WARN MinimalGenotypingEngine - Attempting to genotype more than 50 alleles. Site will be skipped at location chr11:294512
Dear GATK,
Question; any suggestions on how to resolve this?
i run `GenoytypeGVCFs ( gatk/4.1.6.0)` on a cohort of cancer patients but run into this warning message.
`08:19:05.902 WARN MinimalGenotypingEngine - Attempting to genotype more than 50 alleles. Site will be skipped at location chr11:294512`
###exact command used for GenotypeGVCFs, gatk/4.1.6.0
$ gatk --java-options "-Xmx22g -Xms22g" GenotypeGVCFs \
-R /sc/hydra/projects/canan/colon_cancer10312019/intervals_preprocessing/Homo_sapiens_assembly38.fasta \
-V Colon_cohort_combined.g.vcf.gz \
-O output.JointGenotype.Germline41samples.colon.vcf.gz \
--intervals Exome-Agilent_V6_UTR.interval_list \
--tmp-dir /sc/hydra/projects/canan/colon_cancer10312019/joint_calling_colon \
--dbsnp hg38_resources/Homo_sapiens_assembly38.dbsnp138.vcf
### log file after running GenotypeGVCFs
07:56:07.856 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/hpc/packages/minerva-centos7/gatk/4.1.6.0/gatk-4.1.6.0/gatk-package-4.1.6.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
07:56:08.041 INFO GenotypeGVCFs - ------------------------------------------------------------
07:56:08.042 INFO GenotypeGVCFs - The Genome Analysis Toolkit (GATK) v4.1.6.0
07:56:08.042 INFO GenotypeGVCFs - For support and documentation go to https://software.broadinstitute.org/gatk/
07:56:08.042 INFO GenotypeGVCFs - Executing as ahunos01@lh03c01 on Linux v3.10.0-957.el7.x86_64 amd64
07:56:08.042 INFO GenotypeGVCFs - Java runtime: Java HotSpot(TM) 64-Bit Server VM v1.8.0_211-b12
07:56:08.042 INFO GenotypeGVCFs - Start Date/Time: April 4, 2020 7:56:07 AM EDT
07:56:08.042 INFO GenotypeGVCFs - ------------------------------------------------------------
07:56:08.042 INFO GenotypeGVCFs - ------------------------------------------------------------
07:56:08.042 INFO GenotypeGVCFs - HTSJDK Version: 2.21.2
07:56:08.043 INFO GenotypeGVCFs - Picard Version: 2.21.9
07:56:08.043 INFO GenotypeGVCFs - HTSJDK Defaults.COMPRESSION_LEVEL : 2
07:56:08.043 INFO GenotypeGVCFs - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
07:56:08.043 INFO GenotypeGVCFs - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
07:56:08.043 INFO GenotypeGVCFs - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
07:56:08.043 INFO GenotypeGVCFs - Deflater: IntelDeflater
07:56:08.043 INFO GenotypeGVCFs - Inflater: IntelInflater
07:56:08.043 INFO GenotypeGVCFs - GCS max retries/reopens: 20
07:56:08.043 INFO GenotypeGVCFs - Requester pays: disabled
07:56:08.043 INFO GenotypeGVCFs - Initializing engine
07:56:08.409 INFO FeatureManager - Using codec VCFCodec to read file file:///sc/hydra/projects/canan/colon_cancer10312019/joint_calling_colon/hg38_resources/Homo_sapiens_assembly38.dbsnp138.vcf
07:56:08.579 INFO FeatureManager - Using codec VCFCodec to read file file:///sc/hydra/projects/canan/colon_cancer10312019/joint_calling_colon/Colon_cohort_combined.g.vcf.gz
