WARN [2024-03-12 11:57:13] Could not find valid purity and ploidy solution. Error in results[[1]] : subscript out of bounds

[gagank4911]

INFO [2024-03-12 11:54:46] Loading PureCN 2.8.1...
WARN [2024-03-12 11:54:46] Recommended to provide --fun-segmentation Hclust.
INFO [2024-03-12 11:54:46] ------------------------------------------------------------
INFO [2024-03-12 11:54:46] PureCN 2.8.1
INFO [2024-03-12 11:54:46] ------------------------------------------------------------
INFO [2024-03-12 11:54:46] Arguments: -normal.coverage.file -tumor.coverage.file -log.ratio -seg.file ../bam_in/4139.seg -vcf.file ../bam_in/4139_NA_LIB2652_M__S48_TNscope.vcf -normalDB -genome hg38 -sex ? -args.setPriorVcf 6 -args.setMappingBiasVcf ../ref_file/mapping_bias_agilent_v6_hg38.rds -args.filterIntervals 100,0.05 -args.segmentation 0.005,NULL, -sampleid 4139_NA_LIB2652_M__S48_sentieon_match_4.1_deduped -min.ploidy 1.4 -max.ploidy 6 -max.non.clonal 0.2 -max.homozygous.loss 0.05,1e+07 -log.ratio.calibration 0.1 -model.homozygous FALSE -error 0.001 -interval.file ../ref_file/baits_hg38_intervals.txt -min.logr.sdev 0.15 -max.segments 300 -plot.cnv TRUE -vcf.field.prefix PureCN. -cosmic.vcf.file -DB.info.flag DB -POPAF.info.field POP_AF -Cosmic.CNT.info.field Cosmic.CNT -model beta -post.optimize FALSE -BPPARAM -log.file ../out_data//4139_NA_LIB2652_M__S48_sentieon_match_4.1_deduped.log -args.filterVcf -fun.segmentation -test.num.copy -test.purity -speedup.heuristics
INFO [2024-03-12 11:54:46] Loading coverage files...
WARN [2024-03-12 11:54:47] Expecting numeric chromosome names in seg.file, assuming file is properly sorted.
WARN [2024-03-12 11:54:47] Allosome coverage missing, cannot determine sex.
WARN [2024-03-12 11:54:47] Allosome coverage missing, cannot determine sex.
INFO [2024-03-12 11:54:54] Removing 577 intervals with missing log.ratio.
INFO [2024-03-12 11:54:54] Using 70453 intervals (49235 on-target, 21218 off-target).
INFO [2024-03-12 11:54:54] Ratio of mean on-target vs. off-target read counts: NaN
INFO [2024-03-12 11:54:54] Mean off-target bin size: 129575
INFO [2024-03-12 11:54:54] Loading VCF...
INFO [2024-03-12 11:54:55] Found 9603 variants in VCF file.
INFO [2024-03-12 11:54:55] 3431 (35.7%) variants annotated as likely germline (DB INFO flag).
INFO [2024-03-12 11:54:55] 4139_NA_LIB2652_M__S48 is tumor in VCF file.
INFO [2024-03-12 11:54:55] 34 homozygous and 16 heterozygous variants on chrX.
INFO [2024-03-12 11:54:55] Sex from VCF: NA (Fisher's p-value: < 0.0001, odds-ratio: 3.77).
WARN [2024-03-12 11:54:55] Many variants removed by min.base.quality (25) filter. You might want to lower the cutoff.
INFO [2024-03-12 11:54:55] Removing 5215 low quality variants with non-offset BQ < 25.
INFO [2024-03-12 11:54:55] Base quality scores range from 24 to 49 (offset by 1)
INFO [2024-03-12 11:54:55] High median base quality score (49). UMI-barcoded data?
INFO [2024-03-12 11:54:56] Minimum number of supporting reads ranges from 2 to 31, depending on coverage and BQS.
