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abyzovlab / CNVpytor

a python extension of CNVnator -- a tool for CNV analysis from depth-of-coverage by mapped reads
MIT License
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CNVpytor generating empty tsv call files #200

Closed lucsnip closed 9 months ago

lucsnip commented 9 months ago

I am new to CNVpytor. I have created the gc content file and run the following commands with no errors:

cnvpytor -conf mm10_ref_conf.py -root B6MaleKidney_mm10_rd.pytor -rd B6MaleKidney_mapped.bam

cnvpytor -conf mm10_ref_conf.py -root B6MaleKidney_mm10_rd.pytor -his 10000 100000

cnvpytor -conf mm10_ref_conf.py -root B6MaleKidney_mm10_rd.pytor -partition 10000 100000

cnvpytor -conf mm10_ref_conf.py -root B6MaleKidney_mm10_rd.pytor -call 10000 > B6MK_calls.10000.tsv

cnvpytor -root B6MaleKidney_mm10_rd.pytor -call 100000 > B6MK_calls.100000.tsv

However, both call files are empty. Here is the output of the -ls for the root file:

2023-12-13 10:57:36,023 - cnvpytor.genome - INFO - Reading configuration file 'mm10_ref_conf.py'.
2023-12-13 10:57:36,024 - cnvpytor.genome - INFO - Importing reference genome data: 'mm10'.

Filename 'B6MaleKidney_mm10_rd.pytor'

File created: 2023-12-13 10:53 using CNVpytor ver 1.3.1

Chromosomes with RD signal: chr1, chr10, chr11, chr12, chr13, chr14, chr15, chr16, chr17, chr18, chr19, chr1_GL456210_random, chr1_GL456211_random, chr1_GL456212_random, chr1_GL456213_random, chr1_GL456221_random, chr2, chr3, chr4, chr4_GL456216_random, chr4_JH584292_random, chr4_GL456350_random, chr4_JH584293_random, chr4_JH584294_random, chr4_JH584295_random, chr5, chr5_JH584296_random, chr5_JH584297_random, chr5_JH584298_random, chr5_GL456354_random, chr5_JH584299_random, chr6, chr7, chr7_GL456219_random, chr8, chr9, chrM, chrX, chrX_GL456233_random, chrY, chrY_JH584300_random, chrY_JH584301_random, chrY_JH584302_random, chrY_JH584303_random, chrUn_GL456239, chrUn_GL456367, chrUn_GL456378, chrUn_GL456381, chrUn_GL456382, chrUn_GL456383, chrUn_GL456385, chrUn_GL456390, chrUn_GL456392, chrUn_GL456393, chrUn_GL456394, chrUn_GL456359, chrUn_GL456360, chrUn_GL456396, chrUn_GL456372, chrUn_GL456387, chrUn_GL456389, chrUn_GL456370, chrUn_GL456379, chrUn_GL456366, chrUn_GL456368, chrUn_JH584304

Chromosomes with SNP signal: 

Using reference genome: mm10 [ GC: yes, mask: no ]

Chromosomes with RD histograms [bin sizes]:  []

Chromosomes with SNP histograms [bin sizes]:  []

Chromosome lengths: {'chr1': '195471971', 'chr10': '130694993', 'chr11': '122082543', 'chr12': '120129022', 'chr13': '120421639', 'chr14': '124902244', 'chr15': '104043685', 'chr16': '98207768', 'chr17': '94987271', 'chr18': '90702639', 'chr19': '61431566', 'chr1_GL456210_random': '169725', 'chr1_GL456211_random': '241735', 'chr1_GL456212_random': '153618', 'chr1_GL456213_random': '39340', 'chr1_GL456221_random': '206961', 'chr2': '182113224', 'chr3': '160039680', 'chr4': '156508116', 'chr4_GL456216_random': '66673', 'chr4_JH584292_random': '14945', 'chr4_GL456350_random': '227966', 'chr4_JH584293_random': '207968', 'chr4_JH584294_random': '191905', 'chr4_JH584295_random': '1976', 'chr5': '151834684', 'chr5_JH584296_random': '199368', 'chr5_JH584297_random': '205776', 'chr5_JH584298_random': '184189', 'chr5_GL456354_random': '195993', 'chr5_JH584299_random': '953012', 'chr6': '149736546', 'chr7': '145441459', 'chr7_GL456219_random': '175968', 'chr8': '129401213', 'chr9': '124595110', 'chrM': '16299', 'chrX': '171031299', 'chrX_GL456233_random': '336933', 'chrY': '91744698', 'chrY_JH584300_random': '182347', 'chrY_JH584301_random': '259875', 'chrY_JH584302_random': '155838', 'chrY_JH584303_random': '158099', 'chrUn_GL456239': '40056', 'chrUn_GL456367': '42057', 'chrUn_GL456378': '31602', 'chrUn_GL456381': '25871', 'chrUn_GL456382': '23158', 'chrUn_GL456383': '38659', 'chrUn_GL456385': '35240', 'chrUn_GL456390': '24668', 'chrUn_GL456392': '23629', 'chrUn_GL456393': '55711', 'chrUn_GL456394': '24323', 'chrUn_GL456359': '22974', 'chrUn_GL456360': '31704', 'chrUn_GL456396': '21240', 'chrUn_GL456372': '28664', 'chrUn_GL456387': '24685', 'chrUn_GL456389': '28772', 'chrUn_GL456370': '26764', 'chrUn_GL456379': '72385', 'chrUn_GL456366': '47073', 'chrUn_GL456368': '20208', 'chrUn_JH584304': '114452'}

What is my mistake here? Thanks!

arpanda commented 9 months ago

Hi @lucsnip , The histogram panel is empty. Although, you ran the -his step with two bins. i.e., 10000 100000. see this. Chromosomes with RD histograms [bin sizes]: []

Would you mind sharing the content of mm10_ref_conf.py and the log of -his and -rd step. That will help to debug the issue.