07:56:08.773 INFO FeatureManager - Using codec IntervalListCodec to read file file:///sc/hydra/projects/canan/colon_cancer10312019/joint_calling_colon/Exome-Agilent_V6_UTR.interval_list
07:56:10.082 INFO IntervalArgumentCollection - Processing 90463420 bp from intervals
07:56:10.171 INFO GenotypeGVCFs - Done initializing engine
07:56:10.276 INFO ProgressMeter - Starting traversal
07:56:10.276 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
07:56:20.313 INFO ProgressMeter - chr1:2228800 0.2 95000 567898.8
07:56:30.318 INFO ProgressMeter - chr1:9723870 0.3 217000 649668.2
07:56:40.411 INFO ProgressMeter - chr1:15584550 0.5 351000 698878.3
07:56:50.477 INFO ProgressMeter - chr1:20148644 0.7 476000 710447.8
07:57:00.518 INFO ProgressMeter - chr1:25568526 0.8 611000 729668.4
07:57:10.528 INFO ProgressMeter - chr1:31433864 1.0 751000 747859.0
07:57:20.552 INFO ProgressMeter - chr1:36322684 1.2 891000 760714.9
07:57:30.556 INFO ProgressMeter - chr1:42767481 1.3 1036000 774290.0
07:57:40.596 INFO ProgressMeter - chr1:46665627 1.5 1165000 773915.0
07:57:50.658 INFO ProgressMeter - chr1:55138741 1.7 1309000 782411.2
07:58:00.658 INFO ProgressMeter - chr1:74471728 1.8 1460000 793607.7
07:58:10.659 INFO ProgressMeter - chr1:92268130 2.0 1611000 802937.3
07:58:20.704 INFO ProgressMeter - chr1:109297693 2.2 1753000 806421.9
07:58:30.758 INFO ProgressMeter - chr1:114926408 2.3 1889000 806793.8
07:58:40.760 INFO ProgressMeter - chr1:147619504 2.5 2023000 806597.4
07:58:50.796 INFO ProgressMeter - chr1:151714659 2.7 2145000 801769.2
07:59:00.849 INFO ProgressMeter - chr1:155128220 2.8 2265000 796726.3
07:59:10.851 INFO ProgressMeter - chr1:157834419 3.0 2389000 793797.6
07:59:20.869 INFO ProgressMeter - chr1:161631153 3.2 2520000 793313.5
07:59:30.923 INFO ProgressMeter - chr1:173530145 3.3 2669000 798118.1
07:59:40.942 INFO ProgressMeter - chr1:183249742 3.5 2818000 802597.5
07:59:51.036 INFO ProgressMeter - chr1:201209693 3.7 2965000 805852.5
08:00:01.103 INFO ProgressMeter - chr1:205115968 3.8 3100000 805798.3
08:00:11.122 INFO ProgressMeter - chr1:212353127 4.0 3240000 807154.8
08:00:21.172 INFO ProgressMeter - chr1:226548791 4.2 3392000 811176.0
08:00:31.190 INFO ProgressMeter - chr1:235160855 4.3 3534000 812681.6
08:00:41.237 INFO ProgressMeter - chr2:264808 4.5 3679000 814656.0
08:00:51.308 INFO ProgressMeter - chr2:21032277 4.7 3822000 815992.5
08:01:01.423 INFO ProgressMeter - chr2:27503395 4.9 3953000 814640.0
08:01:11.449 INFO ProgressMeter - chr2:38960489 5.0 4095000 815810.2
08:01:21.456 INFO ProgressMeter - chr2:55026559 5.2 4240000 817533.3
08:01:31.485 INFO ProgressMeter - chr2:71078861 5.4 4386000 819279.7
08:01:41.526 INFO ProgressMeter - chr2:85324751 5.5 4522000 819079.2
08:01:51.530 INFO ProgressMeter - chr2:96811119 5.7 4658000 818979.4
08:02:01.567 INFO ProgressMeter - chr2:109502801 5.9 4803000 820345.5
08:02:11.570 INFO ProgressMeter - chr2:127582494 6.0 4948000 821713.1
08:02:21.625 INFO ProgressMeter - chr2:150468533 6.2 5093000 822891.7
08:02:31.645 INFO ProgressMeter - chr2:165899823 6.4 5235000 823611.8
