Using GATK jar /mmfs1/gscratch/srlab/nextflow/bin/miniforge/envs/gatk4/share/gatk4-4.6.2.0-0/gatk-package-4.6.2.0-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 -Xmx400g -jar /mmfs1/gscratch/srlab/nextflow/bin/miniforge/envs/gatk4/share/gatk4-4.6.2.0-0/gatk-package-4.6.2.0-local.jar GenomicsDBImport --genomicsdb-workspace-path GenomicsDB/ -L intervals.bed --sample-name-map sample_map.txt --read-index read_indexes.txt --reader-threads 20 09:00:30.645 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/mmfs1/gscratch/srlab/nextflow/bin/miniforge/envs/gatk4/share/gatk4-4.6.2.0-0/gatk-package-4.6.2.0-local.jar!/com/intel/gkl/native/libgkl_compression.so 09:00:31.909 INFO GenomicsDBImport - ------------------------------------------------------------ 09:00:31.911 INFO GenomicsDBImport - The Genome Analysis Toolkit (GATK) v4.6.2.0 09:00:31.911 INFO GenomicsDBImport - For support and documentation go to https://software.broadinstitute.org/gatk/ 09:00:31.911 INFO GenomicsDBImport - Executing as strigg@n3432 on Linux v4.18.0-513.18.1.el8_9.x86_64 amd64 09:00:31.911 INFO GenomicsDBImport - Java runtime: OpenJDK 64-Bit Server VM v21.0.7+6-LTS 09:00:31.912 INFO GenomicsDBImport - Start Date/Time: July 22, 2025, 9:00:29 AM PDT 09:00:31.912 INFO GenomicsDBImport - ------------------------------------------------------------ 09:00:31.912 INFO GenomicsDBImport - ------------------------------------------------------------ 09:00:31.912 INFO GenomicsDBImport - HTSJDK Version: 4.2.0 09:00:31.912 INFO GenomicsDBImport - Picard Version: 3.4.0 09:00:31.912 INFO GenomicsDBImport - Built for Spark Version: 3.5.0 09:00:31.914 INFO GenomicsDBImport - HTSJDK Defaults.COMPRESSION_LEVEL : 2 09:00:31.914 INFO GenomicsDBImport - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 09:00:31.914 INFO GenomicsDBImport - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 09:00:31.914 INFO GenomicsDBImport - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 09:00:31.914 INFO GenomicsDBImport - Deflater: IntelDeflater 09:00:31.914 INFO GenomicsDBImport - Inflater: IntelInflater 09:00:31.914 INFO GenomicsDBImport - GCS max retries/reopens: 20 09:00:31.922 INFO GenomicsDBImport - Requester pays: disabled 09:00:31.922 INFO GenomicsDBImport - Initializing engine 09:00:33.643 INFO FeatureManager - Using codec BEDCodec to read file file:///mmfs1/gscratch/scrubbed/strigg/analyses/20250714_biscuit/intervals.bed 09:00:33.653 INFO IntervalArgumentCollection - Processing 376579914 bp from intervals 09:00:33.654 WARN GenomicsDBImport - A large number of intervals were specified. Using more than 100 intervals in a single import is not recommended and can cause performance to suffer. If GVCF data only exists within those intervals, performance can be improved by aggregating intervals with the merge-input-intervals argument. 