Can you please provide
a) GATK version used - gatk 4.1.6.0

.(snapshot and seg file attached)

Hello

how can i remove the chr_Un* regions in my copy number plots?
My model final segment file doesn't contain chr_Un fields.

`

sa@sa-mbp ~ % less 8c444e42-2836-489c-8d01-aa8bb6842ec1_CNVSomaticPairWorkflow_8fc68c47-e081-4fde-ba35-69594b5a09f9_call-ModelSegmentsTumor_out_353.hg38.modelFinal.seg | grep -v "^@" | head   

CONTIG START END NUM_POINTS_COPY_RATIO NUM_POINTS_ALLELE_FRACTION LOG2_COPY_RATIO_POSTERIOR_10 LOG2_COPY_RATIO_POSTERIOR_50 LOG2_COPY_RATIO_POSTERIOR_90 MINOR_ALLELE_FRACTION_POSTERIOR_10 MINOR_ALLELE_FRACTION_POSTERIOR_50 MINOR_ALLELE_FRACTION_POSTERIOR_90

chr1 14371 248937297 28109 2392 0.025404 0.035754 0.042479 0.489942 0.496955 0.499533

chr2 667105 15947289 839 95 0.029410 0.037730 0.046698 0.468089 0.488506 0.497851

chr2 16549224 89245753 6359 523 -0.230558 -0.227346 -0.221495 0.384030 0.393627 0.400412

chr2 89268176 89268698 1 0 -29.904706 -29.622139 -29.383854 NaN NaN NaN

chr2 89851557 169206858 5459 339 -0.223373 -0.219118 -0.213770 0.382595 0.391044 0.399919

chr2 169206859 241508948 7952 645 0.035662 0.047521 0.054743 0.487259 0.492968 0.498885

chr3 2238744 89482096 8140 595 -0.241909 -0.231896 -0.229027 0.383767 0.391069 0.400615

chr3 90202096 198177415 8257 782 0.039150 0.045634 0.050130 0.476704 0.493682 0.499261

chr4 1071379 8962092 1229 92 -0.194266 -0.182421 -0.174564 0.436532 0.443561 0.457972

sa@sa-mbp ~ % less 8c444e42-2836-489c-8d01-aa8bb6842ec1_CNVSomaticPairWorkflow_8fc68c47-e081-4fde-ba35-69594b5a09f9_call-ModelSegmentsTumor_out_353.hg38.modelFinal.seg | grep -v "^@" | tail   

chr19 280762 47981260 11936 664 0.040364 0.047642 0.056114 0.474418 0.494501 0.498649

chr19 47991630 58370149 3301 234 0.255312 0.261823 0.270161 0.408744 0.419721 0.428110

chr20 478289 48638171 5009 370 0.023828 0.033652 0.043369 0.482503 0.495500 0.499050

chr20 48639522 64328210 1732 139 0.212166 0.222440 0.230756 0.414498 0.421943 0.429038

chr21 9026773 40369500 1750 168 0.048497 0.059627 0.072271 0.475200 0.491640 0.499016

chr21 40692425 41508499 88 8 0.895854 0.920153 0.938943 0.288503 0.301085 0.323544

chr21 41712533 46267397 854 82 0.112577 0.122776 0.138301 0.459592 0.475863 0.496405

chr22 15527854 50799370 5399 340 0.054828 0.062518 0.070282 0.482935 0.492056 0.498594

chrX 283856 156028226 8918 344 0.043786 0.048812 0.054462 0.474132 0.488578 0.497314

