Full support for GATK4

[lima1]

• [x] Parsing coverage

• [x] Parsing log-ratios

• [x] Mutect2 tumor-only

• [x] Mutect2 tumor/normal

• [ ] CallableBases equivalent

• [x] Parsing segmentations

• [x] PoN VCFs

[andrewrech]

I am comparing MuTectv1.1.7 vs. MuTect2/GATK4 with n = 150 WES

[lima1]

Thank Andrew, that's awesome!

I had no chance to thoroughly compare. I only did quick checks for high-level purity/ploidy concordance in about 20 WES samples, tumor-only and matched.

I have no experience with M2 artifact filtering, so any feedback is highly appreciated.

[andrewrech]

with respect to M2 filtering, it seems experience is very limited across the board. we've struggled with this so we're just going to do the experiment.

I'm sure we can make desensitized results available

[PubuduSaneth]

Hi Markus and Andrew

I'm trying to use PureCN (v1.17.1) to classify Mutect2 variants using segment and log-ratio files from GATK4 (v4.0.6). However, I'm receiving an already reported (but closed) issue - https://github.com/lima1/PureCN/issues/79

I'd be extremely thankful for any guidance that could help me to figure out the issue...

(I followed the GATK4 CNV workflow to generate segment and log-ratio files and PURECN/NormalDB.R to generate the mapping_bias_hg38.rds file)

Following is the command I ran...

Rscript $PURECN/NormalDB.R --outdir $OUT/ --normal_panel pon.vcf.gz --genome hg38 --force

Rscript $PURECN/PureCN.R --out $OUT/  \
--sampleid "P2xxx" \
--tumor P2xxx.tumor.counts.hdf5 \
--logratiofile P2xxx.tumor.clean.denoisedCR.tsv \
--segfile P23993.tumor.clean.modelFinal.seg \
--mappingbiasfile mapping_bias_hg38.rds \
--vcf mutect2_P2xxx.vcf.gz \
--genome hg38 \
--funsegmentation Hclust \
--force --postoptimize --seed 123

and the Error is

Error in which(as.numeric(geno(vcf)$MBQ[, tumor.id.in.vcf]) >= min.base.quality) :
  (list) object cannot be coerced to type 'double'
Calls: runAbsoluteCN ... filterVcfMuTect2 -> filterVcfBasic -> .filterVcfByBQ -> which
In addition: Warning message:
In .bcfHeaderAsSimpleList(header) :
  duplicate keys in header will be forced to unique rownames
Execution halted

The log file

INFO [2019-12-09 14:31:54] ------------------------------------------------------------
INFO [2019-12-09 14:31:54] PureCN 1.17.1
INFO [2019-12-09 14:31:54] ------------------------------------------------------------
INFO [2019-12-09 14:31:54] Arguments: -normal.coverage.file  -seg.file /home/1c53d71ea3b543e2b810f996097930/P2xxx.tumor.clean.modelFinal.seg -vcf.file /home/0495f652ddfd8daa0872f47501bddf/mutect2_P2xxx.vcf.gz -normalDB  -genome hg38 -sex ? -args.setPriorVcf 6 -args.setMappingBiasVcf /home/mapping_bias_hg38.rds -args.segmentation NULL,0.005,NULL -sampleid P2xxx -min.ploidy 1 -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  -max.segments 300 -plot.cnv TRUE -DB.info.flag DB -POPAF.info.field POP_AF -model beta -post.optimize TRUE -BPPARAM  -log.file /home//P2xxx.log -tumor.coverage.file <data> -log.ratio <data> -args.filterVcf <data> -fun.segmentation <data> -test.num.copy <data> -test.purity <data> -speedup.heuristics <data>
INFO [2019-12-09 14:31:54] Loading coverage files...
WARN [2019-12-09 14:31:55] Allosome coverage missing, cannot determine sex.
WARN [2019-12-09 14:31:55] Allosome coverage missing, cannot determine sex.
INFO [2019-12-09 14:31:56] Using 194080 intervals (194080 on-target, 0 off-target).
INFO [2019-12-09 14:31:56] No off-target intervals. If this is hybrid-capture data, consider adding them.
INFO [2019-12-09 14:31:56] Loading VCF...
INFO [2019-12-09 14:31:56] Found 3123 variants in VCF file.
INFO [2019-12-09 14:31:56] Removing 64 triallelic sites.
WARN [2019-12-09 14:31:57] vcf.file has no DB info field for membership in germline databases. Found and used somatic status instead.
INFO [2019-12-09 14:31:57] 3 (0.1%) variants annotated as likely germline (DB INFO flag).
INFO [2019-12-09 14:31:57] tumor.P2xxx is tumor in VCF file.
INFO [2019-12-09 14:31:57] No homozygous variants in VCF, provide unfiltered VCF.
INFO [2019-12-09 14:31:57] Detected MuTect2 VCF.
INFO [2019-12-09 14:31:57] Removing 2360 MuTect2 calls due to blacklisted failure reasons.
INFO [2019-12-09 14:31:58] Removing 3 non heterozygous (in matched normal) germline SNPs.
INFO [2019-12-09 14:31:59] Removing 156 variants with AF < 0.030 or AF >= 1.000 or less than 5 supporting reads or depth < 15.