08:02:41.650 INFO ProgressMeter - chr2:177232690 6.5 5381000 824939.8
08:02:51.682 INFO ProgressMeter - chr2:184598577 6.7 5501000 822259.8
08:03:01.737 INFO ProgressMeter - chr2:200642701 6.9 5648000 823601.8
08:03:11.803 INFO ProgressMeter - chr2:210432135 7.0 5797000 825142.9
08:03:21.910 INFO ProgressMeter - chr2:219223755 7.2 5931000 824448.5
08:03:31.920 INFO ProgressMeter - chr2:230403504 7.4 6061000 823425.3
08:03:41.926 INFO ProgressMeter - chr2:238168114 7.5 6202000 823912.3
08:03:51.959 INFO ProgressMeter - chr3:8532511 7.7 6337000 823552.1
08:04:02.012 INFO ProgressMeter - chr3:14447422 7.9 6473000 823299.5
08:04:12.068 INFO ProgressMeter - chr3:33385759 8.0 6623000 824795.8
08:04:22.120 INFO ProgressMeter - chr3:42745724 8.2 6766000 825383.7
08:04:32.147 INFO ProgressMeter - chr3:48419663 8.4 6910000 826108.7
08:04:42.175 INFO ProgressMeter - chr3:49929714 8.5 7022000 823053.0
08:04:52.189 INFO ProgressMeter - chr3:52651685 8.7 7145000 821401.3
08:05:02.208 INFO ProgressMeter - chr3:64594479 8.9 7284000 821608.8
08:05:12.210 INFO ProgressMeter - chr3:100335066 9.0 7427000 822278.8
08:05:22.239 INFO ProgressMeter - chr3:116445013 9.2 7579000 823859.6
08:05:32.295 INFO ProgressMeter - chr3:126007233 9.4 7730000 825239.0
08:05:42.317 INFO ProgressMeter - chr3:133885762 9.5 7877000 826199.5
08:05:52.334 INFO ProgressMeter - chr3:149520014 9.7 8030000 827752.6
08:06:02.380 INFO ProgressMeter - chr3:170170842 9.9 8182000 829111.1
08:06:12.422 INFO ProgressMeter - chr3:184388927 10.0 8319000 828935.2
08:06:22.470 INFO ProgressMeter - chr3:196782706 10.2 8465000 829639.0
08:06:32.484 INFO ProgressMeter - chr4:3140740 10.4 8598000 829111.8
08:06:42.540 INFO ProgressMeter - chr4:15537023 10.5 8740000 829400.4
08:06:52.544 INFO ProgressMeter - chr4:41935197 10.7 8888000 830308.9
08:07:02.610 INFO ProgressMeter - chr4:67740218 10.9 9036000 831108.0
08:07:12.674 INFO ProgressMeter - chr4:78871841 11.0 9188000 832248.9
08:07:22.706 INFO ProgressMeter - chr4:99219507 11.2 9339000 833306.1
08:07:32.759 INFO ProgressMeter - chr4:118723565 11.4 9490000 834306.5
08:07:42.797 INFO ProgressMeter - chr4:144734885 11.5 9643000 835469.2
08:07:52.805 INFO ProgressMeter - chr4:168220718 11.7 9795000 836549.1
08:08:02.859 INFO ProgressMeter - chr5:850961 11.9 9937000 836702.5
08:08:12.887 INFO ProgressMeter - chr5:33463810 12.0 10082000 837130.9
08:08:22.946 INFO ProgressMeter - chr5:52865099 12.2 10228000 837594.0
08:08:33.018 INFO ProgressMeter - chr5:70925140 12.4 10376000 838192.6
08:08:43.044 INFO ProgressMeter - chr5:86617913 12.5 10527000 839063.3
08:08:53.101 INFO ProgressMeter - chr5:112868319 12.7 10676000 839720.8
08:09:03.207 INFO ProgressMeter - chr5:132708752 12.9 10832000 840851.3
08:09:13.299 INFO ProgressMeter - chr5:140372903 13.1 10972000 840741.6
08:09:23.363 INFO ProgressMeter - chr5:148124962 13.2 11100000 839756.5
08:09:33.397 INFO ProgressMeter - chr5:154055607 13.4 11241000 839798.7
08:09:43.443 INFO ProgressMeter - chr5:172156942 13.6 11395000 840786.7
08:09:53.463 INFO ProgressMeter - chr5:179589736 13.7 11534000 840683.8