Thank you, Arijit

lucsnip commented 9 months ago

mm10 ref conf.py

import_reference_genomes = {
    "mm10": {
        "name": "mm10",
        "species": "Mus musculus",
        "chromosomes": OrderedDict(
            [("chr1", (195471971, "A")), ("chr2", (182113224, "A")), ("chr3", (160039680, "A")),
            ("chr4", (156508116, "A")), ("chr5", (151834684, "A")), ("chr6", (149736546, "A")),
            ("chr7", (145441459, "A")), ("chr8", (129401213, "A")), ("chr9", (124595110, "A")),
            ("chr10", (130694993, "A")), ("chr11", (122082543, "A")), ("chr12", (120129022, "A")),
            ("chr13", (120421639, "A")), ("chr14", (124902244, "A")), ("chr15", (104043685, "A")),
            ("chr16", (98207768, "A")), ("chr17", (94987271, "A")), ("chr18", (90702639, "A")),
            ("chr19", (61431566, "A")), ("chrX", (171031299, "S")), ("chrY", (91744698, "S")),
            ("chrM", (16299, "M"))]),
        "gc_file":"/storage/E_drive/Snipes/genome/mm10_gc_file.pytor"
    }
}

log of his

2023-12-13 12:51:09,651 - cnvpytor - DEBUG - Start logging...
2023-12-13 12:51:09,651 - cnvpytor.genome - DEBUG - Checking reference genome resource files.
2023-12-13 12:51:09,651 - cnvpytor.genome - INFO - Reading configuration file 'mm10_ref_conf.py'.
2023-12-13 12:51:09,652 - cnvpytor.genome - INFO - Importing reference genome data: 'mm10'.
2023-12-13 12:51:09,652 - cnvpytor.root - DEBUG - App class init: filename 'B6MaleKidney_mm10_rd.pytor'; max cores 8.
2023-12-13 12:51:09,652 - cnvpytor.io - DEBUG - Opening h5 file 'B6MaleKidney_mm10_rd.pytor'
2023-12-13 12:51:09,653 - cnvpytor.io - DEBUG - File 'B6MaleKidney_mm10_rd.pytor' successfully opened.
2023-12-13 12:51:09,654 - cnvpytor.root - DEBUG - Using GC content from database for reference genome 'mm10'.
2023-12-13 12:51:09,654 - cnvpytor.io - DEBUG - Opening h5 file '/path/to/mm10_gc_file.pytor'
2023-12-13 12:51:09,654 - cnvpytor.io - DEBUG - File '/path/to/mm10_gc_file.pytor' successfully opened in read-only mode.
2023-12-13 12:51:09,656 - cnvpytor.root - INFO - Calculating global statistics.
2023-12-13 12:51:09,657 - cnvpytor.root - INFO - Calculating global statistics.
2023-12-13 12:51:09,657 - cnvpytor.io - DEBUG - Closing h5 file '/path/to/mm10_gc_file.pytor'
2023-12-13 12:51:09,658 - cnvpytor.io - DEBUG - Closing h5 file 'B6MaleKidney_mm10_rd.pytor'

