-H3K4me3-Duplicate-236
-8_chr2_win250bp_offset0bp.txt
    Selected number of peaks: 0
    2012-02-02 19:53:43 .....................................
Processed 
/mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/Naive-H3K4me3_files/Naive-H3K4me3-Duplicate-236
-8_chr4_win250bp_offset125bp.txt
    Selected number of peaks: 0
    2012-02-02 20:22:28 
Time difference of 1.430973 hours
...
Processed 
/mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/Naive-H3K4me3_files/Naive-H3K4me3-Duplicate-236
-8_chr3_win250bp_offset125bp.txt
    Selected number of peaks: 0
    2012-02-02 20:25:09 
Time difference of 1.476377 hours
.........
Processed 
/mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/Naive-H3K4me3_files/Naive-H3K4me3-Duplicate-236
-8_chr1_win250bp_offset125bp.txt
    Selected number of peaks: 0
    2012-02-02 20:31:53 
Time difference of 1.588956 hours
.........
Processed 
/mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/Naive-H3K4me3_files/Naive-H3K4me3-Duplicate-236
-8_chr2_win250bp_offset125bp.txt
    Selected number of peaks: 0
    2012-02-02 20:38:29 
Time difference of 1.69926 hours
......................................
Processed 
/mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/Naive-H3K4me3_files/Naive-H3K4me3-Duplicate-236
-8_chr6_win250bp_offset0bp.txt
    Selected number of peaks: 0
    2012-02-02 21:02:13 ...
Processed 
/mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/Naive-H3K4me3_files/Naive-H3K4me3-Duplicate-236
-8_chr5_win250bp_offset0bp.txt
    Selected number of peaks: 0
    2012-02-02 21:04:02 .......
Processed 
/mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/Naive-H3K4me3_files/Naive-H3K4me3-Duplicate-236
-8_chr7_win250bp_offset0bp.txt
    Selected number of peaks: 0
    2012-02-02 21:07:24 ..........
Processed 
/mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/Naive-H3K4me3_files/Naive-H3K4me3-Duplicate-236
-8_chrX_win250bp_offset0bp.txt
    Selected number of peaks: 0
    2012-02-02 21:14:10 ..................................
Processed 
/mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/Naive-H3K4me3_files/Naive-H3K4me3-Duplicate-236
-8_chr6_win250bp_offset125bp.txt
    Selected number of peaks: 0
    2012-02-02 21:34:42 
Time difference of 1.158196 hours
..
Processed 
/mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/Naive-H3K4me3_files/Naive-H3K4me3-Duplicate-236
-8_chr7_win250bp_offset125bp.txt
    Selected number of peaks: 0
    2012-02-02 21:36:45 .
Time difference of 1.079499 hours
........
Processed 
/mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/Naive-H3K4me3_files/Naive-H3K4me3-Duplicate-236
-8_chr5_win250bp_offset125bp.txt
    Selected number of peaks: 0
    2012-02-02 21:42:07 
Time difference of 1.327453 hours
.............
Processed 
/mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/Naive-H3K4me3_files/Naive-H3K4me3-Duplicate-236
-8_chrX_win250bp_offset125bp.txt
    Selected number of peaks: 0
    2012-02-02 21:49:12 .
Time difference of 1.176672 hours
............................
Processed 
/mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/Naive-H3K4me3_files/Naive-H3K4me3-Duplicate-236
-8_chr9_win250bp_offset0bp.txt
    Selected number of peaks: 0
    2012-02-02 22:03:02 ..........
Processed 
/mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/Naive-H3K4me3_files/Naive-H3K4me3-Duplicate-236
-8_chr8_win250bp_offset0bp.txt
    Selected number of peaks: 0
    2012-02-02 22:07:47 .......
Processed 
/mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/Naive-H3K4me3_files/Naive-H3K4me3-Duplicate-236
-8_chr10_win250bp_offset0bp.txt
    Selected number of peaks: 0
    2012-02-02 22:11:52 ...............
Processed 
/mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/Naive-H3K4me3_files/Naive-H3K4me3-Duplicate-236
-8_chr11_win250bp_offset0bp.txt
    Selected number of peaks: 0
    2012-02-02 22:18:26 ................
Processed 
/mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/Naive-H3K4me3_files/Naive-H3K4me3-Duplicate-236
-8_chr9_win250bp_offset125bp.txt
    Selected number of peaks: 0
    2012-02-02 22:26:44 
Time difference of 49.93117 mins
.................
Processed 
/mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/Naive-H3K4me3_files/Naive-H3K4me3-Duplicate-236
-8_chr8_win250bp_offset125bp.txt
    Selected number of peaks: 0
    2012-02-02 22:34:32 
Time difference of 59.79024 mins
........
Processed 
/mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/Naive-H3K4me3_files/Naive-H3K4me3-Duplicate-236
-8_chr10_win250bp_offset125bp.txt
    Selected number of peaks: 0
    2012-02-02 22:38:30 
Time difference of 56.30224 mins
..............
Processed 
/mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/Naive-H3K4me3_files/Naive-H3K4me3-Duplicate-236
-8_chr11_win250bp_offset125bp.txt
    Selected number of peaks: 0
    2012-02-02 22:44:17 
Time difference of 55.04764 mins
...............................
Processed 
/mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/Naive-H3K4me3_files/Naive-H3K4me3-Duplicate-236
-8_chr12_win250bp_offset0bp.txt
    Selected number of peaks: 0
    2012-02-02 22:54:45 ..........
Processed 
/mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/Naive-H3K4me3_files/Naive-H3K4me3-Duplicate-236
-8_chr13_win250bp_offset0bp.txt
    Selected number of peaks: 0
    2012-02-02 22:58:31 ...
Processed 
/mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/Naive-H3K4me3_files/Naive-H3K4me3-Duplicate-236
-8_chr14_win250bp_offset0bp.txt
    Selected number of peaks: 0
    2012-02-02 22:59:52 ..............
Processed 
/mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/Naive-H3K4me3_files/Naive-H3K4me3-Duplicate-236
-8_chr15_win250bp_offset0bp.txt
    Selected number of peaks: 0
    2012-02-02 23:04:05 ...................................
Processed 
/mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/Naive-H3K4me3_files/Naive-H3K4me3-Duplicate-236
-8_chr13_win250bp_offset125bp.txt
    Selected number of peaks: 0
    2012-02-02 23:17:07 .
Time difference of 42.52728 mins
..
Processed 
/mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/Naive-H3K4me3_files/Naive-H3K4me3-Duplicate-236
-8_chr14_win250bp_offset125bp.txt
    Selected number of peaks: 0
    2012-02-02 23:17:48 
Time difference of 39.25314 mins
....
Processed 
/mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/Naive-H3K4me3_files/Naive-H3K4me3-Duplicate-236
-8_chr12_win250bp_offset125bp.txt
    Selected number of peaks: 0
    2012-02-02 23:19:29 
Time difference of 52.77208 mins
....
Processed 
/mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/Naive-H3K4me3_files/Naive-H3K4me3-Duplicate-236
-8_chr15_win250bp_offset125bp.txt
    Selected number of peaks: 0
    2012-02-02 23:21:01 
Time difference of 36.67555 mins
........................................................
Processed 
/mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/Naive-H3K4me3_files/Naive-H3K4me3-Duplicate-236
-8_chr20_win250bp_offset0bp.txt
    Selected number of peaks: 0
    2012-02-02 23:34:44 .....
Processed 
/mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/Naive-H3K4me3_files/Naive-H3K4me3-Duplicate-236
-8_chr17_win250bp_offset0bp.txt
    Selected number of peaks: 0
    2012-02-02 23:36:10 ..
Processed 
/mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/Naive-H3K4me3_files/Naive-H3K4me3-Duplicate-236
-8_chr16_win250bp_offset0bp.txt
    Selected number of peaks: 0
    2012-02-02 23:36:34 .....
Processed 
/mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/Naive-H3K4me3_files/Naive-H3K4me3-Duplicate-236
-8_chr18_win250bp_offset0bp.txt
    Selected number of peaks: 0
    2012-02-02 23:37:57 ............................................................
Processed 
/mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/Naive-H3K4me3_files/Naive-H3K4me3-Duplicate-236
-8_chrY_win250bp_offset0bp.txt
    Selected number of peaks: 0
    2012-02-02 23:49:41 ..........
Processed 
/mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/Naive-H3K4me3_files/Naive-H3K4me3-Duplicate-236
-8_chr17_win250bp_offset125bp.txt
    Selected number of peaks: 0
    2012-02-02 23:51:33 
Time difference of 33.73838 mins
.....
Processed 
/mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/Naive-H3K4me3_files/Naive-H3K4me3-Duplicate-236
-8_chr16_win250bp_offset125bp.txt
    Selected number of peaks: 0
    2012-02-02 23:52:40 .
Time difference of 35.524 mins
..
Processed 
/mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/Naive-H3K4me3_files/Naive-H3K4me3-Duplicate-236
-8_chr18_win250bp_offset125bp.txt
    Selected number of peaks: 0
    2012-02-02 23:53:03 .
Time difference of 33.47804 mins
............................................
Processed 
/mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/Naive-H3K4me3_files/Naive-H3K4me3-Duplicate-236
-8_chrY_win250bp_offset125bp.txt
    Selected number of peaks: 0
    2012-02-02 23:58:47 .
Time difference of 18.30639 mins
....................
Processed 
/mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/Naive-H3K4me3_files/Naive-H3K4me3-Duplicate-236
-8_chr22_win250bp_offset0bp.txt
    Selected number of peaks: 0
    2012-02-03 00:01:34 .
Processed 
/mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/Naive-H3K4me3_files/Naive-H3K4me3-Duplicate-236
-8_chr21_win250bp_offset0bp.txt
    Selected number of peaks: 0
    2012-02-03 00:01:40 ...................
Processed 
/mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/Naive-H3K4me3_files/Naive-H3K4me3-Duplicate-236
-8_chr19_win250bp_offset0bp.txt
    Selected number of peaks: 0
    2012-02-03 00:04:58 ...................
Processed 
/mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/Naive-H3K4me3_files/Naive-H3K4me3-Duplicate-236
-8_chr22_win250bp_offset125bp.txt
    Selected number of peaks: 0
    2012-02-03 00:08:27 
Time difference of 15.72667 mins
....
Processed 
/mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/Naive-H3K4me3_files/Naive-H3K4me3-Duplicate-236
-8_chr21_win250bp_offset125bp.txt
    Selected number of peaks: 0
    2012-02-03 00:09:16 
Time difference of 16.16309 mins
........
Processed 
/mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/Naive-H3K4me3_files/Naive-H3K4me3-Duplicate-236
-8_chr19_win250bp_offset125bp.txt
    Selected number of peaks: 0
    2012-02-03 00:14:43 
Time difference of 23.12095 mins
--------WINDOW ANALYSIS COMPLETE-------- 2012-02-03 00:14:47 