chrY 11332178 11396756 3 0 -0.281178 -0.143497 -0.004919 NaN NaN NaN

`

b) Exact GATK commands used 

`Running: java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx6000m -jar /root/gatk.jar PlotModeledSegments --denoised-copy-ratios /cromwell_root/fc-ac4624cb-a8fc-49a2-b071-d3a0ae799418/8c444e42-2836-489c-8d01-aa8bb6842ec1/CNVSomaticPairWorkflow/8fc68c47-e081-4fde-ba35-69594b5a09f9/call-DenoiseReadCountsTumor/353.hg38.denoisedCR.tsv --allelic-counts /cromwell_root/fc-ac4624cb-a8fc-49a2-b071-d3a0ae799418/8c444e42-2836-489c-8d01-aa8bb6842ec1/CNVSomaticPairWorkflow/8fc68c47-e081-4fde-ba35-69594b5a09f9/call-ModelSegmentsTumor/out/353.hg38.hets.tsv --segments /cromwell_root/fc-ac4624cb-a8fc-49a2-b071-d3a0ae799418/8c444e42-2836-489c-8d01-aa8bb6842ec1/CNVSomaticPairWorkflow/8fc68c47-e081-4fde-ba35-69594b5a09f9/call-ModelSegmentsTumor/out/353.hg38.modelFinal.seg --sequence-dictionary /cromwell_root/gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.dict --minimum-contig-length 1000000 --output out --output-prefix 353.hg38`