log of rd

2023-12-13 12:52:19,959 - cnvpytor - DEBUG - Start logging...
2023-12-13 12:52:19,959 - cnvpytor.genome - DEBUG - Checking reference genome resource files.
2023-12-13 12:52:19,959 - cnvpytor.genome - INFO - Reading configuration file 'mm10_ref_conf.py'.
2023-12-13 12:52:19,960 - cnvpytor.genome - INFO - Importing reference genome data: 'mm10'.
2023-12-13 12:52:19,961 - cnvpytor.root - DEBUG - App class init: filename 'B6MaleKidney_mm10_rd.pytor'; max cores 8.
2023-12-13 12:52:19,961 - cnvpytor.io - DEBUG - Opening h5 file 'B6MaleKidney_mm10_rd.pytor'
2023-12-13 12:52:19,961 - cnvpytor.io - DEBUG - File 'B6MaleKidney_mm10_rd.pytor' successfully opened.
2023-12-13 12:52:19,964 - cnvpytor.root - DEBUG - Using GC content from database for reference genome 'mm10'.
2023-12-13 12:52:19,964 - cnvpytor.io - DEBUG - Opening h5 file '/path/to/mm10_gc_file.pytor'
2023-12-13 12:52:19,965 - cnvpytor.io - DEBUG - File '/path/to/mm10_gc_file.pytor' successfully opened in read-only mode.
2023-12-13 12:52:19,968 - cnvpytor.io - DEBUG - Closing h5 file '/path/to/mm10_gc_file.pytor'
2023-12-13 12:52:19,968 - cnvpytor.io - DEBUG - Closing h5 file 'B6MaleKidney_mm10_rd.pytor'
2023-12-13 12:55:00,967 - cnvpytor - DEBUG - Start logging...
2023-12-13 12:55:00,967 - cnvpytor.genome - DEBUG - Checking reference genome resource files.
2023-12-13 12:55:00,967 - cnvpytor.genome - INFO - Reading configuration file 'mm10_ref_conf.py'.
2023-12-13 12:55:00,968 - cnvpytor.genome - INFO - Importing reference genome data: 'mm10'.
2023-12-13 12:55:00,968 - cnvpytor.root - DEBUG - App class init: filename 'B6MaleKidney_mm10_rd.pytor'; max cores 8.
2023-12-13 12:55:00,968 - cnvpytor.io - DEBUG - Opening h5 file 'B6MaleKidney_mm10_rd.pytor'
2023-12-13 12:55:00,968 - cnvpytor.io - DEBUG - File 'B6MaleKidney_mm10_rd.pytor' successfully opened.
2023-12-13 12:55:00,969 - cnvpytor.root - DEBUG - Using GC content from database for reference genome 'mm10'.
2023-12-13 12:55:00,970 - cnvpytor.io - DEBUG - Opening h5 file '/path/to/genome/mm10_gc_file.pytor'
2023-12-13 12:55:00,970 - cnvpytor.io - DEBUG - File '/path/to/mm10_gc_file.pytor' successfully opened in read-only mode.
2023-12-13 12:55:00,987 - cnvpytor.bam - INFO - File: B6MaleKidney_mapped.bam successfully open
2023-12-13 12:55:00,988 - cnvpytor.bam - INFO - Detected reference genome: mm10
2023-12-13 12:55:00,991 - cnvpytor.pool - INFO - Parallel processing using 8 cores
2023-12-13 12:55:01,034 - cnvpytor.root - INFO - Reading data for chromosome chr1 with length 195471971
2023-12-13 12:55:01,034 - cnvpytor.root - INFO - Reading data for chromosome chr10 with length 130694993
2023-12-13 12:55:01,035 - cnvpytor.bam - DEBUG - Reading chromosome chr1 from filename B6MaleKidney_mapped.bam
2023-12-13 12:55:01,035 - cnvpytor.root - INFO - Reading data for chromosome chr11 with length 122082543
2023-12-13 12:55:01,035 - cnvpytor.bam - DEBUG - Reading chromosome chr10 from filename B6MaleKidney_mapped.bam
2023-12-13 12:55:01,035 - cnvpytor.root - INFO - Reading data for chromosome chr14 with length 124902244
2023-12-13 12:55:01,035 - cnvpytor.root - INFO - Reading data for chromosome chr12 with length 120129022
2023-12-13 12:55:01,035 - cnvpytor.root - INFO - Reading data for chromosome chr13 with length 120421639
2023-12-13 12:55:01,035 - cnvpytor.bam - DEBUG - Reading chromosome chr11 from filename B6MaleKidney_mapped.bam
2023-12-13 12:55:01,035 - cnvpytor.bam - DEBUG - Reading chromosome chr14 from filename B6MaleKidney_mapped.bam
2023-12-13 12:55:01,035 - cnvpytor.bam - DEBUG - Reading chromosome chr12 from filename B6MaleKidney_mapped.bam
2023-12-13 12:55:01,035 - cnvpytor.bam - DEBUG - Reading chromosome chr13 from filename B6MaleKidney_mapped.bam
2023-12-13 12:55:01,035 - cnvpytor.root - INFO - Reading data for chromosome chr15 with length 104043685
2023-12-13 12:55:01,035 - cnvpytor.root - INFO - Reading data for chromosome chr16 with length 98207768
2023-12-13 12:55:01,036 - cnvpytor.bam - DEBUG - Reading chromosome chr15 from filename B6MaleKidney_mapped.bam
2023-12-13 12:55:01,036 - cnvpytor.bam - DEBUG - Reading chromosome chr16 from filename B6MaleKidney_mapped.bam
2023-12-13 12:55:09,939 - cnvpytor.root - INFO - Reading data for chromosome chr17 with length 94987271