09:00:33.654 INFO GenomicsDBImport - Done initializing engine 09:00:34.307 INFO GenomicsDBLibLoader - GenomicsDB native library version : 1.5.5-addd795 09:00:34.313 INFO GenomicsDBImport - Vid Map JSON file will be written to /mmfs1/gscratch/scrubbed/strigg/analyses/20250714_biscuit/GenomicsDB/vidmap.json 09:00:34.313 INFO GenomicsDBImport - Callset Map JSON file will be written to /mmfs1/gscratch/scrubbed/strigg/analyses/20250714_biscuit/GenomicsDB/callset.json 09:00:34.313 INFO GenomicsDBImport - Complete VCF Header will be written to /mmfs1/gscratch/scrubbed/strigg/analyses/20250714_biscuit/GenomicsDB/vcfheader.vcf 09:00:34.313 INFO GenomicsDBImport - Importing to workspace - /mmfs1/gscratch/scrubbed/strigg/analyses/20250714_biscuit/GenomicsDB 09:00:34.313 WARN GenomicsDBImport - GenomicsDBImport cannot use multiple VCF reader threads for initialization when the number of intervals is greater than 1. Falling back to serial VCF reader initialization. 09:00:42.040 INFO GenomicsDBImport - Importing batch 1 with 32 samples 12:09:16.909 INFO GenomicsDBImport - Importing batch 1 with 32 samples 15:29:44.006 INFO GenomicsDBImport - Importing batch 1 with 32 samples 17:09:59.360 INFO GenomicsDBImport - Importing batch 1 with 32 samples 18:40:48.520 INFO GenomicsDBImport - Importing batch 1 with 32 samples 19:56:51.199 INFO GenomicsDBImport - Importing batch 1 with 32 samples 21:12:20.468 INFO GenomicsDBImport - Importing batch 1 with 32 samples 21:40:33.601 INFO GenomicsDBImport - Importing batch 1 with 32 samples 22:08:47.310 INFO GenomicsDBImport - Importing batch 1 with 32 samples 22:40:28.452 INFO GenomicsDBImport - Importing batch 1 with 32 samples 22:51:22.508 INFO GenomicsDBImport - Importing batch 1 with 32 samples 23:17:48.372 INFO GenomicsDBImport - Importing batch 1 with 32 samples 23:39:38.670 INFO GenomicsDBImport - Importing batch 1 with 32 samples 23:56:59.598 INFO GenomicsDBImport - Importing batch 1 with 32 samples 00:11:57.337 INFO GenomicsDBImport - Importing batch 1 with 32 samples 00:30:02.523 INFO GenomicsDBImport - Importing batch 1 with 32 samples 00:43:04.015 INFO GenomicsDBImport - Importing batch 1 with 32 samples 00:53:36.306 INFO GenomicsDBImport - Importing batch 1 with 32 samples 01:05:10.078 INFO GenomicsDBImport - Importing batch 1 with 32 samples 01:16:11.992 INFO GenomicsDBImport - Importing batch 1 with 32 samples 01:24:28.962 INFO GenomicsDBImport - Importing batch 1 with 32 samples 01:31:29.238 INFO GenomicsDBImport - Importing batch 1 with 32 samples 01:39:36.514 INFO GenomicsDBImport - Importing batch 1 with 32 samples 01:45:26.856 INFO GenomicsDBImport - Importing batch 1 with 32 samples 01:51:57.264 INFO GenomicsDBImport - Importing batch 1 with 32 samples 01:55:35.315 INFO GenomicsDBImport - Importing batch 1 with 32 samples 02:00:42.730 INFO GenomicsDBImport - Importing batch 1 with 32 samples 02:10:30.117 INFO GenomicsDBImport - Importing batch 1 with 32 samples 02:16:19.267 INFO GenomicsDBImport - Importing batch 1 with 32 samples 02:24:32.733 INFO GenomicsDBImport - Importing batch 1 with 32 samples 02:30:58.846 INFO GenomicsDBImport - Importing batch 1 with 32 samples 02:39:17.618 INFO GenomicsDBImport - Importing batch 1 with 32 samples 02:47:40.250 INFO GenomicsDBImport - Importing batch 1 with 32 samples 02:53:32.567 INFO GenomicsDBImport - Importing batch 1 with 32 samples 02:56:47.176 INFO GenomicsDBImport - Importing batch 1 with 32 samples 03:03:03.770 INFO GenomicsDBImport - Importing batch 1 with 32 samples 03:06:59.392 INFO GenomicsDBImport - Importing