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lima1 / PureCN

Copy number calling and variant classification using targeted short read sequencing
https://bioconductor.org/packages/devel/bioc/html/PureCN.html
Artistic License 2.0
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PureCN.R Error #37

Closed ghost closed 6 years ago

ghost commented 6 years ago

I'm trying to run PureCN.R after Coverage.R and I'm getting a cryptic error (see at the very bottom) that I can't debug. I notice there's a lot of warnings for low coverage but I'm not sure if this is what is causing the error. Any thoughts?

-todd

INFO [2018-06-29 11:17:15] Loading PureCN 1.11.10... WARN [2018-06-29 11:17:34] Multiple chromosomes with very low coverage: 1,10,11,12,13,14,15,16,17,18,19,2,20,21,22,3,4,5,6,7,8,9,X,Y INFO [2018-06-29 11:17:58] Mean coverages: chrX: 0.08, chrY: 0.05, chr1-22: 0.12. INFO [2018-06-29 11:17:58] Sample sex: M INFO [2018-06-29 11:18:06] ------------------------------------------------------------ INFO [2018-06-29 11:18:06] PureCN 1.11.10 INFO [2018-06-29 11:18:06] ------------------------------------------------------------ INFO [2018-06-29 11:18:06] Arguments: -tumor.coverage.file /ts18/ngs/studies/ngs_000261/bwa/G04971TB02_S24.sorted_pos.dedup.recal_coverage_loess.txt -seg.file -vcf.file /ts18/ngs/studies/ngs_000261/bwa/G04971TB02_S24.mutect2_sel.dbsnp.vcf.gz -genome hg19 -sex ? -args.setMappingBiasVcf NULL -args.segmentation NULL,/Biomarker/sih/Databases/PureCN_data/NormalDB/b37/target_weights_SS_v6_b37.txt,0.005,NULL -sampleid G04971TB02_S24 -min.ploidy 1 -max.ploidy 6 -max.non.clonal 0.2 -log.ratio.calibration 0.1 -model.homozygous FALSE -error 0.001 -interval.file /Biomarker/ngs/database/pureCN/b37/baits_b37_V6_intervals.txt -max.segments 300 -plot.cnv TRUE -DB.info.flag DB -model beta -post.optimize FALSE -BPPARAM -log.file /ts18/ngs/studies/ngs_000261/bwa/G04971TB02_S24.log -normal.coverage.file -normalDB -args.filterVcf -fun.segmentation -test.num.copy -test.purity -speedup.heuristics INFO [2018-06-29 11:18:06] Loading coverage files... WARN [2018-06-29 11:18:15] Multiple chromosomes with very low coverage: 1,10,11,12,13,14,15,16,17,18,19,2,20,21,22,3,4,5,6,7,8,9,X,Y INFO [2018-06-29 11:18:20] Mean target coverages: 0X (tumor) 0X (normal). WARN [2018-06-29 11:18:20] Large difference in coverage of tumor and normal. INFO [2018-06-29 11:18:23] Mean coverages: chrX: 0.08, chrY: 0.05, chr1-22: 0.12. INFO [2018-06-29 11:18:25] Mean coverages: chrX: 0.00, chrY: 0.03, chr1-22: 0.00. INFO [2018-06-29 11:19:10] Removing 232918 intervals with missing log.ratio. INFO [2018-06-29 11:19:29] Removing 492 intervals excluded in normalDB. INFO [2018-06-29 11:19:29] Removing 54020 intervals with low total coverage in normal (< 150.00 reads). INFO [2018-06-29 11:19:29] normalDB provided. Setting minimum coverage for segmentation to 0.0015X. INFO [2018-06-29 11:19:29] Using 0 intervals (0 on-target, 0 off-target). INFO [2018-06-29 11:19:29] No off-target intervals. If this is hybrid-capture data, consider adding them. Error in sort(abs(diff(genomdat)))[1:n.keep] : only 0's may be mixed with negative subscripts Calls: runAbsoluteCN -> smooth.CNA -> trimmed.variance Execution halted

ghost commented 6 years ago

Sorry. I'm using the devel version 1.11.10

lima1 commented 6 years ago

Are you sure the input BAM files for Coverage.R are fine? This usually happens with corrupt BAM files. Coverage.R assumes a standard BAM file generated following GATK best practices, with duplicates marked.

ghost commented 6 years ago

You were right. I was using a bad sequencing sample that had very low coverage. I meant to move it out of the way but forgot to. Everything ran fine when I used a good sample.

Thanks!

-todd