[lima1]

Hi,

stable support for Mutect 2 is a top priority for the next release (spring 2020), with beta versions hopefully available in January. Until then, I'd recommend using Mutect 1.1.7.

Thanks, Markus

[PubuduSaneth]

Thank you Markus for getting back so quickly. I'll try Mutect 1.1.7 and looking forward to the PureCN spring 2020 release... Thank you very much for all the work you do...

[lima1]

Still no good callable bases equivalent, but made it less important by estimating callable regions in callMutationBurden. Now GATK4 support in beta.

[genisparra]

Hi, I am using PURECN version 1.21 and Mutect2 from GATK Version 4.0.8.1. And I am getting exactly the same error. Is there anything I can do? Is there any beta version that solves the issue? if not Is there any way to deactivate the vcf filter steep?

Error in which(as.numeric(geno(vcf)$MBQ[, tumor.id.in.vcf]) >= min.base.quality) : (list) object cannot be coerced to type 'double' Calls: runAbsoluteCN ... filterVcfMuTect2 -> filterVcfBasic -> .filterVcfByBQ -> which

I would really appreciate your help and thanks in advance,

Genis

[lima1]

Hi Genis,

can you try the latest versions? They changed the variant annotations quite a lot and it's been difficult to keep up. But things seem to become more stable now.

Markus

[genisparra]

Hi Markus,

Thanks for your fast reply. We know that working with the GATK software and the ever changing versions and formats is a nightmare. Is there any version from Mutect2 GATK4 that PureCN has been test on and you know it should work?

Sincerely,

Genis

-- Genís Parra, PhD Data Analyst - Data Analysis Team Centre Nacional d’Anàlisi Genòmica (CNAG-CRG) Centre de Regulació Genòmica Parc Científic de Barcelona – Torre I Baldiri Reixac, 4 08028 Barcelona Tel +34 93 402 08 46 Email genis.parra@cnag.crg.eu Web http://www.cnag.crg.eu

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---

From: Markus Riester notifications@github.com Sent: Tuesday, February 23, 2021 5:52:23 PM To: lima1/PureCN Cc: Genis Parra Farre; Comment Subject: Re: [lima1/PureCN] Full support for GATK4 (#6)

Hi Genis,

can you try the latest versions? They changed the variant annotations quite a lot and it's been difficult to keep up. But things seem to become more stable now.

Markus

— You are receiving this because you commented. Reply to this email directly, view it on GitHubhttps://github.com/lima1/PureCN/issues/6#issuecomment-784345296, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AIAREDRRKP23PVRCBEB5EL3TAPMMPANCNFSM4D2VSDBA.

[yiolino]

Hi Markus,

I am trying to run pureCN using the Mutect2 vcf file.

Rscript ${PURECN}/PureCN.R --out ${outDir}  \
    --sampleid ${i} \
    --tumor ${i}.cnr \
    --segfile ${i}.seg \
    --vcf ${i}.vcf.gz \
    --statsfile ${i}.vcf.gz.stats \
    --intervals intervals.txt \
    --genome hg38 \
    --funsegmentation Hclust \
    --force --postoptimize --seed 123 \
    --snpblacklist hg38_simpleRepeats.bed

But I got this error. FATAL [2021-02-24 14:12:31] No variants passed filter matched germline.

After tracing the error, it seemed that the problem was with the filterVcfBasic function. This is the location of line 78 vcf <- .testGermline(vcf, tumor.id.in.vcf) in the link. https://github.com/lima1/PureCN/blob/master/R/filterVcf.R

The testGermline function, which starts on line 229, has as.numeric(geno(vcf)$FA. I think this is a typo of as.numeric(geno(vcf)$AF. I don't think there is an INFO Field named FA in vcf files. as.numeric(geno(vcf)$FA　function returns NULL.