batch 1 with 32 samples 03:11:34.876 INFO GenomicsDBImport - Importing batch 1 with 32 samples 03:15:26.110 INFO GenomicsDBImport - Importing batch 1 with 32 samples 03:18:20.626 INFO GenomicsDBImport - Importing batch 1 with 32 samples 03:20:34.698 INFO GenomicsDBImport - Importing batch 1 with 32 samples 03:22:31.783 INFO GenomicsDBImport - Importing batch 1 with 32 samples 03:25:28.053 INFO GenomicsDBImport - Importing batch 1 with 32 samples 03:27:37.910 INFO GenomicsDBImport - Importing batch 1 with 32 samples 03:29:45.656 INFO GenomicsDBImport - Importing batch 1 with 32 samples 03:32:45.799 INFO GenomicsDBImport - Importing batch 1 with 32 samples 03:34:22.172 INFO GenomicsDBImport - Importing batch 1 with 32 samples 03:35:07.931 INFO GenomicsDBImport - Importing batch 1 with 32 samples 03:35:14.790 INFO GenomicsDBImport - Importing batch 1 with 32 samples 03:35:18.814 INFO GenomicsDBImport - Importing batch 1 with 32 samples 03:35:23.811 INFO GenomicsDBImport - Importing batch 1 with 32 samples 03:35:27.231 INFO GenomicsDBImport - Importing batch 1 with 32 samples 03:35:33.526 INFO GenomicsDBImport - Importing batch 1 with 32 samples 03:35:36.122 INFO GenomicsDBImport - Importing batch 1 with 32 samples 03:35:40.247 INFO GenomicsDBImport - Importing batch 1 with 32 samples 03:35:50.611 INFO GenomicsDBImport - Importing batch 1 with 32 samples 03:35:56.340 INFO GenomicsDBImport - Importing batch 1 with 32 samples 03:35:59.503 INFO GenomicsDBImport - Importing batch 1 with 32 samples 03:36:05.201 INFO GenomicsDBImport - Importing batch 1 with 32 samples 03:36:07.945 INFO GenomicsDBImport - Importing batch 1 with 32 samples 03:36:10.500 INFO GenomicsDBImport - Importing batch 1 with 32 samples 03:36:13.566 INFO GenomicsDBImport - Importing batch 1 with 32 samples 03:36:18.216 INFO GenomicsDBImport - Importing batch 1 with 32 samples 03:36:21.034 INFO GenomicsDBImport - Importing batch 1 with 32 samples 03:36:23.250 INFO GenomicsDBImport - Importing batch 1 with 32 samples 03:36:24.566 INFO GenomicsDBImport - Importing batch 1 with 32 samples 03:36:24.769 INFO GenomicsDBImport - Importing batch 1 with 32 samples 03:36:28.738 INFO GenomicsDBImport - Importing batch 1 with 32 samples 03:36:33.088 INFO GenomicsDBImport - Importing batch 1 with 32 samples 03:36:38.107 INFO GenomicsDBImport - Importing batch 1 with 32 samples 03:36:43.383 INFO GenomicsDBImport - Importing batch 1 with 32 samples 03:36:46.514 INFO GenomicsDBImport - Importing batch 1 with 32 samples 03:36:49.488 INFO GenomicsDBImport - Importing batch 1 with 32 samples 03:36:52.251 INFO GenomicsDBImport - Importing batch 1 with 32 samples 03:36:55.142 INFO GenomicsDBImport - Importing batch 1 with 32 samples 03:36:57.834 INFO GenomicsDBImport - Importing batch 1 with 32 samples 03:37:00.782 INFO GenomicsDBImport - Importing batch 1 with 32 samples 03:37:04.960 INFO GenomicsDBImport - Importing batch 1 with 32 samples 03:37:07.905 INFO GenomicsDBImport - Importing batch 1 with 32 samples 03:37:10.928 INFO GenomicsDBImport - Importing batch 1 with 32 samples 03:37:13.747 INFO GenomicsDBImport - Importing batch 1 with 32 samples 03:37:18.316 INFO GenomicsDBImport - Importing batch 