2023-12-13 12:55:10,002 - cnvpytor.bam - DEBUG - Reading chromosome chr17 from filename B6MaleKidney_mapped.bam
2023-12-13 12:55:10,251 - cnvpytor.root - INFO - Reading data for chromosome chr18 with length 90702639
2023-12-13 12:55:10,316 - cnvpytor.bam - DEBUG - Reading chromosome chr18 from filename B6MaleKidney_mapped.bam
2023-12-13 12:55:11,457 - cnvpytor.root - INFO - Reading data for chromosome chr19 with length 61431566
2023-12-13 12:55:11,457 - cnvpytor.bam - DEBUG - Reading chromosome chr19 from filename B6MaleKidney_mapped.bam
2023-12-13 12:55:11,656 - cnvpytor.root - INFO - Reading data for chromosome chr1_GL456210_random with length 169725
2023-12-13 12:55:11,729 - cnvpytor.bam - DEBUG - Reading chromosome chr1_GL456210_random from filename B6MaleKidney_mapped.bam
2023-12-13 12:55:11,800 - cnvpytor.root - INFO - Reading data for chromosome chr1_GL456211_random with length 241735
2023-12-13 12:55:11,800 - cnvpytor.bam - DEBUG - Reading chromosome chr1_GL456211_random from filename B6MaleKidney_mapped.bam
2023-12-13 12:55:11,879 - cnvpytor.root - INFO - Reading data for chromosome chr1_GL456212_random with length 153618
2023-12-13 12:55:11,879 - cnvpytor.bam - DEBUG - Reading chromosome chr1_GL456212_random from filename B6MaleKidney_mapped.bam
2023-12-13 12:55:11,889 - cnvpytor.root - INFO - Reading data for chromosome chr1_GL456221_random with length 206961
2023-12-13 12:55:11,943 - cnvpytor.bam - DEBUG - Reading chromosome chr1_GL456221_random from filename B6MaleKidney_mapped.bam
2023-12-13 12:55:11,887 - cnvpytor.root - INFO - Reading data for chromosome chr1_GL456213_random with length 39340
2023-12-13 12:55:11,958 - cnvpytor.bam - DEBUG - Reading chromosome chr1_GL456213_random from filename B6MaleKidney_mapped.bam
2023-12-13 12:55:11,963 - cnvpytor.root - INFO - Reading data for chromosome chr2 with length 182113224
2023-12-13 12:55:11,963 - cnvpytor.bam - DEBUG - Reading chromosome chr2 from filename B6MaleKidney_mapped.bam
2023-12-13 12:55:12,002 - cnvpytor.root - INFO - Reading data for chromosome chr3 with length 160039680
2023-12-13 12:55:12,002 - cnvpytor.bam - DEBUG - Reading chromosome chr3 from filename B6MaleKidney_mapped.bam
2023-12-13 12:55:12,039 - cnvpytor.root - INFO - Reading data for chromosome chr4 with length 156508116
2023-12-13 12:55:12,039 - cnvpytor.bam - DEBUG - Reading chromosome chr4 from filename B6MaleKidney_mapped.bam
2023-12-13 12:55:12,215 - cnvpytor.root - INFO - Reading data for chromosome chr4_GL456216_random with length 66673
2023-12-13 12:55:12,281 - cnvpytor.bam - DEBUG - Reading chromosome chr4_GL456216_random from filename B6MaleKidney_mapped.bam
2023-12-13 12:55:12,335 - cnvpytor.root - INFO - Reading data for chromosome chr4_JH584292_random with length 14945
2023-12-13 12:55:12,335 - cnvpytor.bam - DEBUG - Reading chromosome chr4_JH584292_random from filename B6MaleKidney_mapped.bam
2023-12-13 12:55:12,387 - cnvpytor.root - INFO - Reading data for chromosome chr4_GL456350_random with length 227966
2023-12-13 12:55:12,387 - cnvpytor.bam - DEBUG - Reading chromosome chr4_GL456350_random from filename B6MaleKidney_mapped.bam
2023-12-13 12:55:12,415 - cnvpytor.root - INFO - Reading data for chromosome chr4_JH584293_random with length 207968
2023-12-13 12:55:12,415 - cnvpytor.bam - DEBUG - Reading chromosome chr4_JH584293_random from filename B6MaleKidney_mapped.bam
2023-12-13 12:55:12,447 - cnvpytor.root - INFO - Reading data for chromosome chr4_JH584294_random with length 191905
2023-12-13 12:55:12,447 - cnvpytor.bam - DEBUG - Reading chromosome chr4_JH584294_random from filename B6MaleKidney_mapped.bam
2023-12-13 12:55:12,480 - cnvpytor.root - INFO - Reading data for chromosome chr4_JH584295_random with length 1976
2023-12-13 12:55:12,480 - cnvpytor.bam - DEBUG - Reading chromosome chr4_JH584295_random from filename B6MaleKidney_mapped.bam
2023-12-13 12:55:12,504 - cnvpytor.root - INFO - Reading data for chromosome chr5 with length 151834684
2023-12-13 12:55:12,504 - cnvpytor.bam - DEBUG - Reading chromosome chr5 from filename B6MaleKidney_mapped.bam
2023-12-13 12:55:16,802 - cnvpytor.root - INFO - Reading data for chromosome chr5_JH584296_random with length 199368
