Using GATK jar /home/shared/gatk-4.2.5.0/gatk-package-4.2.5.0-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 /home/shared/gatk-4.2.5.0/gatk-package-4.2.5.0-local.jar AddOrReplaceReadGroups I=S12M.dedup-split.bam O=S12M.dedup-split-RG.bam RGID=1 RGLB=S12M RGPL=ILLUMINA RGPU=unit1 RGSM=S12M INFO 2022-03-11 09:58:35 AddOrReplaceReadGroups ********** NOTE: Picard's command line syntax is changing. ********** ********** For more information, please see: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** ********** The command line looks like this in the new syntax: ********** ********** AddOrReplaceReadGroups -I S12M.dedup-split.bam -O S12M.dedup-split-RG.bam -RGID 1 -RGLB S12M -RGPL ILLUMINA -RGPU unit1 -RGSM S12M ********** 09:58:35.197 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/shared/gatk-4.2.5.0/gatk-package-4.2.5.0-local.jar!/com/intel/gkl/native/libgkl_compression.so [Fri Mar 11 09:58:35 PST 2022] AddOrReplaceReadGroups INPUT=S12M.dedup-split.bam OUTPUT=S12M.dedup-split-RG.bam RGID=1 RGLB=S12M RGPL=ILLUMINA RGPU=unit1 RGSM=S12M VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=2 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Mar 11, 2022 9:58:35 AM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine INFO: Failed to detect whether we are running on Google Compute Engine. [Fri Mar 11 09:58:35 PST 2022] Executing as sr320@raven on Linux 5.4.0-96-generic amd64; OpenJDK 64-Bit Server VM 11.0.14+9-Ubuntu-0ubuntu2.18.04; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: 4.2.5.0 INFO 2022-03-11 09:58:35 AddOrReplaceReadGroups Created read-group ID=1 PL=ILLUMINA LB=S12M SM=S12M INFO 2022-03-11 09:58:38 AddOrReplaceReadGroups Processed 1,000,000 records. Elapsed time: 00:00:03s. Time for last 1,000,000: 3s. Last read position: NC_035780.1:10,612,562 INFO 2022-03-11 09:58:41 AddOrReplaceReadGroups Processed 2,000,000 records. Elapsed time: 00:00:06s. Time for last 1,000,000: 2s. Last read position: NC_035780.1:22,557,621 INFO 2022-03-11 09:58:44 AddOrReplaceReadGroups Processed 3,000,000 records. Elapsed time: 00:00:08s. Time for last 1,000,000: 2s. Last read position: NC_035780.1:32,603,339 INFO 2022-03-11 09:58:47 AddOrReplaceReadGroups Processed 4,000,000 records. Elapsed time: 00:00:11s. Time for last 1,000,000: 2s. Last read position: NC_035780.1:42,758,474 INFO 2022-03-11 09:58:50 AddOrReplaceReadGroups Processed 5,000,000 records. Elapsed time: 00:00:14s. Time for last 1,000,000: 3s. Last read position: NC_035780.1:57,180,406 INFO 2022-03-11 09:58:53 AddOrReplaceReadGroups Processed 6,000,000 records. Elapsed time: 00:00:17s. Time for last 1,000,000: 3s. Last read position: NC_035781.1:3,202,608 INFO 2022-03-11 09:58:56 AddOrReplaceReadGroups Processed 7,000,000 records. Elapsed time: 00:00:20s. Time for last 1,000,000: 3s. Last read position: NC_035781.1:13,816,583 INFO 2022-03-11 09:58:59 AddOrReplaceReadGroups Processed 8,000,000 records. Elapsed time: 00:00:23s. Time for last 1,000,000: 3s. Last read position: NC_035781.1:24,074,449 INFO 2022-03-11 09:59:02 AddOrReplaceReadGroups Processed 9,000,000 records. Elapsed time: 00:00:26s. Time for last 1,000,000: 3s. Last read position: NC_035781.1:35,952,453 INFO 2022-03-11 09:59:05 AddOrReplaceReadGroups Processed 10,000,000 records. Elapsed time: 00:00:29s. Time for last 1,000,000: 3s. Last read position: NC_035781.1:48,055,742 INFO 2022-03-11 09:59:08 AddOrReplaceReadGroups Processed 11,000,000 records. Elapsed time: 00:00:33s. Time for last 1,000,000: 3s. Last read position: NC_035781.1:58,863,651 INFO 2022-03-11 09:59:14 AddOrReplaceReadGroups Processed 12,000,000 records. Elapsed time: 00:00:39s. Time for last 1,000,000: 6s. Last read position: NC_035782.1:10,021,670 INFO 2022-03-11 09:59:17 AddOrReplaceReadGroups Processed 13,000,000 records. Elapsed time: 00:00:42s. Time for last 1,000,000: 3s. Last read position: NC_035782.1:22,854,463 INFO 2022-03-11 09:59:20 AddOrReplaceReadGroups Processed 14,000,000 records. Elapsed time: 00:00:45s. Time for last 1,000,000: 2s. Last read position: NC_035782.1:34,608,104 INFO 2022-03-11 09:59:23 AddOrReplaceReadGroups Processed 15,000,000 records. Elapsed time: 00:00:48s. Time for last 1,000,000: 2s. Last read position: NC_035782.1:47,505,861 INFO 2022-03-11 09:59:26 AddOrReplaceReadGroups Processed 16,000,000 records. Elapsed time: 00:00:51s. Time for last 1,000,000: 2s. Last read position: NC_035782.1:57,652,448 INFO 2022-03-11 09:59:29 AddOrReplaceReadGroups Processed 17,000,000 records. Elapsed time: 00:00:54s. Time for last 1,000,000: 2s. Last read position: NC_035782.1:68,938,495 INFO 2022-03-11 09:59:32 AddOrReplaceReadGroups Processed 18,000,000 records. Elapsed time: 00:00:57s. Time for last 1,000,000: 3s. Last read position: NC_035783.1:4,767,455 INFO 2022-03-11 09:59:35 AddOrReplaceReadGroups Processed 19,000,000 records. Elapsed time: 00:01:00s. Time for last 1,000,000: 3s. Last read position: NC_035783.1:15,820,621 INFO 2022-03-11 09:59:38 AddOrReplaceReadGroups Processed 20,000,000 records. Elapsed time: 00:01:03s. Time for last 1,000,000: 2s. Last read position: NC_035783.1:25,843,547 INFO 2022-03-11 09:59:41 