--------MERGE WINDOWS AND REFINE PEAKS (no parallelization)-------- 2012-02-03 
00:14:47 

Threshold is 0.05

Getting significant windows from 
/mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/Naive-H3K4me3_files/Naive-H3K4me3.winlist
    Threshold is 0.050000
    Using qvalue as threshold
    Data generated using mixture
    Data format is expanded
    Distance to collapse windows is 0
Getting significant regions from mixture run
    Importing windows from /mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/Naive-H3K4me3_files/Naive-H3K4me3_chr1.wins...
    Importing windows from /mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/Naive-H3K4me3_files/Naive-H3K4me3_chr2.wins...
    Importing windows from /mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/Naive-H3K4me3_files/Naive-H3K4me3_chr3.wins...
    Importing windows from /mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/Naive-H3K4me3_files/Naive-H3K4me3_chr4.wins...
    Importing windows from /mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/Naive-H3K4me3_files/Naive-H3K4me3_chr5.wins...
    Importing windows from /mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/Naive-H3K4me3_files/Naive-H3K4me3_chr6.wins...
    Importing windows from /mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/Naive-H3K4me3_files/Naive-H3K4me3_chr7.wins...
    Importing windows from /mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/Naive-H3K4me3_files/Naive-H3K4me3_chrX.wins...
    Importing windows from /mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/Naive-H3K4me3_files/Naive-H3K4me3_chr8.wins...
    Importing windows from /mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/Naive-H3K4me3_files/Naive-H3K4me3_chr9.wins...
    Importing windows from /mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/Naive-H3K4me3_files/Naive-H3K4me3_chr10.wins...
    Importing windows from /mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/Naive-H3K4me3_files/Naive-H3K4me3_chr11.wins...
    Importing windows from /mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/Naive-H3K4me3_files/Naive-H3K4me3_chr12.wins...
    Importing windows from /mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/Naive-H3K4me3_files/Naive-H3K4me3_chr13.wins...
    Importing windows from /mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/Naive-H3K4me3_files/Naive-H3K4me3_chr14.wins...
    Importing windows from /mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/Naive-H3K4me3_files/Naive-H3K4me3_chr15.wins...
    Importing windows from /mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/Naive-H3K4me3_files/Naive-H3K4me3_chr16.wins...
    Importing windows from /mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/Naive-H3K4me3_files/Naive-H3K4me3_chr17.wins...
    Importing windows from /mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/Naive-H3K4me3_files/Naive-H3K4me3_chr18.wins...
    Importing windows from /mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/Naive-H3K4me3_files/Naive-H3K4me3_chrY.wins...
    Importing windows from /mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/Naive-H3K4me3_files/Naive-H3K4me3_chr19.wins...
    Importing windows from /mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/Naive-H3K4me3_files/Naive-H3K4me3_chr22.wins...
    Importing windows from /mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/Naive-H3K4me3_files/Naive-H3K4me3_chr21.wins...
    Skipping line, /mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/Naive-H3K4me3_files/Naive-H3K4me3_chr21.wins