Thanks,

[lima1]

@genisparra, I have 4.1.6.0 currently installed. Not sure I ran the full set of tests on it, but it should work. Feel free to try the latest version and I'll fix quickly if it doesn't work.

If you are set on 4.0.8.1 in your pipelines, I'm happy to add a fix as well. I won't have time to investigate, but if you point me to the issue and example VCFs for debugging, I'll have a look.

[lima1]

@tetsuro90 , I standardize VCFs to some extend when the file is loaded. So FA should be there and I don't think it is the issue. What version of Mutect 2 are you using? Tumor and normal mode? If so, did you add the flags to make sure that all germline SNPs are not filtered out? Do you follow the complete GATK4 somatic best practices with GnomAD annotation etc.?

Oh, and --statsfile is not required anymore with Mutect2 (in fact I don't know what happens when you provide it). Mutect 2 now adds all information we need to the VCF, so no need to parse the extra file anymore. I will make this clearer in the vignette.

[yiolino]

@lima1 Thank you for your reply. I'm sorry for the misunderstanding.

I used GATK ver4.1.9 and run Mutect2 Matched Normal mode. I followed GATK4 somatic best practice, but it maybe not latest. I used Funcotator to annotation, but input of pureCN vcf was not Funcotator output. Mutect2 output.

If I create a vcf with the right method, will FA appear in the INFO Field? What does FA mean?

I understand that the stats file is not needed. Thank you very much.

[lima1]

@tetsuro90 , PureCN will add the FA field (allelic fraction), you should not need to change anything. Some callers use FA, other AF.

For matched normal mode, you need to add --genotype-germline-sites. Mutect by default only reports somatic variants, but we need the SNPs for copy number and loh calling.

4.1.9 should be fine.

[yiolino]

@lima1 Ok, I fully understand! And I didn't add --genotype-germline-sites option. I'll retry.

Thank you very much for your kind attention.

[yiolino]

Adding the --genotype-germline-sites option was successful. Thank you.

[lima1]

Great @tetsuro90 . Feel free to post the log file (Sampleid.log) and I'll double check that everything looks good.

[genisparra]

Hi,

I find out that my problem was that in GATK Version 4.0.8.1. the vcf generated by Mutect had MBQ in the FORMAT and with two values. I tried version 4.1.7.0 of Mutect and has the MBQ in the INFO column and now it seems to work well.

Thanks for your help,

Genis

[lima1]

ok, great, thanks @genisparra . Like I said, if you need a fix for that in case your locked pipelines need 4.0.8.1, just send me some minimal test vcfs and I'll make sure it parses MBQ correctly.

[yiolino]

