Closed Tintest closed 5 months ago
philippesanio
commented
5 months ago Hi @Tintest
This should not happen, could you be so kind and confirm for me if there are any calls in the bed.gz file from sample1? Do you have by any chance the log of sample1?
Best, Philippe
Tintest
commented
5 months ago Hello, here is the complete log :
singularity exec --bind /srv:/srv spectre.0.2.0.sif spectre CNVCaller \
--coverage mosdepth/Sample2.regions.bed.gz mosdepth/Sample1.regions.bed.gz mosdepth/Sample3.regions.bed.gz mosdepth/Sample4.regions.bed.gz mosdepth/Sample5.regions.bed.gz mosdepth/Sample6.regions.bed.gz mosdepth/Sample7.regions.bed.gz mosdepth/Sample8.regions.bed.gz mosdepth/Sample9.regions.bed.gz mosdepth/Sample10.regions.bed.gz mosdepth/Sample11.regions.bed.gz mosdepth/Sample12.regions.bed.gz mosdepth/Sample13.regions.bed.gz mosdepth/Sample14.regions.bed.gz mosdepth/Sample15.regions.bed.gz mosdepth/Sample16.regions.bed.gz mosdepth/Sample17.regions.bed.gz mosdepth/Sample18.regions.bed.gz mosdepth/Sample19.regions.bed.gz mosdepth/Sample20.regions.bed.gz mosdepth/Sample21.regions.bed.gz mosdepth/Sample22.regions.bed.gz mosdepth/Sample23.regions.bed.gz mosdepth/Sample24.regions.bed.gz mosdepth/Sample25.regions.bed.gz mosdepth/Sample26.regions.bed.gz \
--sample-id Sample2 Sample1 Sample3 Sample4 Sample5 Sample6 Sample7 Sample8 Sample9 Sample10 Sample11 Sample12 Sample13 Sample14 Sample15 Sample16 Sample17 Sample18 Sample19 Sample20 Sample21 Sample22 Sample23 Sample24 Sample25 Sample26 \
--output-dir results/Sample1/ \
--blacklist grch38_blacklist_spectre.bed \
--only-chr chr1,chr2,chr3,chr4,chr5,chr6,chr7,chr8,chr9,chr10,chr11,chr12,chr13,chr14,chr15,chr16,chr17,chr18,chr19,chr20,chr21,chr22,chrX,chrY \
-0 \
--ploidy-chr chrX:1,chrY:1 \
--reference GRCh38.p13.canonical.fa.gz
spectre::2024-04-10 14:07:12,816::INFO::spectre.spectre> Spectre input: CNVCaller --coverage mosdepth/Sample2.regions.bed.gz mosdepth/Sample1.regions.bed.gz mosdepth/Sample3.regions.bed.gz mosdepth/Sample4.regions.bed.gz mosdepth/Sample5.regions.bed.gz mosdepth/Sample6.regions.bed.gz mosdepth/Sample7.regions.bed.gz mosdepth/Sample8.regions.bed.gz mosdepth/Sample9.regions.bed.gz mosdepth/Sample10.regions.bed.gz mosdepth/Sample11.regions.bed.gz mosdepth/Sample12.regions.bed.gz mosdepth/Sample13.regions.bed.gz mosdepth/Sample14.regions.bed.gz mosdepth/Sample15.regions.bed.gz mosdepth/Sample16.regions.bed.gz mosdepth/Sample17.regions.bed.gz mosdepth/Sample18.regions.bed.gz mosdepth/Sample19.regions.bed.gz mosdepth/Sample20.regions.bed.gz mosdepth/Sample21.regions.bed.gz mosdepth/Sample22.regions.bed.gz mosdepth/Sample23.regions.bed.gz mosdepth/Sample24.regions.bed.gz mosdepth/Sample25.regions.bed.gz mosdepth/Sample26.regions.bed.gz --sample-id Sample1 Sample2 Sample3 Sample4 Sample5 Sample6 Sample7 Sample8 Sample9 Sample10 Sample11 Sample12 Sample13 Sample14 Sample15 Sample16 Sample17 Sample18 Sample19 Sample20 Sample21 Sample22 Sample23 Sample24 Sample25 Sample26 --output-dir results --blacklist grch38_blacklist_spectre.bed --only-chr chr1,chr2,chr3,chr4,chr5,chr6,chr7,chr8,chr9,chr10,chr11,chr12,chr13,chr14,chr15,chr16,chr17,chr18,chr19,chr20,chr21,chr22,chrX,chrY -0 --ploidy-chr chrX:1,chrY:1 --reference GRCh38.p13.canonical.fa.gz
spectre::2024-04-10 14:50:39,315::DEBUG::spectre.spectre> Debug output is enabled
spectre::2024-04-10 14:50:39,315::INFO::spectre.spectre> Spectre version: 0.2.0
spectre::2024-04-10 14:50:39,315::INFO::spectre.spectre> Starting spectre
spectre::2024-04-10 14:50:39,315::INFO::spectre.spectre> Evaluate if a new .mdr file needs to be created
spectre::2024-04-10 14:50:39,315::INFO::spectre.spectre> Looking for default metadata.mdr in output directory
spectre::2024-04-10 14:50:39,315::INFO::spectre.spectre> Using existing metadata file
spectre::2024-04-10 14:50:39,316::DEBUG::spectre.spectre> genome: ['chr1', 'chr2', 'chr3', 'chr4', 'chr5', 'chr6', 'chr7', 'chr8', 'chr9', 'chr10', 'chr11', 'chr12', 'chr13', 'chr14', 'chr15', 'chr16', 'chr17', 'chr18', 'chr19', 'chr20', 'chr21', 'chr22', 'chrX', 'chrY']
spectre::2024-04-10 14:50:39,317::INFO::spectre.spectreCNV> Spectre calculating for: mosdepth/Sample2.regions.bed.gz
spectre::2024-04-10 14:50:39,317::INFO::spectre.spectreCNV> Data normalization and outlier removal (right tail)
spectre::2024-04-10 14:50:39,317::DEBUG::spectre.analysis.analysis> coverage file: mosdepth/Sample2.regions.bed.gz
[W::tbx_parse1] Coordinate <= 0 detected. Did you forget to use the -0 option?
spectre::2024-04-10 14:50:39,581::INFO::spectre.analysis.analysis> Determined bin size from Mosdepth coverage: 1000
[W::tbx_parse1] Coordinate <= 0 detected. Did you forget to use the -0 option?
[W::tbx_parse1] Coordinate <= 0 detected. Did you forget to use the -0 option?
[W::tbx_parse1] Coordinate <= 0 detected. Did you forget to use the -0 option?
[W::tbx_parse1] Coordinate <= 0 detected. Did you forget to use the -0 option?
[W::tbx_parse1] Coordinate <= 0 detected. Did you forget to use the -0 option?
[W::tbx_parse1] Coordinate <= 0 detected. Did you forget to use the -0 option?
[W::tbx_parse1] Coordinate <= 0 detected. Did you forget to use the -0 option?
[W::tbx_parse1] Coordinate <= 0 detected. Did you forget to use the -0 option?
[W::tbx_parse1] Coordinate <= 0 detected. Did you forget to use the -0 option?
[W::tbx_parse1] Coordinate <= 0 detected. Did you forget to use the -0 option?
[W::tbx_parse1] Coordinate <= 0 detected. Did you forget to use the -0 option?
[W::tbx_parse1] Coordinate <= 0 detected. Did you forget to use the -0 option?
[W::tbx_parse1] Coordinate <= 0 detected. Did you forget to use the -0 option?
[W::tbx_parse1] Coordinate <= 0 detected. Did you forget to use the -0 option?
[W::tbx_parse1] Coordinate <= 0 detected. Did you forget to use the -0 option?
[W::tbx_parse1] Coordinate <= 0 detected. Did you forget to use the -0 option?
[W::tbx_parse1] Coordinate <= 0 detected. Did you forget to use the -0 option?
[W::tbx_parse1] Coordinate <= 0 detected. Did you forget to use the -0 option?
[W::tbx_parse1] Coordinate <= 0 detected. Did you forget to use the -0 option?
[W::tbx_parse1] Coordinate <= 0 detected. Did you forget to use the -0 option?
[W::tbx_parse1] Coordinate <= 0 detected. Did you forget to use the -0 option?
[W::tbx_parse1] Coordinate <= 0 detected. Did you forget to use the -0 option?
[W::tbx_parse1] Coordinate <= 0 detected. Did you forget to use the -0 option?