08:10:03.520 INFO ProgressMeter - chr6:9750219 13.9 11673000 840546.1
08:10:13.547 INFO ProgressMeter - chr6:26410974 14.1 11814000 840583.9
08:10:23.590 INFO ProgressMeter - chr6:35346970 14.2 11947000 840042.5
08:10:33.650 INFO ProgressMeter - chr6:41792839 14.4 12086000 839914.1
08:10:43.689 INFO ProgressMeter - chr6:45912546 14.6 12209000 838709.8
08:10:53.689 INFO ProgressMeter - chr6:65303580 14.7 12354000 839063.9
08:11:03.757 INFO ProgressMeter - chr6:87530934 14.9 12503000 839614.9
08:11:13.764 INFO ProgressMeter - chr6:109443846 15.1 12652000 840210.4
08:11:23.770 INFO ProgressMeter - chr6:126038654 15.2 12801000 840793.7
08:11:33.797 INFO ProgressMeter - chr6:143339705 15.4 12955000 841670.1
08:11:43.841 INFO ProgressMeter - chr6:157873154 15.6 13106000 842319.5
08:11:53.896 INFO ProgressMeter - chr7:754893 15.7 13242000 841991.5
08:12:03.944 INFO ProgressMeter - chr7:6781247 15.9 13376000 841550.7
08:12:13.997 INFO ProgressMeter - chr7:27141274 16.1 13526000 842110.9
08:12:23.998 INFO ProgressMeter - chr7:42911726 16.2 13679000 842889.4
08:12:34.006 INFO ProgressMeter - chr7:55191930 16.4 13820000 842914.2
08:12:44.047 INFO ProgressMeter - chr7:76000332 16.6 13955000 842548.2
08:12:54.141 INFO ProgressMeter - chr7:92611950 16.7 14106000 843101.4
08:13:04.239 INFO ProgressMeter - chr7:100317043 16.9 14242000 842752.6
08:13:14.276 INFO ProgressMeter - chr7:105113778 17.1 14365000 841699.2
08:13:24.341 INFO ProgressMeter - chr7:123663496 17.2 14523000 842674.3
08:13:34.398 INFO ProgressMeter - chr7:135388520 17.4 14667000 842832.5
08:13:44.426 INFO ProgressMeter - chr7:144284592 17.6 14815000 843238.6
08:13:54.493 INFO ProgressMeter - chr7:152108094 17.7 14935000 842027.5
08:14:04.545 INFO ProgressMeter - chr8:9781617 17.9 15076000 842023.7
08:14:14.560 INFO ProgressMeter - chr8:22109196 18.1 15214000 841882.8
08:14:24.665 INFO ProgressMeter - chr8:28385281 18.2 15351000 841620.3
08:14:34.672 INFO ProgressMeter - chr8:41717637 18.4 15499000 842034.9
08:14:44.728 INFO ProgressMeter - chr8:66460460 18.6 15652000 842674.2
08:14:54.795 INFO ProgressMeter - chr8:87871251 18.7 15809000 843507.3
08:15:04.861 INFO ProgressMeter - chr8:103432650 18.9 15960000 844009.0
08:15:14.900 INFO ProgressMeter - chr8:129749464 19.1 16113000 844626.7
08:15:24.977 INFO ProgressMeter - chr8:143926913 19.2 16263000 845049.9
08:15:35.014 INFO ProgressMeter - chr9:4707650 19.4 16390000 844310.1
08:15:45.053 INFO ProgressMeter - chr9:27061077 19.6 16539000 844705.0
08:15:55.108 INFO ProgressMeter - chr9:35826064 19.7 16671000 844221.0
08:16:05.149 INFO ProgressMeter - chr9:76704941 19.9 16823000 844759.9
08:16:15.208 INFO ProgressMeter - chr9:93649167 20.1 16967000 844877.6
08:16:25.218 INFO ProgressMeter - chr9:104861445 20.2 17116000 845274.9
08:16:35.311 INFO ProgressMeter - chr9:114346080 20.4 17262000 845462.2
08:16:45.322 INFO ProgressMeter - chr9:125066009 20.6 17411000 845847.0
08:16:55.327 INFO ProgressMeter - chr9:129098176 20.8 17549000 845700.3
08:17:05.353 INFO ProgressMeter - chr9:133467795 20.9 17684000 845398.3