AddOrReplaceReadGroups Processed 21,000,000 records. Elapsed time: 00:01:06s. Time for last 1,000,000: 2s. Last read position: NC_035783.1:37,966,262 INFO 2022-03-11 09:59:47 AddOrReplaceReadGroups Processed 22,000,000 records. Elapsed time: 00:01:11s. Time for last 1,000,000: 5s. Last read position: NC_035783.1:48,384,002 INFO 2022-03-11 09:59:50 AddOrReplaceReadGroups Processed 23,000,000 records. Elapsed time: 00:01:15s. Time for last 1,000,000: 3s. Last read position: NC_035784.1:536,576 INFO 2022-03-11 09:59:53 AddOrReplaceReadGroups Processed 24,000,000 records. Elapsed time: 00:01:18s. Time for last 1,000,000: 3s. Last read position: NC_035784.1:12,114,426 INFO 2022-03-11 09:59:56 AddOrReplaceReadGroups Processed 25,000,000 records. Elapsed time: 00:01:21s. Time for last 1,000,000: 3s. Last read position: NC_035784.1:23,651,630 INFO 2022-03-11 09:59:59 AddOrReplaceReadGroups Processed 26,000,000 records. Elapsed time: 00:01:24s. Time for last 1,000,000: 3s. Last read position: NC_035784.1:35,279,342 INFO 2022-03-11 10:00:02 AddOrReplaceReadGroups Processed 27,000,000 records. Elapsed time: 00:01:27s. Time for last 1,000,000: 2s. Last read position: NC_035784.1:44,625,040 INFO 2022-03-11 10:00:05 AddOrReplaceReadGroups Processed 28,000,000 records. Elapsed time: 00:01:30s. Time for last 1,000,000: 2s. Last read position: NC_035784.1:52,215,496 INFO 2022-03-11 10:00:08 AddOrReplaceReadGroups Processed 29,000,000 records. Elapsed time: 00:01:33s. Time for last 1,000,000: 2s. Last read position: NC_035784.1:57,450,071 INFO 2022-03-11 10:00:11 AddOrReplaceReadGroups Processed 30,000,000 records. Elapsed time: 00:01:36s. Time for last 1,000,000: 2s. Last read position: NC_035784.1:68,527,556 INFO 2022-03-11 10:00:14 AddOrReplaceReadGroups Processed 31,000,000 records. Elapsed time: 00:01:39s. Time for last 1,000,000: 3s. Last read position: NC_035784.1:80,981,112 INFO 2022-03-11 10:00:17 AddOrReplaceReadGroups Processed 32,000,000 records. Elapsed time: 00:01:42s. Time for last 1,000,000: 3s. Last read position: NC_035784.1:93,831,614 INFO 2022-03-11 10:00:22 AddOrReplaceReadGroups Processed 33,000,000 records. Elapsed time: 00:01:47s. Time for last 1,000,000: 5s. Last read position: NC_035785.1:7,930,972 INFO 2022-03-11 10:00:26 AddOrReplaceReadGroups Processed 34,000,000 records. Elapsed time: 00:01:50s. Time for last 1,000,000: 3s. Last read position: NC_035785.1:20,686,521 INFO 2022-03-11 10:00:29 AddOrReplaceReadGroups Processed 35,000,000 records. Elapsed time: 00:01:53s. Time for last 1,000,000: 3s. Last read position: NC_035785.1:35,901,877 INFO 2022-03-11 10:00:32 AddOrReplaceReadGroups Processed 36,000,000 records. Elapsed time: 00:01:56s. Time for last 1,000,000: 2s. Last read position: NC_035785.1:47,851,232 INFO 2022-03-11 10:00:35 AddOrReplaceReadGroups Processed 37,000,000 records. Elapsed time: 00:01:59s. Time for last 1,000,000: 2s. Last read position: NC_035786.1:7,267,626 INFO 2022-03-11 10:00:38 AddOrReplaceReadGroups Processed 38,000,000 records. Elapsed time: 00:02:02s. Time for last 1,000,000: 2s. Last read position: NC_035786.1:23,995,070 INFO 2022-03-11 10:00:41 AddOrReplaceReadGroups Processed 39,000,000 records. Elapsed time: 00:02:05s. Time for last 1,000,000: 2s. Last read position: NC_035786.1:38,249,539 Using GATK jar /home/shared/gatk-4.2.5.0/gatk-package-4.2.5.0-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 /home/shared/gatk-4.2.5.0/gatk-package-4.2.5.0-local.jar AddOrReplaceReadGroups I=S12M.dedup-split.bam O=S12M.dedup-split-RG.bam RGID=1 RGLB=S12M RGPL=ILLUMINA RGPU=unit1 RGSM=S12M INFO 2022-03-11 16:11:28 AddOrReplaceReadGroups ********** NOTE: Picard's command line syntax is changing. ********** ********** For more information, please see: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** ********** The command line looks like this in the new syntax: ********** ********** AddOrReplaceReadGroups -I S12M.dedup-split.bam -O S12M.dedup-split-RG.bam -RGID 1 -RGLB S12M -RGPL ILLUMINA -RGPU unit1 -RGSM S12M ********** 16:11:28.364 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/shared/gatk-4.2.5.0/gatk-package-4.2.5.0-local.jar!/com/intel/gkl/native/libgkl_compression.so [Fri Mar 11 16:11:28 PST 2022] AddOrReplaceReadGroups INPUT=S12M.dedup-split.bam OUTPUT=S12M.dedup-split-RG.bam RGID=1 RGLB=S12M RGPL=ILLUMINA RGPU=unit1 RGSM=S12M VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=2 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Mar 11, 2022 4:11:28 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine INFO: Failed to detect whether we are running on Google Compute Engine. [Fri Mar 11 16:11:28 PST 2022] Executing as sr320@raven on Linux 5.4.0-104-generic amd64; OpenJDK 64-Bit Server VM 11.0.14+9-Ubuntu-0ubuntu2.18.04; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: 4.2.5.0 INFO 2022-03-11 16:11:28 AddOrReplaceReadGroups Created read-group ID=1 PL=ILLUMINA LB=S12M SM=S12M INFO 2022-03-11 16:11:32 AddOrReplaceReadGroups Processed 1,000,000 records. Elapsed time: 00:00:03s. Time for last 1,000,000: 3s. Last read position: NC_035780.1:10,612,562 INFO 2022-03-11 16:11:35 AddOrReplaceReadGroups