An unknown error happening

Open MaryGoAround opened this issue 1 year ago • 0 comments
Finally I managed to run PureCN but I get an error after hours
[@login006 ]$ more purecn.out
INFO [2024-10-01 10:25:46] Loading PureCN 2.10.0...
INFO [2024-10-01 10:28:34] Mean coverages: chrX: 24.86, chrY: 0.48, chr1-22: 24.17.
INFO [2024-10-01 10:28:34] Sample sex: F
INFO [2024-10-01 10:28:54] Using default BiocParallel backend. You can change the default in your ~/.Rprofile file.
INFO [2024-10-01 10:28:54] ------------------------------------------------------------
INFO [2024-10-01 10:28:54] PureCN 2.10.0
INFO [2024-10-01 10:28:54] ------------------------------------------------------------
INFO [2024-10-01 10:28:55] Arguments: -tumor.coverage.file LM1.recal_coverage_loess.txt.gz -log.ratio  -seg.file  -vcf.file tumor.vcf.gz -genome hg38 -sex ? -args.setPriorVcf 6 -args.setMappingBiasVcf mapping_bias_wgs_hg38.rds -args.filterIntervals 100,0.05 -args.segmentation 0.005,NULL, -sampleid LM1.recal -min.plo
idy 1.4 -max.ploidy 6 -test.purity 0.9,0.91,0.92,0.93,0.94,0.95 -max.non.clonal 0.3 -max.homozygous.loss 0.5 -log.ratio.calibration 0.1
 -model.homozygous TRUE -error 0.001 -interval.file baits_hg38_intervals.txt -min.logr.sdev 0.15 -max.segments 1000 -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 TRUE -log.file output.log -normal.coverage.file <data> -normalDB <data> -args.filterVcf <data> -fun.segmentation <data> -test.nu
m.copy <data> -speedup.heuristics <data> -BPPARAM <data>
INFO [2024-10-01 10:28:55] Using BiocParallel for parallel optimization.
INFO [2024-10-01 10:28:55] Loading coverage files...
INFO [2024-10-01 10:30:35] Mean target coverages: 24X (tumor) 25X (normal).
INFO [2024-10-01 10:30:56] Mean coverages: chrX: 24.86, chrY: 0.48, chr1-22: 24.17.
INFO [2024-10-01 10:30:57] Mean coverages: chrX: 33.76, chrY: 0.50, chr1-22: 24.43.
INFO [2024-10-01 10:33:13] Removing 34356 intervals with missing log.ratio.
INFO [2024-10-01 10:33:26] Removing 2396 intervals excluded in normalDB.
INFO [2024-10-01 10:33:26] Removing 317 intervals with low total coverage in normal (< 150.00 reads).
INFO [2024-10-01 10:33:26] normalDB provided. Setting minimum coverage for segmentation to 0.0015X.
INFO [2024-10-01 10:33:26] Removing 19125 low count (< 100 total reads) intervals.
INFO [2024-10-01 10:33:30] Removing 52 low coverage (< 0.0015X) intervals.
INFO [2024-10-01 10:33:36] Using 5674884 intervals (5674884 on-target, 0 off-target).
INFO [2024-10-01 10:33:36] No off-target intervals. If this is hybrid-capture data, consider adding them.
INFO [2024-10-01 10:33:52] AT/GC dropout: 1.00 (tumor), 1.00 (normal), 1.01 (coverage log-ratio). 
INFO [2024-10-01 10:33:52] Loading VCF...
INFO [2024-10-01 10:35:49] Found 5209457 variants in VCF file.
INFO [2024-10-01 10:36:06] Removing 114572 triallelic sites.
INFO [2024-10-01 10:36:14] Maximum of POPAF INFO is > 1, assuming -log10 scaled values
WARN [2024-10-01 10:36:18] vcf.file has no DB info field for membership in germline databases. Found and used valid population allele f
requency > 0.001000 instead.
INFO [2024-10-01 10:36:25] 4625437 (90.8%) variants annotated as likely germline (DB INFO flag).