08:17:15.377 INFO ProgressMeter - chr9:137039966 21.1 17805000 844438.5
08:17:25.409 INFO ProgressMeter - chr10:7285564 21.3 17936000 843959.0
08:17:35.413 INFO ProgressMeter - chr10:23318710 21.4 18085000 844345.8
08:17:45.482 INFO ProgressMeter - chr10:45003832 21.6 18228000 844406.2
08:17:55.536 INFO ProgressMeter - chr10:63621240 21.8 18376000 844705.3
08:18:05.558 INFO ProgressMeter - chr10:73425260 21.9 18517000 844701.0
08:18:15.580 INFO ProgressMeter - chr10:87925440 22.1 18656000 844606.2
08:18:25.597 INFO ProgressMeter - chr10:97030705 22.3 18811000 845235.0
08:18:35.646 INFO ProgressMeter - chr10:102141412 22.4 18951000 845165.3
08:18:45.682 INFO ProgressMeter - chr10:113553048 22.6 19085000 844839.1
08:18:55.713 INFO ProgressMeter - chr10:123666529 22.8 19227000 844872.4
08:19:05.788 INFO ProgressMeter - chr11:290494 22.9 19364000 844660.6
08:19:05.902 WARN MinimalGenotypingEngine - Attempting to genotype more than 50 alleles. Site will be skipped at location chr11:294512
08:19:15.827 INFO ProgressMeter - chr11:3827388 23.1 19488000 843909.8
08:19:25.835 INFO ProgressMeter - chr11:8268477 23.3 19628000 843876.9
08:19:35.902 INFO ProgressMeter - chr11:17611250 23.4 19774000 844065.2
08:19:45.921 INFO ProgressMeter - chr11:33551005 23.6 19919000 844237.1
08:19:55.944 INFO ProgressMeter - chr11:47161835 23.8 20061000 844277.9
08:20:05.973 INFO ProgressMeter - chr11:59575357 23.9 20201000 844231.1
08:20:15.990 INFO ProgressMeter - chr11:62665661 24.1 20326000 843569.3
08:20:25.990 INFO ProgressMeter - chr11:65114629 24.3 20454000 843050.2
08:20:36.021 INFO ProgressMeter - chr11:66685715 24.4 20573000 842151.9
08:20:46.034 INFO ProgressMeter - chr11:72013534 24.6 20703000 841723.4
08:20:56.038 INFO ProgressMeter - chr11:77175061 24.8 20848000 841911.4
08:21:06.068 INFO ProgressMeter - chr11:94476477 24.9 21000000 842363.1
08:21:16.074 INFO ProgressMeter - chr11:111456583 25.1 21149000 842702.7
08:21:26.075 INFO ProgressMeter - chr11:118210809 25.3 21283000 842446.8
08:21:36.114 INFO ProgressMeter - chr11:123525904 25.4 21419000 842251.9
08:21:46.136 INFO ProgressMeter - chr11:132435176 25.6 21559000 842225.2
08:21:56.140 INFO ProgressMeter - chr12:6313192 25.8 21698000 842169.8
08:22:06.175 INFO ProgressMeter - chr12:8946431 25.9 21814000 841211.4
08:22:16.236 INFO ProgressMeter - chr12:21438041 26.1 21958000 841324.2
08:22:26.283 INFO ProgressMeter - chr12:39871926 26.3 22102000 841443.0
08:22:36.302 INFO ProgressMeter - chr12:48716820 26.4 22225000 840780.7
08:22:46.351 INFO ProgressMeter - chr12:51354179 26.6 22349000 840148.5
08:22:56.367 INFO ProgressMeter - chr12:54002835 26.8 22476000 839653.5
08:23:06.369 INFO ProgressMeter - chr12:56588850 26.9 22597000 838949.2
08:23:16.419 INFO ProgressMeter - chr12:63780454 27.1 22714000 838081.3
08:23:26.475 INFO ProgressMeter - chr12:76764715 27.3 22863000 838394.4
08:23:36.540 INFO ProgressMeter - chr12:96035657 27.4 23010000 838626.1
08:23:46.553 INFO ProgressMeter - chr12:107658382 27.6 23160000 838990.1