spectre::2024-04-10 14:50:43,310::INFO::spectre.analysis.analysis> Number positions to be tested on chromosome chr1: 248957
spectre::2024-04-10 14:50:43,371::DEBUG::spectre.analysis.analysis> nan_count 39965 v. 248957 self.coverage.size
spectre::2024-04-10 14:50:43,376::DEBUG::spectre.analysis.analysis> Chromsomal Info @ chr1: avg: 16.495551552212532, std: 3.911249453813505, med: 16.3
spectre::2024-04-10 14:50:43,383::INFO::spectre.analysis.analysis> Number positions to be tested on chromosome chr2: 242194
spectre::2024-04-10 14:50:43,439::DEBUG::spectre.analysis.analysis> nan_count 16271 v. 242194 self.coverage.size
spectre::2024-04-10 14:50:43,444::DEBUG::spectre.analysis.analysis> Chromsomal Info @ chr2: avg: 16.384813719718665, std: 3.6760824957335245, med: 16.22
spectre::2024-04-10 14:50:43,450::INFO::spectre.analysis.analysis> Number positions to be tested on chromosome chr3: 198296
spectre::2024-04-10 14:50:43,496::DEBUG::spectre.analysis.analysis> nan_count 6664 v. 198296 self.coverage.size
spectre::2024-04-10 14:50:43,500::DEBUG::spectre.analysis.analysis> Chromsomal Info @ chr3: avg: 16.37970907781581, std: 3.600608108116106, med: 16.23
spectre::2024-04-10 14:50:43,506::INFO::spectre.analysis.analysis> Number positions to be tested on chromosome chr4: 190215
spectre::2024-04-10 14:50:43,560::DEBUG::spectre.analysis.analysis> nan_count 7521 v. 190215 self.coverage.size
spectre::2024-04-10 14:50:43,565::DEBUG::spectre.analysis.analysis> Chromsomal Info @ chr4: avg: 16.28546744830153, std: 3.6505990022680552, med: 16.11
spectre::2024-04-10 14:50:43,570::INFO::spectre.analysis.analysis> Number positions to be tested on chromosome chr5: 181539
spectre::2024-04-10 14:50:43,614::DEBUG::spectre.analysis.analysis> nan_count 10145 v. 181539 self.coverage.size
spectre::2024-04-10 14:50:43,618::DEBUG::spectre.analysis.analysis> Chromsomal Info @ chr5: avg: 16.3648838932518, std: 3.592289743140997, med: 16.21
spectre::2024-04-10 14:50:43,623::INFO::spectre.analysis.analysis> Number positions to be tested on chromosome chr6: 170806
spectre::2024-04-10 14:50:43,664::DEBUG::spectre.analysis.analysis> nan_count 9198 v. 170806 self.coverage.size
spectre::2024-04-10 14:50:43,667::DEBUG::spectre.analysis.analysis> Chromsomal Info @ chr6: avg: 16.504869004009702, std: 4.107705071548058, med: 16.24
spectre::2024-04-10 14:50:43,672::INFO::spectre.analysis.analysis> Number positions to be tested on chromosome chr7: 159346
spectre::2024-04-10 14:50:43,711::DEBUG::spectre.analysis.analysis> nan_count 16339 v. 159346 self.coverage.size
spectre::2024-04-10 14:50:43,714::DEBUG::spectre.analysis.analysis> Chromsomal Info @ chr7: avg: 16.393807435999634, std: 3.883543110869586, med: 16.19
spectre::2024-04-10 14:50:43,719::INFO::spectre.analysis.analysis> Number positions to be tested on chromosome chr8: 145139
spectre::2024-04-10 14:50:43,758::DEBUG::spectre.analysis.analysis> nan_count 11532 v. 145139 self.coverage.size
spectre::2024-04-10 14:50:43,760::DEBUG::spectre.analysis.analysis> Chromsomal Info @ chr8: avg: 16.39050581182124, std: 3.5861119616763686, med: 16.23
spectre::2024-04-10 14:50:43,765::INFO::spectre.analysis.analysis> Number positions to be tested on chromosome chr9: 138395
spectre::2024-04-10 14:50:43,800::DEBUG::spectre.analysis.analysis> nan_count 34657 v. 138395 self.coverage.size
spectre::2024-04-10 14:50:43,803::DEBUG::spectre.analysis.analysis> Chromsomal Info @ chr9: avg: 16.48295908924406, std: 3.828354034671187, med: 16.28
spectre::2024-04-10 14:50:43,808::INFO::spectre.analysis.analysis> Number positions to be tested on chromosome chr10: 133798
spectre::2024-04-10 14:50:43,840::DEBUG::spectre.analysis.analysis> nan_count 9556 v. 133798 self.coverage.size
spectre::2024-04-10 14:50:43,843::DEBUG::spectre.analysis.analysis> Chromsomal Info @ chr10: avg: 16.452156919560213, std: 3.6900969462789814, med: 16.26
spectre::2024-04-10 14:50:43,847::INFO::spectre.analysis.analysis> Number positions to be tested on chromosome chr11: 135087
spectre::2024-04-10 14:50:43,880::DEBUG::spectre.analysis.analysis> nan_count 9712 v. 135087 self.coverage.size
spectre::2024-04-10 14:50:43,883::DEBUG::spectre.analysis.analysis> Chromsomal Info @ chr11: avg: 16.464615274177465, std: 3.8841716871241454, med: 16.27
spectre::2024-04-10 14:50:43,887::INFO::spectre.analysis.analysis> Number positions to be tested on chromosome chr12: 133276
spectre::2024-04-10 14:50:43,920::DEBUG::spectre.analysis.analysis> nan_count 7009 v. 133276 self.coverage.size
spectre::2024-04-10 14:50:43,922::DEBUG::spectre.analysis.analysis> Chromsomal Info @ chr12: avg: 16.405738158030207, std: 3.6570299328368594, med: 16.25
spectre::2024-04-10 14:50:43,927::INFO::spectre.analysis.analysis> Number positions to be tested on chromosome chr13: 114365
spectre::2024-04-10 14:50:43,956::DEBUG::spectre.analysis.analysis> nan_count 20732 v. 114365 self.coverage.size
spectre::2024-04-10 14:50:43,958::DEBUG::spectre.analysis.analysis> Chromsomal Info @ chr13: avg: 16.25281941195946, std: 3.5331951862084674, med: 16.09
spectre::2024-04-10 14:50:43,962::INFO::spectre.analysis.analysis> Number positions to be tested on chromosome chr14: 107044
spectre::2024-04-10 14:50:43,989::DEBUG::spectre.analysis.analysis> nan_count 22399 v. 107044 self.coverage.size
spectre::2024-04-10 14:50:43,992::DEBUG::spectre.analysis.analysis> Chromsomal Info @ chr14: avg: 16.342916888180046, std: 3.480057755307257, med: 16.21
spectre::2024-04-10 14:50:43,995::INFO::spectre.analysis.analysis> Number positions to be tested on chromosome chr15: 101992
spectre::2024-04-10 14:50:44,023::DEBUG::spectre.analysis.analysis> nan_count 31498 v. 101992 self.coverage.size
spectre::2024-04-10 14:50:44,025::DEBUG::spectre.analysis.analysis> Chromsomal Info @ chr15: avg: 16.44266036825829, std: 3.8795770336510373, med: 16.29
spectre::2024-04-10 14:50:44,029::INFO::spectre.analysis.analysis> Number positions to be tested on chromosome chr16: 90339
spectre::2024-04-10 14:50:44,053::DEBUG::spectre.analysis.analysis> nan_count 24142 v. 90339 self.coverage.size
spectre::2024-04-10 14:50:44,055::DEBUG::spectre.analysis.analysis> Chromsomal Info @ chr16: avg: 16.490465277882684, std: 3.802242794613207, med: 16.31
spectre::2024-04-10 14:50:44,058::INFO::spectre.analysis.analysis> Number positions to be tested on chromosome chr17: 83258
spectre::2024-04-10 14:50:44,079::DEBUG::spectre.analysis.analysis> nan_count 15698 v. 83258 self.coverage.size
spectre::2024-04-10 14:50:44,081::DEBUG::spectre.analysis.analysis> Chromsomal Info @ chr17: avg: 16.57192007104796, std: 4.274941666058131, med: 16.3
spectre::2024-04-10 14:50:44,083::INFO::spectre.analysis.analysis> Number positions to be tested on chromosome chr18: 80374
spectre::2024-04-10 14:50:44,103::DEBUG::spectre.analysis.analysis> nan_count 8453 v. 80374 self.coverage.size
spectre::2024-04-10 14:50:44,105::DEBUG::spectre.analysis.analysis> Chromsomal Info @ chr18: avg: 16.344201137359043, std: 3.655624211038385, med: 16.16
spectre::2024-04-10 14:50:44,107::INFO::spectre.analysis.analysis> Number positions to be tested on chromosome chr19: 58618
spectre::2024-04-10 14:50:44,122::DEBUG::spectre.analysis.analysis> nan_count 5916 v. 58618 self.coverage.size
spectre::2024-04-10 14:50:44,123::DEBUG::spectre.analysis.analysis> Chromsomal Info @ chr19: avg: 16.764006679063414, std: 4.790208872549115, med: 16.39
spectre::2024-04-10 14:50:44,125::INFO::spectre.analysis.analysis> Number positions to be tested on chromosome chr20: 64445
spectre::2024-04-10 14:50:44,141::DEBUG::spectre.analysis.analysis> nan_count 7133 v. 64445 self.coverage.size
spectre::2024-04-10 14:50:44,142::DEBUG::spectre.analysis.analysis> Chromsomal Info @ chr20: avg: 16.580571957007262, std: 3.6874092292418705, med: 16.38
spectre::2024-04-10 14:50:44,145::INFO::spectre.analysis.analysis> Number positions to be tested on chromosome chr21: 46710
spectre::2024-04-10 14:50:44,157::DEBUG::spectre.analysis.analysis> nan_count 18970 v. 46710 self.coverage.size
spectre::2024-04-10 14:50:44,159::DEBUG::spectre.analysis.analysis> Chromsomal Info @ chr21: avg: 16.41108904109589, std: 3.772477922474992, med: 16.195
spectre::2024-04-10 14:50:44,160::INFO::spectre.analysis.analysis> Number positions to be tested on chromosome chr22: 50819
spectre::2024-04-10 14:50:44,174::DEBUG::spectre.analysis.analysis> nan_count 19368 v. 50819 self.coverage.size
spectre::2024-04-10 14:50:44,175::DEBUG::spectre.analysis.analysis> Chromsomal Info @ chr22: avg: 16.636215700613654, std: 4.166625828987789, med: 16.38
spectre::2024-04-10 14:50:44,177::INFO::spectre.analysis.analysis> Number positions to be tested on chromosome chrX: 156041
spectre::2024-04-10 14:50:44,216::DEBUG::spectre.analysis.analysis> nan_count 25036 v. 156041 self.coverage.size
spectre::2024-04-10 14:50:44,220::DEBUG::spectre.analysis.analysis> Chromsomal Info @ chrX: avg: 16.322508224876913, std: 3.7127365895852087, med: 16.21
spectre::2024-04-10 14:50:44,225::INFO::spectre.analysis.analysis> Number positions to be tested on chromosome chrY: 57228
spectre::2024-04-10 14:50:44,245::DEBUG::spectre.analysis.analysis> nan_count 57228 v. 57228 self.coverage.size
spectre::2024-04-10 14:50:44,245::WARNING::spectre.analysis.analysis> Chromosome chrY: no data available!