INFO [2024-03-12 11:54:57] Initial testing for significant sample cross-contamination: unlikely
INFO [2024-03-12 11:54:57] Removing 1811 variants with AF < 0.030 or AF >= 0.970 or insufficient supporting reads or depth < 15.
INFO [2024-03-12 11:54:57] Total size of targeted genomic region: 5.92Mb (8.79Mb with 50bp padding).
INFO [2024-03-12 11:54:57] 3.3% of targets contain variants.
INFO [2024-03-12 11:54:57] Removing 381 variants outside intervals.
INFO [2024-03-12 11:54:57] Setting somatic prior probabilities for dbSNP hits to 0.000500 or to 0.500000 otherwise.
INFO [2024-03-12 11:54:57] Loading mapping bias file mapping_bias_agilent_v6_hg38.rds...
INFO [2024-03-12 11:54:57] Found 37415 variants in mapping bias file.
INFO [2024-03-12 11:54:59] Imputing mapping bias for 1850 variants...
INFO [2024-03-12 11:55:32] Excluding 593 novel or poor quality variants from segmentation.
INFO [2024-03-12 11:55:32] Sample sex: ?
INFO [2024-03-12 11:55:32] Segmenting data...
INFO [2024-03-12 11:55:32] Loaded provided segmentation file 4139.seg (format DNAcopy).
WARN [2024-03-12 11:55:32] Expecting numeric chromosome names in seg.file, assuming file is properly sorted.
WARN [2024-03-12 11:55:32] Removing 0 short segments with log-ratio < -8.
INFO [2024-03-12 11:55:32] Re-centering provided segment means (offset 0.7026).
INFO [2024-03-12 11:55:32] Loading pre-computed boundaries for DNAcopy...
INFO [2024-03-12 11:55:32] Setting undo.SD parameter to 0.000000.
Setting multi-figure configuration
INFO [2024-03-12 11:55:34] Setting prune.hclust.h parameter to 0.250000.
INFO [2024-03-12 11:55:34] Found 166 segments with median size of 5.64Mb.
INFO [2024-03-12 11:55:34] Removing 16 variants outside segments.
INFO [2024-03-12 11:55:34] Using 2180 variants.
INFO [2024-03-12 11:55:35] Mean standard deviation of log-ratios: 0.40 (MAPD: 0.00)
INFO [2024-03-12 11:55:35] Mean standard deviation of on-target log-ratios only: 0.00 (MAPD: 0.00)
INFO [2024-03-12 11:55:35] Mean standard deviation of off-target log-ratios only: 0.00 (MAPD: 0.00)
INFO [2024-03-12 11:55:35] 2D-grid search of purity and ploidy...
INFO [2024-03-12 11:56:35] Local optima: 0.42/2.1, 0.52/2.4, 0.52/2, 0.72/3.2, 0.85/3.4, 0.78/2
INFO [2024-03-12 11:56:35] Testing local optimum 1/6 at purity 0.42 and total ploidy 2.10...
INFO [2024-03-12 11:56:37] Recalibrating log-ratios...
INFO [2024-03-12 11:56:37] Testing local optimum 1/6 at purity 0.42 and total ploidy 2.10...
INFO [2024-03-12 11:56:38] Recalibrating log-ratios...
INFO [2024-03-12 11:56:38] Testing local optimum 1/6 at purity 0.42 and total ploidy 2.10...
INFO [2024-03-12 11:56:40] Recalibrating log-ratios...
INFO [2024-03-12 11:56:40] Testing local optimum 1/6 at purity 0.42 and total ploidy 2.10...
INFO [2024-03-12 11:56:42] Testing local optimum 2/6 at purity 0.52 and total ploidy 2.40...
INFO [2024-03-12 11:56:43] Recalibrating log-ratios...
INFO [2024-03-12 11:56:43] Testing local optimum 2/6 at purity 0.52 and total ploidy 2.40...
