gatk CollectVariantCallingMetrics MultiThreadedChunkBased: Unexpected exception encountered in child thread. java.lang.ArrayIndexOutOfBoundsException: Index 1 out of bounds for length 1
I have run the same command on two other .vcf files from different variant callers (deepvariant and gatk), with the same reference genome, bed file/targets, and dbSNP file. They have no issues and I cannot seem to find what is going on. Thank you in advance
REQUIRED for all errors and issues:
a) GATK version used: 4.4.0.0
b) Exact command used:
gatk CollectVariantCallingMetrics -I results/variant_calling/varscan/RM8398_EF_S16.vcf -O results/variant_calling/varscan/post_variant_calling_QC/RM8398_EF_S16 --DBSNP /mnt/scratch_dir/deutekoe/trial/WESP_run/resources/GCF_000001405.40.renamed.vcf.gz --TARGET_INTERVALS /mnt/scratch_dir/deutekoe/trial/WESP_run/resources/hg38_exome_comp_spikein_v2.0.2_targets_sorted.re_annotated.interval --THREAD_COUNT 1 2> log/post_variant_call_metrics/varscan/RM8398_EF_S16.log
c) Entire program log:
Using GATK jar /mnt/scratch_dir/deutekoe/trial/WESP_run/env_db/fd8c46c2bfcd9e9f085ccfbc7267ee19_/share/gatk4-4.4.0.0-0/gatk-package-4.4.0.0-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 -jar /mnt/scratch_dir/deutekoe/trial/WESP_run/env_db/fd8c46c2bfcd9e9f085ccfbc7267ee19_/share/gatk4-4.4.0.0-0/gatk-package-4.4.0.0-local.jar CollectVariantCallingMetrics -I results/variant_calling/varscan/RM8398_EF_S16.vcf -O results/variant_calling/varscan/post_variant_calling_QC/RM8398_EF_S16 --DBSNP /mnt/scratch_dir/deutekoe/trial/WESP_run/resources/GCF_000001405.40.renamed.vcf.gz --TARGET_INTERVALS /mnt/scratch_dir/deutekoe/trial/WESP_run/resources/hg38_exome_comp_spikein_v2.0.2_targets_sorted.re_annotated.interval --THREAD_COUNT 1
08:52:54.212 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/mnt/scratch_dir/deutekoe/trial/WESP_run/env_db/fd8c46c2bfcd9e9f085ccfbc7267ee19_/share/gatk4-4.4.0.0-0/gatk-package-4.4.0.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
[Wed Apr 10 08:52:54 CEST 2024] CollectVariantCallingMetrics --INPUT results/variant_calling/varscan/RM8398_EF_S16.vcf --OUTPUT results/variant_calling/varscan/post_variant_calling_QC/RM8398_EF_S16 --DBSNP /mnt/scratch_dir/deutekoe/trial/WESP_run/resources/GCF_000001405.40.renamed.vcf.gz --TARGET_INTERVALS /mnt/scratch_dir/deutekoe/trial/WESP_run/resources/hg38_exome_comp_spikein_v2.0.2_targets_sorted.re_annotated.interval --THREAD_COUNT 1 --GVCF_INPUT false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 2 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Wed Apr 10 08:52:54 CEST 2024] Executing as deutekoe on Linux 3.10.0-1160.105.1.el7.x86_64 amd64; OpenJDK 64-Bit Server VM 17.0.9-internal+0-adhoc..src; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:4.4.0.0
INFO 2024-04-10 08:52:59 CollectVariantCallingMetrics Loading dbSNP file ...
INFO 2024-04-10 08:53:12 CollectVariantCallingMetrics Read 100,000 variants. Elapsed time: 00:00:13s. Time for last 100,000: 11s. Last read position: chr1:6,602,199
INFO 2024-04-10 08:53:21 CollectVariantCallingMetrics Read 200,000 variants. Elapsed time: 00:00:22s. Time for last 100,000: 9s. Last read position: chr1:15,935,947
INFO 2024-04-10 08:53:32 CollectVariantCallingMetrics Read 300,000 variants. Elapsed time: 00:00:33s. Time for last 100,000: 10s. Last read position: chr1:25,290,674
INFO 2024-04-10 08:53:42 CollectVariantCallingMetrics Read 400,000 variants. Elapsed time: 00:00:43s. Time for last 100,000: 9s. Last read position: chr1:34,988,566
INFO 2024-04-10 08:53:52 CollectVariantCallingMetrics Read 500,000 variants. Elapsed time: 00:00:52s. Time for last 100,000: 9s. Last read position: chr1:43,992,201
INFO 2024-04-10 08:54:04 CollectVariantCallingMetrics Read 600,000 variants. Elapsed time: 00:01:04s. Time for last 100,000: 11s. Last read position: chr1:58,576,446
INFO 2024-04-10 08:54:15 CollectVariantCallingMetrics Read 700,000 variants. Elapsed time: 00:01:15s. Time for last 100,000: 10s. Last read position: chr1:89,706,316
INFO 2024-04-10 08:54:26 CollectVariantCallingMetrics Read 800,000 variants. Elapsed time: 00:01:27s. Time for last 100,000: 11s. Last read position: chr1:112,416,204
INFO 2024-04-10 08:54:37 CollectVariantCallingMetrics Read 900,000 variants. Elapsed time: 00:01:37s. Time for last 100,000: 10s. Last read position: chr1:148,937,814
INFO 2024-04-10 08:54:44 CollectVariantCallingMetrics Read 1,000,000 variants. Elapsed time: 00:01:44s. Time for last 100,000: 6s. Last read position: chr1:154,029,981
INFO 2024-04-10 08:54:53 CollectVariantCallingMetrics Read 1,100,000 variants. Elapsed time: 00:01:54s. Time for last 100,000: 9s. Last read position: chr1:159,068,600
INFO 2024-04-10 08:55:05 CollectVariantCallingMetrics Read 1,200,000 variants. Elapsed time: 00:02:05s. Time for last 100,000: 11s. Last read position: chr1:173,961,136
INFO 2024-04-10 08:55:15 CollectVariantCallingMetrics Read 1,300,000 variants. Elapsed time: 00:02:16s. Time for last 100,000: 10s. Last read position: chr1:198,694,051
INFO 2024-04-10 08:55:25 CollectVariantCallingMetrics Read 1,400,000 variants. Elapsed time: 00:02:25s. Time for last 100,000: 9s. Last read position: chr1:209,776,040
INFO 2024-04-10 08:55:35 CollectVariantCallingMetrics Read 1,500,000 variants. Elapsed time: 00:02:36s. Time for last 100,000: 10s. Last read position: chr1:228,281,966
INFO 2024-04-10 08:55:46 CollectVariantCallingMetrics Read 1,600,000 variants. Elapsed time: 00:02:47s. Time for last 100,000: 11s. Last read position: chr1:246,740,243
INFO 2024-04-10 08:55:55 CollectVariantCallingMetrics Read 1,700,000 variants. Elapsed time: 00:02:56s. Time for last 100,000: 8s. Last read position: chr2:21,008,133
INFO 2024-04-10 08:56:07 CollectVariantCallingMetrics Read 1,800,000 variants. Elapsed time: 00:03:08s. Time for last 100,000: 11s. Last read position: chr2:32,469,491
INFO 2024-04-10 08:56:22 CollectVariantCallingMetrics Read 1,900,000 variants. Elapsed time: 00:03:23s. Time for last 100,000: 15s. Last read position: chr2:54,911,017
INFO 2024-04-10 08:56:34 CollectVariantCallingMetrics Read 2,000,000 variants. Elapsed time: 00:03:34s. Time for last 100,000: 11s. Last read position: chr2:74,460,269