Imported 0 coordinates
*** glibc detected *** /usr/lib64/R/bin/exec/R: double free or corruption 
(out): 0x00007fff32499cb0 ***
======= Backtrace: =========
/lib64/libc.so.6(+0x74c06)[0x7f004fd73c06]
/usr/lib64/R/library/zinba/libs/zinba.so(+0x3af4a)[0x7f004c6c2f4a]
/usr/lib64/R/library/zinba/libs/zinba.so(_ZN8analysis12importCoordsEPKcdS1_iii+0
x18f)[0x7f004c6c480f]
/usr/lib64/R/library/zinba/libs/zinba.so(getSeqCountProfile+0x109)[0x7f004c710fa
9]
/usr/lib64/R/lib/libR.so(+0xb2f97)[0x7f005035df97]
/usr/lib64/R/lib/libR.so(Rf_eval+0x739)[0x7f005038e129]
/usr/lib64/R/lib/libR.so(+0xe5da0)[0x7f0050390da0]
/usr/lib64/R/lib/libR.so(Rf_eval+0x55b)[0x7f005038df4b]
/usr/lib64/R/lib/libR.so(+0xe5f29)[0x7f0050390f29]
/usr/lib64/R/lib/libR.so(Rf_eval+0x55b)[0x7f005038df4b]
/usr/lib64/R/lib/libR.so(Rf_applyClosure+0x322)[0x7f0050392142]
/usr/lib64/R/lib/libR.so(Rf_eval+0x430)[0x7f005038de20]
/usr/lib64/R/lib/libR.so(+0xe5f29)[0x7f0050390f29]
/usr/lib64/R/lib/libR.so(Rf_eval+0x55b)[0x7f005038df4b]
/usr/lib64/R/lib/libR.so(Rf_applyClosure+0x322)[0x7f0050392142]
/usr/lib64/R/lib/libR.so(Rf_eval+0x430)[0x7f005038de20]
/usr/lib64/R/lib/libR.so(+0xe5f29)[0x7f0050390f29]
/usr/lib64/R/lib/libR.so(Rf_eval+0x55b)[0x7f005038df4b]
/usr/lib64/R/lib/libR.so(Rf_eval+0x55b)[0x7f005038df4b]
/usr/lib64/R/lib/libR.so(+0xe5f29)[0x7f0050390f29]
/usr/lib64/R/lib/libR.so(Rf_eval+0x55b)[0x7f005038df4b]
/usr/lib64/R/lib/libR.so(Rf_eval+0x55b)[0x7f005038df4b]
/usr/lib64/R/lib/libR.so(Rf_eval+0x55b)[0x7f005038df4b]
/usr/lib64/R/lib/libR.so(Rf_eval+0x55b)[0x7f005038df4b]
/usr/lib64/R/lib/libR.so(+0xe5f29)[0x7f0050390f29]
/usr/lib64/R/lib/libR.so(Rf_eval+0x55b)[0x7f005038df4b]
/usr/lib64/R/lib/libR.so(Rf_applyClosure+0x322)[0x7f0050392142]
/usr/lib64/R/lib/libR.so(Rf_eval+0x430)[0x7f005038de20]
/usr/lib64/R/lib/libR.so(+0xe5f29)[0x7f0050390f29]
/usr/lib64/R/lib/libR.so(Rf_eval+0x55b)[0x7f005038df4b]
/usr/lib64/R/lib/libR.so(Rf_eval+0x55b)[0x7f005038df4b]
/usr/lib64/R/lib/libR.so(+0xe5f29)[0x7f0050390f29]
/usr/lib64/R/lib/libR.so(Rf_eval+0x55b)[0x7f005038df4b]
/usr/lib64/R/lib/libR.so(Rf_applyClosure+0x322)[0x7f0050392142]
/usr/lib64/R/lib/libR.so(Rf_eval+0x430)[0x7f005038de20]
/usr/lib64/R/lib/libR.so(+0xe425d)[0x7f005038f25d]
/usr/lib64/R/lib/libR.so(+0xd7d23)[0x7f0050382d23]
/usr/lib64/R/lib/libR.so(Rf_eval+0x17a)[0x7f005038db6a]
/usr/lib64/R/lib/libR.so(Rf_applyClosure+0x322)[0x7f0050392142]
/usr/lib64/R/lib/libR.so(+0xded84)[0x7f0050389d84]
/usr/lib64/R/lib/libR.so(Rf_eval+0x17a)[0x7f005038db6a]
/usr/lib64/R/lib/libR.so(Rf_applyClosure+0x322)[0x7f0050392142]
/usr/lib64/R/lib/libR.so(Rf_eval+0x430)[0x7f005038de20]
/usr/lib64/R/lib/libR.so(Rf_ReplIteration+0x1e3)[0x7f00503c34d3]
/usr/lib64/R/lib/libR.so(+0x118760)[0x7f00503c3760]
/usr/lib64/R/lib/libR.so(run_Rmainloop+0x50)[0x7f00503c3c80]
/usr/lib64/R/bin/exec/R(main+0x1b)[0x4007fb]
/lib64/libc.so.6(__libc_start_main+0xed)[0x7f004fd2023d]
/usr/lib64/R/bin/exec/R[0x40082d]
======= Memory map: ========
00400000-00401000 r-xp 00000000 08:01 1462739                            
/usr/lib64/R/bin/exec/R
00600000-00601000 r--p 00000000 08:01 1462739                            
/usr/lib64/R/bin/exec/R
00601000-00602000 rw-p 00001000 08:01 1462739                            
/usr/lib64/R/bin/exec/R
00602000-05b4f000 rw-p 00000000 00:00 0                                  [heap]
7f004bf74000-7f004bf79000 r-xp 00000000 08:01 272620                     