That would be very helpful. Here is the log file

[1] "/mysample_dir"
INFO [2021-02-25 14:55:00] Loading PureCN 1.20.0...
INFO [2021-02-25 14:55:00] ------------------------------------------------------------
INFO [2021-02-25 14:55:00] PureCN 1.20.0
INFO [2021-02-25 14:55:00] ------------------------------------------------------------
INFO [2021-02-25 14:55:00] Arguments: -normal.coverage.file  -tumor.coverage.file /myinput_dir/my_sample/my_sample_sorted_deup_recal.cnr -log.ratio  -seg.file /myseg_dir/my_sample.seg -vcf.file /bam_dir/my_sample/my_sample_somatic.vcf.gz -normalDB  -genome hg38 -sex ? -args.setPriorVcf 6 -args.setMappingBiasVcf NULL -args.segmentation 0.005,NULL -sampleid my_sample -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 baits_hg38_intervals.txt -max.segments 300 -plot.cnv TRUE -vcf.field.prefix PureCN. -DB.info.flag DB -POPAF.info.field POP_AF -model beta -post.optimize TRUE -BPPARAM  -log.file /my_logdir/my_sample/my_sample.log -args.filterVcf <data> -fun.segmentation <data> -test.num.copy <data> -test.purity <data> -speedup.heuristics <data>
INFO [2021-02-25 14:55:00] Loading coverage files...
INFO [2021-02-25 14:55:06] Found log2-ratio in tumor coverage data.
WARN [2021-02-25 14:55:06] log2-ratio contains outliers < -8, ignoring them...
INFO [2021-02-25 14:55:06] Mean coverages: chrX: 297.98, chrY: 61.26, chr1-22: 235.59.
INFO [2021-02-25 14:55:06] Mean coverages: chrX: 297.98, chrY: 61.26, chr1-22: 235.59.
WARN [2021-02-25 14:55:12] tumor.coverage.file and interval.file do not align.
INFO [2021-02-25 14:55:24] Removing 13 intervals with missing log.ratio.
INFO [2021-02-25 14:55:24] Using 265358 intervals (228699 on-target, 36659 off-target).
INFO [2021-02-25 14:55:24] Ratio of mean on-target vs. off-target read counts: NaN
INFO [2021-02-25 14:55:24] Mean off-target bin size: 62245
INFO [2021-02-25 14:55:24] Loading VCF...
INFO [2021-02-25 14:55:25] Found 7356 variants in VCF file.
INFO [2021-02-25 14:55:25] Removing 189 triallelic sites.
WARN [2021-02-25 14:55:25] Found GERMQ info field with Phred scaled germline probabilities.
INFO [2021-02-25 14:55:25] Maximum of POPAP INFO is > 1, assuming -log10 scaled values
WARN [2021-02-25 14:55:25] vcf.file has no DB info field for membership in germline databases. Found and used valid population allele frequency > 0.001000 instead.
INFO [2021-02-25 14:55:25] 3630 (50.6%) variants annotated as likely germline (DB INFO flag).
WARN [2021-02-25 14:55:26] Found 28 variants with missing allelic fraction starting with chr2:87771410_T/G. Removing them.
INFO [2021-02-25 14:55:26] my_sample is tumor in VCF file.
INFO [2021-02-25 14:55:26] 21 homozygous and 203 heterozygous variants on chrX.
INFO [2021-02-25 14:55:26] Sex from VCF: F (Fisher's p-value: 0.017, odds-ratio: 0.59).
WARN [2021-02-25 14:55:26] Sex mismatch of coverage and VCF. Could be because of noisy data, contamination, loss of chrY or a mis-alignment of coverage and VCF.
INFO [2021-02-25 14:55:26] Detected MuTect2 VCF.
INFO [2021-02-25 14:55:26] Removing 0 Mutect2 calls due to blacklisted failure reasons.
INFO [2021-02-25 14:55:26] Removing 4715 non heterozygous (in matched normal) germline SNPs.
INFO [2021-02-25 14:55:27] Removing 42 variants with AF < 0.030 or AF >= 1.000 or less than 5 supporting reads or depth < 15.
INFO [2021-02-25 14:55:32] Removing 208 blacklisted variants.
WARN [2021-02-25 14:55:32] Variant ids contain NAs at filter step BQ.
INFO [2021-02-25 14:55:32] Removing 0 low quality variants with BQ < 25.
INFO [2021-02-25 14:55:32] Total size of targeted genomic region: 33.95Mb (54.09Mb with 50bp padding).
INFO [2021-02-25 14:55:33] 0.8% of targets contain variants.
INFO [2021-02-25 14:55:33] Removing 335 variants outside intervals.