INFO 2024-04-10 08:56:45 CollectVariantCallingMetrics Read 2,100,000 variants. Elapsed time: 00:03:45s. Time for last 100,000: 11s. Last read position: chr2:98,230,121
INFO 2024-04-10 08:56:56 CollectVariantCallingMetrics Read 2,200,000 variants. Elapsed time: 00:03:56s. Time for last 100,000: 10s. Last read position: chr2:121,407,577
INFO 2024-04-10 08:57:05 CollectVariantCallingMetrics Read 2,300,000 variants. Elapsed time: 00:04:06s. Time for last 100,000: 9s. Last read position: chr2:151,659,062
INFO 2024-04-10 08:57:19 CollectVariantCallingMetrics Read 2,400,000 variants. Elapsed time: 00:04:19s. Time for last 100,000: 13s. Last read position: chr2:173,359,269
INFO 2024-04-10 08:57:31 CollectVariantCallingMetrics Read 2,500,000 variants. Elapsed time: 00:04:31s. Time for last 100,000: 11s. Last read position: chr2:186,590,343
INFO 2024-04-10 08:57:44 CollectVariantCallingMetrics Read 2,600,000 variants. Elapsed time: 00:04:44s. Time for last 100,000: 13s. Last read position: chr2:208,248,601
INFO 2024-04-10 08:57:54 CollectVariantCallingMetrics Read 2,700,000 variants. Elapsed time: 00:04:55s. Time for last 100,000: 10s. Last read position: chr2:224,401,493
INFO 2024-04-10 08:58:07 CollectVariantCallingMetrics Read 2,800,000 variants. Elapsed time: 00:05:08s. Time for last 100,000: 12s. Last read position: chr2:240,030,359
INFO 2024-04-10 08:58:21 CollectVariantCallingMetrics Read 2,900,000 variants. Elapsed time: 00:05:21s. Time for last 100,000: 13s. Last read position: chr3:13,323,393
INFO 2024-04-10 08:58:34 CollectVariantCallingMetrics Read 3,000,000 variants. Elapsed time: 00:05:35s. Time for last 100,000: 13s. Last read position: chr3:38,739,551
INFO 2024-04-10 08:58:43 CollectVariantCallingMetrics Read 3,100,000 variants. Elapsed time: 00:05:44s. Time for last 100,000: 8s. Last read position: chr3:48,464,937
INFO 2024-04-10 08:58:54 CollectVariantCallingMetrics Read 3,200,000 variants. Elapsed time: 00:05:54s. Time for last 100,000: 10s. Last read position: chr3:52,487,506
INFO 2024-04-10 08:59:05 CollectVariantCallingMetrics Read 3,300,000 variants. Elapsed time: 00:06:06s. Time for last 100,000: 11s. Last read position: chr3:88,139,587
INFO 2024-04-10 08:59:15 CollectVariantCallingMetrics Read 3,400,000 variants. Elapsed time: 00:06:16s. Time for last 100,000: 9s. Last read position: chr3:121,488,474
INFO 2024-04-10 08:59:26 CollectVariantCallingMetrics Read 3,500,000 variants. Elapsed time: 00:06:27s. Time for last 100,000: 10s. Last read position: chr3:133,644,359
INFO 2024-04-10 08:59:36 CollectVariantCallingMetrics Read 3,600,000 variants. Elapsed time: 00:06:37s. Time for last 100,000: 10s. Last read position: chr3:159,888,886
INFO 2024-04-10 08:59:48 CollectVariantCallingMetrics Read 3,700,000 variants. Elapsed time: 00:06:48s. Time for last 100,000: 11s. Last read position: chr3:187,291,678
INFO 2024-04-10 08:59:57 CollectVariantCallingMetrics Read 3,800,000 variants. Elapsed time: 00:06:57s. Time for last 100,000: 8s. Last read position: chr4:1,900,986
INFO 2024-04-10 09:00:07 CollectVariantCallingMetrics Read 3,900,000 variants. Elapsed time: 00:07:07s. Time for last 100,000: 10s. Last read position: chr4:20,554,319
INFO 2024-04-10 09:00:19 CollectVariantCallingMetrics Read 4,000,000 variants. Elapsed time: 00:07:19s. Time for last 100,000: 11s. Last read position: chr4:56,511,275
INFO 2024-04-10 09:00:30 CollectVariantCallingMetrics Read 4,100,000 variants. Elapsed time: 00:07:30s. Time for last 100,000: 11s. Last read position: chr4:86,701,676
INFO 2024-04-10 09:00:41 CollectVariantCallingMetrics Read 4,200,000 variants. Elapsed time: 00:07:42s. Time for last 100,000: 11s. Last read position: chr4:118,294,985
INFO 2024-04-10 09:00:51 CollectVariantCallingMetrics Read 4,300,000 variants. Elapsed time: 00:07:51s. Time for last 100,000: 9s. Last read position: chr4:154,324,353
INFO 2024-04-10 09:01:01 CollectVariantCallingMetrics Read 4,400,000 variants. Elapsed time: 00:08:02s. Time for last 100,000: 10s. Last read position: chr5:139,531
INFO 2024-04-10 09:01:12 CollectVariantCallingMetrics Read 4,500,000 variants. Elapsed time: 00:08:13s. Time for last 100,000: 11s. Last read position: chr5:35,618,017
INFO 2024-04-10 09:01:25 CollectVariantCallingMetrics Read 4,600,000 variants. Elapsed time: 00:08:26s. Time for last 100,000: 12s. Last read position: chr5:69,116,397
INFO 2024-04-10 09:01:36 CollectVariantCallingMetrics Read 4,700,000 variants. Elapsed time: 00:08:36s. Time for last 100,000: 10s. Last read position: chr5:95,783,813
INFO 2024-04-10 09:01:52 CollectVariantCallingMetrics Read 4,800,000 variants. Elapsed time: 00:08:53s. Time for last 100,000: 16s. Last read position: chr5:132,726,125
INFO 2024-04-10 09:01:59 CollectVariantCallingMetrics Read 4,900,000 variants. Elapsed time: 00:09:00s. Time for last 100,000: 7s. Last read position: chr5:141,200,872
INFO 2024-04-10 09:02:09 CollectVariantCallingMetrics Read 5,000,000 variants. Elapsed time: 00:09:10s. Time for last 100,000: 10s. Last read position: chr5:151,537,822
INFO 2024-04-10 09:02:21 CollectVariantCallingMetrics Read 5,100,000 variants. Elapsed time: 00:09:22s. Time for last 100,000: 11s. Last read position: chr5:177,402,385
INFO 2024-04-10 09:02:31 CollectVariantCallingMetrics Read 5,200,000 variants. Elapsed time: 00:09:32s. Time for last 100,000: 10s. Last read position: chr6:13,470,501
INFO 2024-04-10 09:02:38 CollectVariantCallingMetrics Read 5,300,000 variants. Elapsed time: 00:09:39s. Time for last 100,000: 7s. Last read position: chr6:30,888,945
INFO 2024-04-10 09:02:47 CollectVariantCallingMetrics Read 5,400,000 variants. Elapsed time: 00:09:48s. Time for last 100,000: 8s. Last read position: chr6:35,214,469
INFO 2024-04-10 09:02:58 CollectVariantCallingMetrics Read 5,500,000 variants. Elapsed time: 00:09:58s. Time for last 100,000: 10s. Last read position: chr6:44,265,060
INFO 2024-04-10 09:03:09 CollectVariantCallingMetrics Read 5,600,000 variants. Elapsed time: 00:10:09s. Time for last 100,000: 11s. Last read position: chr6:73,803,265
