PureCN
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lima1
Error in PureCN.R
Describe the issue A error had happened whenI'm running PureCN.R.
To Reproduce FATAL [2022-08-04 15:23:30] f not in expected range.
FATAL [2022-08-04 15:23:30]
FATAL [2022-08-04 15:23:30] This is most likely a user error due to invalid input data or
FATAL [2022-08-04 15:23:30] parameters (PureCN 2.0.2).
Expected behavior A clear and concise description of what you expected to happen.
Log file INFO [2022-08-04 14:57:13] Loading coverage files... INFO [2022-08-04 14:57:14] Mean target coverages: 405X (tumor) 406X (normal). INFO [2022-08-04 14:57:15] Mean coverages: chrX: 201.04, chrY: 154.85, chr1-22: 403.43. INFO [2022-08-04 14:57:15] Mean coverages: chrX: 208.06, chrY: 154.85, chr1-22: 407.28. INFO [2022-08-04 14:57:22] Removing 119 intervals with missing log.ratio. INFO [2022-08-04 14:57:22] Removing 26 low/high GC targets. INFO [2022-08-04 14:57:22] Removing 667 intervals excluded in normalDB. INFO [2022-08-04 14:57:22] normalDB provided. Setting minimum coverage for segmentation to 0.0015X. INFO [2022-08-04 14:57:22] Removing 1337 low count (< 100 total reads) intervals. INFO [2022-08-04 14:57:22] Using 29201 intervals (14583 on-target, 14618 off-target). INFO [2022-08-04 14:57:22] Ratio of mean on-target vs. off-target read counts: 6.89 INFO [2022-08-04 14:57:22] Mean off-target bin size: 173456 INFO [2022-08-04 14:57:23] AT/GC dropout: 0.97 (tumor), 0.97 (normal), 1.00 (coverage log-ratio). INFO [2022-08-04 14:57:23] Loading VCF... INFO [2022-08-04 14:57:25] Found 7400 variants in VCF file. WARN [2022-08-04 14:57:25] vcf.file has no DB or POP_AF info field for membership in germline databases. Guessing it based on available dbSNP ID. INFO [2022-08-04 14:57:26] 6441 (87.0%) variants annotated as likely germline (DB INFO flag). INFO [2022-08-04 14:57:27] Y22S00143-B1TA is tumor in VCF file. INFO [2022-08-04 14:57:27] 57 homozygous and 3 heterozygous variants on chrX. INFO [2022-08-04 14:57:27] Sex from VCF: M (Fisher's p-value: < 0.0001, odds-ratio: 38.95). INFO [2022-08-04 14:57:28] Initial testing for significant sample cross-contamination: unlikely INFO [2022-08-04 14:57:29] Removing 13 variants with AF < 0.030 or AF >= Inf or less than 6 supporting reads or depth < 15. WARN [2022-08-04 14:57:29] Variant ids contain NAs at filter step BQ. INFO [2022-08-04 14:57:29] Removing 0 low quality variants with BQ < 25. INFO [2022-08-04 14:57:29] Total size of targeted genomic region: 3.40Mb (4.58Mb with 50bp padding). INFO [2022-08-04 14:57:30] 38.0% of targets contain variants. INFO [2022-08-04 14:57:30] Removing 345 variants outside intervals. INFO [2022-08-04 14:57:31] Reading COSMIC VCF... INFO [2022-08-04 14:59:43] Found COSMIC annotation in VCF. Requiring 6 hits. INFO [2022-08-04 14:59:43] Setting somatic prior probabilities for hits to 0.995000 or to 0.500000 if in both COSMIC and dbSNP. INFO [2022-08-04 14:59:43] Loading mapping bias file mapping_bias_PRCC-Normal-PoN_hg19.rds... INFO [2022-08-04 14:59:43] Found 43496 variants in mapping bias file. INFO [2022-08-04 14:59:46] Imputing mapping bias for 937 variants... INFO [2022-08-04 15:00:15] Excluding 1944 novel or poor quality variants from segmentation. INFO [2022-08-04 15:00:15] Excluding 937 variants not in pool of normals from segmentation. INFO [2022-08-04 15:00:15] Sample sex: M INFO [2022-08-04 15:00:15] Segmenting data... INFO [2022-08-04 15:00:15] Interval weights found, will use weighted CBS. INFO [2022-08-04 15:00:16] Loading pre-computed boundaries for