c) The entire error log if applicable

`

2020/07/28 02:33:29 Starting container setup.
2020/07/28 02:33:34 Done container setup.
2020/07/28 02:33:35 Starting localization.
2020/07/28 02:33:42 Localization script execution started...
2020/07/28 02:33:42 Localizing input gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.dict -> /cromwell_root/gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.dict
2020/07/28 02:33:43 Localizing input gs://fc-ac4624cb-a8fc-49a2-b071-d3a0ae799418/8c444e42-2836-489c-8d01-aa8bb6842ec1/CNVSomaticPairWorkflow/8fc68c47-e081-4fde-ba35-69594b5a09f9/call-PlotModeledSegmentsTumor/script -> /cromwell_root/script
2020/07/28 02:33:44 Localizing input gs://fc-ac4624cb-a8fc-49a2-b071-d3a0ae799418/8c444e42-2836-489c-8d01-aa8bb6842ec1/CNVSomaticPairWorkflow/8fc68c47-e081-4fde-ba35-69594b5a09f9/call-DenoiseReadCountsTumor/353.hg38.denoisedCR.tsv -> /cromwell_root/fc-ac4624cb-a8fc-49a2-b071-d3a0ae799418/8c444e42-2836-489c-8d01-aa8bb6842ec1/CNVSomaticPairWorkflow/8fc68c47-e081-4fde-ba35-69594b5a09f9/call-DenoiseReadCountsTumor/353.hg38.denoisedCR.tsv
2020/07/28 02:33:45 Localizing input gs://fc-ac4624cb-a8fc-49a2-b071-d3a0ae799418/8c444e42-2836-489c-8d01-aa8bb6842ec1/CNVSomaticPairWorkflow/8fc68c47-e081-4fde-ba35-69594b5a09f9/call-ModelSegmentsTumor/out/353.hg38.hets.tsv -> /cromwell_root/fc-ac4624cb-a8fc-49a2-b071-d3a0ae799418/8c444e42-2836-489c-8d01-aa8bb6842ec1/CNVSomaticPairWorkflow/8fc68c47-e081-4fde-ba35-69594b5a09f9/call-ModelSegmentsTumor/out/353.hg38.hets.tsv
2020/07/28 02:33:47 Localizing input gs://fc-ac4624cb-a8fc-49a2-b071-d3a0ae799418/8c444e42-2836-489c-8d01-aa8bb6842ec1/CNVSomaticPairWorkflow/8fc68c47-e081-4fde-ba35-69594b5a09f9/call-ModelSegmentsTumor/out/353.hg38.modelFinal.seg -> /cromwell_root/fc-ac4624cb-a8fc-49a2-b071-d3a0ae799418/8c444e42-2836-489c-8d01-aa8bb6842ec1/CNVSomaticPairWorkflow/8fc68c47-e081-4fde-ba35-69594b5a09f9/call-ModelSegmentsTumor/out/353.hg38.modelFinal.seg
Copying gs://fc-ac4624cb-a8fc-49a2-b071-d3a0ae799418/8c444e42-2836-489c-8d01-aa8bb6842ec1/CNVSomaticPairWorkflow/8fc68c47-e081-4fde-ba35-69594b5a09f9/call-ModelSegmentsTumor/out/353.hg38.modelFinal.seg...
/ [0/1 files][    0.0 B/590.2 KiB]   0% Done                                    
/ [1/1 files][590.2 KiB/590.2 KiB] 100% Done                                    
Operation completed over 1 objects/590.2 KiB.                                    
2020/07/28 02:33:49 Localization script execution complete.
2020/07/28 02:33:52 Done localization.
2020/07/28 02:33:53 Running user action: docker run -v /mnt/local-disk:/cromwell_root --entrypoint= us.gcr.io/broad-gatk/gatk@sha256:2c0e2ba20c9beb58842ba2149efc29059bc52a5178ce05debf0f38238c0bde86 /bin/bash /cromwell_root/script
Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/cromwell_root/tmp.fb074081
02:33:57.924 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk/gatk-package-4.1.6.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
02:33:58.235 INFO  PlotModeledSegments - ------------------------------------------------------------
02:33:58.236 INFO  PlotModeledSegments - The Genome Analysis Toolkit (GATK) v4.1.6.0
02:33:58.236 INFO  PlotModeledSegments - For support and documentation go to https://software.broadinstitute.org/gatk/
02:33:58.237 INFO  PlotModeledSegments - Executing as root@ca5cc1d6b4e5 on Linux v4.19.112+ amd64
02:33:58.237 INFO  PlotModeledSegments - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_212-8u212-b03-0ubuntu1.16.04.1-b03
02:33:58.237 INFO  PlotModeledSegments - Start Date/Time: July 28, 2020 2:33:57 AM UTC
02:33:58.237 INFO  PlotModeledSegments - ------------------------------------------------------------
02:33:58.237 INFO  PlotModeledSegments - ------------------------------------------------------------
02:33:58.240 INFO  PlotModeledSegments - HTSJDK Version: 2.21.2
02:33:58.240 INFO  PlotModeledSegments - Picard Version: 2.21.9
02:33:58.240 INFO  PlotModeledSegments - HTSJDK Defaults.COMPRESSION_LEVEL : 2
02:33:58.240 INFO  PlotModeledSegments - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
02:33:58.245 INFO  PlotModeledSegments - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
02:33:58.246 INFO  PlotModeledSegments - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
02:33:58.246 INFO  PlotModeledSegments - Deflater: IntelDeflater
02:33:58.246 INFO  PlotModeledSegments - Inflater: IntelInflater