INFO 2024-04-10 09:03:20 CollectVariantCallingMetrics Read 5,700,000 variants. Elapsed time: 00:10:21s. Time for last 100,000: 11s. Last read position: chr6:109,270,049
INFO 2024-04-10 09:03:31 CollectVariantCallingMetrics Read 5,800,000 variants. Elapsed time: 00:10:32s. Time for last 100,000: 10s. Last read position: chr6:135,455,750
INFO 2024-04-10 09:03:43 CollectVariantCallingMetrics Read 5,900,000 variants. Elapsed time: 00:10:43s. Time for last 100,000: 11s. Last read position: chr6:158,069,626
INFO 2024-04-10 09:03:52 CollectVariantCallingMetrics Read 6,000,000 variants. Elapsed time: 00:10:53s. Time for last 100,000: 9s. Last read position: chr7:4,017,186
INFO 2024-04-10 09:04:04 CollectVariantCallingMetrics Read 6,100,000 variants. Elapsed time: 00:11:05s. Time for last 100,000: 11s. Last read position: chr7:26,844,076
INFO 2024-04-10 09:04:14 CollectVariantCallingMetrics Read 6,200,000 variants. Elapsed time: 00:11:15s. Time for last 100,000: 9s. Last read position: chr7:48,520,164
INFO 2024-04-10 09:04:25 CollectVariantCallingMetrics Read 6,300,000 variants. Elapsed time: 00:11:25s. Time for last 100,000: 10s. Last read position: chr7:83,155,697
INFO 2024-04-10 09:04:37 CollectVariantCallingMetrics Read 6,400,000 variants. Elapsed time: 00:11:38s. Time for last 100,000: 12s. Last read position: chr7:100,488,801
INFO 2024-04-10 09:04:46 CollectVariantCallingMetrics Read 6,500,000 variants. Elapsed time: 00:11:47s. Time for last 100,000: 8s. Last read position: chr7:108,109,244
INFO 2024-04-10 09:04:59 CollectVariantCallingMetrics Read 6,600,000 variants. Elapsed time: 00:12:00s. Time for last 100,000: 13s. Last read position: chr7:135,578,830
INFO 2024-04-10 09:05:09 CollectVariantCallingMetrics Read 6,700,000 variants. Elapsed time: 00:12:09s. Time for last 100,000: 9s. Last read position: chr7:149,795,591
INFO 2024-04-10 09:05:19 CollectVariantCallingMetrics Read 6,800,000 variants. Elapsed time: 00:12:19s. Time for last 100,000: 10s. Last read position: chr8:6,757,163
INFO 2024-04-10 09:05:29 CollectVariantCallingMetrics Read 6,900,000 variants. Elapsed time: 00:12:30s. Time for last 100,000: 10s. Last read position: chr8:24,339,467
INFO 2024-04-10 09:05:42 CollectVariantCallingMetrics Read 7,000,000 variants. Elapsed time: 00:12:42s. Time for last 100,000: 12s. Last read position: chr8:48,731,380
INFO 2024-04-10 09:05:54 CollectVariantCallingMetrics Read 7,100,000 variants. Elapsed time: 00:12:55s. Time for last 100,000: 12s. Last read position: chr8:90,791,917
INFO 2024-04-10 09:06:04 CollectVariantCallingMetrics Read 7,200,000 variants. Elapsed time: 00:13:05s. Time for last 100,000: 10s. Last read position: chr8:123,126,079
INFO 2024-04-10 09:06:14 CollectVariantCallingMetrics Read 7,300,000 variants. Elapsed time: 00:13:14s. Time for last 100,000: 9s. Last read position: chr8:143,868,295
INFO 2024-04-10 09:06:26 CollectVariantCallingMetrics Read 7,400,000 variants. Elapsed time: 00:13:26s. Time for last 100,000: 11s. Last read position: chr9:6,256,059
INFO 2024-04-10 09:06:37 CollectVariantCallingMetrics Read 7,500,000 variants. Elapsed time: 00:13:38s. Time for last 100,000: 11s. Last read position: chr9:35,301,452
INFO 2024-04-10 09:06:47 CollectVariantCallingMetrics Read 7,600,000 variants. Elapsed time: 00:13:48s. Time for last 100,000: 9s. Last read position: chr9:79,627,422
INFO 2024-04-10 09:06:57 CollectVariantCallingMetrics Read 7,700,000 variants. Elapsed time: 00:13:58s. Time for last 100,000: 10s. Last read position: chr9:99,151,396
INFO 2024-04-10 09:07:09 CollectVariantCallingMetrics Read 7,800,000 variants. Elapsed time: 00:14:10s. Time for last 100,000: 12s. Last read position: chr9:121,154,727
INFO 2024-04-10 09:07:20 CollectVariantCallingMetrics Read 7,900,000 variants. Elapsed time: 00:14:21s. Time for last 100,000: 10s. Last read position: chr9:130,422,680
INFO 2024-04-10 09:07:33 CollectVariantCallingMetrics Read 8,000,000 variants. Elapsed time: 00:14:33s. Time for last 100,000: 12s. Last read position: chr9:136,523,042
INFO 2024-04-10 09:07:43 CollectVariantCallingMetrics Read 8,100,000 variants. Elapsed time: 00:14:44s. Time for last 100,000: 10s. Last read position: chr10:12,760,948
INFO 2024-04-10 09:07:55 CollectVariantCallingMetrics Read 8,200,000 variants. Elapsed time: 00:14:55s. Time for last 100,000: 11s. Last read position: chr10:42,592,721
INFO 2024-04-10 09:08:05 CollectVariantCallingMetrics Read 8,300,000 variants. Elapsed time: 00:15:06s. Time for last 100,000: 10s. Last read position: chr10:68,786,178
INFO 2024-04-10 09:08:18 CollectVariantCallingMetrics Read 8,400,000 variants. Elapsed time: 00:15:18s. Time for last 100,000: 12s. Last read position: chr10:87,505,116
INFO 2024-04-10 09:08:31 CollectVariantCallingMetrics Read 8,500,000 variants. Elapsed time: 00:15:31s. Time for last 100,000: 12s. Last read position: chr10:100,944,044
INFO 2024-04-10 09:08:42 CollectVariantCallingMetrics Read 8,600,000 variants. Elapsed time: 00:15:43s. Time for last 100,000: 11s. Last read position: chr10:119,431,519
INFO 2024-04-10 09:08:52 CollectVariantCallingMetrics Read 8,700,000 variants. Elapsed time: 00:15:53s. Time for last 100,000: 10s. Last read position: chr11:533,875
INFO 2024-04-10 09:09:01 CollectVariantCallingMetrics Read 8,800,000 variants. Elapsed time: 00:16:01s. Time for last 100,000: 8s. Last read position: chr11:4,923,499
INFO 2024-04-10 09:09:09 CollectVariantCallingMetrics Read 8,900,000 variants. Elapsed time: 00:16:10s. Time for last 100,000: 8s. Last read position: chr11:14,294,847
INFO 2024-04-10 09:09:22 CollectVariantCallingMetrics Read 9,000,000 variants. Elapsed time: 00:16:23s. Time for last 100,000: 12s. Last read position: chr11:44,234,211
INFO 2024-04-10 09:09:31 CollectVariantCallingMetrics Read 9,100,000 variants. Elapsed time: 00:16:31s. Time for last 100,000: 8s. Last read position: chr11:58,267,528
INFO 2024-04-10 09:09:39 CollectVariantCallingMetrics Read 9,200,000 variants. Elapsed time: 00:16:39s. Time for last 100,000: 8s. Last read position: chr11:64,315,138
INFO 2024-04-10 09:09:49 CollectVariantCallingMetrics Read 9,300,000 variants. Elapsed time: 00:16:49s. Time for last 100,000: 9s. Last read position: chr11:67,434,412