spectre::2024-04-10 14:50:44,246::DEBUG::spectre.analysis.cnv_metrics> Convert Genome analysis to coverage dataframe
spectre::2024-04-10 14:50:44,945::DEBUG::spectre.analysis.cnv_metrics> Converting blacklist to exclusion zone
spectre::2024-04-10 14:50:45,001::DEBUG::spectre.analysis.cnv_metrics> Preparing all parameters for the cnv evaluation
spectre::2024-04-10 14:50:59,733::DEBUG::spectre.analysis.cnv_metrics> Getting exclusion zone indices in mosdepth coverage data
spectre::2024-04-10 14:51:03,683::DEBUG::spectre.analysis.cnv_metrics> Generating random coverage sample indices
spectre::2024-04-10 14:51:03,915::DEBUG::spectre.analysis.cnv_metrics> CNV-Metrics: Writing random samples to file
spectre::2024-04-10 14:51:05,922::DEBUG::spectre.analysis.cnv_metrics> Calculationg DEL/DUP thresholds based on quantiles: 0.1 and 0.9
spectre::2024-04-10 14:51:05,934::DEBUG::spectre.analysis.cnv_metrics> CNV-Metrics: Calculated thresholds for DEL: 1.4809815950920244 and DUP: 2.510429447852761
spectre::2024-04-10 14:51:05,934::DEBUG::spectre.analysis.cnv_metrics> Calculated thresholds for DEL: 1.4809815950920244 and DUP: 2.510429447852761
spectre::2024-04-10 14:51:05,935::INFO::spectre.analysis.analysis> Selected threshold for DEL=1.481 and DUP=2.5104 for a ploidy of 2
spectre::2024-04-10 14:51:06,000::INFO::spectre.spectreCNV> CNV calling - Coverage for sample: Sample2
spectre::2024-04-10 14:51:06,000::INFO::spectre.analysis.analysis> Calculating CNVs for Sample2 @ chromosome chr1
spectre::2024-04-10 14:51:06,273::INFO::spectre.analysis.analysis> Calculating CNVs for Sample2 @ chromosome chr2
spectre::2024-04-10 14:51:06,557::INFO::spectre.analysis.analysis> Calculating CNVs for Sample2 @ chromosome chr3
spectre::2024-04-10 14:51:06,800::INFO::spectre.analysis.analysis> Calculating CNVs for Sample2 @ chromosome chr4
spectre::2024-04-10 14:51:07,035::INFO::spectre.analysis.analysis> Calculating CNVs for Sample2 @ chromosome chr5
spectre::2024-04-10 14:51:07,274::INFO::spectre.analysis.analysis> Calculating CNVs for Sample2 @ chromosome chr6
spectre::2024-04-10 14:51:07,490::INFO::spectre.analysis.analysis> Calculating CNVs for Sample2 @ chromosome chr7
spectre::2024-04-10 14:51:07,701::INFO::spectre.analysis.analysis> Calculating CNVs for Sample2 @ chromosome chr8
spectre::2024-04-10 14:51:07,883::INFO::spectre.analysis.analysis> Calculating CNVs for Sample2 @ chromosome chr9
spectre::2024-04-10 14:51:08,049::INFO::spectre.analysis.analysis> Calculating CNVs for Sample2 @ chromosome chr10
spectre::2024-04-10 14:51:08,199::INFO::spectre.analysis.analysis> Calculating CNVs for Sample2 @ chromosome chr11
spectre::2024-04-10 14:51:08,352::INFO::spectre.analysis.analysis> Calculating CNVs for Sample2 @ chromosome chr12
spectre::2024-04-10 14:51:08,500::INFO::spectre.analysis.analysis> Calculating CNVs for Sample2 @ chromosome chr13
spectre::2024-04-10 14:51:08,624::INFO::spectre.analysis.analysis> Calculating CNVs for Sample2 @ chromosome chr14
spectre::2024-04-10 14:51:08,740::INFO::spectre.analysis.analysis> Calculating CNVs for Sample2 @ chromosome chr15
spectre::2024-04-10 14:51:08,849::INFO::spectre.analysis.analysis> Calculating CNVs for Sample2 @ chromosome chr16
spectre::2024-04-10 14:51:08,950::INFO::spectre.analysis.analysis> Calculating CNVs for Sample2 @ chromosome chr17
spectre::2024-04-10 14:51:09,041::INFO::spectre.analysis.analysis> Calculating CNVs for Sample2 @ chromosome chr18
spectre::2024-04-10 14:51:09,131::INFO::spectre.analysis.analysis> Calculating CNVs for Sample2 @ chromosome chr19
spectre::2024-04-10 14:51:09,200::INFO::spectre.analysis.analysis> Calculating CNVs for Sample2 @ chromosome chr20
spectre::2024-04-10 14:51:09,271::INFO::spectre.analysis.analysis> Calculating CNVs for Sample2 @ chromosome chr21
spectre::2024-04-10 14:51:09,317::INFO::spectre.analysis.analysis> Calculating CNVs for Sample2 @ chromosome chr22
spectre::2024-04-10 14:51:09,373::INFO::spectre.analysis.analysis> Calculating CNVs for Sample2 @ chromosome chrX
spectre::2024-04-10 14:51:09,543::DEBUG::spectre.analysis.cnv_metrics> Evaluating all CNVs
spectre::2024-04-10 14:51:09,543::DEBUG::spectre.analysis.cnv_metrics> Recalculating
spectre::2024-04-10 14:51:09,543::DEBUG::spectre.analysis.cnv_metrics> Converting cnv calls to exclusion zone
spectre::2024-04-10 14:51:09,544::DEBUG::spectre.analysis.cnv_metrics> Merging exclusion zones
spectre::2024-04-10 14:51:24,020::DEBUG::spectre.analysis.cnv_metrics> Getting exclusion zone indices in mosdepth coverage data
spectre::2024-04-10 14:51:28,214::DEBUG::spectre.analysis.cnv_metrics> Generating random coverage sample indices
spectre::2024-04-10 14:51:28,467::INFO::spectre.analysis.cnv_metrics> DEL border:1.4809815950920244 DUP border:2.510429447852761
spectre::2024-04-10 14:51:28,479::DEBUG::spectre.analysis.cnv_metrics> Creating CNV distribution plot
spectre::2024-04-10 14:51:28,573::DEBUG::spectre.analysis.cnv_metrics> Plot path: /srv/scratch/testardqu/tickets/28452/Spectre/results/Sample2/debug/genome_coverage_distribution-Sample2.png
spectre::2024-04-10 14:51:28,653::INFO::spectre.analysis.analysis> refining cnv calls
spectre::2024-04-10 14:51:28,658::DEBUG::spectre.analysis.analysis> Writing coverage to /srv/scratch/testardqu/tickets/28452/Spectre/results/Sample2/debug/cnv_Sample2_byCoverage_chrchr1.csv
spectre::2024-04-10 14:51:29,484::DEBUG::spectre.analysis.analysis> total cnv candidates in chr1: 46 before merge
spectre::2024-04-10 14:51:29,484::DEBUG::spectre.analysis.analysis> Current merge cycle 1
spectre::2024-04-10 14:51:29,489::DEBUG::spectre.analysis.analysis> Current merge cycle 2
spectre::2024-04-10 14:51:29,493::DEBUG::spectre.analysis.analysis> Total merge rounds: 2
spectre::2024-04-10 14:51:29,493::DEBUG::spectre.analysis.analysis> Trying to merge over blacklisted regions for chr1
spectre::2024-04-10 14:51:29,493::DEBUG::spectre.analysis.analysis> Current blacklist merge cycle 1
spectre::2024-04-10 14:51:29,496::DEBUG::spectre.analysis.analysis> Total merge rounds over blacklisted region: 1
spectre::2024-04-10 14:51:29,876::DEBUG::spectre.analysis.cnv_metrics> CNV-Metrics: Calculated thresholds for DEL: 1.153806708360109 and DUP: 2.87418633303406
spectre::2024-04-10 14:51:29,877::DEBUG::spectre.analysis.analysis> Clean by threshold: 41 -> 33. Cleaned: 8
spectre::2024-04-10 14:51:29,877::DEBUG::spectre.analysis.analysis> Clean by size: 33 -> 0. Cleaned: 33
spectre::2024-04-10 14:51:29,877::DEBUG::spectre.analysis.analysis> Clean by size: 41 -> 0. Cleaned: 41
spectre::2024-04-10 14:51:29,881::DEBUG::spectre.analysis.analysis> Writing coverage to /srv/scratch/testardqu/tickets/28452/Spectre/results/Sample2/debug/cnv_Sample2_byCoverage_chrchr2.csv
spectre::2024-04-10 14:51:30,728::DEBUG::spectre.analysis.analysis> total cnv candidates in chr2: 24 before merge
spectre::2024-04-10 14:51:30,728::DEBUG::spectre.analysis.analysis> Current merge cycle 1
spectre::2024-04-10 14:51:30,730::DEBUG::spectre.analysis.analysis> Current merge cycle 2
spectre::2024-04-10 14:51:30,731::DEBUG::spectre.analysis.analysis> Total merge rounds: 2
spectre::2024-04-10 14:51:30,731::DEBUG::spectre.analysis.analysis> Trying to merge over blacklisted regions for chr2
spectre::2024-04-10 14:51:30,731::DEBUG::spectre.analysis.analysis> Current blacklist merge cycle 1
spectre::2024-04-10 14:51:30,733::DEBUG::spectre.analysis.analysis> Total merge rounds over blacklisted region: 1
spectre::2024-04-10 14:51:30,938::DEBUG::spectre.analysis.cnv_metrics> CNV-Metrics: Calculated thresholds for DEL: 1.153806708360109 and DUP: 2.87418633303406
spectre::2024-04-10 14:51:30,939::DEBUG::spectre.analysis.analysis> Clean by threshold: 23 -> 15. Cleaned: 8