Processed 2,000,000 records. Elapsed time: 00:00:07s. Time for last 1,000,000: 3s. Last read position: NC_035780.1:22,557,621 INFO 2022-03-11 16:11:38 AddOrReplaceReadGroups Processed 3,000,000 records. Elapsed time: 00:00:10s. Time for last 1,000,000: 3s. Last read position: NC_035780.1:32,603,339 INFO 2022-03-11 16:11:41 AddOrReplaceReadGroups Processed 4,000,000 records. Elapsed time: 00:00:13s. Time for last 1,000,000: 2s. Last read position: NC_035780.1:42,758,474 INFO 2022-03-11 16:11:45 AddOrReplaceReadGroups Processed 5,000,000 records. Elapsed time: 00:00:17s. Time for last 1,000,000: 4s. Last read position: NC_035780.1:57,180,406 INFO 2022-03-11 16:11:48 AddOrReplaceReadGroups Processed 6,000,000 records. Elapsed time: 00:00:20s. Time for last 1,000,000: 3s. Last read position: NC_035781.1:3,202,608 INFO 2022-03-11 16:11:51 AddOrReplaceReadGroups Processed 7,000,000 records. Elapsed time: 00:00:23s. Time for last 1,000,000: 3s. Last read position: NC_035781.1:13,816,583 INFO 2022-03-11 16:11:54 AddOrReplaceReadGroups Processed 8,000,000 records. Elapsed time: 00:00:26s. Time for last 1,000,000: 3s. Last read position: NC_035781.1:24,074,449 INFO 2022-03-11 16:11:57 AddOrReplaceReadGroups Processed 9,000,000 records. Elapsed time: 00:00:29s. Time for last 1,000,000: 3s. Last read position: NC_035781.1:35,952,453 INFO 2022-03-11 16:12:00 AddOrReplaceReadGroups Processed 10,000,000 records. Elapsed time: 00:00:32s. Time for last 1,000,000: 3s. Last read position: NC_035781.1:48,055,742 INFO 2022-03-11 16:12:03 AddOrReplaceReadGroups Processed 11,000,000 records. Elapsed time: 00:00:35s. Time for last 1,000,000: 2s. Last read position: NC_035781.1:58,863,651 INFO 2022-03-11 16:12:09 AddOrReplaceReadGroups Processed 12,000,000 records. Elapsed time: 00:00:40s. Time for last 1,000,000: 5s. Last read position: NC_035782.1:10,021,670 INFO 2022-03-11 16:12:12 AddOrReplaceReadGroups Processed 13,000,000 records. Elapsed time: 00:00:43s. Time for last 1,000,000: 3s. Last read position: NC_035782.1:22,854,463 INFO 2022-03-11 16:12:15 AddOrReplaceReadGroups Processed 14,000,000 records. Elapsed time: 00:00:46s. Time for last 1,000,000: 3s. Last read position: NC_035782.1:34,608,104 INFO 2022-03-11 16:12:18 AddOrReplaceReadGroups Processed 15,000,000 records. Elapsed time: 00:00:49s. Time for last 1,000,000: 3s. Last read position: NC_035782.1:47,505,861 INFO 2022-03-11 16:12:21 AddOrReplaceReadGroups Processed 16,000,000 records. Elapsed time: 00:00:53s. Time for last 1,000,000: 3s. Last read position: NC_035782.1:57,652,448 INFO 2022-03-11 16:12:24 AddOrReplaceReadGroups Processed 17,000,000 records. Elapsed time: 00:00:56s. Time for last 1,000,000: 3s. Last read position: NC_035782.1:68,938,495 INFO 2022-03-11 16:12:27 AddOrReplaceReadGroups Processed 18,000,000 records. Elapsed time: 00:00:59s. Time for last 1,000,000: 3s. Last read position: NC_035783.1:4,767,455 INFO 2022-03-11 16:12:30 AddOrReplaceReadGroups Processed 19,000,000 records. Elapsed time: 00:01:02s. Time for last 1,000,000: 3s. Last read position: NC_035783.1:15,820,621 INFO 2022-03-11 16:12:33 AddOrReplaceReadGroups Processed 20,000,000 records. Elapsed time: 00:01:05s. Time for last 1,000,000: 3s. Last read position: NC_035783.1:25,843,547 INFO 2022-03-11 16:12:37 AddOrReplaceReadGroups Processed 21,000,000 records. Elapsed time: 00:01:08s. Time for last 1,000,000: 3s. Last read position: NC_035783.1:37,966,262 INFO 2022-03-11 16:12:43 AddOrReplaceReadGroups Processed 22,000,000 records. Elapsed time: 00:01:14s. Time for last 1,000,000: 6s. Last read position: NC_035783.1:48,384,002 INFO 2022-03-11 16:12:46 AddOrReplaceReadGroups Processed 23,000,000 records. Elapsed time: 00:01:18s. Time for last 1,000,000: 3s. Last read position: NC_035784.1:536,576 INFO 2022-03-11 16:12:49 AddOrReplaceReadGroups Processed 24,000,000 records. Elapsed time: 00:01:21s. Time for last 1,000,000: 3s. Last read position: NC_035784.1:12,114,426 INFO 2022-03-11 16:12:52 AddOrReplaceReadGroups Processed 25,000,000 records. Elapsed time: 00:01:24s. Time for last 1,000,000: 3s. Last read position: NC_035784.1:23,651,630 INFO 2022-03-11 16:12:56 AddOrReplaceReadGroups Processed 26,000,000 records. Elapsed time: 00:01:27s. Time for last 1,000,000: 3s. Last read position: NC_035784.1:35,279,342 INFO 2022-03-11 16:12:59 AddOrReplaceReadGroups Processed 27,000,000 records. Elapsed time: 00:01:30s. Time for last 1,000,000: 3s. Last read position: NC_035784.1:44,625,040 INFO 2022-03-11 16:13:02 AddOrReplaceReadGroups Processed 28,000,000 records. Elapsed time: 00:01:33s. Time for last 1,000,000: 2s. Last read position: NC_035784.1:52,215,496 INFO 2022-03-11 16:13:04 AddOrReplaceReadGroups Processed 29,000,000 records. Elapsed time: 00:01:36s. Time for last 1,000,000: 2s. Last read position: NC_035784.1:57,450,071 INFO 2022-03-11 16:13:07 AddOrReplaceReadGroups Processed 30,000,000 records. Elapsed time: 00:01:39s. Time for last 1,000,000: 3s. Last read position: NC_035784.1:68,527,556 INFO 2022-03-11 16:13:11 AddOrReplaceReadGroups Processed 31,000,000 records. Elapsed time: 00:01:42s. Time for last 1,000,000: 3s. Last read