INFO [2024-03-12 11:56:45] Recalibrating log-ratios...
INFO [2024-03-12 11:56:45] Testing local optimum 2/6 at purity 0.52 and total ploidy 2.40...
INFO [2024-03-12 11:56:47] Recalibrating log-ratios...
INFO [2024-03-12 11:56:47] Testing local optimum 2/6 at purity 0.52 and total ploidy 2.40...
INFO [2024-03-12 11:56:48] Testing local optimum 3/6 at purity 0.52 and total ploidy 2.00...
INFO [2024-03-12 11:56:50] Recalibrating log-ratios...
INFO [2024-03-12 11:56:50] Testing local optimum 3/6 at purity 0.52 and total ploidy 2.00...
INFO [2024-03-12 11:56:51] Recalibrating log-ratios...
INFO [2024-03-12 11:56:51] Testing local optimum 3/6 at purity 0.52 and total ploidy 2.00...
INFO [2024-03-12 11:56:53] Recalibrating log-ratios...
INFO [2024-03-12 11:56:53] Testing local optimum 3/6 at purity 0.52 and total ploidy 2.00...
INFO [2024-03-12 11:56:55] Testing local optimum 4/6 at purity 0.72 and total ploidy 3.20...
INFO [2024-03-12 11:56:56] Recalibrating log-ratios...
INFO [2024-03-12 11:56:56] Testing local optimum 4/6 at purity 0.72 and total ploidy 3.20...
INFO [2024-03-12 11:56:58] Recalibrating log-ratios...
INFO [2024-03-12 11:56:58] Testing local optimum 4/6 at purity 0.72 and total ploidy 3.20...
INFO [2024-03-12 11:56:59] Recalibrating log-ratios...
INFO [2024-03-12 11:56:59] Testing local optimum 4/6 at purity 0.72 and total ploidy 3.20...
INFO [2024-03-12 11:57:01] Testing local optimum 5/6 at purity 0.85 and total ploidy 3.40...
INFO [2024-03-12 11:57:03] Recalibrating log-ratios...
INFO [2024-03-12 11:57:03] Testing local optimum 5/6 at purity 0.85 and total ploidy 3.40...
INFO [2024-03-12 11:57:04] Recalibrating log-ratios...
INFO [2024-03-12 11:57:04] Testing local optimum 5/6 at purity 0.85 and total ploidy 3.40...
INFO [2024-03-12 11:57:06] Recalibrating log-ratios...
INFO [2024-03-12 11:57:06] Testing local optimum 5/6 at purity 0.85 and total ploidy 3.40...
INFO [2024-03-12 11:57:07] Testing local optimum 6/6 at purity 0.78 and total ploidy 2.00...
INFO [2024-03-12 11:57:09] Recalibrating log-ratios...
INFO [2024-03-12 11:57:09] Testing local optimum 6/6 at purity 0.78 and total ploidy 2.00...
INFO [2024-03-12 11:57:10] Recalibrating log-ratios...
INFO [2024-03-12 11:57:10] Testing local optimum 6/6 at purity 0.78 and total ploidy 2.00...
INFO [2024-03-12 11:57:12] Recalibrating log-ratios...
INFO [2024-03-12 11:57:12] Testing local optimum 6/6 at purity 0.78 and total ploidy 2.00...
INFO [2024-03-12 11:57:13] Skipping 6 solutions exceeding max.non.clonal (0.20): 0.15/7.32151366171102e+69, 0.29/6.4975043500027e+69, 0.15/1.75075056629748e+70, 0.93/4.62651304294153e+67, 0.95/4.9331070195215e+69, 0.29/1.14927951762391e+71 (purity/tumor ploidy)
WARN [2024-03-12 11:57:13] Could not find valid purity and ploidy solution.
Error in results[[1]] : subscript out of bounds
Calls: runAbsoluteCN -> grepl -> is.factor
Execution halted
root@095bb1c61e92:/opt#