spectre::2024-04-10 14:51:30,939::DEBUG::spectre.analysis.analysis> Clean by size: 15 -> 0. Cleaned: 15
spectre::2024-04-10 14:51:30,939::DEBUG::spectre.analysis.analysis> Clean by size: 23 -> 0. Cleaned: 23
spectre::2024-04-10 14:51:30,943::DEBUG::spectre.analysis.analysis> Writing coverage to /srv/scratch/testardqu/tickets/28452/Spectre/results/Sample2/debug/cnv_Sample2_byCoverage_chrchr3.csv
spectre::2024-04-10 14:51:31,648::DEBUG::spectre.analysis.analysis> total cnv candidates in chr3: 25 before merge
spectre::2024-04-10 14:51:31,648::DEBUG::spectre.analysis.analysis> Current merge cycle 1
spectre::2024-04-10 14:51:31,650::DEBUG::spectre.analysis.analysis> Current merge cycle 2
spectre::2024-04-10 14:51:31,652::DEBUG::spectre.analysis.analysis> Current merge cycle 3
spectre::2024-04-10 14:51:31,653::DEBUG::spectre.analysis.analysis> Total merge rounds: 3
spectre::2024-04-10 14:51:31,653::DEBUG::spectre.analysis.analysis> Trying to merge over blacklisted regions for chr3
spectre::2024-04-10 14:51:31,653::DEBUG::spectre.analysis.analysis> Current blacklist merge cycle 1
spectre::2024-04-10 14:51:31,654::DEBUG::spectre.analysis.analysis> Total merge rounds over blacklisted region: 1
spectre::2024-04-10 14:51:31,848::DEBUG::spectre.analysis.cnv_metrics> CNV-Metrics: Calculated thresholds for DEL: 1.153806708360109 and DUP: 2.87418633303406
spectre::2024-04-10 14:51:31,848::DEBUG::spectre.analysis.analysis> Clean by threshold: 21 -> 14. Cleaned: 7
spectre::2024-04-10 14:51:31,848::DEBUG::spectre.analysis.analysis> Clean by size: 14 -> 0. Cleaned: 14
spectre::2024-04-10 14:51:31,848::DEBUG::spectre.analysis.analysis> Clean by size: 21 -> 0. Cleaned: 21
spectre::2024-04-10 14:51:31,852::DEBUG::spectre.analysis.analysis> Writing coverage to /srv/scratch/testardqu/tickets/28452/Spectre/results/Sample2/debug/cnv_Sample2_byCoverage_chrchr4.csv
spectre::2024-04-10 14:51:32,530::DEBUG::spectre.analysis.analysis> total cnv candidates in chr4: 24 before merge
spectre::2024-04-10 14:51:32,530::DEBUG::spectre.analysis.analysis> Current merge cycle 1
spectre::2024-04-10 14:51:32,532::DEBUG::spectre.analysis.analysis> Current merge cycle 2
spectre::2024-04-10 14:51:32,533::DEBUG::spectre.analysis.analysis> Current merge cycle 3
spectre::2024-04-10 14:51:32,535::DEBUG::spectre.analysis.analysis> Total merge rounds: 3
spectre::2024-04-10 14:51:32,535::DEBUG::spectre.analysis.analysis> Trying to merge over blacklisted regions for chr4
spectre::2024-04-10 14:51:32,535::DEBUG::spectre.analysis.analysis> Current blacklist merge cycle 1
spectre::2024-04-10 14:51:32,536::DEBUG::spectre.analysis.analysis> Total merge rounds over blacklisted region: 1
spectre::2024-04-10 14:51:32,720::DEBUG::spectre.analysis.cnv_metrics> CNV-Metrics: Calculated thresholds for DEL: 1.153806708360109 and DUP: 2.87418633303406
spectre::2024-04-10 14:51:32,721::DEBUG::spectre.analysis.analysis> Clean by threshold: 21 -> 16. Cleaned: 5
spectre::2024-04-10 14:51:32,721::DEBUG::spectre.analysis.analysis> Clean by size: 16 -> 0. Cleaned: 16
spectre::2024-04-10 14:51:32,721::DEBUG::spectre.analysis.analysis> Clean by size: 21 -> 0. Cleaned: 21
spectre::2024-04-10 14:51:32,724::DEBUG::spectre.analysis.analysis> Writing coverage to /srv/scratch/testardqu/tickets/28452/Spectre/results/Sample2/debug/cnv_Sample2_byCoverage_chrchr5.csv
spectre::2024-04-10 14:51:33,367::DEBUG::spectre.analysis.analysis> total cnv candidates in chr5: 24 before merge
spectre::2024-04-10 14:51:33,367::DEBUG::spectre.analysis.analysis> Current merge cycle 1
spectre::2024-04-10 14:51:33,368::DEBUG::spectre.analysis.analysis> Current merge cycle 2
spectre::2024-04-10 14:51:33,370::DEBUG::spectre.analysis.analysis> Current merge cycle 3
spectre::2024-04-10 14:51:33,371::DEBUG::spectre.analysis.analysis> Total merge rounds: 3
spectre::2024-04-10 14:51:33,371::DEBUG::spectre.analysis.analysis> Trying to merge over blacklisted regions for chr5
spectre::2024-04-10 14:51:33,371::DEBUG::spectre.analysis.analysis> Current blacklist merge cycle 1
spectre::2024-04-10 14:51:33,373::DEBUG::spectre.analysis.analysis> Total merge rounds over blacklisted region: 1
spectre::2024-04-10 14:51:33,556::DEBUG::spectre.analysis.cnv_metrics> CNV-Metrics: Calculated thresholds for DEL: 1.153806708360109 and DUP: 2.87418633303406
spectre::2024-04-10 14:51:33,557::DEBUG::spectre.analysis.analysis> Clean by threshold: 20 -> 16. Cleaned: 4
spectre::2024-04-10 14:51:33,557::DEBUG::spectre.analysis.analysis> Clean by size: 16 -> 0. Cleaned: 16
spectre::2024-04-10 14:51:33,557::DEBUG::spectre.analysis.analysis> Clean by size: 20 -> 0. Cleaned: 20
spectre::2024-04-10 14:51:33,560::DEBUG::spectre.analysis.analysis> Writing coverage to /srv/scratch/testardqu/tickets/28452/Spectre/results/Sample2/debug/cnv_Sample2_byCoverage_chrchr6.csv
spectre::2024-04-10 14:51:34,169::DEBUG::spectre.analysis.analysis> total cnv candidates in chr6: 38 before merge
spectre::2024-04-10 14:51:34,169::DEBUG::spectre.analysis.analysis> Current merge cycle 1
spectre::2024-04-10 14:51:34,172::DEBUG::spectre.analysis.analysis> Current merge cycle 2
spectre::2024-04-10 14:51:34,174::DEBUG::spectre.analysis.analysis> Current merge cycle 3
spectre::2024-04-10 14:51:34,176::DEBUG::spectre.analysis.analysis> Total merge rounds: 3
spectre::2024-04-10 14:51:34,176::DEBUG::spectre.analysis.analysis> Trying to merge over blacklisted regions for chr6
spectre::2024-04-10 14:51:34,176::DEBUG::spectre.analysis.analysis> Current blacklist merge cycle 1
spectre::2024-04-10 14:51:34,178::DEBUG::spectre.analysis.analysis> Total merge rounds over blacklisted region: 1
spectre::2024-04-10 14:51:34,472::DEBUG::spectre.analysis.cnv_metrics> CNV-Metrics: Calculated thresholds for DEL: 1.153806708360109 and DUP: 2.87418633303406
spectre::2024-04-10 14:51:34,473::DEBUG::spectre.analysis.analysis> Clean by threshold: 33 -> 24. Cleaned: 9
spectre::2024-04-10 14:51:34,473::DEBUG::spectre.analysis.analysis> Clean by size: 24 -> 0. Cleaned: 24
spectre::2024-04-10 14:51:34,473::DEBUG::spectre.analysis.analysis> Clean by size: 33 -> 0. Cleaned: 33
spectre::2024-04-10 14:51:34,476::DEBUG::spectre.analysis.analysis> Writing coverage to /srv/scratch/testardqu/tickets/28452/Spectre/results/Sample2/debug/cnv_Sample2_byCoverage_chrchr7.csv
spectre::2024-04-10 14:51:35,024::DEBUG::spectre.analysis.analysis> total cnv candidates in chr7: 37 before merge
spectre::2024-04-10 14:51:35,024::DEBUG::spectre.analysis.analysis> Current merge cycle 1
spectre::2024-04-10 14:51:35,027::DEBUG::spectre.analysis.analysis> Current merge cycle 2
spectre::2024-04-10 14:51:35,029::DEBUG::spectre.analysis.analysis> Current merge cycle 3
spectre::2024-04-10 14:51:35,031::DEBUG::spectre.analysis.analysis> Total merge rounds: 3
spectre::2024-04-10 14:51:35,031::DEBUG::spectre.analysis.analysis> Trying to merge over blacklisted regions for chr7
spectre::2024-04-10 14:51:35,031::DEBUG::spectre.analysis.analysis> Current blacklist merge cycle 1
spectre::2024-04-10 14:51:35,033::DEBUG::spectre.analysis.analysis> Total merge rounds over blacklisted region: 1
spectre::2024-04-10 14:51:35,339::DEBUG::spectre.analysis.cnv_metrics> CNV-Metrics: Calculated thresholds for DEL: 1.153806708360109 and DUP: 2.87418633303406
spectre::2024-04-10 14:51:35,339::DEBUG::spectre.analysis.analysis> Clean by threshold: 30 -> 25. Cleaned: 5
spectre::2024-04-10 14:51:35,339::DEBUG::spectre.analysis.analysis> Clean by size: 25 -> 0. Cleaned: 25
spectre::2024-04-10 14:51:35,339::DEBUG::spectre.analysis.analysis> Clean by size: 30 -> 0. Cleaned: 30
spectre::2024-04-10 14:51:35,343::DEBUG::spectre.analysis.analysis> Writing coverage to /srv/scratch/testardqu/tickets/28452/Spectre/results/Sample2/debug/cnv_Sample2_byCoverage_chrchr8.csv