1 with 32 samples 03:37:20.827 INFO GenomicsDBImport - Importing batch 1 with 32 samples 03:37:25.727 INFO GenomicsDBImport - Importing batch 1 with 32 samples 03:37:30.235 INFO GenomicsDBImport - Importing batch 1 with 32 samples 03:37:40.307 INFO GenomicsDBImport - Importing batch 1 with 32 samples 03:37:51.680 INFO GenomicsDBImport - Importing batch 1 with 32 samples 03:38:04.072 INFO GenomicsDBImport - Importing batch 1 with 32 samples 03:38:09.460 INFO GenomicsDBImport - Importing batch 1 with 32 samples 03:38:14.366 INFO GenomicsDBImport - Importing batch 1 with 32 samples 03:38:18.708 INFO GenomicsDBImport - Importing batch 1 with 32 samples 03:38:24.145 INFO GenomicsDBImport - Importing batch 1 with 32 samples 03:38:30.691 INFO GenomicsDBImport - Importing batch 1 with 32 samples 03:38:34.246 INFO GenomicsDBImport - Importing batch 1 with 32 samples 03:38:37.141 INFO GenomicsDBImport - Importing batch 1 with 32 samples 03:38:42.946 INFO GenomicsDBImport - Importing batch 1 with 32 samples 03:38:49.042 INFO GenomicsDBImport - Importing batch 1 with 32 samples 03:38:53.340 INFO GenomicsDBImport - Importing batch 1 with 32 samples 03:38:56.654 INFO GenomicsDBImport - Importing batch 1 with 32 samples 03:39:02.734 INFO GenomicsDBImport - Importing batch 1 with 32 samples 03:39:09.577 INFO GenomicsDBImport - Importing batch 1 with 32 samples 03:39:14.715 INFO GenomicsDBImport - Importing batch 1 with 32 samples 03:39:21.331 INFO GenomicsDBImport - Importing batch 1 with 32 samples 03:39:28.119 INFO GenomicsDBImport - Importing batch 1 with 32 samples 03:39:35.218 INFO GenomicsDBImport - Importing batch 1 with 32 samples 03:39:38.910 INFO GenomicsDBImport - Importing batch 1 with 32 samples 03:39:45.405 INFO GenomicsDBImport - Importing batch 1 with 32 samples 03:39:49.405 INFO GenomicsDBImport - Importing batch 1 with 32 samples 03:39:55.304 INFO GenomicsDBImport - Importing batch 1 with 32 samples 03:39:59.435 INFO GenomicsDBImport - Importing batch 1 with 32 samples 03:40:05.192 INFO GenomicsDBImport - Importing batch 1 with 32 samples 03:40:08.447 INFO GenomicsDBImport - Importing batch 1 with 32 samples 03:40:12.104 INFO GenomicsDBImport - Importing batch 1 with 32 samples 03:40:16.328 INFO GenomicsDBImport - Importing batch 1 with 32 samples 03:40:21.003 INFO GenomicsDBImport - Importing batch 1 with 32 samples 03:40:25.219 INFO GenomicsDBImport - Importing batch 1 with 32 samples 03:40:29.995 INFO GenomicsDBImport - Importing batch 1 with 32 samples 03:40:34.634 INFO GenomicsDBImport - Importing batch 1 with 32 samples 03:40:39.185 INFO GenomicsDBImport - Importing batch 1 with 32 samples 03:40:43.804 INFO GenomicsDBImport - Importing batch 1 with 32 samples 03:40:49.799 INFO GenomicsDBImport - Importing batch 1 with 32 samples 03:40:54.485 INFO GenomicsDBImport - Importing batch 1 with 32 samples 03:41:02.462 INFO GenomicsDBImport - Importing batch 1 with 32 samples 03:41:07.832 INFO GenomicsDBImport - Importing batch 1 with 32 samples 03:41:13.309 INFO GenomicsDBImport - Importing batch 1 with 32 samples 03:41:17.756 INFO GenomicsDBImport - Importing batch 1 with 32 samples 03:41:22.494 INFO GenomicsDBImport - Importing batch 1 with 