WARN [2024-10-01 10:39:30] Found 111 variants with missing allelic fraction starting with chr1:152196088_T/C. Removing them.
INFO [2024-10-01 10:40:09] LM1 is tumor in VCF file.
INFO [2024-10-01 10:40:51] 40704 homozygous and 83308 heterozygous variants on chrX.
INFO [2024-10-01 10:40:52] Sex from VCF: F (Fisher's p-value: < 0.0001, odds-ratio: 1.06).
INFO [2024-10-01 10:40:55] Detected MuTect2 VCF.
INFO [2024-10-01 10:41:26] Removing 0 Mutect2 calls due to blacklisted failure reasons.
INFO [2024-10-01 10:41:49] Removing 27429 low quality variants with non-offset BQ < 20.
INFO [2024-10-01 10:41:57] Base quality scores range from 19 to 36 (offset by 1)
INFO [2024-10-01 10:41:59] Minimum number of supporting reads ranges from 1 to 41, depending on coverage and BQS.
INFO [2024-10-01 11:23:05] Initial testing for significant sample cross-contamination: unlikely
INFO [2024-10-01 11:23:46] Removing 867833 variants with AF < 0.030 or AF >= Inf or insufficient supporting reads or depth < 15.
INFO [2024-10-01 11:23:46] Total size of targeted genomic region: 2269.94Mb (2332.15Mb with 50bp padding).
INFO [2024-10-01 11:24:08] 42.3% of targets contain variants.
INFO [2024-10-01 11:24:32] Removing 923690 variants outside intervals.
INFO [2024-10-01 11:24:34] Setting somatic prior probabilities for likely germline hits to 0.000500 or to 0.500000 otherwise.
INFO [2024-10-01 11:24:41] Loading mapping bias file mapping_bias_wgs_hg38.rds...
INFO [2024-10-01 11:24:44] Found 7147265 variants in mapping bias file.
INFO [2024-10-01 11:30:03] Imputing mapping bias for 663118 variants...
INFO [2024-10-01 16:40:14] Excluding 249449 novel or poor quality variants from segmentation.
INFO [2024-10-01 16:40:22] Sample sex: F
INFO [2024-10-01 16:40:22] Segmenting data...
INFO [2024-10-01 16:40:27] Interval weights found, will use weighted PSCBS.
INFO [2024-10-01 16:40:44] MAPD of 2937956 allelic fractions: 0.09 (0.09 adjusted).
INFO [2024-10-01 16:41:10] Setting undo.SD parameter to 0.750000.
INFO [2024-10-01 18:11:06] Found 36352 segments, exceeding max.segments threshold of 1000.
INFO [2024-10-01 18:11:06] Setting undo.SD parameter to 1.125000.
INFO [2024-10-01 19:24:57] Found 33924 segments, exceeding max.segments threshold of 1000.
INFO [2024-10-01 21:39:44] Setting prune.hclust.h parameter to 0.150000.
INFO [2024-10-01 23:26:34] Found 33918 segments with median size of 0.02Mb.
INFO [2024-10-01 23:26:39] Removing 5 variants outside segments.
INFO [2024-10-01 23:26:40] Using 3275817 variants.
INFO [2024-10-01 23:36:21] Mean standard deviation of log-ratios: 0.24 (MAPD: 0.20)
INFO [2024-10-01 23:36:21] 2D-grid search of purity and ploidy...
INFO [2024-10-01 23:40:49] Local optima: 0.93/4.8, 0.9/5.6, 0.9/3.8, 0.9/2.8, 0.9/2

[@login006]$ more purecn.err 
INFO [2024-10-01 23:40:51] Testing local optimum 5/5 at purity 0.90 and total ploidy 2.00...

Stop worker failed with the error: wrong args for environment subassignment
Error: BiocParallel errors
  0 remote errors, element index: 
  5 unevaluated and other errors
  first remote error:
Execution halted
Thanks for any help
Oct 02 '24 08:10 MaryGoAround