position: NC_035784.1:80,981,112 INFO 2022-03-11 16:13:14 AddOrReplaceReadGroups Processed 32,000,000 records. Elapsed time: 00:01:45s. Time for last 1,000,000: 3s. Last read position: NC_035784.1:93,831,614 INFO 2022-03-11 16:13:20 AddOrReplaceReadGroups Processed 33,000,000 records. Elapsed time: 00:01:51s. Time for last 1,000,000: 6s. Last read position: NC_035785.1:7,930,972 INFO 2022-03-11 16:13:23 AddOrReplaceReadGroups Processed 34,000,000 records. Elapsed time: 00:01:54s. Time for last 1,000,000: 3s. Last read position: NC_035785.1:20,686,521 INFO 2022-03-11 16:13:26 AddOrReplaceReadGroups Processed 35,000,000 records. Elapsed time: 00:01:57s. Time for last 1,000,000: 3s. Last read position: NC_035785.1:35,901,877 INFO 2022-03-11 16:13:29 AddOrReplaceReadGroups Processed 36,000,000 records. Elapsed time: 00:02:00s. Time for last 1,000,000: 3s. Last read position: NC_035785.1:47,851,232 INFO 2022-03-11 16:13:32 AddOrReplaceReadGroups Processed 37,000,000 records. Elapsed time: 00:02:03s. Time for last 1,000,000: 3s. Last read position: NC_035786.1:7,267,626 INFO 2022-03-11 16:13:35 AddOrReplaceReadGroups Processed 38,000,000 records. Elapsed time: 00:02:06s. Time for last 1,000,000: 3s. Last read position: NC_035786.1:23,995,070 INFO 2022-03-11 16:13:38 AddOrReplaceReadGroups Processed 39,000,000 records. Elapsed time: 00:02:09s. Time for last 1,000,000: 3s. Last read position: NC_035786.1:38,249,539 INFO 2022-03-11 16:13:41 AddOrReplaceReadGroups Processed 40,000,000 records. Elapsed time: 00:02:13s. Time for last 1,000,000: 3s. Last read position: NC_035786.1:51,608,830 INFO 2022-03-11 16:13:44 AddOrReplaceReadGroups Processed 41,000,000 records. Elapsed time: 00:02:16s. Time for last 1,000,000: 3s. Last read position: NC_035787.1:7,158,266 INFO 2022-03-11 16:13:47 AddOrReplaceReadGroups Processed 42,000,000 records. Elapsed time: 00:02:19s. Time for last 1,000,000: 3s. Last read position: NC_035787.1:22,843,638 INFO 2022-03-11 16:13:54 AddOrReplaceReadGroups Processed 43,000,000 records. Elapsed time: 00:02:25s. Time for last 1,000,000: 6s. Last read position: NC_035787.1:38,366,459 INFO 2022-03-11 16:13:57 AddOrReplaceReadGroups Processed 44,000,000 records. Elapsed time: 00:02:28s. Time for last 1,000,000: 3s. Last read position: NC_035787.1:50,188,829 INFO 2022-03-11 16:14:00 AddOrReplaceReadGroups Processed 45,000,000 records. Elapsed time: 00:02:31s. Time for last 1,000,000: 3s. Last read position: NC_035787.1:61,963,186 INFO 2022-03-11 16:14:03 AddOrReplaceReadGroups Processed 46,000,000 records. Elapsed time: 00:02:34s. Time for last 1,000,000: 3s. Last read position: NC_035787.1:75,892,095 INFO 2022-03-11 16:14:06 AddOrReplaceReadGroups Processed 47,000,000 records. Elapsed time: 00:02:37s. Time for last 1,000,000: 3s. Last read position: NC_035788.1:15,304,845 INFO 2022-03-11 16:14:09 AddOrReplaceReadGroups Processed 48,000,000 records. Elapsed time: 00:02:40s. Time for last 1,000,000: 3s. Last read position: NC_035788.1:27,549,406 INFO 2022-03-11 16:14:12 AddOrReplaceReadGroups Processed 49,000,000 records. Elapsed time: 00:02:43s. Time for last 1,000,000: 3s. Last read position: NC_035788.1:44,917,050 INFO 2022-03-11 16:14:15 AddOrReplaceReadGroups Processed 50,000,000 records. Elapsed time: 00:02:46s. Time for last 1,000,000: 3s. Last read position: NC_035788.1:55,731,071 INFO 2022-03-11 16:14:18 AddOrReplaceReadGroups Processed 51,000,000 records. Elapsed time: 00:02:49s. Time for last 1,000,000: 3s. Last read position: NC_035788.1:67,723,623 INFO 2022-03-11 16:14:21 AddOrReplaceReadGroups Processed 52,000,000 records. Elapsed time: 00:02:53s. Time for last 1,000,000: 3s. Last read position: NC_035788.1:79,065,929 INFO 2022-03-11 16:14:26 AddOrReplaceReadGroups Processed 53,000,000 records. Elapsed time: 00:02:58s. Time for last 1,000,000: 5s. Last read position: NC_035788.1:92,003,022 INFO 2022-03-11 16:14:30 AddOrReplaceReadGroups Processed 54,000,000 records. Elapsed time: 00:03:02s. Time for last 1,000,000: 3s. Last read position: NC_035789.1:1,455,061 INFO 2022-03-11 16:14:33 AddOrReplaceReadGroups Processed 55,000,000 records. Elapsed time: 00:03:05s. Time for last 1,000,000: 3s. Last read position: NC_035789.1:12,897,226 INFO 2022-03-11 16:14:36 AddOrReplaceReadGroups Processed 56,000,000 records. Elapsed time: 00:03:08s. Time for last 1,000,000: 3s. Last read position: NC_035789.1:23,212,850 INFO 2022-03-11 16:14:39 AddOrReplaceReadGroups Processed 57,000,000 records. Elapsed time: 00:03:11s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 16:14:42 AddOrReplaceReadGroups Processed 58,000,000 records. Elapsed time: 00:03:14s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 16:14:45 AddOrReplaceReadGroups Processed 59,000,000 records. Elapsed time: 00:03:17s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 16:14:48 AddOrReplaceReadGroups Processed 60,000,000 records. Elapsed time: 00:03:19s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 16:14:51 AddOrReplaceReadGroups Processed 61,000,000 records. Elapsed time: 00:03:22s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 16:14:54 AddOrReplaceReadGroups Processed 