spectre::2024-04-10 14:51:35,848::DEBUG::spectre.analysis.analysis> total cnv candidates in chr8: 14 before merge
spectre::2024-04-10 14:51:35,848::DEBUG::spectre.analysis.analysis> Current merge cycle 1
spectre::2024-04-10 14:51:35,849::DEBUG::spectre.analysis.analysis> Total merge rounds: 1
spectre::2024-04-10 14:51:35,849::DEBUG::spectre.analysis.analysis> Trying to merge over blacklisted regions for chr8
spectre::2024-04-10 14:51:35,849::DEBUG::spectre.analysis.analysis> Current blacklist merge cycle 1
spectre::2024-04-10 14:51:35,850::DEBUG::spectre.analysis.analysis> Total merge rounds over blacklisted region: 1
spectre::2024-04-10 14:51:35,971::DEBUG::spectre.analysis.cnv_metrics> CNV-Metrics: Calculated thresholds for DEL: 1.153806708360109 and DUP: 2.87418633303406
spectre::2024-04-10 14:51:35,972::DEBUG::spectre.analysis.analysis> Clean by threshold: 14 -> 6. Cleaned: 8
spectre::2024-04-10 14:51:35,972::DEBUG::spectre.analysis.analysis> Clean by size: 6 -> 0. Cleaned: 6
spectre::2024-04-10 14:51:35,972::DEBUG::spectre.analysis.analysis> Clean by size: 14 -> 0. Cleaned: 14
spectre::2024-04-10 14:51:35,975::DEBUG::spectre.analysis.analysis> Writing coverage to /srv/scratch/testardqu/tickets/28452/Spectre/results/Sample2/debug/cnv_Sample2_byCoverage_chrchr9.csv
spectre::2024-04-10 14:51:36,404::DEBUG::spectre.analysis.analysis> total cnv candidates in chr9: 26 before merge
spectre::2024-04-10 14:51:36,404::DEBUG::spectre.analysis.analysis> Current merge cycle 1
spectre::2024-04-10 14:51:36,406::DEBUG::spectre.analysis.analysis> Current merge cycle 2
spectre::2024-04-10 14:51:36,408::DEBUG::spectre.analysis.analysis> Total merge rounds: 2
spectre::2024-04-10 14:51:36,408::DEBUG::spectre.analysis.analysis> Trying to merge over blacklisted regions for chr9
spectre::2024-04-10 14:51:36,408::DEBUG::spectre.analysis.analysis> Current blacklist merge cycle 1
spectre::2024-04-10 14:51:36,410::DEBUG::spectre.analysis.analysis> Total merge rounds over blacklisted region: 1
spectre::2024-04-10 14:51:36,607::DEBUG::spectre.analysis.cnv_metrics> CNV-Metrics: Calculated thresholds for DEL: 1.153806708360109 and DUP: 2.87418633303406
spectre::2024-04-10 14:51:36,608::DEBUG::spectre.analysis.analysis> Clean by threshold: 22 -> 17. Cleaned: 5
spectre::2024-04-10 14:51:36,608::DEBUG::spectre.analysis.analysis> Clean by size: 17 -> 0. Cleaned: 17
spectre::2024-04-10 14:51:36,608::DEBUG::spectre.analysis.analysis> Clean by size: 22 -> 0. Cleaned: 22
spectre::2024-04-10 14:51:36,611::DEBUG::spectre.analysis.analysis> Writing coverage to /srv/scratch/testardqu/tickets/28452/Spectre/results/Sample2/debug/cnv_Sample2_byCoverage_chrchr10.csv
spectre::2024-04-10 14:51:37,085::DEBUG::spectre.analysis.analysis> total cnv candidates in chr10: 20 before merge
spectre::2024-04-10 14:51:37,085::DEBUG::spectre.analysis.analysis> Current merge cycle 1
spectre::2024-04-10 14:51:37,086::DEBUG::spectre.analysis.analysis> Total merge rounds: 1
spectre::2024-04-10 14:51:37,087::DEBUG::spectre.analysis.analysis> Trying to merge over blacklisted regions for chr10
spectre::2024-04-10 14:51:37,087::DEBUG::spectre.analysis.analysis> Current blacklist merge cycle 1
spectre::2024-04-10 14:51:37,088::DEBUG::spectre.analysis.analysis> Total merge rounds over blacklisted region: 1
spectre::2024-04-10 14:51:37,259::DEBUG::spectre.analysis.cnv_metrics> CNV-Metrics: Calculated thresholds for DEL: 1.153806708360109 and DUP: 2.87418633303406
spectre::2024-04-10 14:51:37,260::DEBUG::spectre.analysis.analysis> Clean by threshold: 19 -> 13. Cleaned: 6
spectre::2024-04-10 14:51:37,260::DEBUG::spectre.analysis.analysis> Clean by size: 13 -> 0. Cleaned: 13
spectre::2024-04-10 14:51:37,260::DEBUG::spectre.analysis.analysis> Clean by size: 19 -> 0. Cleaned: 19
spectre::2024-04-10 14:51:37,263::DEBUG::spectre.analysis.analysis> Writing coverage to /srv/scratch/testardqu/tickets/28452/Spectre/results/Sample2/debug/cnv_Sample2_byCoverage_chrchr11.csv
spectre::2024-04-10 14:51:37,743::DEBUG::spectre.analysis.analysis> total cnv candidates in chr11: 30 before merge
spectre::2024-04-10 14:51:37,743::DEBUG::spectre.analysis.analysis> Current merge cycle 1
spectre::2024-04-10 14:51:37,745::DEBUG::spectre.analysis.analysis> Current merge cycle 2
spectre::2024-04-10 14:51:37,747::DEBUG::spectre.analysis.analysis> Total merge rounds: 2
spectre::2024-04-10 14:51:37,747::DEBUG::spectre.analysis.analysis> Trying to merge over blacklisted regions for chr11
spectre::2024-04-10 14:51:37,747::DEBUG::spectre.analysis.analysis> Current blacklist merge cycle 1
spectre::2024-04-10 14:51:37,749::DEBUG::spectre.analysis.analysis> Total merge rounds over blacklisted region: 1
spectre::2024-04-10 14:51:37,995::DEBUG::spectre.analysis.cnv_metrics> CNV-Metrics: Calculated thresholds for DEL: 1.153806708360109 and DUP: 2.87418633303406
spectre::2024-04-10 14:51:37,996::DEBUG::spectre.analysis.analysis> Clean by threshold: 29 -> 23. Cleaned: 6
spectre::2024-04-10 14:51:37,996::DEBUG::spectre.analysis.analysis> Clean by size: 23 -> 0. Cleaned: 23
spectre::2024-04-10 14:51:37,996::DEBUG::spectre.analysis.analysis> Clean by size: 29 -> 0. Cleaned: 29
spectre::2024-04-10 14:51:37,999::DEBUG::spectre.analysis.analysis> Writing coverage to /srv/scratch/testardqu/tickets/28452/Spectre/results/Sample2/debug/cnv_Sample2_byCoverage_chrchr12.csv
spectre::2024-04-10 14:51:38,478::DEBUG::spectre.analysis.analysis> total cnv candidates in chr12: 15 before merge
spectre::2024-04-10 14:51:38,478::DEBUG::spectre.analysis.analysis> Current merge cycle 1
spectre::2024-04-10 14:51:38,479::DEBUG::spectre.analysis.analysis> Total merge rounds: 1
spectre::2024-04-10 14:51:38,479::DEBUG::spectre.analysis.analysis> Trying to merge over blacklisted regions for chr12
spectre::2024-04-10 14:51:38,479::DEBUG::spectre.analysis.analysis> Current blacklist merge cycle 1
spectre::2024-04-10 14:51:38,480::DEBUG::spectre.analysis.analysis> Total merge rounds over blacklisted region: 1
spectre::2024-04-10 14:51:38,609::DEBUG::spectre.analysis.cnv_metrics> CNV-Metrics: Calculated thresholds for DEL: 1.153806708360109 and DUP: 2.87418633303406
spectre::2024-04-10 14:51:38,610::DEBUG::spectre.analysis.analysis> Clean by threshold: 15 -> 7. Cleaned: 8
spectre::2024-04-10 14:51:38,610::DEBUG::spectre.analysis.analysis> Clean by size: 7 -> 0. Cleaned: 7
spectre::2024-04-10 14:51:38,610::DEBUG::spectre.analysis.analysis> Clean by size: 15 -> 0. Cleaned: 15
spectre::2024-04-10 14:51:38,613::DEBUG::spectre.analysis.analysis> Writing coverage to /srv/scratch/testardqu/tickets/28452/Spectre/results/Sample2/debug/cnv_Sample2_byCoverage_chrchr13.csv
spectre::2024-04-10 14:51:38,992::DEBUG::spectre.analysis.analysis> total cnv candidates in chr13: 7 before merge
spectre::2024-04-10 14:51:38,992::DEBUG::spectre.analysis.analysis> Current merge cycle 1
spectre::2024-04-10 14:51:38,992::DEBUG::spectre.analysis.analysis> Total merge rounds: 1
spectre::2024-04-10 14:51:38,992::DEBUG::spectre.analysis.analysis> Trying to merge over blacklisted regions for chr13
spectre::2024-04-10 14:51:38,992::DEBUG::spectre.analysis.analysis> Current blacklist merge cycle 1
spectre::2024-04-10 14:51:38,993::DEBUG::spectre.analysis.analysis> Total merge rounds over blacklisted region: 1
spectre::2024-04-10 14:51:39,055::DEBUG::spectre.analysis.cnv_metrics> CNV-Metrics: Calculated thresholds for DEL: 1.153806708360109 and DUP: 2.87418633303406
spectre::2024-04-10 14:51:39,055::DEBUG::spectre.analysis.analysis> Clean by threshold: 7 -> 5. Cleaned: 2
spectre::2024-04-10 14:51:39,055::DEBUG::spectre.analysis.analysis> Clean by size: 5 -> 0. Cleaned: 5