DNAcopy... INFO [2022-08-04 15:00:16] Setting undo.SD parameter to 0.500000. INFO [2022-08-04 15:00:20] Setting prune.hclust.h parameter to 0.100000. INFO [2022-08-04 15:00:20] Found 43 segments with median size of 50.03Mb. INFO [2022-08-04 15:00:20] Using 7042 variants. INFO [2022-08-04 15:00:21] Mean standard deviation of log-ratios: 0.25 (MAPD: 0.19) INFO [2022-08-04 15:00:21] Mean standard deviation of on-target log-ratios only: 0.18 (MAPD: 0.13) INFO [2022-08-04 15:00:21] Mean standard deviation of off-target log-ratios only: 0.31 (MAPD: 0.28) INFO [2022-08-04 15:00:21] 2D-grid search of purity and ploidy... INFO [2022-08-04 15:01:16] Local optima: 0.1/2.2, 0.12/2, 0.14/2.4, 0.3/3.2, 0.18/1.8, 0.45/3.8, 0.26/2, 0.55/4.2, 0.42/2.8, 0.52/3, 0.45/2.4, 0.62/5, 0.82/6, 0.38/1.6, 0.65/2.6, 0.85/2.8, 0.58/1.4, 0.52/2, 0.78/2 INFO [2022-08-04 15:01:16] Testing local optimum 1/19 at purity 0.10 and total ploidy 2.20... INFO [2022-08-04 15:01:20] Testing local optimum 2/19 at purity 0.12 and total ploidy 2.00... INFO [2022-08-04 15:01:24] Testing local optimum 3/19 at purity 0.14 and total ploidy 2.40... INFO [2022-08-04 15:01:29] Testing local optimum 4/19 at purity 0.30 and total ploidy 3.20... INFO [2022-08-04 15:01:43] Recalibrating log-ratios... INFO [2022-08-04 15:01:43] Testing local optimum 4/19 at purity 0.30 and total ploidy 3.20... INFO [2022-08-04 15:01:53] Testing local optimum 5/19 at purity 0.18 and total ploidy 1.80... INFO [2022-08-04 15:01:58] Testing local optimum 6/19 at purity 0.45 and total ploidy 3.80... INFO [2022-08-04 15:02:01] Testing local optimum 7/19 at purity 0.26 and total ploidy 2.00... INFO [2022-08-04 15:02:05] Testing local optimum 8/19 at purity 0.55 and total ploidy 4.20... INFO [2022-08-04 15:02:08] Testing local optimum 9/19 at purity 0.42 and total ploidy 2.80... INFO [2022-08-04 15:02:11] Testing local optimum 10/19 at purity 0.52 and total ploidy 3.00... INFO [2022-08-04 15:02:14] Testing local optimum 11/19 at purity 0.45 and total ploidy 2.40... INFO [2022-08-04 15:02:18] Testing local optimum 12/19 at purity 0.62 and total ploidy 5.00... INFO [2022-08-04 15:02:31] Recalibrating log-ratios... INFO [2022-08-04 15:02:31] Testing local optimum 12/19 at purity 0.62 and total ploidy 5.00... INFO [2022-08-04 15:02:35] Recalibrating log-ratios... INFO [2022-08-04 15:02:35] Testing local optimum 12/19 at purity 0.62 and total ploidy 5.00... INFO [2022-08-04 15:02:41] Recalibrating log-ratios... INFO [2022-08-04 15:02:41] Testing local optimum 12/19 at purity 0.62 and total ploidy 5.00... INFO [2022-08-04 15:02:51] Testing local optimum 13/19 at purity 0.82 and total ploidy 6.00... INFO [2022-08-04 15:03:02] Testing local optimum 14/19 at purity 0.38 and total ploidy 1.60... INFO [2022-08-04 15:03:14] Recalibrating log-ratios... INFO [2022-08-04 15:03:14] Testing local optimum 14/19 at purity 0.38 and total ploidy 1.60... INFO [2022-08-04 15:04:19] Recalibrating log-ratios... INFO [2022-08-04 15:04:19] Testing local optimum 14/19 at purity 0.38 and total ploidy 1.60... INFO [2022-08-04 15:04:31] Testing local optimum 15/19 at purity 0.65 and total ploidy 2.60... INFO [2022-08-04 15:04:35] Testing local optimum 16/19 at purity 0.85 and total ploidy 2.80... INFO [2022-08-04 15:04:38] Testing local optimum 17/19 at purity 0.58 and total ploidy 1.40... INFO [2022-08-04 15:04:52] Recalibrating log-ratios... INFO [2022-08-04 15:04:52] Testing local optimum 17/19 at purity 0.58 and total ploidy 1.40... INFO [2022-08-04 15:06:18] Recalibrating log-ratios... INFO [2022-08-04 15:06:18] Testing