INFO 2024-04-10 09:09:59 CollectVariantCallingMetrics Read 9,400,000 variants. Elapsed time: 00:16:59s. Time for last 100,000: 10s. Last read position: chr11:77,622,028
INFO 2024-04-10 09:10:09 CollectVariantCallingMetrics Read 9,500,000 variants. Elapsed time: 00:17:09s. Time for last 100,000: 9s. Last read position: chr11:105,035,133
INFO 2024-04-10 09:10:22 CollectVariantCallingMetrics Read 9,600,000 variants. Elapsed time: 00:17:23s. Time for last 100,000: 13s. Last read position: chr11:119,090,009
INFO 2024-04-10 09:10:34 CollectVariantCallingMetrics Read 9,700,000 variants. Elapsed time: 00:17:34s. Time for last 100,000: 11s. Last read position: chr12:175,005
INFO 2024-04-10 09:10:46 CollectVariantCallingMetrics Read 9,800,000 variants. Elapsed time: 00:17:46s. Time for last 100,000: 11s. Last read position: chr12:9,841,885
INFO 2024-04-10 09:10:56 CollectVariantCallingMetrics Read 9,900,000 variants. Elapsed time: 00:17:57s. Time for last 100,000: 10s. Last read position: chr12:32,327,784
INFO 2024-04-10 09:11:07 CollectVariantCallingMetrics Read 10,000,000 variants. Elapsed time: 00:18:07s. Time for last 100,000: 10s. Last read position: chr12:49,603,193
INFO 2024-04-10 09:11:15 CollectVariantCallingMetrics Read 10,100,000 variants. Elapsed time: 00:18:16s. Time for last 100,000: 8s. Last read position: chr12:55,743,749
INFO 2024-04-10 09:11:27 CollectVariantCallingMetrics Read 10,200,000 variants. Elapsed time: 00:18:27s. Time for last 100,000: 11s. Last read position: chr12:69,697,713
INFO 2024-04-10 09:11:37 CollectVariantCallingMetrics Read 10,300,000 variants. Elapsed time: 00:18:38s. Time for last 100,000: 10s. Last read position: chr12:101,288,993
INFO 2024-04-10 09:11:50 CollectVariantCallingMetrics Read 10,400,000 variants. Elapsed time: 00:18:50s. Time for last 100,000: 12s. Last read position: chr12:113,463,394
INFO 2024-04-10 09:12:00 CollectVariantCallingMetrics Read 10,500,000 variants. Elapsed time: 00:19:01s. Time for last 100,000: 10s. Last read position: chr12:128,696,041
INFO 2024-04-10 09:12:11 CollectVariantCallingMetrics Read 10,600,000 variants. Elapsed time: 00:19:12s. Time for last 100,000: 10s. Last read position: chr13:28,339,199
INFO 2024-04-10 09:12:26 CollectVariantCallingMetrics Read 10,700,000 variants. Elapsed time: 00:19:26s. Time for last 100,000: 14s. Last read position: chr13:50,013,057
INFO 2024-04-10 09:12:36 CollectVariantCallingMetrics Read 10,800,000 variants. Elapsed time: 00:19:37s. Time for last 100,000: 10s. Last read position: chr13:106,494,959
INFO 2024-04-10 09:12:45 CollectVariantCallingMetrics Read 10,900,000 variants. Elapsed time: 00:19:45s. Time for last 100,000: 8s. Last read position: chr14:22,132,823
INFO 2024-04-10 09:12:56 CollectVariantCallingMetrics Read 11,000,000 variants. Elapsed time: 00:19:56s. Time for last 100,000: 10s. Last read position: chr14:36,680,714
INFO 2024-04-10 09:13:06 CollectVariantCallingMetrics Read 11,100,000 variants. Elapsed time: 00:20:07s. Time for last 100,000: 10s. Last read position: chr14:64,024,913
INFO 2024-04-10 09:13:17 CollectVariantCallingMetrics Read 11,200,000 variants. Elapsed time: 00:20:17s. Time for last 100,000: 10s. Last read position: chr14:77,027,010
INFO 2024-04-10 09:13:29 CollectVariantCallingMetrics Read 11,300,000 variants. Elapsed time: 00:20:29s. Time for last 100,000: 11s. Last read position: chr14:100,729,076
INFO 2024-04-10 09:13:37 CollectVariantCallingMetrics Read 11,400,000 variants. Elapsed time: 00:20:37s. Time for last 100,000: 8s. Last read position: chr15:22,866,820
INFO 2024-04-10 09:13:48 CollectVariantCallingMetrics Read 11,500,000 variants. Elapsed time: 00:20:48s. Time for last 100,000: 11s. Last read position: chr15:40,659,407
INFO 2024-04-10 09:13:58 CollectVariantCallingMetrics Read 11,600,000 variants. Elapsed time: 00:20:59s. Time for last 100,000: 10s. Last read position: chr15:48,241,584
INFO 2024-04-10 09:14:11 CollectVariantCallingMetrics Read 11,700,000 variants. Elapsed time: 00:21:11s. Time for last 100,000: 12s. Last read position: chr15:64,418,555
INFO 2024-04-10 09:14:21 CollectVariantCallingMetrics Read 11,800,000 variants. Elapsed time: 00:21:21s. Time for last 100,000: 9s. Last read position: chr15:75,650,561
INFO 2024-04-10 09:14:30 CollectVariantCallingMetrics Read 11,900,000 variants. Elapsed time: 00:21:31s. Time for last 100,000: 9s. Last read position: chr15:89,791,093
INFO 2024-04-10 09:14:42 CollectVariantCallingMetrics Read 12,000,000 variants. Elapsed time: 00:21:43s. Time for last 100,000: 11s. Last read position: chr16:882,137
INFO 2024-04-10 09:14:55 CollectVariantCallingMetrics Read 12,100,000 variants. Elapsed time: 00:21:55s. Time for last 100,000: 12s. Last read position: chr16:3,204,243
INFO 2024-04-10 09:15:07 CollectVariantCallingMetrics Read 12,200,000 variants. Elapsed time: 00:22:08s. Time for last 100,000: 12s. Last read position: chr16:15,586,779
INFO 2024-04-10 09:15:19 CollectVariantCallingMetrics Read 12,300,000 variants. Elapsed time: 00:22:19s. Time for last 100,000: 11s. Last read position: chr16:28,592,316
INFO 2024-04-10 09:15:28 CollectVariantCallingMetrics Read 12,400,000 variants. Elapsed time: 00:22:29s. Time for last 100,000: 9s. Last read position: chr16:48,561,689
INFO 2024-04-10 09:15:40 CollectVariantCallingMetrics Read 12,500,000 variants. Elapsed time: 00:22:41s. Time for last 100,000: 12s. Last read position: chr16:67,563,665
INFO 2024-04-10 09:15:50 CollectVariantCallingMetrics Read 12,600,000 variants. Elapsed time: 00:22:50s. Time for last 100,000: 9s. Last read position: chr16:75,222,676
INFO 2024-04-10 09:16:01 CollectVariantCallingMetrics Read 12,700,000 variants. Elapsed time: 00:23:02s. Time for last 100,000: 11s. Last read position: chr16:88,864,364
INFO 2024-04-10 09:16:12 CollectVariantCallingMetrics Read 12,800,000 variants. Elapsed time: 00:23:12s. Time for last 100,000: 10s. Last read position: chr17:4,008,909
INFO 2024-04-10 09:16:23 CollectVariantCallingMetrics Read 12,900,000 variants. Elapsed time: 00:23:23s. Time for last 100,000: 10s. Last read position: chr17:7,898,022