08:23:56.577 INFO ProgressMeter - chr12:112216771 27.8 23305000 839164.1
08:24:06.617 INFO ProgressMeter - chr12:120577162 27.9 23448000 839256.5
08:24:16.660 INFO ProgressMeter - chr12:125078346 28.1 23585000 839132.7
08:24:26.701 INFO ProgressMeter - chr13:23756019 28.3 23718000 838870.0
08:24:36.734 INFO ProgressMeter - chr13:37574758 28.4 23864000 839071.3
08:24:46.784 INFO ProgressMeter - chr13:52156468 28.6 24015000 839436.8
08:24:56.813 INFO ProgressMeter - chr13:98881934 28.8 24166000 839808.2
08:25:06.891 INFO ProgressMeter - chr14:19499676 28.9 24308000 839840.7
08:25:16.922 INFO ProgressMeter - chr14:23052282 29.1 24432000 839277.1
08:25:26.964 INFO ProgressMeter - chr14:24576341 29.3 24543000 838270.7
08:25:36.978 INFO ProgressMeter - chr14:50727359 29.4 24692000 838579.5
08:25:46.997 INFO ProgressMeter - chr14:61570478 29.6 24836000 838714.0
08:25:57.027 INFO ProgressMeter - chr14:70730809 29.8 24983000 838941.7
08:26:07.095 INFO ProgressMeter - chr14:76870002 29.9 25123000 838916.4
08:26:17.101 INFO ProgressMeter - chr14:94448713 30.1 25270000 839151.6
08:26:27.128 INFO ProgressMeter - chr14:103120958 30.3 25412000 839209.8
08:26:37.130 INFO ProgressMeter - chr15:23566798 30.4 25536000 838687.7
08:26:47.157 INFO ProgressMeter - chr15:38499072 30.6 25679000 838780.5
08:26:57.173 INFO ProgressMeter - chr15:42006149 30.8 25802000 838227.6
08:27:07.201 INFO ProgressMeter - chr15:45171367 30.9 25929000 837804.4
08:27:17.250 INFO ProgressMeter - chr15:55850759 31.1 26080000 838147.7
08:27:27.296 INFO ProgressMeter - chr15:65155049 31.3 26230000 838456.7
08:27:37.347 INFO ProgressMeter - chr15:72686440 31.5 26374000 838569.4
08:27:47.352 INFO ProgressMeter - chr15:78169309 31.6 26516000 838638.0
08:27:57.415 INFO ProgressMeter - chr15:87876523 31.8 26663000 838837.7
08:28:07.563 INFO ProgressMeter - chr15:99098406 32.0 26800000 838685.1
08:28:17.678 INFO ProgressMeter - chr16:740270 32.1 26913000 837801.4
08:28:27.717 INFO ProgressMeter - chr16:2326535 32.3 27024000 836897.7
08:28:37.747 INFO ProgressMeter - chr16:5030558 32.5 27151000 836500.7
08:28:47.776 INFO ProgressMeter - chr16:19578758 32.6 27293000 836567.0
08:28:57.823 INFO ProgressMeter - chr16:27403236 32.8 27440000 836778.0
08:29:07.900 INFO ProgressMeter - chr16:30670484 33.0 27572000 836519.0
08:29:17.934 INFO ProgressMeter - chr16:50315695 33.1 27705000 836310.9
08:29:27.964 INFO ProgressMeter - chr16:58020244 33.3 27844000 836286.7
08:29:37.973 INFO ProgressMeter - chr16:67954379 33.5 27971000 835913.0
08:29:47.989 INFO ProgressMeter - chr16:71970066 33.6 28106000 835778.3
08:29:57.988 INFO ProgressMeter - chr16:84410645 33.8 28242000 835680.8
08:30:07.999 INFO ProgressMeter - chr16:89816145 34.0 28362000 835108.6
08:30:18.047 INFO ProgressMeter - chr17:4531137 34.1 28500000 835054.3
08:30:28.105 INFO ProgressMeter - chr17:7389144 34.3 28618000 834413.4
08:30:38.165 INFO ProgressMeter - chr17:10355176 34.5 28742000 833951.9
08:30:46.205 WARN MinimalGenotypingEngine - Attempting to genotype more than 50 alleles. Site will be skipped at location chr17:17816189