local optimum 17/19 at purity 0.58 and total ploidy 1.40... INFO [2022-08-04 15:07:59] Testing local optimum 18/19 at purity 0.52 and total ploidy 2.00... INFO [2022-08-04 15:08:02] Testing local optimum 19/19 at purity 0.78 and total ploidy 2.00... INFO [2022-08-04 15:08:06] Skipping 2 solutions that converged to the same optima. INFO [2022-08-04 15:08:06] Fitting variants with betabin model for local optimum 1/19... INFO [2022-08-04 15:08:06] Fitting variants for purity 0.12, tumor ploidy 4.42 and contamination 0.01. INFO [2022-08-04 15:09:00] Optimized purity: 0.12 INFO [2022-08-04 15:09:00] Fitting variants with betabin model for local optimum 2/19... INFO [2022-08-04 15:09:00] Fitting variants for purity 0.13, tumor ploidy 2.21 and contamination 0.01. INFO [2022-08-04 15:09:54] Optimized purity: 0.13 INFO [2022-08-04 15:09:54] Fitting variants with betabin model for local optimum 3/19... INFO [2022-08-04 15:09:54] Fitting variants for purity 0.16, tumor ploidy 5.20 and contamination 0.01. INFO [2022-08-04 15:10:47] Optimized purity: 0.16 INFO [2022-08-04 15:10:47] Fitting variants with betabin model for local optimum 4/19... INFO [2022-08-04 15:10:47] Fitting variants for purity 0.34, tumor ploidy 5.08 and contamination 0.01. INFO [2022-08-04 15:11:41] Optimized purity: 0.34 INFO [2022-08-04 15:11:41] Fitting variants with betabin model for local optimum 5/19... INFO [2022-08-04 15:11:42] Fitting variants for purity 0.10, tumor ploidy 5.30 and contamination 0.01. INFO [2022-08-04 15:12:32] Optimized purity: 0.10 INFO [2022-08-04 15:12:32] Fitting variants with betabin model for local optimum 6/19... INFO [2022-08-04 15:12:33] Fitting variants for purity 0.47, tumor ploidy 5.96 and contamination 0.01. INFO [2022-08-04 15:13:26] Optimized purity: 0.47 INFO [2022-08-04 15:13:26] Fitting variants with betabin model for local optimum 8/19... INFO [2022-08-04 15:13:26] Fitting variants for purity 0.57, tumor ploidy 5.96 and contamination 0.01. INFO [2022-08-04 15:14:18] Optimized purity: 0.57 INFO [2022-08-04 15:14:18] Fitting variants with betabin model for local optimum 9/19... INFO [2022-08-04 15:14:19] Fitting variants for purity 0.46, tumor ploidy 4.05 and contamination 0.01. INFO [2022-08-04 15:15:10] Optimized purity: 0.46 INFO [2022-08-04 15:15:11] Fitting variants with betabin model for local optimum 10/19... INFO [2022-08-04 15:15:11] Fitting variants for purity 0.55, tumor ploidy 4.00 and contamination 0.01. INFO [2022-08-04 15:16:03] Optimized purity: 0.55 INFO [2022-08-04 15:16:03] Fitting variants with betabin model for local optimum 11/19... INFO [2022-08-04 15:16:03] Fitting variants for purity 0.50, tumor ploidy 3.00 and contamination 0.01. INFO [2022-08-04 15:16:56] Optimized purity: 0.50 INFO [2022-08-04 15:16:56] Fitting variants with betabin model for local optimum 12/19... INFO [2022-08-04 15:16:56] Fitting variants for purity 0.51, tumor ploidy 5.15 and contamination 0.01. INFO [2022-08-04 15:17:48] Optimized purity: 0.51 INFO [2022-08-04 15:17:48] Fitting variants with betabin model for local optimum 13/19... INFO [2022-08-04 15:17:48] Fitting variants for purity 0.77, tumor ploidy 6.00 and contamination 0.01. INFO [2022-08-04 15:18:40] Optimized purity: 0.77 INFO [2022-08-04 15:18:40] Fitting variants with betabin model for local optimum 15/19... INFO [2022-08-04 15:18:41] Fitting variants for purity 0.69, tumor ploidy 3.00 and contamination 0.01. INFO [2022-08-04 15:19:33] Optimized purity: 0.69 INFO [2022-08-04 15:19:33] Fitting variants with betabin model for local optimum 