INFO 2024-04-10 09:16:33 CollectVariantCallingMetrics Read 13,000,000 variants. Elapsed time: 00:23:33s. Time for last 100,000: 10s. Last read position: chr17:18,123,346
INFO 2024-04-10 09:16:44 CollectVariantCallingMetrics Read 13,100,000 variants. Elapsed time: 00:23:45s. Time for last 100,000: 11s. Last read position: chr17:31,326,125
INFO 2024-04-10 09:16:55 CollectVariantCallingMetrics Read 13,200,000 variants. Elapsed time: 00:23:55s. Time for last 100,000: 10s. Last read position: chr17:40,416,028
INFO 2024-04-10 09:17:13 CollectVariantCallingMetrics Read 13,300,000 variants. Elapsed time: 00:24:13s. Time for last 100,000: 18s. Last read position: chr17:44,353,994
INFO 2024-04-10 09:17:24 CollectVariantCallingMetrics Read 13,400,000 variants. Elapsed time: 00:24:25s. Time for last 100,000: 11s. Last read position: chr17:55,773,730
INFO 2024-04-10 09:17:36 CollectVariantCallingMetrics Read 13,500,000 variants. Elapsed time: 00:24:36s. Time for last 100,000: 11s. Last read position: chr17:67,911,014
INFO 2024-04-10 09:17:47 CollectVariantCallingMetrics Read 13,600,000 variants. Elapsed time: 00:24:48s. Time for last 100,000: 11s. Last read position: chr17:76,626,069
INFO 2024-04-10 09:17:58 CollectVariantCallingMetrics Read 13,700,000 variants. Elapsed time: 00:24:58s. Time for last 100,000: 10s. Last read position: chr17:82,237,567
INFO 2024-04-10 09:18:09 CollectVariantCallingMetrics Read 13,800,000 variants. Elapsed time: 00:25:09s. Time for last 100,000: 10s. Last read position: chr18:24,080,872
INFO 2024-04-10 09:18:22 CollectVariantCallingMetrics Read 13,900,000 variants. Elapsed time: 00:25:22s. Time for last 100,000: 12s. Last read position: chr18:57,662,594
INFO 2024-04-10 09:18:31 CollectVariantCallingMetrics Read 14,000,000 variants. Elapsed time: 00:25:31s. Time for last 100,000: 9s. Last read position: chr19:1,043,385
INFO 2024-04-10 09:18:41 CollectVariantCallingMetrics Read 14,100,000 variants. Elapsed time: 00:25:41s. Time for last 100,000: 9s. Last read position: chr19:4,343,771
INFO 2024-04-10 09:18:51 CollectVariantCallingMetrics Read 14,200,000 variants. Elapsed time: 00:25:52s. Time for last 100,000: 10s. Last read position: chr19:8,897,567
INFO 2024-04-10 09:19:00 CollectVariantCallingMetrics Read 14,300,000 variants. Elapsed time: 00:26:00s. Time for last 100,000: 8s. Last read position: chr19:12,145,940
INFO 2024-04-10 09:19:09 CollectVariantCallingMetrics Read 14,400,000 variants. Elapsed time: 00:26:09s. Time for last 100,000: 8s. Last read position: chr19:16,876,510
INFO 2024-04-10 09:19:17 CollectVariantCallingMetrics Read 14,500,000 variants. Elapsed time: 00:26:17s. Time for last 100,000: 7s. Last read position: chr19:22,180,967
INFO 2024-04-10 09:19:25 CollectVariantCallingMetrics Read 14,600,000 variants. Elapsed time: 00:26:26s. Time for last 100,000: 8s. Last read position: chr19:36,818,974
INFO 2024-04-10 09:19:34 CollectVariantCallingMetrics Read 14,700,000 variants. Elapsed time: 00:26:34s. Time for last 100,000: 8s. Last read position: chr19:41,194,657
INFO 2024-04-10 09:19:41 CollectVariantCallingMetrics Read 14,800,000 variants. Elapsed time: 00:26:41s. Time for last 100,000: 7s. Last read position: chr19:45,499,204
INFO 2024-04-10 09:19:50 CollectVariantCallingMetrics Read 14,900,000 variants. Elapsed time: 00:26:50s. Time for last 100,000: 8s. Last read position: chr19:49,476,124
INFO 2024-04-10 09:19:57 CollectVariantCallingMetrics Read 15,000,000 variants. Elapsed time: 00:26:57s. Time for last 100,000: 7s. Last read position: chr19:53,140,855
INFO 2024-04-10 09:20:05 CollectVariantCallingMetrics Read 15,100,000 variants. Elapsed time: 00:27:05s. Time for last 100,000: 7s. Last read position: chr19:57,130,000
INFO 2024-04-10 09:20:11 CollectVariantCallingMetrics Read 15,200,000 variants. Elapsed time: 00:27:12s. Time for last 100,000: 6s. Last read position: chr20:3,964,010
INFO 2024-04-10 09:20:23 CollectVariantCallingMetrics Read 15,300,000 variants. Elapsed time: 00:27:23s. Time for last 100,000: 11s. Last read position: chr20:33,083,296
INFO 2024-04-10 09:20:33 CollectVariantCallingMetrics Read 15,400,000 variants. Elapsed time: 00:27:33s. Time for last 100,000: 10s. Last read position: chr20:45,425,646
INFO 2024-04-10 09:20:43 CollectVariantCallingMetrics Read 15,500,000 variants. Elapsed time: 00:27:44s. Time for last 100,000: 10s. Last read position: chr20:62,322,722
INFO 2024-04-10 09:20:53 CollectVariantCallingMetrics Read 15,600,000 variants. Elapsed time: 00:27:54s. Time for last 100,000: 9s. Last read position: chr21:33,262,567
INFO 2024-04-10 09:21:05 CollectVariantCallingMetrics Read 15,700,000 variants. Elapsed time: 00:28:06s. Time for last 100,000: 11s. Last read position: chr21:45,918,399
INFO 2024-04-10 09:21:17 CollectVariantCallingMetrics Read 15,800,000 variants. Elapsed time: 00:28:18s. Time for last 100,000: 12s. Last read position: chr22:22,721,029
INFO 2024-04-10 09:21:27 CollectVariantCallingMetrics Read 15,900,000 variants. Elapsed time: 00:28:28s. Time for last 100,000: 9s. Last read position: chr22:31,874,384
INFO 2024-04-10 09:21:38 CollectVariantCallingMetrics Read 16,000,000 variants. Elapsed time: 00:28:38s. Time for last 100,000: 10s. Last read position: chr22:41,781,690
INFO 2024-04-10 09:21:49 CollectVariantCallingMetrics Read 16,100,000 variants. Elapsed time: 00:28:50s. Time for last 100,000: 11s. Last read position: chrX:386,569
INFO 2024-04-10 09:21:59 CollectVariantCallingMetrics Read 16,200,000 variants. Elapsed time: 00:29:00s. Time for last 100,000: 9s. Last read position: chrX:40,598,692
INFO 2024-04-10 09:22:08 CollectVariantCallingMetrics Read 16,300,000 variants. Elapsed time: 00:29:09s. Time for last 100,000: 9s. Last read position: chrX:70,277,435
INFO 2024-04-10 09:22:17 CollectVariantCallingMetrics Read 16,400,000 variants. Elapsed time: 00:29:18s. Time for last 100,000: 8s. Last read position: chrX:111,735,118
INFO 2024-04-10 09:22:25 CollectVariantCallingMetrics Read 16,500,000 variants. Elapsed time: 00:29:26s. Time for last 100,000: 8s. Last read position: chrX:153,671,362
INFO 2024-04-10 09:22:31 CollectVariantCallingMetrics Starting iteration of variants.