INFO [2021-02-25 14:55:33] Found SOMATIC annotation in VCF.
INFO [2021-02-25 14:55:33] Setting somatic prior probabilities for somatic variants to 0.999000 or to 0.000100 otherwise.
INFO [2021-02-25 14:55:33] Found SOMATIC annotation in VCF. Setting mapping bias to 0.985.
INFO [2021-02-25 14:55:33] Excluding 0 novel or poor quality variants from segmentation.
INFO [2021-02-25 14:55:33] Sample sex: M
INFO [2021-02-25 14:55:33] Segmenting data...
INFO [2021-02-25 14:55:33] Loaded provided segmentation file my_sample.seg (format DNAcopy).
WARN [2021-02-25 14:55:33] Expecting numeric chromosome names in seg.file, assuming file is properly sorted.
WARN [2021-02-25 14:55:33] Provided sampleid (my_sample) does not match my_sample_sorted_deup_recal found in segmentation.
INFO [2021-02-25 14:55:33] Re-centering provided segment means (offset -0.0155).
INFO [2021-02-25 14:55:33] Setting prune.hclust.h parameter to 0.100000.
INFO [2021-02-25 14:55:33] Found 431 segments with median size of 1.62Mb.
INFO [2021-02-25 14:55:33] Using 1839 variants.
INFO [2021-02-25 14:55:35] Mean standard deviation of log-ratios: 0.30
INFO [2021-02-25 14:55:35] Mean standard deviation of on-target log-ratios only: 0.30
INFO [2021-02-25 14:55:35] Mean standard deviation of off-target log-ratios only: 0.30
INFO [2021-02-25 14:55:35] 2D-grid search of purity and ploidy...
INFO [2021-02-25 14:59:40] Local optima: 0.17/2.4, 0.27/3, 0.58/4.2, 0.52/4.4, 0.48/3.4, 0.19/2,
0.72/5.4, 0.85/6, 0.72/4, 0.52/3, 0.95/4.8, 0.62/2.6, 0.38/1.6, 0.52/2,
0.82/2.8, 0.78/2, 0.58/1.4
INFO [2021-02-25 14:59:40] Testing local optimum 1/17 at purity 0.17 and total ploidy 2.40...
INFO [2021-02-25 15:00:01] Testing local optimum 2/17 at purity 0.27 and total ploidy 3.00...
INFO [2021-02-25 15:00:24] Testing local optimum 3/17 at purity 0.58 and total ploidy 4.20...
INFO [2021-02-25 15:00:42] Testing local optimum 4/17 at purity 0.52 and total ploidy 4.40...
INFO [2021-02-25 15:00:48] Recalibrating log-ratios...
INFO [2021-02-25 15:00:48] Testing local optimum 4/17 at purity 0.52 and total ploidy 4.40...
INFO [2021-02-25 15:01:14] Recalibrating log-ratios...
INFO [2021-02-25 15:01:14] Testing local optimum 4/17 at purity 0.52 and total ploidy 4.40...
INFO [2021-02-25 15:01:44] Recalibrating log-ratios...
INFO [2021-02-25 15:01:44] Testing local optimum 4/17 at purity 0.52 and total ploidy 4.40...
INFO [2021-02-25 15:02:15] Testing local optimum 5/17 at purity 0.48 and total ploidy 3.40...
INFO [2021-02-25 15:02:33] Testing local optimum 6/17 at purity 0.19 and total ploidy 2.00...
INFO [2021-02-25 15:03:05] Testing local optimum 7/17 at purity 0.72 and total ploidy 5.40...
INFO [2021-02-25 15:03:10] Recalibrating log-ratios...
INFO [2021-02-25 15:03:10] Testing local optimum 7/17 at purity 0.72 and total ploidy 5.40...
INFO [2021-02-25 15:03:27] Recalibrating log-ratios...
INFO [2021-02-25 15:03:27] Testing local optimum 7/17 at purity 0.72 and total ploidy 5.40...
INFO [2021-02-25 15:03:53] Recalibrating log-ratios...
INFO [2021-02-25 15:03:53] Testing local optimum 7/17 at purity 0.72 and total ploidy 5.40...
INFO [2021-02-25 15:04:23] Testing local optimum 8/17 at purity 0.85 and total ploidy 6.00...
INFO [2021-02-25 15:04:28] Recalibrating log-ratios...
INFO [2021-02-25 15:04:28] Testing local optimum 8/17 at purity 0.85 and total ploidy 6.00...
INFO [2021-02-25 15:04:48] Recalibrating log-ratios...
INFO [2021-02-25 15:04:48] Testing local optimum 8/17 at purity 0.85 and total ploidy 6.00...
INFO [2021-02-25 15:05:09] Recalibrating log-ratios...
INFO [2021-02-25 15:05:09] Testing local optimum 8/17 at purity 0.85 and total ploidy 6.00...