spectre::2024-04-10 14:51:39,055::DEBUG::spectre.analysis.analysis> Clean by size: 7 -> 0. Cleaned: 7
spectre::2024-04-10 14:51:39,057::DEBUG::spectre.analysis.analysis> Writing coverage to /srv/scratch/testardqu/tickets/28452/Spectre/results/Sample2/debug/cnv_Sample2_byCoverage_chrchr14.csv
spectre::2024-04-10 14:51:39,404::DEBUG::spectre.analysis.analysis> total cnv candidates in chr14: 7 before merge
spectre::2024-04-10 14:51:39,404::DEBUG::spectre.analysis.analysis> Current merge cycle 1
spectre::2024-04-10 14:51:39,405::DEBUG::spectre.analysis.analysis> Total merge rounds: 1
spectre::2024-04-10 14:51:39,405::DEBUG::spectre.analysis.analysis> Trying to merge over blacklisted regions for chr14
spectre::2024-04-10 14:51:39,405::DEBUG::spectre.analysis.analysis> Current blacklist merge cycle 1
spectre::2024-04-10 14:51:39,405::DEBUG::spectre.analysis.analysis> Total merge rounds over blacklisted region: 1
spectre::2024-04-10 14:51:39,467::DEBUG::spectre.analysis.cnv_metrics> CNV-Metrics: Calculated thresholds for DEL: 1.153806708360109 and DUP: 2.87418633303406
spectre::2024-04-10 14:51:39,467::DEBUG::spectre.analysis.analysis> Clean by threshold: 7 -> 3. Cleaned: 4
spectre::2024-04-10 14:51:39,468::DEBUG::spectre.analysis.analysis> Clean by size: 3 -> 0. Cleaned: 3
spectre::2024-04-10 14:51:39,468::DEBUG::spectre.analysis.analysis> Clean by size: 7 -> 0. Cleaned: 7
spectre::2024-04-10 14:51:39,470::DEBUG::spectre.analysis.analysis> Writing coverage to /srv/scratch/testardqu/tickets/28452/Spectre/results/Sample2/debug/cnv_Sample2_byCoverage_chrchr15.csv
spectre::2024-04-10 14:51:39,777::DEBUG::spectre.analysis.analysis> total cnv candidates in chr15: 13 before merge
spectre::2024-04-10 14:51:39,777::DEBUG::spectre.analysis.analysis> Current merge cycle 1
spectre::2024-04-10 14:51:39,778::DEBUG::spectre.analysis.analysis> Current merge cycle 2
spectre::2024-04-10 14:51:39,779::DEBUG::spectre.analysis.analysis> Current merge cycle 3
spectre::2024-04-10 14:51:39,779::DEBUG::spectre.analysis.analysis> Total merge rounds: 3
spectre::2024-04-10 14:51:39,779::DEBUG::spectre.analysis.analysis> Trying to merge over blacklisted regions for chr15
spectre::2024-04-10 14:51:39,779::DEBUG::spectre.analysis.analysis> Current blacklist merge cycle 1
spectre::2024-04-10 14:51:39,780::DEBUG::spectre.analysis.analysis> Total merge rounds over blacklisted region: 1
spectre::2024-04-10 14:51:39,868::DEBUG::spectre.analysis.cnv_metrics> CNV-Metrics: Calculated thresholds for DEL: 1.153806708360109 and DUP: 2.87418633303406
spectre::2024-04-10 14:51:39,868::DEBUG::spectre.analysis.analysis> Clean by threshold: 9 -> 7. Cleaned: 2
spectre::2024-04-10 14:51:39,868::DEBUG::spectre.analysis.analysis> Clean by size: 7 -> 0. Cleaned: 7
spectre::2024-04-10 14:51:39,868::DEBUG::spectre.analysis.analysis> Clean by size: 9 -> 0. Cleaned: 9
spectre::2024-04-10 14:51:39,870::DEBUG::spectre.analysis.analysis> Writing coverage to /srv/scratch/testardqu/tickets/28452/Spectre/results/Sample2/debug/cnv_Sample2_byCoverage_chrchr16.csv
spectre::2024-04-10 14:51:40,160::DEBUG::spectre.analysis.analysis> total cnv candidates in chr16: 21 before merge
spectre::2024-04-10 14:51:40,160::DEBUG::spectre.analysis.analysis> Current merge cycle 1
spectre::2024-04-10 14:51:40,162::DEBUG::spectre.analysis.analysis> Current merge cycle 2
spectre::2024-04-10 14:51:40,163::DEBUG::spectre.analysis.analysis> Current merge cycle 3
spectre::2024-04-10 14:51:40,164::DEBUG::spectre.analysis.analysis> Total merge rounds: 3
spectre::2024-04-10 14:51:40,164::DEBUG::spectre.analysis.analysis> Trying to merge over blacklisted regions for chr16
spectre::2024-04-10 14:51:40,164::DEBUG::spectre.analysis.analysis> Current blacklist merge cycle 1
spectre::2024-04-10 14:51:40,166::DEBUG::spectre.analysis.analysis> Total merge rounds over blacklisted region: 1
spectre::2024-04-10 14:51:40,326::DEBUG::spectre.analysis.cnv_metrics> CNV-Metrics: Calculated thresholds for DEL: 1.153806708360109 and DUP: 2.87418633303406
spectre::2024-04-10 14:51:40,327::DEBUG::spectre.analysis.analysis> Clean by threshold: 17 -> 12. Cleaned: 5
spectre::2024-04-10 14:51:40,327::DEBUG::spectre.analysis.analysis> Clean by size: 12 -> 0. Cleaned: 12
spectre::2024-04-10 14:51:40,327::DEBUG::spectre.analysis.analysis> Clean by size: 17 -> 0. Cleaned: 17
spectre::2024-04-10 14:51:40,329::DEBUG::spectre.analysis.analysis> Writing coverage to /srv/scratch/testardqu/tickets/28452/Spectre/results/Sample2/debug/cnv_Sample2_byCoverage_chrchr17.csv
spectre::2024-04-10 14:51:40,606::DEBUG::spectre.analysis.analysis> total cnv candidates in chr17: 34 before merge
spectre::2024-04-10 14:51:40,606::DEBUG::spectre.analysis.analysis> Current merge cycle 1
spectre::2024-04-10 14:51:40,609::DEBUG::spectre.analysis.analysis> Current merge cycle 2
spectre::2024-04-10 14:51:40,611::DEBUG::spectre.analysis.analysis> Current merge cycle 3
spectre::2024-04-10 14:51:40,613::DEBUG::spectre.analysis.analysis> Total merge rounds: 3
spectre::2024-04-10 14:51:40,613::DEBUG::spectre.analysis.analysis> Trying to merge over blacklisted regions for chr17
spectre::2024-04-10 14:51:40,613::DEBUG::spectre.analysis.analysis> Current blacklist merge cycle 1
spectre::2024-04-10 14:51:40,615::DEBUG::spectre.analysis.analysis> Total merge rounds over blacklisted region: 1
spectre::2024-04-10 14:51:40,890::DEBUG::spectre.analysis.cnv_metrics> CNV-Metrics: Calculated thresholds for DEL: 1.153806708360109 and DUP: 2.87418633303406
spectre::2024-04-10 14:51:40,891::DEBUG::spectre.analysis.analysis> Clean by threshold: 27 -> 18. Cleaned: 9
spectre::2024-04-10 14:51:40,891::DEBUG::spectre.analysis.analysis> Clean by size: 18 -> 0. Cleaned: 18
spectre::2024-04-10 14:51:40,891::DEBUG::spectre.analysis.analysis> Clean by size: 27 -> 0. Cleaned: 27
spectre::2024-04-10 14:51:40,893::DEBUG::spectre.analysis.analysis> Writing coverage to /srv/scratch/testardqu/tickets/28452/Spectre/results/Sample2/debug/cnv_Sample2_byCoverage_chrchr18.csv
spectre::2024-04-10 14:51:41,201::DEBUG::spectre.analysis.analysis> total cnv candidates in chr18: 9 before merge
spectre::2024-04-10 14:51:41,202::DEBUG::spectre.analysis.analysis> Current merge cycle 1
spectre::2024-04-10 14:51:41,202::DEBUG::spectre.analysis.analysis> Total merge rounds: 1
spectre::2024-04-10 14:51:41,202::DEBUG::spectre.analysis.analysis> Trying to merge over blacklisted regions for chr18
spectre::2024-04-10 14:51:41,202::DEBUG::spectre.analysis.analysis> Current blacklist merge cycle 1
spectre::2024-04-10 14:51:41,203::DEBUG::spectre.analysis.analysis> Total merge rounds over blacklisted region: 1
spectre::2024-04-10 14:51:41,280::DEBUG::spectre.analysis.cnv_metrics> CNV-Metrics: Calculated thresholds for DEL: 1.153806708360109 and DUP: 2.87418633303406
spectre::2024-04-10 14:51:41,281::DEBUG::spectre.analysis.analysis> Clean by threshold: 9 -> 7. Cleaned: 2
spectre::2024-04-10 14:51:41,281::DEBUG::spectre.analysis.analysis> Clean by size: 7 -> 0. Cleaned: 7
spectre::2024-04-10 14:51:41,281::DEBUG::spectre.analysis.analysis> Clean by size: 9 -> 0. Cleaned: 9
spectre::2024-04-10 14:51:41,282::DEBUG::spectre.analysis.analysis> Writing coverage to /srv/scratch/testardqu/tickets/28452/Spectre/results/Sample2/debug/cnv_Sample2_byCoverage_chrchr19.csv
spectre::2024-04-10 14:51:41,489::DEBUG::spectre.analysis.analysis> total cnv candidates in chr19: 48 before merge
spectre::2024-04-10 14:51:41,489::DEBUG::spectre.analysis.analysis> Current merge cycle 1
spectre::2024-04-10 14:51:41,492::DEBUG::spectre.analysis.analysis> Current merge cycle 2
spectre::2024-04-10 14:51:41,495::DEBUG::spectre.analysis.analysis> Total merge rounds: 2
spectre::2024-04-10 14:51:41,495::DEBUG::spectre.analysis.analysis> Trying to merge over blacklisted regions for chr19