62,000,000 records. Elapsed time: 00:03:25s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 16:14:57 AddOrReplaceReadGroups Processed 63,000,000 records. Elapsed time: 00:03:28s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 16:15:04 AddOrReplaceReadGroups Processed 64,000,000 records. Elapsed time: 00:03:35s. Time for last 1,000,000: 6s. Last read position: */* INFO 2022-03-11 16:15:06 AddOrReplaceReadGroups Processed 65,000,000 records. Elapsed time: 00:03:38s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 16:15:09 AddOrReplaceReadGroups Processed 66,000,000 records. Elapsed time: 00:03:41s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 16:15:12 AddOrReplaceReadGroups Processed 67,000,000 records. Elapsed time: 00:03:44s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 16:15:15 AddOrReplaceReadGroups Processed 68,000,000 records. Elapsed time: 00:03:46s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 16:15:18 AddOrReplaceReadGroups Processed 69,000,000 records. Elapsed time: 00:03:49s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 16:15:21 AddOrReplaceReadGroups Processed 70,000,000 records. Elapsed time: 00:03:52s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 16:15:24 AddOrReplaceReadGroups Processed 71,000,000 records. Elapsed time: 00:03:55s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 16:15:27 AddOrReplaceReadGroups Processed 72,000,000 records. Elapsed time: 00:03:58s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 16:15:30 AddOrReplaceReadGroups Processed 73,000,000 records. Elapsed time: 00:04:01s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 16:15:32 AddOrReplaceReadGroups Processed 74,000,000 records. Elapsed time: 00:04:04s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 16:15:40 AddOrReplaceReadGroups Processed 75,000,000 records. Elapsed time: 00:04:11s. Time for last 1,000,000: 7s. Last read position: */* INFO 2022-03-11 16:15:43 AddOrReplaceReadGroups Processed 76,000,000 records. Elapsed time: 00:04:14s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 16:15:46 AddOrReplaceReadGroups Processed 77,000,000 records. Elapsed time: 00:04:17s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 16:15:49 AddOrReplaceReadGroups Processed 78,000,000 records. Elapsed time: 00:04:20s. Time for last 1,000,000: 2s. Last read position: */* [Fri Mar 11 16:15:51 PST 2022] picard.sam.AddOrReplaceReadGroups done. Elapsed time: 4.38 minutes. Runtime.totalMemory()=2755657728 Tool returned: 0 Using GATK jar /home/shared/gatk-4.2.5.0/gatk-package-4.2.5.0-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 /home/shared/gatk-4.2.5.0/gatk-package-4.2.5.0-local.jar AddOrReplaceReadGroups I=S13M.dedup-split.bam O=S13M.dedup-split-RG.bam RGID=1 RGLB=S13M RGPL=ILLUMINA RGPU=unit1 RGSM=S13M INFO 2022-03-11 16:15:52 AddOrReplaceReadGroups ********** NOTE: Picard's command line syntax is changing. ********** ********** For more information, please see: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** ********** The command line looks like this in the new syntax: ********** ********** AddOrReplaceReadGroups -I S13M.dedup-split.bam -O S13M.dedup-split-RG.bam -RGID 1 -RGLB S13M -RGPL ILLUMINA -RGPU unit1 -RGSM S13M ********** 16:15:52.854 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/shared/gatk-4.2.5.0/gatk-package-4.2.5.0-local.jar!/com/intel/gkl/native/libgkl_compression.so [Fri Mar 11 16:15:52 PST 2022] AddOrReplaceReadGroups INPUT=S13M.dedup-split.bam OUTPUT=S13M.dedup-split-RG.bam RGID=1 RGLB=S13M RGPL=ILLUMINA RGPU=unit1 RGSM=S13M VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=2 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Mar 11, 2022 4:15:52 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine INFO: Failed to detect whether we are running on Google Compute Engine. [Fri Mar 11 16:15:52 PST 2022] Executing as sr320@raven on Linux 5.4.0-104-generic amd64; OpenJDK 64-Bit Server VM 11.0.14+9-Ubuntu-0ubuntu2.18.04; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: 4.2.5.0 INFO 2022-03-11 16:15:52 AddOrReplaceReadGroups Created read-group ID=1 PL=ILLUMINA LB=S13M SM=S13M INFO 2022-03-11 16:15:56 AddOrReplaceReadGroups Processed 1,000,000 records. Elapsed time: 00:00:03s. Time for last 1,000,000: 3s. Last read position: NC_035780.1:13,357,714 INFO 2022-03-11 16:15:58 AddOrReplaceReadGroups Processed 2,000,000 records. Elapsed time: 00:00:05s. Time for last 1,000,000: 2s. Last read position: NC_035780.1:26,317,179 INFO 2022-03-11 16:16:01 AddOrReplaceReadGroups Processed 3,000,000 records. Elapsed time: 00:00:08s. Time for last 1,000,000: 2s. Last read position: NC_035780.1:41,313,918 INFO 2022-03-11 16:16:05 AddOrReplaceReadGroups Processed 4,000,000 records. Elapsed time: 00:00:11s. Time for last 1,000,000: 3s. Last read position: NC_035780.1:59,557,206 INFO 2022-03-11 16:16:08 AddOrReplaceReadGroups Processed 5,000,000 records. Elapsed time: 00:00:14s. Time for last 1,000,000: 2s. Last read position: NC_035781.1:9,179,091 INFO 2022-03-11 16:16:10 AddOrReplaceReadGroups Processed 6,000,000 records. Elapsed time: 00:00:17s. Time for last 1,000,000: 2s. Last read