08:30:48.210 INFO ProgressMeter - chr17:18162399 34.6 28871000 833645.3
08:30:58.230 INFO ProgressMeter - chr17:28702401 34.8 29004000 833466.6
08:31:08.288 INFO ProgressMeter - chr17:35006795 35.0 29142000 833417.5
08:31:18.289 INFO ProgressMeter - chr17:40627436 35.1 29279000 833363.4
08:31:28.294 INFO ProgressMeter - chr17:43171185 35.3 29403000 832939.1
08:31:38.300 INFO ProgressMeter - chr17:47649839 35.5 29536000 832772.6
08:31:48.344 INFO ProgressMeter - chr17:50667842 35.6 29661000 832368.3
08:31:58.351 INFO ProgressMeter - chr17:62267147 35.8 29805000 832512.8
08:32:08.365 INFO ProgressMeter - chr17:69285899 36.0 29938000 832347.5
08:32:18.381 INFO ProgressMeter - chr17:75843036 36.1 30069000 832127.6
08:32:28.394 INFO ProgressMeter - chr17:79738063 36.3 30193000 831718.0
08:32:38.431 INFO ProgressMeter - chr17:82128516 36.5 30314000 831220.8
08:32:48.449 INFO ProgressMeter - chr18:11689681 36.6 30454000 831254.0
08:32:58.482 INFO ProgressMeter - chr18:32672981 36.8 30604000 831552.9
08:33:08.570 INFO ProgressMeter - chr18:50283028 37.0 30754000 831828.4
08:33:18.597 INFO ProgressMeter - chr18:70328488 37.1 30903000 832097.4
08:33:28.661 INFO ProgressMeter - chr19:1275755 37.3 31029000 831733.6
08:33:38.704 INFO ProgressMeter - chr19:3731700 37.5 31157000 831434.2
08:33:45.175 WARN MinimalGenotypingEngine - Attempting to genotype more than 50 alleles. Site will be skipped at location chr19:5787204
08:33:48.738 INFO ProgressMeter - chr19:6857215 37.6 31285000 831140.8
08:33:58.816 INFO ProgressMeter - chr19:9214838 37.8 31402000 830543.0
08:34:08.852 INFO ProgressMeter - chr19:12317771 38.0 31531000 830281.7
08:34:18.886 INFO ProgressMeter - chr19:15264406 38.1 31657000 829944.8
08:34:28.907 INFO ProgressMeter - chr19:18211630 38.3 31789000 829772.2
08:34:38.990 INFO ProgressMeter - chr19:23934503 38.5 31918000 829500.8
08:34:48.995 INFO ProgressMeter - chr19:35872651 38.6 32048000 829285.5
08:34:59.030 INFO ProgressMeter - chr19:39031871 38.8 32182000 829164.4
08:35:09.104 INFO ProgressMeter - chr19:41993807 39.0 32313000 828953.6
08:35:19.171 INFO ProgressMeter - chr19:45471684 39.1 32447000 828823.8
08:35:29.223 INFO ProgressMeter - chr19:48472531 39.3 32587000 828852.9
08:35:39.223 INFO ProgressMeter - chr19:50378493 39.5 32707000 828393.4
08:35:49.293 INFO ProgressMeter - chr19:53725404 39.7 32840000 828241.2
08:35:59.351 INFO ProgressMeter - chr19:57154517 39.8 32971000 828044.3
08:36:09.390 INFO ProgressMeter - chr20:2144171 40.0 33112000 828106.1
08:36:19.409 INFO ProgressMeter - chr20:13072265 40.2 33255000 828223.3
08:36:29.425 INFO ProgressMeter - chr20:32031065 40.3 33403000 828465.2
08:36:39.430 INFO ProgressMeter - chr20:36255737 40.5 33545000 828560.1
08:36:49.468 INFO ProgressMeter - chr20:44943193 40.7 33695000 828840.0
08:36:59.488 INFO ProgressMeter - chr20:50582818 40.8 33833000 828829.8
08:37:09.552 INFO ProgressMeter - chr20:62395090 41.0 33967000 828707.3
08:37:19.580 INFO ProgressMeter - chr21:25880612 41.2 34095000 828452.4