spectre::2024-04-10 14:51:41,495::DEBUG::spectre.analysis.analysis> Current blacklist merge cycle 1
spectre::2024-04-10 14:51:41,497::DEBUG::spectre.analysis.analysis> Total merge rounds over blacklisted region: 1
spectre::2024-04-10 14:51:41,874::DEBUG::spectre.analysis.cnv_metrics> CNV-Metrics: Calculated thresholds for DEL: 1.153806708360109 and DUP: 2.87418633303406
spectre::2024-04-10 14:51:41,875::DEBUG::spectre.analysis.analysis> Clean by threshold: 45 -> 32. Cleaned: 13
spectre::2024-04-10 14:51:41,875::DEBUG::spectre.analysis.analysis> Clean by size: 32 -> 0. Cleaned: 32
spectre::2024-04-10 14:51:41,875::DEBUG::spectre.analysis.analysis> Clean by size: 45 -> 0. Cleaned: 45
spectre::2024-04-10 14:51:41,877::DEBUG::spectre.analysis.analysis> Writing coverage to /srv/scratch/testardqu/tickets/28452/Spectre/results/Sample2/debug/cnv_Sample2_byCoverage_chrchr20.csv
spectre::2024-04-10 14:51:42,104::DEBUG::spectre.analysis.analysis> total cnv candidates in chr20: 5 before merge
spectre::2024-04-10 14:51:42,105::DEBUG::spectre.analysis.analysis> Current merge cycle 1
spectre::2024-04-10 14:51:42,105::DEBUG::spectre.analysis.analysis> Total merge rounds: 1
spectre::2024-04-10 14:51:42,105::DEBUG::spectre.analysis.analysis> Trying to merge over blacklisted regions for chr20
spectre::2024-04-10 14:51:42,105::DEBUG::spectre.analysis.analysis> Current blacklist merge cycle 1
spectre::2024-04-10 14:51:42,106::DEBUG::spectre.analysis.analysis> Total merge rounds over blacklisted region: 1
spectre::2024-04-10 14:51:42,151::DEBUG::spectre.analysis.cnv_metrics> CNV-Metrics: Calculated thresholds for DEL: 1.153806708360109 and DUP: 2.87418633303406
spectre::2024-04-10 14:51:42,151::DEBUG::spectre.analysis.analysis> Clean by threshold: 5 -> 5. Cleaned: 0
spectre::2024-04-10 14:51:42,151::DEBUG::spectre.analysis.analysis> Clean by size: 5 -> 0. Cleaned: 5
spectre::2024-04-10 14:51:42,151::DEBUG::spectre.analysis.analysis> Clean by size: 5 -> 0. Cleaned: 5
spectre::2024-04-10 14:51:42,152::DEBUG::spectre.analysis.analysis> Writing coverage to /srv/scratch/testardqu/tickets/28452/Spectre/results/Sample2/debug/cnv_Sample2_byCoverage_chrchr21.csv
spectre::2024-04-10 14:51:42,285::DEBUG::spectre.analysis.analysis> total cnv candidates in chr21: 3 before merge
spectre::2024-04-10 14:51:42,285::DEBUG::spectre.analysis.analysis> Current merge cycle 1
spectre::2024-04-10 14:51:42,286::DEBUG::spectre.analysis.analysis> Total merge rounds: 1
spectre::2024-04-10 14:51:42,286::DEBUG::spectre.analysis.analysis> Trying to merge over blacklisted regions for chr21
spectre::2024-04-10 14:51:42,286::DEBUG::spectre.analysis.analysis> Current blacklist merge cycle 1
spectre::2024-04-10 14:51:42,286::DEBUG::spectre.analysis.analysis> Total merge rounds over blacklisted region: 1
spectre::2024-04-10 14:51:42,313::DEBUG::spectre.analysis.cnv_metrics> CNV-Metrics: Calculated thresholds for DEL: 1.153806708360109 and DUP: 2.87418633303406
spectre::2024-04-10 14:51:42,313::DEBUG::spectre.analysis.analysis> Clean by threshold: 3 -> 1. Cleaned: 2
spectre::2024-04-10 14:51:42,313::DEBUG::spectre.analysis.analysis> Clean by size: 1 -> 0. Cleaned: 1
spectre::2024-04-10 14:51:42,313::DEBUG::spectre.analysis.analysis> Clean by size: 3 -> 0. Cleaned: 3
spectre::2024-04-10 14:51:42,315::DEBUG::spectre.analysis.analysis> Writing coverage to /srv/scratch/testardqu/tickets/28452/Spectre/results/Sample2/debug/cnv_Sample2_byCoverage_chrchr22.csv
spectre::2024-04-10 14:51:42,461::DEBUG::spectre.analysis.analysis> total cnv candidates in chr22: 18 before merge
spectre::2024-04-10 14:51:42,461::DEBUG::spectre.analysis.analysis> Current merge cycle 1
spectre::2024-04-10 14:51:42,462::DEBUG::spectre.analysis.analysis> Current merge cycle 2
spectre::2024-04-10 14:51:42,464::DEBUG::spectre.analysis.analysis> Total merge rounds: 2
spectre::2024-04-10 14:51:42,464::DEBUG::spectre.analysis.analysis> Trying to merge over blacklisted regions for chr22
spectre::2024-04-10 14:51:42,464::DEBUG::spectre.analysis.analysis> Current blacklist merge cycle 1
spectre::2024-04-10 14:51:42,465::DEBUG::spectre.analysis.analysis> Total merge rounds over blacklisted region: 1
spectre::2024-04-10 14:51:42,588::DEBUG::spectre.analysis.cnv_metrics> CNV-Metrics: Calculated thresholds for DEL: 1.153806708360109 and DUP: 2.87418633303406
spectre::2024-04-10 14:51:42,588::DEBUG::spectre.analysis.analysis> Clean by threshold: 14 -> 11. Cleaned: 3
spectre::2024-04-10 14:51:42,588::DEBUG::spectre.analysis.analysis> Clean by size: 11 -> 0. Cleaned: 11
spectre::2024-04-10 14:51:42,588::DEBUG::spectre.analysis.analysis> Clean by size: 14 -> 0. Cleaned: 14
spectre::2024-04-10 14:51:42,591::DEBUG::spectre.analysis.analysis> Writing coverage to /srv/scratch/testardqu/tickets/28452/Spectre/results/Sample2/debug/cnv_Sample2_byCoverage_chrchrX.csv
spectre::2024-04-10 14:51:43,113::DEBUG::spectre.analysis.analysis> total cnv candidates in chrX: 31 before merge
spectre::2024-04-10 14:51:43,113::DEBUG::spectre.analysis.analysis> Current merge cycle 1
spectre::2024-04-10 14:51:43,116::DEBUG::spectre.analysis.analysis> Current merge cycle 2
spectre::2024-04-10 14:51:43,118::DEBUG::spectre.analysis.analysis> Total merge rounds: 2
spectre::2024-04-10 14:51:43,118::DEBUG::spectre.analysis.analysis> Trying to merge over blacklisted regions for chrX
spectre::2024-04-10 14:51:43,118::DEBUG::spectre.analysis.analysis> Current blacklist merge cycle 1
spectre::2024-04-10 14:51:43,120::DEBUG::spectre.analysis.analysis> Total merge rounds over blacklisted region: 1
spectre::2024-04-10 14:51:43,363::DEBUG::spectre.analysis.cnv_metrics> CNV-Metrics: Calculated thresholds for DEL: 1.153806708360109 and DUP: 2.87418633303406
spectre::2024-04-10 14:51:43,364::DEBUG::spectre.analysis.analysis> Clean by threshold: 27 -> 25. Cleaned: 2
spectre::2024-04-10 14:51:43,364::DEBUG::spectre.analysis.analysis> Clean by size: 25 -> 0. Cleaned: 25
spectre::2024-04-10 14:51:43,364::DEBUG::spectre.analysis.analysis> Clean by size: 27 -> 0. Cleaned: 27
spectre::2024-04-10 14:51:43,364::INFO::spectre.spectreCNV> Calculate CNV metrics
spectre::2024-04-10 14:51:43,364::DEBUG::spectre.analysis.cnv_metrics> Evaluating all CNVs
spectre::2024-04-10 14:51:43,364::DEBUG::spectre.analysis.cnv_metrics> Recalculating
spectre::2024-04-10 14:51:43,364::DEBUG::spectre.analysis.cnv_metrics> Converting cnv calls to exclusion zone
spectre::2024-04-10 14:51:43,364::DEBUG::spectre.analysis.cnv_metrics> Merging exclusion zones
spectre::2024-04-10 14:51:57,744::DEBUG::spectre.analysis.cnv_metrics> Getting exclusion zone indices in mosdepth coverage data
spectre::2024-04-10 14:52:01,500::DEBUG::spectre.analysis.cnv_metrics> Generating random coverage sample indices
spectre::2024-04-10 14:52:01,749::INFO::spectre.analysis.cnv_metrics> DEL border:1.4809815950920244 DUP border:2.510429447852761
spectre::2024-04-10 14:52:01,750::DEBUG::spectre.analysis.cnv_metrics> Creating CNV distribution plot
spectre::2024-04-10 14:52:01,825::DEBUG::spectre.analysis.cnv_metrics> Plot path: /srv/scratch/testardqu/tickets/28452/Spectre/results/Sample2/debug/genome_coverage_distribution-Sample2.png
spectre::2024-04-10 14:52:01,888::INFO::spectre.spectreCNV> Merge CNV and LoH candidates
spectre::2024-04-10 14:52:01,888::DEBUG::spectre.classes.loh_candidate> CNV cand: 0
spectre::2024-04-10 14:52:01,888::INFO::spectre.spectreCNV> Final candidates are written to .spc file
spectre::2024-04-10 14:52:02,024::INFO::spectre.spectreCNV> Results are writen to bed file
spectre::2024-04-10 14:52:02,047::INFO::spectre.spectreCNV> Results are writen to VCF file
spectre::2024-04-10 14:52:02,047::INFO::spectre.spectreCNV> Result plot in progress