position: NC_035781.1:22,181,635 INFO 2022-03-11 16:16:13 AddOrReplaceReadGroups Processed 7,000,000 records. Elapsed time: 00:00:20s. Time for last 1,000,000: 3s. Last read position: NC_035781.1:37,724,947 INFO 2022-03-11 16:16:16 AddOrReplaceReadGroups Processed 8,000,000 records. Elapsed time: 00:00:23s. Time for last 1,000,000: 2s. Last read position: NC_035781.1:53,452,378 INFO 2022-03-11 16:16:19 AddOrReplaceReadGroups Processed 9,000,000 records. Elapsed time: 00:00:26s. Time for last 1,000,000: 2s. Last read position: NC_035782.1:6,665,248 INFO 2022-03-11 16:16:22 AddOrReplaceReadGroups Processed 10,000,000 records. Elapsed time: 00:00:29s. Time for last 1,000,000: 2s. Last read position: NC_035782.1:24,472,575 INFO 2022-03-11 16:16:26 AddOrReplaceReadGroups Processed 11,000,000 records. Elapsed time: 00:00:33s. Time for last 1,000,000: 3s. Last read position: NC_035782.1:41,064,184 INFO 2022-03-11 16:16:32 AddOrReplaceReadGroups Processed 12,000,000 records. Elapsed time: 00:00:39s. Time for last 1,000,000: 5s. Last read position: NC_035782.1:56,569,555 INFO 2022-03-11 16:16:35 AddOrReplaceReadGroups Processed 13,000,000 records. Elapsed time: 00:00:42s. Time for last 1,000,000: 2s. Last read position: NC_035782.1:72,098,919 INFO 2022-03-11 16:16:38 AddOrReplaceReadGroups Processed 14,000,000 records. Elapsed time: 00:00:45s. Time for last 1,000,000: 2s. Last read position: NC_035783.1:11,702,901 INFO 2022-03-11 16:16:41 AddOrReplaceReadGroups Processed 15,000,000 records. Elapsed time: 00:00:48s. Time for last 1,000,000: 2s. Last read position: NC_035783.1:24,658,804 INFO 2022-03-11 16:16:44 AddOrReplaceReadGroups Processed 16,000,000 records. Elapsed time: 00:00:51s. Time for last 1,000,000: 2s. Last read position: NC_035783.1:40,822,556 INFO 2022-03-11 16:16:47 AddOrReplaceReadGroups Processed 17,000,000 records. Elapsed time: 00:00:53s. Time for last 1,000,000: 2s. Last read position: NC_035783.1:55,147,509 INFO 2022-03-11 16:16:49 AddOrReplaceReadGroups Processed 18,000,000 records. Elapsed time: 00:00:56s. Time for last 1,000,000: 2s. Last read position: NC_035784.1:10,917,481 INFO 2022-03-11 16:16:52 AddOrReplaceReadGroups Processed 19,000,000 records. Elapsed time: 00:00:59s. Time for last 1,000,000: 2s. Last read position: NC_035784.1:26,906,124 INFO 2022-03-11 16:16:55 AddOrReplaceReadGroups Processed 20,000,000 records. Elapsed time: 00:01:02s. Time for last 1,000,000: 2s. Last read position: NC_035784.1:43,047,478 INFO 2022-03-11 16:16:58 AddOrReplaceReadGroups Processed 21,000,000 records. Elapsed time: 00:01:05s. Time for last 1,000,000: 2s. Last read position: NC_035784.1:52,194,915 INFO 2022-03-11 16:17:02 AddOrReplaceReadGroups Processed 22,000,000 records. Elapsed time: 00:01:09s. Time for last 1,000,000: 3s. Last read position: NC_035784.1:52,276,632 INFO 2022-03-11 16:17:06 AddOrReplaceReadGroups Processed 23,000,000 records. Elapsed time: 00:01:13s. Time for last 1,000,000: 4s. Last read position: NC_035784.1:63,027,048 INFO 2022-03-11 16:17:09 AddOrReplaceReadGroups Processed 24,000,000 records. Elapsed time: 00:01:16s. Time for last 1,000,000: 2s. Last read position: NC_035784.1:77,987,906 INFO 2022-03-11 16:17:12 AddOrReplaceReadGroups Processed 25,000,000 records. Elapsed time: 00:01:19s. Time for last 1,000,000: 2s. Last read position: NC_035784.1:95,550,220 INFO 2022-03-11 16:17:15 AddOrReplaceReadGroups Processed 26,000,000 records. Elapsed time: 00:01:22s. Time for last 1,000,000: 2s. Last read position: NC_035785.1:14,576,115 INFO 2022-03-11 16:17:18 AddOrReplaceReadGroups Processed 27,000,000 records. Elapsed time: 00:01:25s. Time for last 1,000,000: 2s. Last read position: NC_035785.1:32,449,345 INFO 2022-03-11 16:17:21 AddOrReplaceReadGroups Processed 28,000,000 records. Elapsed time: 00:01:28s. Time for last 1,000,000: 2s. Last read position: NC_035785.1:48,895,033 INFO 2022-03-11 16:17:24 AddOrReplaceReadGroups Processed 29,000,000 records. Elapsed time: 00:01:31s. Time for last 1,000,000: 2s. Last read position: NC_035786.1:14,169,123 INFO 2022-03-11 16:17:27 AddOrReplaceReadGroups Processed 30,000,000 records. Elapsed time: 00:01:34s. Time for last 1,000,000: 2s. Last read position: NC_035786.1:36,445,608 INFO 2022-03-11 16:17:30 AddOrReplaceReadGroups Processed 31,000,000 records. Elapsed time: 00:01:37s. Time for last 1,000,000: 2s. Last read position: NC_035786.1:55,109,231 INFO 2022-03-11 16:17:32 AddOrReplaceReadGroups Processed 32,000,000 records. Elapsed time: 00:01:39s. Time for last 1,000,000: 2s. Last read position: NC_035787.1:16,647,025 INFO 2022-03-11 16:17:36 AddOrReplaceReadGroups Processed 33,000,000 records. Elapsed time: 00:01:43s. Time for last 1,000,000: 3s. Last read position: NC_035787.1:37,592,076 INFO 2022-03-11 16:17:42 AddOrReplaceReadGroups Processed 34,000,000 records. Elapsed time: 00:01:49s. Time for last 1,000,000: 5s. Last read position: NC_035787.1:52,199,977 INFO 2022-03-11 16:17:45 AddOrReplaceReadGroups Processed 35,000,000 records. Elapsed time: 00:01:52s. Time for last 1,000,000: 2s. Last read position: NC_035787.1:67,126,704 INFO 2022-03-11 16:17:48 AddOrReplaceReadGroups Processed 