16/19... INFO [2022-08-04 15:19:34] Fitting variants for purity 0.95, tumor ploidy 3.00 and contamination 0.01. INFO [2022-08-04 15:20:25] Optimized purity: 0.95 INFO [2022-08-04 15:20:25] Fitting variants with betabin model for local optimum 17/19... INFO [2022-08-04 15:20:25] Fitting variants for purity 0.95, tumor ploidy 0.35 and contamination 0.01. INFO [2022-08-04 15:21:18] Optimized purity: 0.95 INFO [2022-08-04 15:21:18] Fitting variants with betabin model for local optimum 18/19... INFO [2022-08-04 15:21:18] Fitting variants for purity 0.32, tumor ploidy 2.00 and contamination 0.01. INFO [2022-08-04 15:22:10] Optimized purity: 0.32 INFO [2022-08-04 15:22:10] Fitting variants with betabin model for local optimum 19/19... INFO [2022-08-04 15:22:10] Fitting variants for purity 0.59, tumor ploidy 2.00 and contamination 0.01. INFO [2022-08-04 15:23:02] Optimized purity: 0.59 INFO [2022-08-04 15:23:02] Done. INFO [2022-08-04 15:23:02] ------------------------------------------------------------ INFO [2022-08-04 15:23:06] Generating output files... FATAL [2022-08-04 15:23:30] f not in expected range.
FATAL [2022-08-04 15:23:30]
FATAL [2022-08-04 15:23:30] This is most likely a user error due to invalid input data or
FATAL [2022-08-04 15:23:30] parameters (PureCN 2.0.2).
Session Info
sessionInfo() R version 4.1.1 (2021-08-10) Platform: x86_64-conda-linux-gnu (64-bit) Running under: CentOS release 6.8 (Final)
Matrix products: default BLAS/LAPACK: /share/work4/zhangyk4498/sysoft/anaconda3/envs/PureCN2.0.2/lib/libopenblasp-r0.3.20.so
locale: [1] LC_CTYPE=zh_CN.UTF-8 LC_NUMERIC=C [3] LC_TIME=zh_CN.UTF-8 LC_COLLATE=zh_CN.UTF-8 [5] LC_MONETARY=zh_CN.UTF-8 LC_MESSAGES=zh_CN.UTF-8 [7] LC_PAPER=zh_CN.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=zh_CN.UTF-8 LC_IDENTIFICATION=C
attached base packages: [1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached): [1] compiler_4.1.1
Thanks, haven't seen this before. Which files does it generate (so I can figure out where it crashes)?
Thanks, haven't seen this before. Which files does it generate (so I can figure out where it crashes)?
Thank you for your reply。 The error happened when generate sample.pdf.
PureCN.R -> plotAbs(ret, type = "all") -> .plotTypeAF -> calculatePowerDetectSomatic
Since the PureCN version 2.0.2 is required, how should I resolve this error.
Thank you very much.
Hi lina1:
Thank you for your reply.
The error happened when generate sample.pdf.
PureCN.R -> plotAbs(ret, type = "all") -> .plotTypeAF -> calculatePowerDetectSomatic
Since the PureCN version 2.0.2 is required, how should I resolve this error.
Thank you very much.
2022年8月18日 23:50，Markus Riester @.***> 写道：
Thanks, haven't seen this before. Which files does it generate (so I can figure out where it crashes)?
— Reply to this email directly, view it on GitHub https://github.com/lima1/PureCN/issues/248#issuecomment-1219657738, or unsubscribe https://github.com/notifications/unsubscribe-auth/A2LZLBFIJIKOUB5XJ6GT6PLVZZLVZANCNFSM55RWKXVQ. You are receiving this because you authored the thread.
Hmm, never seen this before. Any chance you can share the Sampleid.rds and Sampleid.log files by mail with me?
Hi:
The attachment is an RDS file. I hope to find a solution. Thank you very much!
At 2022-08-29 22:51:26, "Markus Riester" @.***> wrote:
Hmm, never seen this before. Any chance you can share the Sampleid.rds file by mail with me?
— Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you authored the thread.Message ID: @.***>
从网易163邮箱发来的超大附件 Y22S0033204-J1TA.rds (27.5M, 2022年9月14日 11:36 到期) 下载