/usr/lib64/R/library/MASS/libs/MASS.so
7f004bf79000-7f004c178000 ---p 00005000 08:01 272620                     
/usr/lib64/R/library/MASS/libs/MASS.so
7f004c178000-7f004c179000 r--p 00004000 08:01 272620                     
/usr/lib64/R/library/MASS/libs/MASS.so
7f004c179000-7f004c17a000 rw-p 00005000 08:01 272620                     
/usr/lib64/R/library/MASS/libs/MASS.so
7f004c17a000-7f004c17d000 r-xp 00000000 08:01 1723848                    
/usr/lib64/R/library/multicore/libs/multicore.so
7f004c17d000-7f004c37c000 ---p 00003000 08:01 1723848                    
/usr/lib64/R/library/multicore/libs/multicore.so
7f004c37c000-7f004c37d000 r--p 00002000 08:01 1723848                    
/usr/lib64/R/library/multicore/libs/multicore.so
7f004c37d000-7f004c37e000 rw-p 00003000 08:01 1723848                    
/usr/lib64/R/library/multicore/libs/multicore.so
7f004c37e000-7f004c46a000 r-xp 00000000 08:01 1449542                    
/usr/lib64/libstdc++.so.6.0.16
7f004c46a000-7f004c669000 ---p 000ec000 08:01 1449542                    
/usr/lib64/libstdc++.so.6.0.16
7f004c669000-7f004c671000 r--p 000eb000 08:01 1449542                    
/usr/lib64/libstdc++.so.6.0.16
7f004c671000-7f004c673000 rw-p 000f3000 08:01 1449542                    
/usr/lib64/libstdc++.so.6.0.16
7f004c673000-7f004c688000 rw-p 00000000 00:00 0 
7f004c688000-7f004c797000 r-xp 00000000 08:01 1724137                    
/usr/lib64/R/library/zinba/libs/zinba.so
7f004c797000-7f004c997000 ---p 0010f000 08:01 1724137                    
/usr/lib64/R/library/zinba/libs/zinba.so
7f004c997000-7f004c998000 r--p 0010f000 08:01 1724137                    
/usr/lib64/R/library/zinba/libs/zinba.so
7f004c998000-7f004c9b7000 rw-p 00110000 08:01 1724137                    
/usr/lib64/R/library/zinba/libs/zinba.so
7f004c9b7000-7f004ca80000 rw-p 00000000 00:00 0 
7f004ca80000-7f004cab5000 r-xp 00000000 08:01 1452701                    
/usr/lib64/libquadmath.so.0.0.0
7f004cab5000-7f004ccb4000 ---p 00035000 08:01 1452701                    
/usr/lib64/libquadmath.so.0.0.0
7f004ccb4000-7f004ccb5000 r--p 00034000 08:01 1452701                    
/usr/lib64/libquadmath.so.0.0.0
7f004ccb5000-7f004ccb6000 rw-p 00035000 08:01 1452701                    
/usr/lib64/libquadmath.so.0.0.0
7f004ccb6000-7f004cdcc000 r-xp 00000000 08:01 1457192                    
/usr/lib64/libgfortran.so.3.0.0
7f004cdcc000-7f004cfcb000 ---p 00116000 08:01 1457192                    
/usr/lib64/libgfortran.so.3.0.0
7f004cfcb000-7f004cfcc000 r--p 00115000 08:01 1457192                    
/usr/lib64/libgfortran.so.3.0.0
7f004cfcc000-7f004cfce000 rw-p 00116000 08:01 1457192                    
/usr/lib64/libgfortran.so.3.0.0
7f004cfce000-7f004d03c000 r-xp 00000000 08:01 660380                     
/usr/lib64/R/library/stats/libs/stats.so
7f004d03c000-7f004d23b000 ---p 0006e000 08:01 660380                     
/usr/lib64/R/library/stats/libs/stats.so
7f004d23b000-7f004d23d000 r--p 0006d000 08:01 660380                     
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7f004d23d000-7f004d23f000 rw-p 0006f000 08:01 660380                     
/usr/lib64/R/library/stats/libs/stats.so
7f004d23f000-7f004d36e000 rw-p 00000000 00:00 0 
7f004d36e000-7f004d39c000 r-xp 00000000 08:01 398975                     
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7f004d39c000-7f004d59b000 ---p 0002e000 08:01 398975                     