36,000,000 records. Elapsed time: 00:01:55s. Time for last 1,000,000: 2s. Last read position: NC_035788.1:13,081,634 INFO 2022-03-11 16:17:51 AddOrReplaceReadGroups Processed 37,000,000 records. Elapsed time: 00:01:57s. Time for last 1,000,000: 2s. Last read position: NC_035788.1:33,839,714 INFO 2022-03-11 16:17:53 AddOrReplaceReadGroups Processed 38,000,000 records. Elapsed time: 00:02:00s. Time for last 1,000,000: 2s. Last read position: NC_035788.1:51,444,616 INFO 2022-03-11 16:17:56 AddOrReplaceReadGroups Processed 39,000,000 records. Elapsed time: 00:02:03s. Time for last 1,000,000: 2s. Last read position: NC_035788.1:66,972,853 INFO 2022-03-11 16:17:59 AddOrReplaceReadGroups Processed 40,000,000 records. Elapsed time: 00:02:06s. Time for last 1,000,000: 2s. Last read position: NC_035788.1:81,657,001 INFO 2022-03-11 16:18:02 AddOrReplaceReadGroups Processed 41,000,000 records. Elapsed time: 00:02:09s. Time for last 1,000,000: 2s. Last read position: NC_035788.1:101,714,044 INFO 2022-03-11 16:18:05 AddOrReplaceReadGroups Processed 42,000,000 records. Elapsed time: 00:02:12s. Time for last 1,000,000: 2s. Last read position: NC_035789.1:13,041,973 INFO 2022-03-11 16:18:08 AddOrReplaceReadGroups Processed 43,000,000 records. Elapsed time: 00:02:15s. Time for last 1,000,000: 2s. Last read position: NC_035789.1:28,614,319 INFO 2022-03-11 16:18:14 AddOrReplaceReadGroups Processed 44,000,000 records. Elapsed time: 00:02:21s. Time for last 1,000,000: 5s. Last read position: */* INFO 2022-03-11 16:18:17 AddOrReplaceReadGroups Processed 45,000,000 records. Elapsed time: 00:02:24s. Time for last 1,000,000: 3s. Last read position: */* INFO 2022-03-11 16:18:20 AddOrReplaceReadGroups Processed 46,000,000 records. Elapsed time: 00:02:27s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 16:18:22 AddOrReplaceReadGroups Processed 47,000,000 records. Elapsed time: 00:02:29s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 16:18:25 AddOrReplaceReadGroups Processed 48,000,000 records. Elapsed time: 00:02:32s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 16:18:28 AddOrReplaceReadGroups Processed 49,000,000 records. Elapsed time: 00:02:35s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 16:18:31 AddOrReplaceReadGroups Processed 50,000,000 records. Elapsed time: 00:02:38s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 16:18:33 AddOrReplaceReadGroups Processed 51,000,000 records. Elapsed time: 00:02:40s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 16:18:36 AddOrReplaceReadGroups Processed 52,000,000 records. Elapsed time: 00:02:43s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 16:18:39 AddOrReplaceReadGroups Processed 53,000,000 records. Elapsed time: 00:02:46s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 16:18:42 AddOrReplaceReadGroups Processed 54,000,000 records. Elapsed time: 00:02:49s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 16:18:44 AddOrReplaceReadGroups Processed 55,000,000 records. Elapsed time: 00:02:51s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 16:18:52 AddOrReplaceReadGroups Processed 56,000,000 records. Elapsed time: 00:02:59s. Time for last 1,000,000: 7s. Last read position: */* INFO 2022-03-11 16:18:55 AddOrReplaceReadGroups Processed 57,000,000 records. Elapsed time: 00:03:02s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 16:18:58 AddOrReplaceReadGroups Processed 58,000,000 records. Elapsed time: 00:03:04s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 16:19:00 AddOrReplaceReadGroups Processed 59,000,000 records. Elapsed time: 00:03:07s. Time for last 1,000,000: 2s. Last read position: */* [Fri Mar 11 16:19:02 PST 2022] picard.sam.AddOrReplaceReadGroups done. Elapsed time: 3.16 minutes. Runtime.totalMemory()=2722103296 Tool returned: 0 Using GATK jar /home/shared/gatk-4.2.5.0/gatk-package-4.2.5.0-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 /home/shared/gatk-4.2.5.0/gatk-package-4.2.5.0-local.jar AddOrReplaceReadGroups I=S16F.dedup-split.bam O=S16F.dedup-split-RG.bam RGID=1 RGLB=S16F RGPL=ILLUMINA RGPU=unit1 RGSM=S16F INFO 2022-03-11 16:19:04 AddOrReplaceReadGroups ********** NOTE: Picard's command line syntax is changing. ********** ********** For more information, please see: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** ********** The command line looks like this in the new syntax: ********** ********** AddOrReplaceReadGroups -I S16F.dedup-split.bam -O S16F.dedup-split-RG.bam -RGID 1 -RGLB S16F -RGPL ILLUMINA -RGPU unit1 -RGSM S16F ********** 16:19:04.274 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/shared/gatk-4.2.5.0/gatk-package-4.2.5.0-local.jar!