ERROR 2024-04-10 09:22:33 MultiThreadedChunkBased Unexpected exception encountered in child thread.
java.lang.ArrayIndexOutOfBoundsException: Index 1 out of bounds for length 1
at picard.vcf.CallingMetricAccumulator.updateSummaryMetric(CallingMetricAccumulator.java:244)
at picard.vcf.CallingMetricAccumulator.updateDetailMetric(CallingMetricAccumulator.java:180)
at picard.vcf.CallingMetricAccumulator.lambda$accumulate$3(CallingMetricAccumulator.java:127)
at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.accept(ForEachOps.java:183)
at java.base/java.util.stream.ReferencePipeline$2$1.accept(ReferencePipeline.java:179)
at java.base/java.util.HashMap$KeySpliterator.forEachRemaining(HashMap.java:1707)
at java.base/java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:509)
at java.base/java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:499)
at java.base/java.util.stream.ForEachOps$ForEachOp.evaluateSequential(ForEachOps.java:150)
at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.evaluateSequential(ForEachOps.java:173)
at java.base/java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234)
at java.base/java.util.stream.ReferencePipeline.forEach(ReferencePipeline.java:596)
at picard.vcf.CallingMetricAccumulator.accumulate(CallingMetricAccumulator.java:126)
at picard.vcf.processor.VariantAccumulatorExecutor$MultiThreadedChunkBased$Worker.run(VariantAccumulatorExecutor.java:142)
at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:539)
at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1136)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:635)
at java.base/java.lang.Thread.run(Thread.java:840)
[Wed Apr 10 09:22:33 CEST 2024] picard.vcf.CollectVariantCallingMetrics done. Elapsed time: 29.65 minutes.
Runtime.totalMemory()=2379735040
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
picard.vcf.processor.VariantAccumulatorExecutor$MultiThreadedChunkBased$MultiException: Children threads encountered exceptions:
Index 1 out of bounds for length 1
at picard.vcf.processor.VariantAccumulatorExecutor$MultiThreadedChunkBased.awaitCompletion(VariantAccumulatorExecutor.java:109)
at picard.vcf.processor.VariantProcessor.process(VariantProcessor.java:97)
at picard.vcf.CollectVariantCallingMetrics.doWork(CollectVariantCallingMetrics.java:129)
at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:289)
at org.broadinstitute.hellbender.cmdline.PicardCommandLineProgramExecutor.instanceMain(PicardCommandLineProgramExecutor.java:37)
at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:160)
at org.broadinstitute.hellbender.Main.mainEntry(Main.java:203)
at org.broadinstitute.hellbender.Main.main(Main.java:289)
-
Can you run ValidateVariants tool on your callset to see if any of the records is causing any errors?
-
Hi ah yeah, I did run that. It seemed ok to me, but I might have missed something. For completeness, this is what I did:
- updated to gatk 4.5.0.0. Did not work, broke my other stuff
- adjusted threads (1 to 8)
- ran:
gatk ValidateVariants -V WESP_run/results/variant_calling/varscan/RM8398_EF_S16.vcf -D WESP_run/resources/GCF_000001405.40.renamed.vcf.gz"
Using GATK jar /mnt/scratch_dir/deutekoe/conda/envs/gatk4/share/gatk4-4.5.0.0-0/gatk-package-4.5.0.0-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 -jar /mnt/scratch_dir/deutekoe/conda/envs/gatk4/share/gatk4-4.5.0.0-0/gatk-package-4.5.0.0-local.jar ValidateVariants -V WESP_run/results/variant_calling/varscan/RM8398_EF_S16.vcf -D WESP_run/resources/GCF_000001405.40.renamed.vcf.gz
13:59:25.707 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/mnt/scratch_dir/deutekoe/conda/envs/gatk4/share/gatk4-4.5.0.0-0/gatk-package-4.5.0.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
13:59:26.175 INFO ValidateVariants - ------------------------------------------------------------
13:59:26.179 INFO ValidateVariants - The Genome Analysis Toolkit (GATK) v4.5.0.0
13:59:26.179 INFO ValidateVariants - For support and documentation go to https://software.broadinstitute.org/gatk/
13:59:26.179 INFO ValidateVariants - Executing as deutekoe on Linux v3.10.0-1160.105.1.el7.x86_64 amd64
13:59:26.179 INFO ValidateVariants - Java runtime: OpenJDK 64-Bit Server VM v17.0.10-internal+0-adhoc..src
13:59:26.179 INFO ValidateVariants - Start Date/Time: April 10, 2024 at 1:59:25 PM CEST
13:59:26.180 INFO ValidateVariants - ------------------------------------------------------------
13:59:26.180 INFO ValidateVariants - ------------------------------------------------------------
13:59:26.180 INFO ValidateVariants - HTSJDK Version: 4.1.0
13:59:26.180 INFO ValidateVariants - Picard Version: 3.1.1
13:59:26.180 INFO ValidateVariants - Built for Spark Version: 3.5.0
13:59:26.181 INFO ValidateVariants - HTSJDK Defaults.COMPRESSION_LEVEL : 2
13:59:26.181 INFO ValidateVariants - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
13:59:26.182 INFO ValidateVariants - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
13:59:26.183 INFO ValidateVariants - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
13:59:26.183 INFO ValidateVariants - Deflater: IntelDeflater
13:59:26.183 INFO ValidateVariants - Inflater: IntelInflater
13:59:26.183 INFO ValidateVariants - GCS max retries/reopens: 20
13:59:26.183 INFO ValidateVariants - Requester pays: disabled
13:59:26.184 INFO ValidateVariants - Initializing engine
13:59:26.414 INFO FeatureManager - Using codec VCFCodec to read file file:///mnt/scratch_dir/deutekoe/trial/WESP_run/resources/GCF_000001405.40.renamed.vcf.gz
13:59:27.064 INFO FeatureManager - Using codec VCFCodec to read file file:///mnt/scratch_dir/deutekoe/trial/WESP_run/results/variant_calling/varscan/RM8398_EF_S16.vcf