08:37:29.619 INFO ProgressMeter - chr21:38122446 41.3 34238000 828558.5
08:37:39.705 INFO ProgressMeter - chr21:45128545 41.5 34380000 828623.8
08:37:49.764 INFO ProgressMeter - chr22:19724636 41.7 34510000 828409.7
08:37:59.787 INFO ProgressMeter - chr22:24096258 41.8 34639000 828185.3
08:38:09.804 INFO ProgressMeter - chr22:30606826 42.0 34784000 828345.6
08:38:19.857 INFO ProgressMeter - chr22:37519541 42.2 34927000 828445.5
08:38:29.928 INFO ProgressMeter - chr22:41216065 42.3 35065000 828420.6
08:38:39.960 INFO ProgressMeter - chr22:46678481 42.5 35207000 828502.7
08:38:49.984 INFO ProgressMeter - chrX:10567036 42.7 35339000 828352.3
08:39:00.031 INFO ProgressMeter - chrX:24316621 42.8 35499000 828849.4
08:39:10.068 INFO ProgressMeter - chrX:47240185 43.0 35657000 829299.4
08:39:20.082 INFO ProgressMeter - chrX:53192178 43.2 35793000 829243.6
08:39:30.102 INFO ProgressMeter - chrX:69530129 43.3 35940000 829440.1
08:39:40.148 INFO ProgressMeter - chrX:78125723 43.5 36086000 829603.9
08:39:50.180 INFO ProgressMeter - chrX:106823405 43.7 36239000 829931.2
08:40:00.227 INFO ProgressMeter - chrX:120430826 43.8 36402000 830479.4
08:40:10.308 INFO ProgressMeter - chrX:137566190 44.0 36556000 830808.1
08:40:20.357 INFO ProgressMeter - chrX:153886167 44.2 36698000 830872.7
08:40:28.887 INFO ProgressMeter - chrY:24806563 44.3 36816983 830892.1
08:40:28.887 INFO ProgressMeter - Traversal complete. Processed 36816983 total variants in 44.3 minutes.
08:40:28.952 INFO GenotypeGVCFs - Shutting down engine
[April 4, 2020 8:40:28 AM EDT] org.broadinstitute.hellbender.tools.walkers.GenotypeGVCFs done. Elapsed time: 44.35 minutes.
Runtime.totalMemory()=23615504384
Using GATK jar /hpc/packages/minerva-centos7/gatk/4.1.6.0/gatk-4.1.6.0/gatk-package-4.1.6.0-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 -Xmx22g -Xms22g -jar /hpc/packages/minerva-centos7/gatk/4.1.6.0/gatk-4.1.6.0/gatk-package-4.1.6.0-local.jar GenotypeGVCFs -R /sc/hydra/projects/canan/colon_cancer10312019/intervals_preprocessing/Homo_sapiens_assembly38.fasta -V Colon_cohort_combined.g.vcf.gz -O output.JointGenotype.Germline41samples.colon.vcf.gz --intervals Exome-Agilent_V6_UTR.interval_list --tmp-dir /sc/hydra/projects/canan/colon_cancer10312019/joint_calling_colon --dbsnp hg38_resources/Homo_sapiens_assembly38.dbsnp138.vcf
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Hi sahuno
Is your question about how to resolve the warnings? Its just saying that its skipping particular locations due to low confidence calls. You don't have to worry about warnings.
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how can i resolve these warnings?
thanks for the response
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As I said above, these warning are just stating that there are regions of low confidence calls in your data. These warnings are not a problem and you shouldn't worry about resolving them. There is a --verbosity argument that you can set to ERROR to only show you error instead of the warnings.
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