INFO [2021-02-25 15:05:28] Testing local optimum 9/17 at purity 0.72 and total ploidy 4.00...
INFO [2021-02-25 15:05:50] Testing local optimum 10/17 at purity 0.52 and total ploidy 3.00...
INFO [2021-02-25 15:06:10] Testing local optimum 11/17 at purity 0.95 and total ploidy 4.80...
INFO [2021-02-25 15:06:24] Testing local optimum 12/17 at purity 0.62 and total ploidy 2.60...
INFO [2021-02-25 15:06:52] Testing local optimum 13/17 at purity 0.38 and total ploidy 1.60...
INFO [2021-02-25 15:06:57] Recalibrating log-ratios...
INFO [2021-02-25 15:06:57] Testing local optimum 13/17 at purity 0.38 and total ploidy 1.60...
INFO [2021-02-25 15:07:03] Recalibrating log-ratios...
INFO [2021-02-25 15:07:03] Testing local optimum 13/17 at purity 0.38 and total ploidy 1.60...
INFO [2021-02-25 15:07:08] Recalibrating log-ratios...
INFO [2021-02-25 15:07:08] Testing local optimum 13/17 at purity 0.38 and total ploidy 1.60...
INFO [2021-02-25 15:07:14] Testing local optimum 14/17 at purity 0.52 and total ploidy 2.00...
INFO [2021-02-25 15:07:35] Testing local optimum 15/17 at purity 0.82 and total ploidy 2.80...
INFO [2021-02-25 15:07:56] Testing local optimum 16/17 at purity 0.78 and total ploidy 2.00...
INFO [2021-02-25 15:08:13] Testing local optimum 17/17 at purity 0.58 and total ploidy 1.40...
INFO [2021-02-25 15:08:18] Recalibrating log-ratios...
INFO [2021-02-25 15:08:18] Testing local optimum 17/17 at purity 0.58 and total ploidy 1.40...
INFO [2021-02-25 15:08:24] Recalibrating log-ratios...
INFO [2021-02-25 15:08:24] Testing local optimum 17/17 at purity 0.58 and total ploidy 1.40...
INFO [2021-02-25 15:08:29] Recalibrating log-ratios...
INFO [2021-02-25 15:08:29] Testing local optimum 17/17 at purity 0.58 and total ploidy 1.40...
INFO [2021-02-25 15:08:35] Skipping 1 solutions that converged to the same optima.
INFO [2021-02-25 15:08:35] Skipping 2 solutions exceeding max.non.clonal (0.20).
INFO [2021-02-25 15:08:35] Fitting variants with beta model for local optimum 2/17...
INFO [2021-02-25 15:08:36] Fitting variants for purity 0.28, tumor ploidy 5.80 and contamination 0.01.
INFO [2021-02-25 15:08:57] Rare karyotype solution. Skipping post-optimization.
INFO [2021-02-25 15:08:57] Optimized purity: 0.28
INFO [2021-02-25 15:08:57] Fitting variants with beta model for local optimum 3/17...
INFO [2021-02-25 15:08:59] Fitting variants for purity 0.61, tumor ploidy 5.85 and contamination 0.01.
INFO [2021-02-25 15:09:21] Rare karyotype solution. Skipping post-optimization.
INFO [2021-02-25 15:09:21] Optimized purity: 0.61
INFO [2021-02-25 15:09:21] Fitting variants with beta model for local optimum 4/17...
INFO [2021-02-25 15:09:22] Fitting variants for purity 0.22, tumor ploidy 4.66 and contamination 0.01.
INFO [2021-02-25 15:09:44] Rare karyotype solution. Skipping post-optimization.
INFO [2021-02-25 15:09:44] Optimized purity: 0.22
INFO [2021-02-25 15:09:44] Fitting variants with beta model for local optimum 5/17...
INFO [2021-02-25 15:09:45] Fitting variants for purity 0.48, tumor ploidy 4.86 and contamination 0.01.
INFO [2021-02-25 15:10:07] Rare karyotype solution. Skipping post-optimization.
INFO [2021-02-25 15:10:07] Optimized purity: 0.48
INFO [2021-02-25 15:10:07] Fitting variants with beta model for local optimum 6/17...
INFO [2021-02-25 15:10:09] Fitting variants for purity 0.25, tumor ploidy 1.88 and contamination 0.01.
INFO [2021-02-25 15:10:30] Fitting variants for purity 0.21, tumor ploidy 1.88 and contamination 0.01.
INFO [2021-02-25 15:10:51] Fitting variants for purity 0.22, tumor ploidy 1.88 and contamination 0.01.
INFO [2021-02-25 15:11:13] Fitting variants for purity 0.23, tumor ploidy 1.88 and contamination 0.01.
INFO [2021-02-25 15:11:33] Fitting variants for purity 0.24, tumor ploidy 1.88 and contamination 0.01.