02:33:58.246 INFO  PlotModeledSegments - GCS max retries/reopens: 20
02:33:58.246 INFO  PlotModeledSegments - Requester pays: disabled
02:33:58.246 INFO  PlotModeledSegments - Initializing engine
02:33:58.247 INFO  PlotModeledSegments - Done initializing engine
02:33:58.265 INFO  PlotModeledSegments - Reading and validating input files...
02:34:00.585 INFO  PlotModeledSegments - Contigs above length threshold: {chr1=248956422, chr2=242193529, chr3=198295559, chr4=190214555, chr5=181538259, chr6=170805979, chr7=159345973, chr8=145138636, chr9=138394717, chr10=133797422, chr11=135086622, chr12=133275309, chr13=114364328, chr14=107043718, chr15=101991189, chr16=90338345, chr17=83257441, chr18=80373285, chr19=58617616, chr20=64444167, chr21=46709983, chr22=50818468, chrX=156040895, chrY=57227415, chr16_KI270728v1_random=1872759, chr5_GL339449v2_alt=1612928, chr6_GL000250v2_alt=4672374, chr7_KI270803v1_alt=1111570, chr14_KI270847v1_alt=1511111, chr14_KI270846v1_alt=1351393, chr16_KI270853v1_alt=2659700, chr17_KI270857v1_alt=2877074, chr17_GL000258v2_alt=1821992, chr5_KI270897v1_alt=1144418, chr6_GL000251v2_alt=4795265, chr15_KI270905v1_alt=5161414, chr17_KI270908v1_alt=1423190, chr6_GL000252v2_alt=4604811, chr19_GL949748v2_alt=1064304, chr6_GL000253v2_alt=4677643, chr19_GL949749v2_alt=1091841, chr6_GL000254v2_alt=4827813, chr19_GL949750v2_alt=1066390, chr6_GL000255v2_alt=4606388, chr19_GL949751v2_alt=1002683, chr6_GL000256v2_alt=4929269, chr19_KI270938v1_alt=1066800}
02:34:00.763 INFO  PlotModeledSegments - Writing plot to /cromwell_root/out/353.hg38.modeled.png...
02:34:02.224 INFO  PlotModeledSegments - PlotModeledSegments complete.
02:34:02.224 INFO  PlotModeledSegments - Shutting down engine
[July 28, 2020 2:34:02 AM UTC] org.broadinstitute.hellbender.tools.copynumber.plotting.PlotModeledSegments done. Elapsed time: 0.07 minutes.
Runtime.totalMemory()=311951360
Using GATK jar /root/gatk.jar defined in environment variable GATK_LOCAL_JAR
Running:
    java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx6000m -jar /root/gatk.jar PlotModeledSegments --denoised-copy-ratios /cromwell_root/fc-ac4624cb-a8fc-49a2-b071-d3a0ae799418/8c444e42-2836-489c-8d01-aa8bb6842ec1/CNVSomaticPairWorkflow/8fc68c47-e081-4fde-ba35-69594b5a09f9/call-DenoiseReadCountsTumor/353.hg38.denoisedCR.tsv --allelic-counts /cromwell_root/fc-ac4624cb-a8fc-49a2-b071-d3a0ae799418/8c444e42-2836-489c-8d01-aa8bb6842ec1/CNVSomaticPairWorkflow/8fc68c47-e081-4fde-ba35-69594b5a09f9/call-ModelSegmentsTumor/out/353.hg38.hets.tsv --segments /cromwell_root/fc-ac4624cb-a8fc-49a2-b071-d3a0ae799418/8c444e42-2836-489c-8d01-aa8bb6842ec1/CNVSomaticPairWorkflow/8fc68c47-e081-4fde-ba35-69594b5a09f9/call-ModelSegmentsTumor/out/353.hg38.modelFinal.seg --sequence-dictionary /cromwell_root/gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.dict --minimum-contig-length 1000000 --output out --output-prefix 353.hg38
2020/07/28 02:34:03 Starting delocalization.
2020/07/28 02:34:04 Delocalization script execution started...
2020/07/28 02:34:04 Delocalizing output /cromwell_root/memory_retry_rc -> gs://fc-ac4624cb-a8fc-49a2-b071-d3a0ae799418/8c444e42-2836-489c-8d01-aa8bb6842ec1/CNVSomaticPairWorkflow/8fc68c47-e081-4fde-ba35-69594b5a09f9/call-PlotModeledSegmentsTumor/memory_retry_rc
2020/07/28 02:34:04 Delocalizing output /cromwell_root/rc -> gs://fc-ac4624cb-a8fc-49a2-b071-d3a0ae799418/8c444e42-2836-489c-8d01-aa8bb6842ec1/CNVSomaticPairWorkflow/8fc68c47-e081-4fde-ba35-69594b5a09f9/call-PlotModeledSegmentsTumor/rc
2020/07/28 02:34:06 Delocalizing output /cromwell_root/stdout -> gs://fc-ac4624cb-a8fc-49a2-b071-d3a0ae799418/8c444e42-2836-489c-8d01-aa8bb6842ec1/CNVSomaticPairWorkflow/8fc68c47-e081-4fde-ba35-69594b5a09f9/call-PlotModeledSegmentsTumor/stdout
2020/07/28 02:34:07 Delocalizing output /cromwell_root/stderr -> gs://fc-ac4624cb-a8fc-49a2-b071-d3a0ae799418/8c444e42-2836-489c-8d01-aa8bb6842ec1/CNVSomaticPairWorkflow/8fc68c47-e081-4fde-ba35-69594b5a09f9/call-PlotModeledSegmentsTumor/stderr
2020/07/28 02:34:08 Delocalizing output /cromwell_root/out/353.hg38.modeled.png -> gs://fc-ac4624cb-a8fc-49a2-b071-d3a0ae799418/8c444e42-2836-489c-8d01-aa8bb6842ec1/CNVSomaticPairWorkflow/8fc68c47-e081-4fde-ba35-69594b5a09f9/call-PlotModeledSegmentsTumor/out/353.hg38.modeled.png
2020/07/28 02:34:09 Delocalization script execution complete.
2020/07/28 02:34:10 Done delocalization.

`

Thanks
Sam