13:59:27.498 INFO ValidateVariants - Done initializing engine
13:59:27.500 WARN ValidateVariants - REF validation cannot be done because no reference file was provided
13:59:27.500 WARN ValidateVariants - Other possible validations will still be performed
13:59:27.501 INFO ProgressMeter - Starting traversal
13:59:27.501 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
13:59:50.095 INFO ProgressMeter - chr1:11059842 0.4 1000 2655.9
14:00:02.661 INFO ProgressMeter - chr1:16698167 0.6 2000 3413.1
14:00:22.193 INFO ProgressMeter - chr1:26255600 0.9 3000 3291.2
14:00:51.201 INFO ProgressMeter - chr1:43172261 1.4 4000 2867.4
14:01:22.646 INFO ProgressMeter - chr1:62263166 1.9 5000 2605.4
14:02:02.527 INFO ProgressMeter - chr1:92333594 2.6 6000 2322.2
14:02:35.105 INFO ProgressMeter - chr1:115857214 3.1 7000 2238.8
14:02:56.543 INFO ProgressMeter - chr1:147056188 3.5 8000 2296.2
14:03:15.743 INFO ProgressMeter - chr1:155287701 3.8 9000 2365.9
14:03:35.202 INFO ProgressMeter - chr1:165769074 4.1 10000 2422.3
14:04:06.600 INFO ProgressMeter - chr1:185147026 4.7 11000 2364.8
14:04:33.726 INFO ProgressMeter - chr1:206012565 5.1 12000 2351.2
14:05:08.835 INFO ProgressMeter - chr1:227493453 5.7 13000 2285.2
14:05:33.144 INFO ProgressMeter - chr1:241957759 6.1 14000 2297.3
14:05:58.800 INFO ProgressMeter - chr2:10792081 6.5 15000 2300.0
14:06:26.722 INFO ProgressMeter - chr2:32144832 7.0 16000 2290.0
14:07:13.877 INFO ProgressMeter - chr2:61380375 7.8 17000 2187.1
14:07:48.306 INFO ProgressMeter - chr2:87120739 8.3 18000 2156.5
14:08:04.851 INFO ProgressMeter - chr2:97995531 8.6 19000 2203.5
14:08:28.792 INFO ProgressMeter - chr2:113612069 9.0 20000 2216.9
14:08:53.732 INFO ProgressMeter - chr2:135788274 9.4 21000 2225.2
14:09:33.767 INFO ProgressMeter - chr2:169661081 10.1 22000 2177.3
14:10:06.149 INFO ProgressMeter - chr2:191386000 10.6 23000 2160.8
14:10:40.816 INFO ProgressMeter - chr2:217760858 11.2 24000 2138.7
14:11:03.525 INFO ProgressMeter - chr2:233190156 11.6 25000 2155.1
14:11:32.210 INFO ProgressMeter - chr3:8992874 12.1 26000 2152.6
14:12:07.068 INFO ProgressMeter - chr3:33132664 12.7 27000 2132.8
14:12:39.820 INFO ProgressMeter - chr3:52472266 13.2 28000 2120.4
14:13:12.385 INFO ProgressMeter - chr3:75665415 13.7 29000 2109.4
14:13:43.758 INFO ProgressMeter - chr3:113450525 14.3 30000 2102.2
14:14:11.951 INFO ProgressMeter - chr3:131016043 14.7 31000 2103.0
14:14:51.251 INFO ProgressMeter - chr3:161504060 15.4 32000 2078.5
14:15:30.704 INFO ProgressMeter - chr3:193993393 16.1 33000 2055.6
14:15:45.196 INFO ProgressMeter - chr4:2291194 16.3 34000 2086.5
14:16:05.170 INFO ProgressMeter - chr4:9779606 16.6 35000 2104.9
14:16:42.894 INFO ProgressMeter - chr4:48510685 17.3 36000 2086.2
14:17:12.298 INFO ProgressMeter - chr4:73543766 17.7 37000 2084.9
14:17:48.647 INFO ProgressMeter - chr4:103140688 18.4 38000 2070.6
14:18:26.725 INFO ProgressMeter - chr4:140947908 19.0 39000 2054.0
14:19:06.610 INFO ProgressMeter - chr4:176222576 19.7 40000 2035.4
14:19:25.780 INFO ProgressMeter - chr5:1094274 20.0 41000 2052.9
14:19:59.926 INFO ProgressMeter - chr5:36217895 20.5 42000 2044.7
14:20:35.955 INFO ProgressMeter - chr5:69313357 21.1 43000 2034.0
14:21:07.042 INFO ProgressMeter - chr5:96996381 21.7 44000 2031.5
14:21:54.215 INFO ProgressMeter - chr5:137936279 22.4 45000 2004.9
14:22:21.551 INFO ProgressMeter - chr5:157087442 22.9 46000 2008.7
14:22:49.902 INFO ProgressMeter - chr5:179708070 23.4 47000 2010.8
14:23:21.194 INFO ProgressMeter - chr6:21602321 23.9 48000 2008.8
14:23:33.219 INFO ProgressMeter - chr6:29945653 24.1 49000 2033.6
14:23:50.717 INFO ProgressMeter - chr6:38807898 24.4 52000 2132.3
14:24:25.788 INFO ProgressMeter - chr6:64388875 25.0 53000 2122.4
14:25:05.920 INFO ProgressMeter - chr6:100879659 25.6 54000 2106.1
14:25:44.267 INFO ProgressMeter - chr6:132374478 26.3 55000 2092.9
14:26:17.106 INFO ProgressMeter - chr6:159323887 26.8 56000 2087.5
14:26:43.962 INFO ProgressMeter - chr7:4079346 27.3 57000 2089.9
14:27:18.397 INFO ProgressMeter - chr7:25154999 27.8 58000 2082.7
14:27:50.755 INFO ProgressMeter - chr7:48489568 28.4 59000 2078.4
14:28:22.006 INFO ProgressMeter - chr7:75063485 28.9 60000 2075.5
14:28:54.346 INFO ProgressMeter - chr7:100107173 29.4 61000 2071.5
14:29:40.884 INFO ProgressMeter - chr7:135415152 30.2 63000 2084.5
14:29:52.164 INFO ProgressMeter - chr7:142774011 30.4 64000 2104.5
14:30:15.461 INFO ProgressMeter - chr7:158683579 30.8 65000 2110.4
14:30:45.032 INFO ProgressMeter - chr8:11999355 31.3 66000 2109.2
14:31:13.165 INFO ProgressMeter - chr8:27397851 31.8 67000 2109.5
14:31:53.730 INFO ProgressMeter - chr8:62999559 32.4 68000 2096.4
14:32:43.796 INFO ProgressMeter - chr8:108479170 33.3 69000 2073.8
14:33:18.307 INFO ProgressMeter - chr8:142543729 33.8 70000 2068.1
14:33:38.316 INFO ProgressMeter - chr9:6606746 34.2 71000 2077.2
14:34:16.849 INFO ProgressMeter - chr9:34725050 34.8 72000 2067.6
14:34:33.430 INFO ProgressMeter - chr9:62844107 35.1 73000 2079.8
14:34:51.858 INFO ProgressMeter - chr9:76489898 35.4 74000 2090.0
14:35:28.174 INFO ProgressMeter - chr9:104604727 36.0 75000 2082.7
14:36:01.880 INFO ProgressMeter - chr9:127579231 36.6 76000 2078.0
14:36:17.836 INFO ProgressMeter - chr9:134079343 36.8 77000 2090.2
14:36:32.198 INFO ProgressMeter - chr10:2501466 37.1 78000 2103.7
14:37:00.309 INFO ProgressMeter - chr10:20787378 37.5 79000 2104.0
14:37:34.439 INFO ProgressMeter - chr10:45000672 38.1 80000 2098.9
14:37:54.943 INFO ProgressMeter - chr10:60080702 38.5 81000 2106.2
14:38:24.933 INFO ProgressMeter - chr10:84081630 39.0 82000 2104.9