INFO [2021-02-25 15:11:54] Fitting variants for purity 0.26, tumor ploidy 1.88 and contamination 0.01.
INFO [2021-02-25 15:12:14] Fitting variants for purity 0.27, tumor ploidy 1.88 and contamination 0.01.
INFO [2021-02-25 15:12:35] Fitting variants for purity 0.28, tumor ploidy 1.88 and contamination 0.01.
INFO [2021-02-25 15:12:57] Fitting variants for purity 0.29, tumor ploidy 1.88 and contamination 0.01.
INFO [2021-02-25 15:13:18] Optimized purity: 0.25
INFO [2021-02-25 15:13:18] Fitting variants with beta model for local optimum 7/17...
INFO [2021-02-25 15:13:19] Fitting variants for purity 0.36, tumor ploidy 3.88 and contamination 0.01.
INFO [2021-02-25 15:13:42] Fitting variants for purity 0.32, tumor ploidy 3.88 and contamination 0.01.
INFO [2021-02-25 15:14:02] Fitting variants for purity 0.33, tumor ploidy 3.88 and contamination 0.01.
INFO [2021-02-25 15:14:21] Fitting variants for purity 0.34, tumor ploidy 3.88 and contamination 0.01.
INFO [2021-02-25 15:14:42] Fitting variants for purity 0.35, tumor ploidy 3.88 and contamination 0.01.
INFO [2021-02-25 15:15:04] Fitting variants for purity 0.37, tumor ploidy 3.88 and contamination 0.01.
INFO [2021-02-25 15:15:25] Fitting variants for purity 0.38, tumor ploidy 3.88 and contamination 0.01.
INFO [2021-02-25 15:15:46] Fitting variants for purity 0.39, tumor ploidy 3.88 and contamination 0.01.
INFO [2021-02-25 15:16:07] Fitting variants for purity 0.40, tumor ploidy 3.88 and contamination 0.01.
INFO [2021-02-25 15:16:29] Optimized purity: 0.32
INFO [2021-02-25 15:16:29] Fitting variants with beta model for local optimum 8/17...
INFO [2021-02-25 15:16:30] Fitting variants for purity 0.57, tumor ploidy 4.90 and contamination 0.01.
INFO [2021-02-25 15:16:52] Rare karyotype solution. Skipping post-optimization.
INFO [2021-02-25 15:16:52] Optimized purity: 0.57
INFO [2021-02-25 15:16:52] Fitting variants with beta model for local optimum 9/17...
INFO [2021-02-25 15:16:53] Fitting variants for purity 0.77, tumor ploidy 4.92 and contamination 0.01.
INFO [2021-02-25 15:17:17] Rare karyotype solution. Skipping post-optimization.
INFO [2021-02-25 15:17:17] Optimized purity: 0.77
INFO [2021-02-25 15:17:17] Fitting variants with beta model for local optimum 10/17...
INFO [2021-02-25 15:17:18] Fitting variants for purity 0.43, tumor ploidy 3.89 and contamination 0.01.
INFO [2021-02-25 15:17:41] High ploidy solution in highly balanced genome. Skipping post-optimization.
INFO [2021-02-25 15:17:41] Optimized purity: 0.43
INFO [2021-02-25 15:17:41] Fitting variants with beta model for local optimum 11/17...
INFO [2021-02-25 15:17:42] Fitting variants for purity 0.95, tumor ploidy 4.95 and contamination 0.01.
INFO [2021-02-25 15:18:05] Rare karyotype solution. Skipping post-optimization.
INFO [2021-02-25 15:18:05] Optimized purity: 0.95
INFO [2021-02-25 15:18:05] Fitting variants with beta model for local optimum 12/17...
INFO [2021-02-25 15:18:07] Fitting variants for purity 0.42, tumor ploidy 2.92 and contamination 0.01.
INFO [2021-02-25 15:18:30] Fitting variants for purity 0.38, tumor ploidy 2.92 and contamination 0.01.
INFO [2021-02-25 15:18:53] Fitting variants for purity 0.39, tumor ploidy 2.92 and contamination 0.01.
INFO [2021-02-25 15:19:16] Fitting variants for purity 0.40, tumor ploidy 2.92 and contamination 0.01.
INFO [2021-02-25 15:19:40] Fitting variants for purity 0.41, tumor ploidy 2.92 and contamination 0.01.
INFO [2021-02-25 15:20:02] Fitting variants for purity 0.43, tumor ploidy 2.92 and contamination 0.01.
INFO [2021-02-25 15:20:25] Fitting variants for purity 0.44, tumor ploidy 2.92 and contamination 0.01.