2023-12-13 12:55:16,802 - cnvpytor.bam - DEBUG - Reading chromosome chr5_JH584296_random from filename B6MaleKidney_mapped.bam
2023-12-13 12:55:16,835 - cnvpytor.root - INFO - Reading data for chromosome chr5_JH584297_random with length 205776
2023-12-13 12:55:16,835 - cnvpytor.bam - DEBUG - Reading chromosome chr5_JH584297_random from filename B6MaleKidney_mapped.bam
2023-12-13 12:55:16,879 - cnvpytor.root - INFO - Reading data for chromosome chr5_JH584298_random with length 184189
2023-12-13 12:55:16,879 - cnvpytor.bam - DEBUG - Reading chromosome chr5_JH584298_random from filename B6MaleKidney_mapped.bam
2023-12-13 12:55:16,919 - cnvpytor.root - INFO - Reading data for chromosome chr5_GL456354_random with length 195993
2023-12-13 12:55:16,919 - cnvpytor.bam - DEBUG - Reading chromosome chr5_GL456354_random from filename B6MaleKidney_mapped.bam
2023-12-13 12:55:16,961 - cnvpytor.root - INFO - Reading data for chromosome chr5_JH584299_random with length 953012
2023-12-13 12:55:16,961 - cnvpytor.bam - DEBUG - Reading chromosome chr5_JH584299_random from filename B6MaleKidney_mapped.bam
2023-12-13 12:55:17,070 - cnvpytor.root - INFO - Reading data for chromosome chr6 with length 149736546
2023-12-13 12:55:17,070 - cnvpytor.bam - DEBUG - Reading chromosome chr6 from filename B6MaleKidney_mapped.bam
2023-12-13 12:55:18,489 - cnvpytor.root - INFO - Reading data for chromosome chr7 with length 145441459
2023-12-13 12:55:18,490 - cnvpytor.root - INFO - Reading data for chromosome chr7_GL456219_random with length 175968
2023-12-13 12:55:18,490 - cnvpytor.bam - DEBUG - Reading chromosome chr7 from filename B6MaleKidney_mapped.bam
2023-12-13 12:55:18,490 - cnvpytor.bam - DEBUG - Reading chromosome chr7_GL456219_random from filename B6MaleKidney_mapped.bam
2023-12-13 12:55:18,557 - cnvpytor.root - INFO - Reading data for chromosome chr8 with length 129401213
2023-12-13 12:55:18,557 - cnvpytor.bam - DEBUG - Reading chromosome chr8 from filename B6MaleKidney_mapped.bam
2023-12-13 12:55:18,913 - cnvpytor.root - INFO - Reading data for chromosome chr9 with length 124595110
2023-12-13 12:55:18,913 - cnvpytor.bam - DEBUG - Reading chromosome chr9 from filename B6MaleKidney_mapped.bam
2023-12-13 12:55:25,493 - cnvpytor.root - INFO - Reading data for chromosome chrM with length 16299
2023-12-13 12:55:25,494 - cnvpytor.bam - DEBUG - Reading chromosome chrM from filename B6MaleKidney_mapped.bam
2023-12-13 12:55:25,859 - cnvpytor.root - INFO - Reading data for chromosome chrX with length 171031299
2023-12-13 12:55:25,860 - cnvpytor.bam - DEBUG - Reading chromosome chrX from filename B6MaleKidney_mapped.bam
2023-12-13 12:55:26,050 - cnvpytor.root - INFO - Reading data for chromosome chrX_GL456233_random with length 336933
2023-12-13 12:55:26,051 - cnvpytor.bam - DEBUG - Reading chromosome chrX_GL456233_random from filename B6MaleKidney_mapped.bam
2023-12-13 12:55:26,096 - cnvpytor.root - INFO - Reading data for chromosome chrY with length 91744698
2023-12-13 12:55:26,096 - cnvpytor.bam - DEBUG - Reading chromosome chrY from filename B6MaleKidney_mapped.bam
2023-12-13 12:55:26,108 - cnvpytor.root - INFO - Reading data for chromosome chrY_JH584300_random with length 182347
2023-12-13 12:55:26,108 - cnvpytor.bam - DEBUG - Reading chromosome chrY_JH584300_random from filename B6MaleKidney_mapped.bam
2023-12-13 12:55:26,138 - cnvpytor.root - INFO - Reading data for chromosome chrY_JH584301_random with length 259875
2023-12-13 12:55:26,138 - cnvpytor.bam - DEBUG - Reading chromosome chrY_JH584301_random from filename B6MaleKidney_mapped.bam
2023-12-13 12:55:26,169 - cnvpytor.root - INFO - Reading data for chromosome chrY_JH584302_random with length 155838
2023-12-13 12:55:26,169 - cnvpytor.bam - DEBUG - Reading chromosome chrY_JH584302_random from filename B6MaleKidney_mapped.bam
2023-12-13 12:55:26,200 - cnvpytor.root - INFO - Reading data for chromosome chrY_JH584303_random with length 158099
2023-12-13 12:55:26,200 - cnvpytor.bam - DEBUG - Reading chromosome chrY_JH584303_random from filename B6MaleKidney_mapped.bam
2023-12-13 12:55:26,227 - cnvpytor.root - INFO - Reading data for chromosome chrUn_GL456239 with length 40056
2023-12-13 12:55:26,228 - cnvpytor.bam - DEBUG - Reading chromosome chrUn_GL456239 from filename B6MaleKidney_mapped.bam