14:38:51.185 INFO ProgressMeter - chr10:100204555 39.4 83000 2106.9
14:39:21.154 INFO ProgressMeter - chr10:123040356 39.9 84000 2105.6
14:39:37.791 INFO ProgressMeter - chr11:236871 40.2 85000 2115.9
14:40:05.583 INFO ProgressMeter - chr11:12002226 40.6 87000 2141.0
14:40:44.381 INFO ProgressMeter - chr11:43798658 41.3 88000 2131.7
14:41:10.761 INFO ProgressMeter - chr11:60175636 41.7 89000 2133.2
14:41:28.381 INFO ProgressMeter - chr11:67715957 42.0 90000 2142.1
14:41:54.165 INFO ProgressMeter - chr11:83980415 42.4 91000 2144.0
14:42:27.941 INFO ProgressMeter - chr11:111870102 43.0 92000 2139.2
14:42:50.565 INFO ProgressMeter - chr11:126293229 43.4 93000 2143.6
14:43:15.758 INFO ProgressMeter - chr12:7189790 43.8 94000 2145.9
14:43:29.658 INFO ProgressMeter - chr12:13569728 44.0 95000 2157.3
14:43:58.537 INFO ProgressMeter - chr12:38028645 44.5 96000 2156.5
14:44:21.531 INFO ProgressMeter - chr12:52286153 44.9 97000 2160.3
14:44:40.291 INFO ProgressMeter - chr12:64275111 45.2 98000 2167.5
14:45:17.946 INFO ProgressMeter - chr12:96952177 45.8 99000 2159.7
14:45:50.924 INFO ProgressMeter - chr12:120447081 46.4 100000 2155.6
14:46:13.836 INFO ProgressMeter - chr12:132811208 46.8 101000 2159.4
14:46:33.874 INFO ProgressMeter - chr13:26680030 47.1 102000 2165.3
14:47:06.991 INFO ProgressMeter - chr13:49541661 47.7 103000 2161.2
14:47:49.212 INFO ProgressMeter - chr13:102733766 48.4 104000 2150.5
14:48:04.208 INFO ProgressMeter - chr14:19402012 48.6 105000 2160.0
14:48:17.128 INFO ProgressMeter - chr14:26597507 48.8 106000 2170.9
14:48:52.159 INFO ProgressMeter - chr14:59610065 49.4 107000 2165.5
14:49:18.642 INFO ProgressMeter - chr14:77330298 49.9 108000 2166.4
14:49:48.662 INFO ProgressMeter - chr14:102930369 50.4 109000 2164.7
14:49:59.577 INFO ProgressMeter - chr15:20741838 50.5 110000 2176.7
14:50:17.677 INFO ProgressMeter - chr15:32804465 50.8 111000 2183.5
14:50:35.923 INFO ProgressMeter - chr15:43924361 51.1 112000 2190.1
14:51:07.439 INFO ProgressMeter - chr15:64824129 51.7 113000 2187.1
14:51:28.603 INFO ProgressMeter - chr15:78200244 52.0 114000 2191.5
14:51:44.551 INFO ProgressMeter - chr15:88512809 52.3 115000 2199.5
14:52:05.962 INFO ProgressMeter - chr16:370338 52.6 116000 2203.6
14:52:18.814 INFO ProgressMeter - chr16:4564054 52.9 117000 2213.6
14:52:43.778 INFO ProgressMeter - chr16:19487243 53.3 118000 2215.1
14:53:05.568 INFO ProgressMeter - chr16:33598996 53.6 119000 2218.7
14:53:22.463 INFO ProgressMeter - chr16:57249818 53.9 120000 2225.7
14:53:46.713 INFO ProgressMeter - chr16:75463442 54.3 121000 2227.5
14:54:15.434 INFO ProgressMeter - chr16:88738326 54.8 122000 2226.3
14:54:32.308 INFO ProgressMeter - chr17:4499508 55.1 123000 2233.1
14:54:47.097 INFO ProgressMeter - chr17:12717444 55.3 124000 2241.2
14:55:00.760 INFO ProgressMeter - chr17:21415276 55.6 125000 2250.1
14:55:19.849 INFO ProgressMeter - chr17:36493853 55.9 126000 2255.1
14:55:34.053 INFO ProgressMeter - chr17:43202523 56.1 127000 2263.4
14:55:57.230 INFO ProgressMeter - chr17:58973004 56.5 128000 2265.7
14:56:19.629 INFO ProgressMeter - chr17:74613950 56.9 129000 2268.4
14:56:33.938 INFO ProgressMeter - chr17:80998620 57.1 130000 2276.4
14:56:52.263 INFO ProgressMeter - chr18:9594802 57.4 131000 2281.7
14:57:17.323 INFO ProgressMeter - chr18:35140225 57.8 132000 2282.5
14:57:54.552 INFO ProgressMeter - chr18:71226775 58.5 133000 2275.4
14:58:13.076 INFO ProgressMeter - chr19:2811833 58.8 134000 2280.5
14:58:26.574 INFO ProgressMeter - chr19:7814132 59.0 135000 2288.7
14:58:41.032 INFO ProgressMeter - chr19:14107208 59.2 136000 2296.3
14:58:53.069 INFO ProgressMeter - chr19:19280064 59.4 137000 2305.4
14:59:14.095 INFO ProgressMeter - chr19:34931904 59.8 138000 2308.6
14:59:26.984 INFO ProgressMeter - chr19:41025920 60.0 139000 2317.0
14:59:41.737 INFO ProgressMeter - chr19:47353079 60.2 140000 2324.1
14:59:52.918 INFO ProgressMeter - chr19:51645551 60.4 141000 2333.5
15:00:08.045 INFO ProgressMeter - chr19:57244250 60.7 143000 2356.8
15:00:28.216 INFO ProgressMeter - chr20:13792926 61.0 144000 2360.2
15:00:46.810 INFO ProgressMeter - chr20:30391498 61.3 145000 2364.6
15:01:12.135 INFO ProgressMeter - chr20:47169235 61.7 146000 2364.6
15:01:35.009 INFO ProgressMeter - chr20:64083430 62.1 147000 2366.2
15:01:57.016 INFO ProgressMeter - chr21:30601197 62.5 148000 2368.3
15:02:18.331 INFO ProgressMeter - chr21:44558616 62.8 149000 2370.8
15:02:40.358 INFO ProgressMeter - chr22:22117897 63.2 151000 2388.7
15:02:54.575 INFO ProgressMeter - chr22:30534399 63.5 152000 2395.5
15:03:16.348 INFO ProgressMeter - chr22:42140302 63.8 153000 2397.6
15:03:35.331 INFO ProgressMeter - chrX:1352649 64.1 154000 2401.4
15:04:04.124 INFO ProgressMeter - chrX:48975236 64.6 155000 2399.0
15:04:38.762 INFO ProgressMeter - chrX:106901299 65.2 156000 2393.1
15:05:06.766 INFO ProgressMeter - chrX:154470399 65.7 157000 2391.3
15:05:11.906 INFO ProgressMeter - chrUn_JTFH01001117v1_decoy:1104 65.7 168977 2570.4
15:05:11.906 INFO ProgressMeter - Traversal complete. Processed 168977 total variants in 65.7 minutes.
15:05:11.906 INFO ValidateVariants - Shutting down engine
[April 10, 2024 at 3:05:11 PM CEST] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 65.77 minutes.
Runtime.totalMemory()=558624768 -
This looks like a bug. Can you share your input vcf with us so that we can replicate the problem?
You may use the below article to submit your files. Once you are done let us know the file name so that we can check.
https://gatk.broadinstitute.org/hc/en-us/articles/360035889671-How-do-I-submit-a-detailed-bug-report
Regards.
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