INFO [2021-02-25 15:20:48] Fitting variants for purity 0.45, tumor ploidy 2.92 and contamination 0.01.
INFO [2021-02-25 15:21:10] Fitting variants for purity 0.46, tumor ploidy 2.92 and contamination 0.01.
INFO [2021-02-25 15:21:31] Optimized purity: 0.38
INFO [2021-02-25 15:21:31] Fitting variants with beta model for local optimum 14/17...
INFO [2021-02-25 15:21:33] Fitting variants for purity 0.32, tumor ploidy 1.90 and contamination 0.01.
INFO [2021-02-25 15:21:56] Fitting variants for purity 0.28, tumor ploidy 1.90 and contamination 0.01.
INFO [2021-02-25 15:22:19] Fitting variants for purity 0.29, tumor ploidy 1.90 and contamination 0.01.
INFO [2021-02-25 15:22:41] Fitting variants for purity 0.30, tumor ploidy 1.90 and contamination 0.01.
INFO [2021-02-25 15:23:04] Fitting variants for purity 0.31, tumor ploidy 1.90 and contamination 0.01.
INFO [2021-02-25 15:23:25] Fitting variants for purity 0.33, tumor ploidy 1.90 and contamination 0.01.
INFO [2021-02-25 15:23:48] Fitting variants for purity 0.34, tumor ploidy 1.90 and contamination 0.01.
INFO [2021-02-25 15:24:11] Fitting variants for purity 0.35, tumor ploidy 1.90 and contamination 0.01.
INFO [2021-02-25 15:24:33] Fitting variants for purity 0.36, tumor ploidy 1.90 and contamination 0.01.
INFO [2021-02-25 15:24:56] Optimized purity: 0.28
INFO [2021-02-25 15:24:56] Fitting variants with beta model for local optimum 15/17...
INFO [2021-02-25 15:24:57] Fitting variants for purity 0.62, tumor ploidy 2.95 and contamination 0.01.
INFO [2021-02-25 15:25:20] Fitting variants for purity 0.58, tumor ploidy 2.95 and contamination 0.01.
INFO [2021-02-25 15:25:44] Fitting variants for purity 0.59, tumor ploidy 2.95 and contamination 0.01.
INFO [2021-02-25 15:26:06] Fitting variants for purity 0.60, tumor ploidy 2.95 and contamination 0.01.
INFO [2021-02-25 15:26:26] Fitting variants for purity 0.61, tumor ploidy 2.95 and contamination 0.01.
INFO [2021-02-25 15:26:47] Fitting variants for purity 0.63, tumor ploidy 2.95 and contamination 0.01.
INFO [2021-02-25 15:27:08] Fitting variants for purity 0.64, tumor ploidy 2.95 and contamination 0.01.
INFO [2021-02-25 15:27:28] Fitting variants for purity 0.65, tumor ploidy 2.95 and contamination 0.01.
INFO [2021-02-25 15:27:49] Fitting variants for purity 0.66, tumor ploidy 2.95 and contamination 0.01.
INFO [2021-02-25 15:28:10] Optimized purity: 0.58
INFO [2021-02-25 15:28:10] Fitting variants with beta model for local optimum 16/17...
INFO [2021-02-25 15:28:11] Fitting variants for purity 0.59, tumor ploidy 1.97 and contamination 0.01.
INFO [2021-02-25 15:28:32] Fitting variants for purity 0.55, tumor ploidy 1.97 and contamination 0.01.
INFO [2021-02-25 15:28:52] Fitting variants for purity 0.56, tumor ploidy 1.97 and contamination 0.01.
INFO [2021-02-25 15:29:12] Fitting variants for purity 0.57, tumor ploidy 1.97 and contamination 0.01.
INFO [2021-02-25 15:29:32] Fitting variants for purity 0.58, tumor ploidy 1.97 and contamination 0.01.
INFO [2021-02-25 15:29:51] Fitting variants for purity 0.60, tumor ploidy 1.97 and contamination 0.01.
INFO [2021-02-25 15:30:10] Fitting variants for purity 0.61, tumor ploidy 1.97 and contamination 0.01.
INFO [2021-02-25 15:30:30] Fitting variants for purity 0.62, tumor ploidy 1.97 and contamination 0.01.
INFO [2021-02-25 15:30:51] Fitting variants for purity 0.63, tumor ploidy 1.97 and contamination 0.01.
INFO [2021-02-25 15:31:11] Optimized purity: 0.55
INFO [2021-02-25 15:31:11] Done.
INFO [2021-02-25 15:31:11] ------------------------------------------------------------
Warning message : 
In .checkSeg(seg, sampleid, model.homozygous, verbose): 
  NA was generated by forced transformation
INFO [2021-02-25 15:31:13] Generating output files...

Thank you