32 samples 03:41:24.905 INFO GenomicsDBImport - Importing batch 1 with 32 samples 03:41:30.871 INFO GenomicsDBImport - Importing batch 1 with 32 samples 03:41:34.925 INFO GenomicsDBImport - Importing batch 1 with 32 samples 03:41:39.709 INFO GenomicsDBImport - Importing batch 1 with 32 samples 03:41:44.195 INFO GenomicsDBImport - Importing batch 1 with 32 samples 03:41:47.171 INFO GenomicsDBImport - Importing batch 1 with 32 samples 03:41:54.277 INFO GenomicsDBImport - Importing batch 1 with 32 samples 03:41:59.486 INFO GenomicsDBImport - Importing batch 1 with 32 samples 03:42:04.206 INFO GenomicsDBImport - Importing batch 1 with 32 samples 03:42:08.248 INFO GenomicsDBImport - Importing batch 1 with 32 samples 03:42:14.018 INFO GenomicsDBImport - Importing batch 1 with 32 samples 03:42:20.674 INFO GenomicsDBImport - Importing batch 1 with 32 samples 03:42:26.448 INFO GenomicsDBImport - Importing batch 1 with 32 samples 03:42:30.617 INFO GenomicsDBImport - Importing batch 1 with 32 samples 03:42:36.682 INFO GenomicsDBImport - Importing batch 1 with 32 samples 03:42:40.612 INFO GenomicsDBImport - Importing batch 1 with 32 samples 03:42:45.721 INFO GenomicsDBImport - Importing batch 1 with 32 samples 03:42:50.489 INFO GenomicsDBImport - Importing batch 1 with 32 samples 03:42:55.074 INFO GenomicsDBImport - Importing batch 1 with 32 samples 03:43:00.452 INFO GenomicsDBImport - Importing batch 1 with 32 samples 03:43:07.179 INFO GenomicsDBImport - Importing batch 1 with 32 samples 03:43:12.279 INFO GenomicsDBImport - Importing batch 1 with 32 samples 03:43:16.936 INFO GenomicsDBImport - Importing batch 1 with 32 samples 03:43:20.815 INFO GenomicsDBImport - Importing batch 1 with 32 samples 03:43:25.031 INFO GenomicsDBImport - Importing batch 1 with 32 samples 03:43:29.777 INFO GenomicsDBImport - Importing batch 1 with 32 samples 03:43:34.320 INFO GenomicsDBImport - Importing batch 1 with 32 samples 03:43:39.343 INFO GenomicsDBImport - Importing batch 1 with 32 samples 03:43:44.057 INFO GenomicsDBImport - Importing batch 1 with 32 samples 03:43:48.785 INFO GenomicsDBImport - Importing batch 1 with 32 samples 03:43:53.838 INFO GenomicsDBImport - Importing batch 1 with 32 samples 03:43:59.071 INFO GenomicsDBImport - Importing batch 1 with 32 samples 03:44:04.372 INFO GenomicsDBImport - Importing batch 1 with 32 samples 03:44:08.320 INFO GenomicsDBImport - Importing batch 1 with 32 samples 03:44:13.156 INFO GenomicsDBImport - Importing batch 1 with 32 samples 03:44:18.808 INFO GenomicsDBImport - Importing batch 1 with 32 samples 03:44:24.444 INFO GenomicsDBImport - Importing batch 1 with 32 samples 03:44:28.150 INFO GenomicsDBImport - Importing batch 1 with 32 samples 03:44:31.417 INFO GenomicsDBImport - Importing batch 1 with 32 samples 03:44:34.591 INFO GenomicsDBImport - Importing batch 1 with 32 samples 03:44:40.600 INFO GenomicsDBImport - Importing batch 1 with 32 samples 03:44:44.586 INFO GenomicsDBImport - Importing batch 1 with 32 samples 03:44:50.442 INFO GenomicsDBImport - Importing batch 1 with 32 samples 03:44:57.018 INFO GenomicsDBImport - Importing batch 1 with 32 samples 03:45:00.503 INFO GenomicsDBImport - Importing batch 1 with 32 