2023-12-13 12:55:26,307 - cnvpytor.root - INFO - Reading data for chromosome chrUn_GL456367 with length 42057
2023-12-13 12:55:26,308 - cnvpytor.bam - DEBUG - Reading chromosome chrUn_GL456367 from filename B6MaleKidney_mapped.bam
2023-12-13 12:55:26,336 - cnvpytor.root - INFO - Reading data for chromosome chrUn_GL456378 with length 31602
2023-12-13 12:55:26,336 - cnvpytor.bam - DEBUG - Reading chromosome chrUn_GL456378 from filename B6MaleKidney_mapped.bam
2023-12-13 12:55:26,367 - cnvpytor.root - INFO - Reading data for chromosome chrUn_GL456381 with length 25871
2023-12-13 12:55:26,367 - cnvpytor.bam - DEBUG - Reading chromosome chrUn_GL456381 from filename B6MaleKidney_mapped.bam
2023-12-13 12:55:26,398 - cnvpytor.root - INFO - Reading data for chromosome chrUn_GL456382 with length 23158
2023-12-13 12:55:26,399 - cnvpytor.bam - DEBUG - Reading chromosome chrUn_GL456382 from filename B6MaleKidney_mapped.bam
2023-12-13 12:55:26,424 - cnvpytor.root - INFO - Reading data for chromosome chrUn_GL456383 with length 38659
2023-12-13 12:55:26,425 - cnvpytor.bam - DEBUG - Reading chromosome chrUn_GL456383 from filename B6MaleKidney_mapped.bam
2023-12-13 12:55:26,477 - cnvpytor.root - INFO - Reading data for chromosome chrUn_GL456385 with length 35240
2023-12-13 12:55:26,478 - cnvpytor.bam - DEBUG - Reading chromosome chrUn_GL456385 from filename B6MaleKidney_mapped.bam
2023-12-13 12:55:26,506 - cnvpytor.root - INFO - Reading data for chromosome chrUn_GL456390 with length 24668
2023-12-13 12:55:26,507 - cnvpytor.bam - DEBUG - Reading chromosome chrUn_GL456390 from filename B6MaleKidney_mapped.bam
2023-12-13 12:55:26,604 - cnvpytor.root - INFO - Reading data for chromosome chrUn_GL456392 with length 23629
2023-12-13 12:55:26,604 - cnvpytor.bam - DEBUG - Reading chromosome chrUn_GL456392 from filename B6MaleKidney_mapped.bam
2023-12-13 12:55:26,657 - cnvpytor.root - INFO - Reading data for chromosome chrUn_GL456393 with length 55711
2023-12-13 12:55:26,657 - cnvpytor.bam - DEBUG - Reading chromosome chrUn_GL456393 from filename B6MaleKidney_mapped.bam
2023-12-13 12:55:26,709 - cnvpytor.root - INFO - Reading data for chromosome chrUn_GL456394 with length 24323
2023-12-13 12:55:26,709 - cnvpytor.bam - DEBUG - Reading chromosome chrUn_GL456394 from filename B6MaleKidney_mapped.bam
2023-12-13 12:55:26,742 - cnvpytor.root - INFO - Reading data for chromosome chrUn_GL456359 with length 22974
2023-12-13 12:55:26,742 - cnvpytor.bam - DEBUG - Reading chromosome chrUn_GL456359 from filename B6MaleKidney_mapped.bam
2023-12-13 12:55:26,772 - cnvpytor.root - INFO - Reading data for chromosome chrUn_GL456360 with length 31704
2023-12-13 12:55:26,772 - cnvpytor.bam - DEBUG - Reading chromosome chrUn_GL456360 from filename B6MaleKidney_mapped.bam
2023-12-13 12:55:26,800 - cnvpytor.root - INFO - Reading data for chromosome chrUn_GL456396 with length 21240
2023-12-13 12:55:26,801 - cnvpytor.bam - DEBUG - Reading chromosome chrUn_GL456396 from filename B6MaleKidney_mapped.bam
2023-12-13 12:55:26,894 - cnvpytor.root - INFO - Reading data for chromosome chrUn_GL456372 with length 28664
2023-12-13 12:55:26,895 - cnvpytor.bam - DEBUG - Reading chromosome chrUn_GL456372 from filename B6MaleKidney_mapped.bam
2023-12-13 12:55:26,920 - cnvpytor.root - INFO - Reading data for chromosome chrUn_GL456387 with length 24685
2023-12-13 12:55:26,921 - cnvpytor.bam - DEBUG - Reading chromosome chrUn_GL456387 from filename B6MaleKidney_mapped.bam
2023-12-13 12:55:26,977 - cnvpytor.root - INFO - Reading data for chromosome chrUn_GL456389 with length 28772
2023-12-13 12:55:26,977 - cnvpytor.bam - DEBUG - Reading chromosome chrUn_GL456389 from filename B6MaleKidney_mapped.bam
2023-12-13 12:55:27,019 - cnvpytor.root - INFO - Reading data for chromosome chrUn_GL456370 with length 26764
2023-12-13 12:55:27,020 - cnvpytor.bam - DEBUG - Reading chromosome chrUn_GL456370 from filename B6MaleKidney_mapped.bam
2023-12-13 12:55:27,070 - cnvpytor.root - INFO - Reading data for chromosome chrUn_GL456379 with length 72385
2023-12-13 12:55:27,070 - cnvpytor.bam - DEBUG - Reading chromosome chrUn_GL456379 from filename B6MaleKidney_mapped.bam