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7f004d59b000-7f004d59c000 r--p 0002d000 08:01 398975                     
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7f004d59c000-7f004d59d000 rw-p 0002e000 08:01 398975                     
/usr/lib64/R/library/grDevices/libs/grDevices.so
7f004d5dd000-7f004d5f2000 r-xp 00000000 08:01 786717                     
/lib64/libgcc_s.so.1
7f004d5f2000-7f004d7f1000 ---p 00015000 08:01 786717                     
/lib64/libgcc_s.so.1
7f004d7f1000-7f004d7f2000 r--p 00014000 08:01 786717                     
/lib64/libgcc_s.so.1
7f004d7f2000-7f004d7f3000 rw-p 00015000 08:01 786717                     
/lib64/libgcc_s.so.1
7f004d7f3000-7f004e9fa000 rw-p 00000000 00:00 0 
7f004e9fa000-7f004ea01000 r-xp 00000000 08:01 660119                     
/usr/lib64/R/library/methods/libs/methods.so
7f004ea01000-7f004ec00000 ---p 00007000 08:01 660119                     
/usr/lib64/R/library/methods/libs/methods.so
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7f004ec01000-7f004ec02000 rw-p 00007000 08:01 660119                     
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/usr/lib64/libgomp.so.1.0.0
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/usr/lib64/libgomp.so.1.0.0
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/usr/lib64/R/lib/libRblas.so
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/lib64/libc-2.14.1.so
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/lib64/libc-2.14.1.so
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/lib64/libpthread-2.14.1.so
7f00500a6000-7f00502a5000 ---p 00018000 08:01 786583                     
/lib64/libpthread-2.14.1.so
7f00502a5000-7f00502a6000 r--p 00017000 08:01 786583                     
/lib64/libpthread-2.14.1.so
7f00502a6000-7f00502a7000 rw-p 00018000 08:01 786583                     
/lib64/libpthread-2.14.1.so
7f00502a7000-7f00502ab000 rw-p 00000000 00:00 0 
7f00502ab000-7f005059e000 r-xp 00000000 08:01 1587687                    
/usr/lib64/R/lib/libR.so
7f005059e000-7f005079e000 ---p 002f3000 08:01 1587687                    
/usr/lib64/R/lib/libR.so
7f005079e000-7f00507a4000 r--p 002f3000 08:01 1587687                    
/usr/lib64/R/lib/libR.so
7f00507a4000-7f00507b4000 rw-p 002f9000 08:01 1587687                    
/usr/lib64/R/lib/libR.so
7f00507b4000-7f0050835000 rw-p 00000000 00:00 0 
7f0050835000-7f0050855000 r-xp 00000000 08:01 786571                     
/lib64/ld-2.14.1.so
7f0050863000-7f00509f9000 rw-p 00000000 00:00 0 
7f00509f9000-7f0050a38000 r--p 00000000 08:01 1575179                    
/usr/lib/locale/en_US.utf8/LC_CTYPE
7f0050a38000-7f0050a3f000 rw-p 00000000 00:00 0 
7f0050a4b000-7f0050a4d000 rw-p 00000000 00:00 0 
7f0050a4d000-7f0050a54000 r--s 00000000 08:01 1442599                    
/usr/lib64/gconv/gconv-modules.cache
7f0050a54000-7f0050a55000 rw-p 00000000 00:00 0 
7f0050a55000-7f0050a56000 r--p 00020000 08:01 786571                     
/lib64/ld-2.14.1.so
7f0050a56000-7f0050a57000 rw-p 00021000 08:01 786571                     
/lib64/ld-2.14.1.so
7f0050a57000-7f0050a58000 rw-p 00000000 00:00 0 
7fff3245c000-7fff324a2000 rw-p 00000000 00:00 0                          [stack]
7fff325ff000-7fff32600000 r-xp 00000000 00:00 0                          [vdso]
ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0                  
[vsyscall]
Aborted