samples 03:45:07.780 INFO GenomicsDBImport - Importing batch 1 with 32 samples 03:45:12.164 INFO GenomicsDBImport - Importing batch 1 with 32 samples 03:45:16.803 INFO GenomicsDBImport - Importing batch 1 with 32 samples 03:45:21.167 INFO GenomicsDBImport - Importing batch 1 with 32 samples 03:45:26.199 INFO GenomicsDBImport - Importing batch 1 with 32 samples 03:45:30.228 INFO GenomicsDBImport - Importing batch 1 with 32 samples 03:45:33.607 INFO GenomicsDBImport - Importing batch 1 with 32 samples 03:45:35.874 INFO GenomicsDBImport - Importing batch 1 with 32 samples 03:45:38.966 INFO GenomicsDBImport - Importing batch 1 with 32 samples 03:45:40.710 INFO GenomicsDBImport - Importing batch 1 with 32 samples 03:45:41.147 INFO GenomicsDBImport - Importing batch 1 with 32 samples 03:45:43.610 INFO GenomicsDBImport - Importing batch 1 with 32 samples 03:45:46.955 INFO GenomicsDBImport - Importing batch 1 with 32 samples 03:45:50.782 INFO GenomicsDBImport - Importing batch 1 with 32 samples 03:45:54.287 INFO GenomicsDBImport - Importing batch 1 with 32 samples 03:45:56.394 INFO GenomicsDBImport - Importing batch 1 with 32 samples 03:46:00.628 INFO GenomicsDBImport - Importing batch 1 with 32 samples 03:46:05.322 INFO GenomicsDBImport - Importing batch 1 with 32 samples 03:46:09.750 INFO GenomicsDBImport - Importing batch 1 with 32 samples 03:46:13.427 INFO GenomicsDBImport - Importing batch 1 with 32 samples 03:46:17.282 INFO GenomicsDBImport - Importing batch 1 with 32 samples 03:46:21.801 INFO GenomicsDBImport - Importing batch 1 with 32 samples 03:46:26.010 INFO GenomicsDBImport - Importing batch 1 with 32 samples 03:46:29.490 INFO GenomicsDBImport - Importing batch 1 with 32 samples 03:46:32.691 INFO GenomicsDBImport - Importing batch 1 with 32 samples 03:46:37.383 INFO GenomicsDBImport - Importing batch 1 with 32 samples 03:46:40.825 INFO GenomicsDBImport - Importing batch 1 with 32 samples 03:46:44.400 INFO GenomicsDBImport - Importing batch 1 with 32 samples 03:46:47.402 INFO GenomicsDBImport - Importing batch 1 with 32 samples 03:46:51.731 INFO GenomicsDBImport - Importing batch 1 with 32 samples 03:46:59.923 INFO GenomicsDBImport - Importing batch 1 with 32 samples 03:47:04.280 INFO GenomicsDBImport - Importing batch 1 with 32 samples 03:47:07.552 INFO GenomicsDBImport - Importing batch 1 with 32 samples 03:47:10.801 INFO GenomicsDBImport - Importing batch 1 with 32 samples 03:47:13.950 INFO GenomicsDBImport - Importing batch 1 with 32 samples 03:47:17.994 INFO GenomicsDBImport - Importing batch 1 with 32 samples 03:47:21.855 INFO GenomicsDBImport - Importing batch 1 with 32 samples 03:47:25.821 INFO GenomicsDBImport - Importing batch 1 with 32 samples 03:47:30.169 INFO GenomicsDBImport - Importing batch 1 with 32 samples 03:47:33.237 INFO GenomicsDBImport - Importing batch 1 with 32 samples 03:47:33.816 INFO GenomicsDBImport - Done importing batch 1/1 03:47:33.818 INFO GenomicsDBImport - Import completed! 03:47:33.818 INFO GenomicsDBImport - Shutting down engine [July 23, 2025, 3:47:33 AM PDT] org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport done. Elapsed time: 1,127.07 minutes. Runtime.totalMemory()=2076049408 Tool returned: true