spectre::2024-04-10 14:52:02,076::INFO::spectre.plots.plot> CNVs in chromosome: chr1
spectre::2024-04-10 14:52:02,940::INFO::spectre.plots.plot> Plot saved: img/Sample2_plot_cnv_chr1.png
spectre::2024-04-10 14:52:02,997::INFO::spectre.plots.plot> CNVs in chromosome: chr2
spectre::2024-04-10 14:52:04,138::INFO::spectre.plots.plot> Plot saved: img/Sample2_plot_cnv_chr2.png
spectre::2024-04-10 14:52:04,195::INFO::spectre.plots.plot> CNVs in chromosome: chr3
spectre::2024-04-10 14:52:05,332::INFO::spectre.plots.plot> Plot saved: img/Sample2_plot_cnv_chr3.png
spectre::2024-04-10 14:52:05,461::INFO::spectre.plots.plot> CNVs in chromosome: chr4
spectre::2024-04-10 14:52:06,519::INFO::spectre.plots.plot> Plot saved: img/Sample2_plot_cnv_chr4.png
spectre::2024-04-10 14:52:06,577::INFO::spectre.plots.plot> CNVs in chromosome: chr5
spectre::2024-04-10 14:52:07,554::INFO::spectre.plots.plot> Plot saved: img/Sample2_plot_cnv_chr5.png
spectre::2024-04-10 14:52:07,610::INFO::spectre.plots.plot> CNVs in chromosome: chr6
spectre::2024-04-10 14:52:08,544::INFO::spectre.plots.plot> Plot saved: img/Sample2_plot_cnv_chr6.png
spectre::2024-04-10 14:52:08,600::INFO::spectre.plots.plot> CNVs in chromosome: chr7
spectre::2024-04-10 14:52:09,472::INFO::spectre.plots.plot> Plot saved: img/Sample2_plot_cnv_chr7.png
spectre::2024-04-10 14:52:09,526::INFO::spectre.plots.plot> CNVs in chromosome: chr8
spectre::2024-04-10 14:52:10,351::INFO::spectre.plots.plot> Plot saved: img/Sample2_plot_cnv_chr8.png
spectre::2024-04-10 14:52:10,404::INFO::spectre.plots.plot> CNVs in chromosome: chr9
spectre::2024-04-10 14:52:11,098::INFO::spectre.plots.plot> Plot saved: img/Sample2_plot_cnv_chr9.png
spectre::2024-04-10 14:52:11,151::INFO::spectre.plots.plot> CNVs in chromosome: chr10
spectre::2024-04-10 14:52:11,965::INFO::spectre.plots.plot> Plot saved: img/Sample2_plot_cnv_chr10.png
spectre::2024-04-10 14:52:12,018::INFO::spectre.plots.plot> CNVs in chromosome: chr11
spectre::2024-04-10 14:52:12,813::INFO::spectre.plots.plot> Plot saved: img/Sample2_plot_cnv_chr11.png
spectre::2024-04-10 14:52:12,867::INFO::spectre.plots.plot> CNVs in chromosome: chr12
spectre::2024-04-10 14:52:13,660::INFO::spectre.plots.plot> Plot saved: img/Sample2_plot_cnv_chr12.png
spectre::2024-04-10 14:52:13,728::INFO::spectre.plots.plot> CNVs in chromosome: chr13
spectre::2024-04-10 14:52:14,384::INFO::spectre.plots.plot> Plot saved: img/Sample2_plot_cnv_chr13.png
spectre::2024-04-10 14:52:14,453::INFO::spectre.plots.plot> CNVs in chromosome: chr14
spectre::2024-04-10 14:52:15,096::INFO::spectre.plots.plot> Plot saved: img/Sample2_plot_cnv_chr14.png
spectre::2024-04-10 14:52:15,168::INFO::spectre.plots.plot> CNVs in chromosome: chr15
spectre::2024-04-10 14:52:15,767::INFO::spectre.plots.plot> Plot saved: img/Sample2_plot_cnv_chr15.png
spectre::2024-04-10 14:52:15,819::INFO::spectre.plots.plot> CNVs in chromosome: chr16
spectre::2024-04-10 14:52:16,351::INFO::spectre.plots.plot> Plot saved: img/Sample2_plot_cnv_chr16.png
spectre::2024-04-10 14:52:16,403::INFO::spectre.plots.plot> CNVs in chromosome: chr17
spectre::2024-04-10 14:52:16,950::INFO::spectre.plots.plot> Plot saved: img/Sample2_plot_cnv_chr17.png
spectre::2024-04-10 14:52:17,002::INFO::spectre.plots.plot> CNVs in chromosome: chr18
spectre::2024-04-10 14:52:17,604::INFO::spectre.plots.plot> Plot saved: img/Sample2_plot_cnv_chr18.png
/usr/local/lib/python3.11/site-packages/spectre/plots/plot.py:39: RuntimeWarning: More than 20 figures have been opened. Figures created through the pyplot interface (`matplotlib.pyplot.figure`) are retained until explicitly closed and may consume too much memory. (To control this warning, see the rcParam `figure.max_open_warning`). Consider using `matplotlib.pyplot.close()`.
self.figure = plot_engine.figure(figsize=(8, 4))
spectre::2024-04-10 14:52:17,657::INFO::spectre.plots.plot> CNVs in chromosome: chr19
spectre::2024-04-10 14:52:18,150::INFO::spectre.plots.plot> Plot saved: img/Sample2_plot_cnv_chr19.png
spectre::2024-04-10 14:52:18,202::INFO::spectre.plots.plot> CNVs in chromosome: chr20
spectre::2024-04-10 14:52:18,720::INFO::spectre.plots.plot> Plot saved: img/Sample2_plot_cnv_chr20.png
spectre::2024-04-10 14:52:18,784::INFO::spectre.plots.plot> CNVs in chromosome: chr21
spectre::2024-04-10 14:52:19,119::INFO::spectre.plots.plot> Plot saved: img/Sample2_plot_cnv_chr21.png
spectre::2024-04-10 14:52:19,185::INFO::spectre.plots.plot> CNVs in chromosome: chr22
spectre::2024-04-10 14:52:19,550::INFO::spectre.plots.plot> Plot saved: img/Sample2_plot_cnv_chr22.png
spectre::2024-04-10 14:52:19,609::INFO::spectre.plots.plot> CNVs in chromosome: chrX
spectre::2024-04-10 14:52:20,434::INFO::spectre.plots.plot> Plot saved: img/Sample2_plot_cnv_chrX.png
spectre::2024-04-10 14:52:20,465::INFO::spectre.spectreCNV> Output dir: /srv/scratch/testardqu/tickets/28452/Spectre/results/Sample2
spectre::2024-04-10 14:52:20,465::INFO::spectre.spectreCNV> Done with sample Sample2
spectre::2024-04-10 14:52:20,465::INFO::spectre.spectre> Spectre finishedThanks.
philippesanio
commented
5 months ago Hi @Tintest,
The log looks normal to me. Can could you be so kind and check the BED file for me if it contains any calls, since it is directly linked to the VCF output?
Thanks, Philippe
Tintest
commented
5 months ago The Sample2_cnv.bed.gz is empty. Do you need the debug bed files ?
Tintest
commented
5 months ago I just noticed that every sample with an empty VCF file instead of an VCF.GZ file are females. All the other VCF.GZ files are males except for two samples. One is non-empty with a CNV on chr15 and the other has numerous deletions on the X chromosome, in the same way as in #16. This sample may have a particular sexual phenotype that I'll have to investigate.
This "bug" would therefore seem to occur when no CNV is detected for the sample in question, and therefore when the VCF is empty.
philippesanio
commented
5 months ago Hi @Tintest my apologies for the delay, I am currently slammed with tasks.
I have pushed some changes 0e96275, that will address your issues. I also added instructions in the README.md on how to install the latest Spectre version using a local installation with pip.
I have reviewed your command again and found that you were running Spectre in the single sample mode. Our intention was only to provide multiple samples when used with the population mode. The main idea was to give the user the option to bundle multiple similar samples together, thus all the results from the samples are located in the one output directory. As a little add-on we offer to run the standalone population mode on the batch on samples when the --population flag has been provided.
Please keep in mind, all flags that have been set are applied to all provided samples. This could become an issue when running male or female samples on, e.g. chrX.
If you want to run Spectre on multiple samples with different properties (e.g. male or female), please run Spectre in single sample mode by providing only one Mosdepth coverage file at each time. This will give you the flexibility to adjust the setting according to the sample. Furthermore, In the end of each run, Spectre produces an SPC file that you can then use with the population mode in a later step of your workflow.
I hope this will help you. Feel free to reach out anytime.
Cheers, Philippe
Hello,
I noticed that for some samples in my cohort, the final files produced were empty vcf files instead of vcf.gz files when these included CNVs. Is this the expected behavior when simply no CNV is called ?
There don't seem to be any errors in the logs.
There is a blank line at the end of the vcf file.
Thanks.