Original comment by por...@porter.st on 3 Feb 2012 at 3:27

GoogleCodeExporter commented 8 years ago 

> 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)
> library(zinba)

version of zinba is 2.01

Original comment by por...@porter.st on 3 Feb 2012 at 3:28

GoogleCodeExporter commented 8 years ago 
From what it looks like ZINBA could not detect any peaks regions with 
confidence in your data set, so did not create any output in the enrichment 
detection step (leading to a problem in the later step).  It appears your read 
depth seems to be too low to detect peaks with the default parameters.  You can 
try using the run.zinba function (detailed in the Using Zinba wiki) and use a 
larger window size and see if that improves the results.  If you want to get a 
better picture of what your data looks like, you can load your .basecount file 
(it is in .wig format) into a locally installed version of the UCSC genome 
browser.

I am working on an update coming out this weekend that will prevent the above 
segfault from occurring when no peaks are selected.  It may also be useful for 
ZINBA to  print out some chromosome-level window read count summary information 
to provide an idea of what the level of signal that ZINBA is working with.

Original comment by homer...@gmail.com on 3 Feb 2012 at 4:02

GoogleCodeExporter commented 8 years ago 
Sounds good. Also I found that I've used mappability 36bp when data is 25bp, is 
it a big problem, should I recreate my own mappability file for 25bp reads?

Original comment by por...@porter.st on 3 Feb 2012 at 4:19

GoogleCodeExporter commented 8 years ago 
One more option is to use the run.zinba function with the default window size 
(250bp) and modelselect=F, specifying your own formulas.  For example, the 
formula selected in your output is the following

background:  exp_count ~ input_count + 1
enrichment: exp_count ~  1
zero-inflation: exp_count ~ 1

With just input as a covariate, I've only seen these formulas chosen in cases 
where ZINBA cannot detect any signal that differs above background.  Using the 
following formulas in run.zinba may alleviate the low coverage situation, but 
no guarantee:

modelselect=F, 
formula= exp_count ~ input_count + 1,
formulaE= exp_count ~ input_count + 1,
formulaZ= exp_count ~ 1,

Original comment by homer...@gmail.com on 3 Feb 2012 at 4:20

GoogleCodeExporter commented 8 years ago 
I dont think it will make much of a difference 25 vs 36, so you should be ok

Original comment by homer...@gmail.com on 3 Feb 2012 at 4:27

GoogleCodeExporter commented 8 years ago 
Also, in some cases modeling your data without input control (leaving 
input='none' in zinba() function ) may be more beneficial in low depth cases 
than using input control, so that may be a better option.  If this works better 
for you let me know.