2023-12-13 12:55:27,100 - cnvpytor.root - INFO - Reading data for chromosome chrUn_GL456366 with length 47073
2023-12-13 12:55:27,100 - cnvpytor.bam - DEBUG - Reading chromosome chrUn_GL456366 from filename B6MaleKidney_mapped.bam
2023-12-13 12:55:27,135 - cnvpytor.root - INFO - Reading data for chromosome chrUn_GL456368 with length 20208
2023-12-13 12:55:27,135 - cnvpytor.bam - DEBUG - Reading chromosome chrUn_GL456368 from filename B6MaleKidney_mapped.bam
2023-12-13 12:55:27,163 - cnvpytor.root - INFO - Reading data for chromosome chrUn_JH584304 with length 114452
2023-12-13 12:55:27,163 - cnvpytor.bam - DEBUG - Reading chromosome chrUn_JH584304 from filename B6MaleKidney_mapped.bam
2023-12-13 12:55:41,636 - cnvpytor.io - INFO - Adding RD data for chromosome 'chr1'.
2023-12-13 12:55:43,436 - cnvpytor.io - INFO - Adding RD data for chromosome 'chr10'.
2023-12-13 12:55:44,554 - cnvpytor.io - INFO - Adding RD data for chromosome 'chr11'.
2023-12-13 12:55:45,716 - cnvpytor.io - INFO - Adding RD data for chromosome 'chr12'.
2023-12-13 12:55:46,751 - cnvpytor.io - INFO - Adding RD data for chromosome 'chr13'.
2023-12-13 12:55:47,773 - cnvpytor.io - INFO - Adding RD data for chromosome 'chr14'.
2023-12-13 12:55:48,832 - cnvpytor.io - INFO - Adding RD data for chromosome 'chr15'.
2023-12-13 12:55:49,711 - cnvpytor.io - INFO - Adding RD data for chromosome 'chr16'.
2023-12-13 12:55:50,534 - cnvpytor.io - INFO - Adding RD data for chromosome 'chr17'.
2023-12-13 12:55:51,389 - cnvpytor.io - INFO - Adding RD data for chromosome 'chr18'.
2023-12-13 12:55:52,156 - cnvpytor.io - INFO - Adding RD data for chromosome 'chr19'.
2023-12-13 12:55:52,678 - cnvpytor.io - INFO - Adding RD data for chromosome 'chr1_GL456210_random'.
2023-12-13 12:55:52,684 - cnvpytor.io - INFO - Adding RD data for chromosome 'chr1_GL456211_random'.
2023-12-13 12:55:52,691 - cnvpytor.io - INFO - Adding RD data for chromosome 'chr1_GL456212_random'.
2023-12-13 12:55:52,696 - cnvpytor.io - INFO - Adding RD data for chromosome 'chr1_GL456213_random'.
2023-12-13 12:55:52,701 - cnvpytor.io - INFO - Adding RD data for chromosome 'chr1_GL456221_random'.
2023-12-13 12:55:52,710 - cnvpytor.io - INFO - Adding RD data for chromosome 'chr2'.
2023-12-13 12:55:54,289 - cnvpytor.io - INFO - Adding RD data for chromosome 'chr3'.
2023-12-13 12:55:55,670 - cnvpytor.io - INFO - Adding RD data for chromosome 'chr4'.
2023-12-13 12:55:57,009 - cnvpytor.io - INFO - Adding RD data for chromosome 'chr4_GL456216_random'.
2023-12-13 12:55:57,018 - cnvpytor.io - INFO - Adding RD data for chromosome 'chr4_JH584292_random'.
2023-12-13 12:55:57,025 - cnvpytor.io - INFO - Adding RD data for chromosome 'chr4_GL456350_random'.
2023-12-13 12:55:57,032 - cnvpytor.io - INFO - Adding RD data for chromosome 'chr4_JH584293_random'.
2023-12-13 12:55:57,040 - cnvpytor.io - INFO - Adding RD data for chromosome 'chr4_JH584294_random'.
2023-12-13 12:55:57,048 - cnvpytor.io - INFO - Adding RD data for chromosome 'chr4_JH584295_random'.
2023-12-13 12:55:57,056 - cnvpytor.io - INFO - Adding RD data for chromosome 'chr5'.
2023-12-13 12:55:58,497 - cnvpytor.io - INFO - Adding RD data for chromosome 'chr5_JH584296_random'.
2023-12-13 12:55:58,505 - cnvpytor.io - INFO - Adding RD data for chromosome 'chr5_JH584297_random'.
2023-12-13 12:55:58,513 - cnvpytor.io - INFO - Adding RD data for chromosome 'chr5_JH584298_random'.
2023-12-13 12:55:58,519 - cnvpytor.io - INFO - Adding RD data for chromosome 'chr5_GL456354_random'.
2023-12-13 12:55:58,525 - cnvpytor.io - INFO - Adding RD data for chromosome 'chr5_JH584299_random'.
2023-12-13 12:55:58,537 - cnvpytor.io - INFO - Adding RD data for chromosome 'chr6'.
2023-12-13 12:55:59,833 - cnvpytor.io - INFO - Adding RD data for chromosome 'chr7'.
2023-12-13 12:56:01,118 - cnvpytor.io - INFO - Adding RD data for chromosome 'chr7_GL456219_random'.
2023-12-13 12:56:01,126 - cnvpytor.io - INFO - Adding RD data for chromosome 'chr8'.
2023-12-13 12:56:02,227 - cnvpytor.io - INFO - Adding RD data for chromosome 'chr9'.
2023-12-13 12:56:03,276 - cnvpytor.io - INFO - Adding RD data for chromosome 'chrM'.
2023-12-13 12:56:03,281 - cnvpytor.io - INFO - Adding RD data for chromosome 'chrX'.
2023-12-13 12:56:04,051 - cnvpytor.io - INFO - Adding RD data for chromosome 'chrX_GL456233_random'.
2023-12-13 12:56:04,060 - cnvpytor.io - INFO - Adding RD data for chromosome 'chrY'.
2023-12-13 12:56:04,567 - cnvpytor.io - INFO - Adding RD data for chromosome 'chrY_JH584300_random'.
2023-12-13 12:56:04,574 - cnvpytor.io - INFO - Adding RD data for chromosome 'chrY_JH584301_random'.
2023-12-13 12:56:04,580 - cnvpytor.io - INFO - Adding RD data for chromosome 'chrY_JH584302_random'.
2023-12-13 12:56:04,585 - cnvpytor.io - INFO - Adding RD data for chromosome 'chrY_JH584303_random'.
2023-12-13 12:56:04,593 - cnvpytor.io - INFO - Adding RD data for chromosome 'chrUn_GL456239'.
2023-12-13 12:56:04,602 - cnvpytor.io - INFO - Adding RD data for chromosome 'chrUn_GL456367'.
2023-12-13 12:56:04,609 - cnvpytor.io - INFO - Adding RD data for chromosome 'chrUn_GL456378'.
2023-12-13 12:56:04,616 - cnvpytor.io - INFO - Adding RD data for chromosome 'chrUn_GL456381'.
2023-12-13 12:56:04,621 - cnvpytor.io - INFO - Adding RD data for chromosome 'chrUn_GL456382'.
2023-12-13 12:56:04,626 - cnvpytor.io - INFO - Adding RD data for chromosome 'chrUn_GL456383'.
2023-12-13 12:56:04,631 - cnvpytor.io - INFO - Adding RD data for chromosome 'chrUn_GL456385'.
2023-12-13 12:56:04,636 - cnvpytor.io - INFO - Adding RD data for chromosome 'chrUn_GL456390'.
2023-12-13 12:56:04,640 - cnvpytor.io - INFO - Adding RD data for chromosome 'chrUn_GL456392'.
2023-12-13 12:56:04,645 - cnvpytor.io - INFO - Adding RD data for chromosome 'chrUn_GL456393'.
2023-12-13 12:56:04,650 - cnvpytor.io - INFO - Adding RD data for chromosome 'chrUn_GL456394'.
2023-12-13 12:56:04,654 - cnvpytor.io - INFO - Adding RD data for chromosome 'chrUn_GL456359'.
2023-12-13 12:56:04,658 - cnvpytor.io - INFO - Adding RD data for chromosome 'chrUn_GL456360'.
2023-12-13 12:56:04,663 - cnvpytor.io - INFO - Adding RD data for chromosome 'chrUn_GL456396'.
2023-12-13 12:56:04,667 - cnvpytor.io - INFO - Adding RD data for chromosome 'chrUn_GL456372'.
2023-12-13 12:56:04,671 - cnvpytor.io - INFO - Adding RD data for chromosome 'chrUn_GL456387'.
2023-12-13 12:56:04,676 - cnvpytor.io - INFO - Adding RD data for chromosome 'chrUn_GL456389'.
2023-12-13 12:56:04,680 - cnvpytor.io - INFO - Adding RD data for chromosome 'chrUn_GL456370'.
2023-12-13 12:56:04,684 - cnvpytor.io - INFO - Adding RD data for chromosome 'chrUn_GL456379'.
2023-12-13 12:56:04,688 - cnvpytor.io - INFO - Adding RD data for chromosome 'chrUn_GL456366'.
2023-12-13 12:56:04,693 - cnvpytor.io - INFO - Adding RD data for chromosome 'chrUn_GL456368'.
2023-12-13 12:56:04,701 - cnvpytor.io - INFO - Adding RD data for chromosome 'chrUn_JH584304'.
2023-12-13 12:56:04,817 - h5py._conv - DEBUG - Creating converter from 5 to 3
2023-12-13 12:56:04,818 - cnvpytor.root - INFO - GC content for reference genome 'mm10' found in database.
2023-12-13 12:56:04,818 - cnvpytor.io - DEBUG - Opening h5 file '/path/to/mm10_gc_file.pytor'
2023-12-13 12:56:04,819 - cnvpytor.io - DEBUG - File '/path/to/mm10_gc_file.pytor' successfully opened in read-only mode.
2023-12-13 12:56:04,819 - cnvpytor.io - DEBUG - Closing h5 file '/path/to/mm10_gc_file.pytor'
2023-12-13 12:56:04,820 - cnvpytor.io - DEBUG - Closing h5 file '/path/to/mm10_gc_file.pytor'
2023-12-13 12:56:04,820 - cnvpytor.io - DEBUG - Closing h5 file 'B6MaleKidney_mm10_rd.pytor'
arpanda commented 9 months ago

I think, the reference genome was not set properly during/after the rd step. Could you please run the step for setting reference genome after the rd and then other steps.

As, you already have the rd results, there is no need to rerun the rd step. Run the following. 

cnvpytor -conf mm10_ref_conf.py -root B6MaleKidney_mm10_rd.pytor -rg mm10
cnvpytor -conf mm10_ref_conf.py -root B6MaleKidney_mm10_rd.pytor -stat 100

then -his step


cnvpytor -conf mm10_ref_conf.py -root B6MaleKidney_mm10_rd.pytor -his 10000 100000

After this, please check if there is any change for the histogram or not via ls command. i.e, 

 Chromosomes with RD histograms [bin sizes]:  []

If you have change, please proceed with other steps. If not, would you mind sharing pytor file, I can check in details. Email: panda.arijit@mayo.edu

Thank you, Arijit

arpanda commented 9 months ago

The GC file was empty, resulting in error in subsequent steps.