Original comment by homer...@gmail.com on 3 Feb 2012 at 4:29

GoogleCodeExporter commented 8 years ago 
I'll try all these variations and report back a result.
Thanks

Original comment by por...@porter.st on 3 Feb 2012 at 4:35

GoogleCodeExporter commented 8 years ago 
I'm really sorry, I used your parameters and received this error

source("./ZINBA/com.R")
Error in zinba(align = "/mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/output_150/",  : 
  unused argument(s) (winSize = 250, modelselect = F, formula = exp_count ~ input_count + 1, formulaE = exp_count ~ input_count + 1, formulaZ = exp_count ~ 1)

command is: 

zinba(
  align='/mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/output_150/',
  numProc=4,
  seq='/mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/Naive-H3K4me3-Duplicate-236-8.hits',
  basecountfile='/mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/Naive-H3K4me3-Duplicate-236-8.basecount',
  filetype='bowtie',
  outfile='/mnt/sf_G_DRIVE/FASTQ-DATA/ZINBA/Naive-H3K4me3',
  twoBit='/mnt/sf_G_DRIVE/FASTQ-DATA/b_indexes/hg19.2bit',
  extension=150,
  printFullOut=1,
  refinepeaks=1,
  broad=F,
  winSize=250,
  modelselect=F,
  formula= exp_count ~ input_count + 1,
  formulaE= exp_count ~ input_count + 1,
  formulaZ= exp_count ~ 1
)

Original comment by por...@porter.st on 3 Feb 2012 at 5:44

GoogleCodeExporter commented 8 years ago 
If you look at the Using ZINBA tutorial, the zinba() function does not use 
these functions.  To specify them, you have to use the *run.zinba* function, as 
mentioned earlier.

Original comment by homer...@gmail.com on 3 Feb 2012 at 5:58

GoogleCodeExporter commented 8 years ago 
I've attached two error files with different winSize parameter, R still crushed.

Original comment by por...@porter.st on 3 Feb 2012 at 7:43

Attachments:

GoogleCodeExporter commented 8 years ago 
Please follow the run.zinba example here on the Using Zinba page here, using 
the *CHiP-seq example* as a template for how to run the function:  
http://code.google.com/p/zinba/wiki/UsingZINBA#Custom_Analysis .  You are 
ignoring several parameters, leading to the crashes.  The new version coming 
this weekend will be more stable with this function.

Original comment by homer...@gmail.com on 3 Feb 2012 at 8:16

GoogleCodeExporter commented 8 years ago 
I've made as you said, and it done looks like well. I did not test 2.02, I'll 
do it on next week. Also I almost add .bam file loading (like "bowtie" type) 
are you interested in that ?

Zinba done well on histone precipitation and not so understandable on DNase. 
Maybe on DNase data, I should play with some sensitivity parameters, because 
near highly enreached regions it found some times peaks where they look like 
background. I'm not a  big professional, so maybe I'm wrong somewhere.

Original comment by por...@porter.st on 12 Feb 2012 at 4:54

GoogleCodeExporter commented 8 years ago 
Here are some suggested parameters by one of our users that applied zinba to 
DNAse data.  In general the results seemed ok to them, except with the FDR=T 
option there was some overcalling of peak (may need a more strict threshold).  
Feel free to contact me directly at homeriq5@gmail.com with any suggests or 
comments.

zinba(
   align='[% alignability_directory %]',
   numProc=[% number_of_processors %],
   seq='[% seq_file %]',
   basecountfile='[% basecount_file %]',
   filetype='[% seq_file_type %]',
   outfile='[% output_dir_prefix %]',
   threshold=.05,
   twoBit='[% two_bit_file %]',
   extension=1,
   refinepeaks=1,
   printFullOut=1,
   broad=F,
   input="none"
)

Original comment by homer...@gmail.com on 16 Feb 2012 at 7:39

GoogleCodeExporter commented 8 years ago

Original comment by homer...@gmail.com on 16 Feb 2012 at 7:39