/com/intel/gkl/native/libgkl_compression.so [Fri Mar 11 16:19:04 PST 2022] AddOrReplaceReadGroups INPUT=S16F.dedup-split.bam OUTPUT=S16F.dedup-split-RG.bam RGID=1 RGLB=S16F RGPL=ILLUMINA RGPU=unit1 RGSM=S16F VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=2 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Mar 11, 2022 4:19:04 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine INFO: Failed to detect whether we are running on Google Compute Engine. [Fri Mar 11 16:19:04 PST 2022] Executing as sr320@raven on Linux 5.4.0-104-generic amd64; OpenJDK 64-Bit Server VM 11.0.14+9-Ubuntu-0ubuntu2.18.04; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: 4.2.5.0 INFO 2022-03-11 16:19:04 AddOrReplaceReadGroups Created read-group ID=1 PL=ILLUMINA LB=S16F SM=S16F INFO 2022-03-11 16:19:07 AddOrReplaceReadGroups Processed 1,000,000 records. Elapsed time: 00:00:03s. Time for last 1,000,000: 3s. Last read position: NC_035780.1:15,501,139 INFO 2022-03-11 16:19:10 AddOrReplaceReadGroups Processed 2,000,000 records. Elapsed time: 00:00:05s. Time for last 1,000,000: 2s. Last read position: NC_035780.1:30,377,809 INFO 2022-03-11 16:19:13 AddOrReplaceReadGroups Processed 3,000,000 records. Elapsed time: 00:00:09s. Time for last 1,000,000: 3s. Last read position: NC_035780.1:46,822,750 INFO 2022-03-11 16:19:16 AddOrReplaceReadGroups Processed 4,000,000 records. Elapsed time: 00:00:12s. Time for last 1,000,000: 3s. Last read position: NC_035780.1:59,961,442 INFO 2022-03-11 16:19:19 AddOrReplaceReadGroups Processed 5,000,000 records. Elapsed time: 00:00:15s. Time for last 1,000,000: 3s. Last read position: NC_035781.1:4,885,738 INFO 2022-03-11 16:19:22 AddOrReplaceReadGroups Processed 6,000,000 records. Elapsed time: 00:00:18s. Time for last 1,000,000: 2s. Last read position: NC_035781.1:11,588,938 INFO 2022-03-11 16:19:25 AddOrReplaceReadGroups Processed 7,000,000 records. Elapsed time: 00:00:21s. Time for last 1,000,000: 2s. Last read position: NC_035781.1:20,577,759 INFO 2022-03-11 16:19:28 AddOrReplaceReadGroups Processed 8,000,000 records. Elapsed time: 00:00:24s. Time for last 1,000,000: 2s. Last read position: NC_035781.1:31,342,901 INFO 2022-03-11 16:19:31 AddOrReplaceReadGroups Processed 9,000,000 records. Elapsed time: 00:00:27s. Time for last 1,000,000: 3s. Last read position: NC_035781.1:42,349,649 INFO 2022-03-11 16:19:34 AddOrReplaceReadGroups Processed 10,000,000 records. Elapsed time: 00:00:30s. Time for last 1,000,000: 2s. Last read position: NC_035781.1:52,623,439 INFO 2022-03-11 16:19:37 AddOrReplaceReadGroups Processed 11,000,000 records. Elapsed time: 00:00:33s. Time for last 1,000,000: 3s. Last read position: NC_035782.1:7,491,623 INFO 2022-03-11 16:19:43 AddOrReplaceReadGroups Processed 12,000,000 records. Elapsed time: 00:00:39s. Time for last 1,000,000: 6s. Last read position: NC_035782.1:20,948,031 INFO 2022-03-11 16:19:46 AddOrReplaceReadGroups Processed 13,000,000 records. Elapsed time: 00:00:42s. Time for last 1,000,000: 2s. Last read position: NC_035782.1:26,262,725 INFO 2022-03-11 16:19:49 AddOrReplaceReadGroups Processed 14,000,000 records. Elapsed time: 00:00:45s. Time for last 1,000,000: 2s. Last read position: NC_035782.1:35,851,025 INFO 2022-03-11 16:19:52 AddOrReplaceReadGroups Processed 15,000,000 records. Elapsed time: 00:00:48s. Time for last 1,000,000: 3s. Last read position: NC_035782.1:47,264,312 INFO 2022-03-11 16:19:55 AddOrReplaceReadGroups Processed 16,000,000 records. Elapsed time: 00:00:51s. Time for last 1,000,000: 3s. Last read position: NC_035782.1:57,052,788 INFO 2022-03-11 16:19:58 AddOrReplaceReadGroups Processed 17,000,000 records. Elapsed time: 00:00:54s. Time for last 1,000,000: 3s. Last read position: NC_035782.1:67,322,039 INFO 2022-03-11 16:20:01 AddOrReplaceReadGroups Processed 18,000,000 records. Elapsed time: 00:00:57s. Time for last 1,000,000: 3s. Last read position: NC_035783.1:4,675,434 INFO 2022-03-11 16:20:04 AddOrReplaceReadGroups Processed 19,000,000 records. Elapsed time: 00:01:00s. Time for last 1,000,000: 3s. Last read position: NC_035783.1:16,430,903 INFO 2022-03-11 16:20:07 AddOrReplaceReadGroups Processed 20,000,000 records. Elapsed time: 00:01:03s. Time for last 1,000,000: 3s. Last read position: NC_035783.1:27,569,126 INFO 2022-03-11 16:20:10 AddOrReplaceReadGroups Processed 21,000,000 records. Elapsed time: 00:01:06s. Time for last 1,000,000: 2s. Last read position: NC_035783.1:34,438,846 INFO 2022-03-11 16:20:16 AddOrReplaceReadGroups Processed 22,000,000 records. Elapsed time: 00:01:12s. Time for last 1,000,000: 5s. Last read position: NC_035783.1:34,526,976 INFO 2022-03-11 16:20:19 AddOrReplaceReadGroups Processed 23,000,000 records. Elapsed time: 00:01:14s. Time for last 1,000,000: 2s. Last read position: NC_035783.1:34,538,622 INFO 2022-03-11 16:20:22 AddOrReplaceReadGroups Processed 24,000,000 records. Elapsed time: 00:01:17s. Time for last 1,000,000: 2s. Last read position: NC_035783.1:42,646,758 INFO 2022-03-11 16:20:25 AddOrReplaceReadGroups Processed 25,000,000 records. Elapsed time: 00:01:20s. Time for last 1,000,000: 3s. Last read position: NC_035783.1:56,659,345 INFO 2022-03-11 16:20:28 AddOrReplaceReadGroups Processed 26,000,000 records. Elapsed time: 00:01:23s. Time for last 1,000,000: 3s. Last read position: NC_035784.1:8,480,227 INFO 2022-03-11 16:20:31 AddOrReplaceReadGroups Processed 27,000,000 records. Elapsed time: 00:01:27s. Time for last 1,000,000: 3s. Last read position: NC_035784.1:21,002,002 INFO 2022-03-11 16:20:34 AddOrReplaceReadGroups Processed 28,000,000 records. Elapsed time: 00:01:30s. Time for last 1,000,000: 3s. Last read position: NC_035784.1:35,086,292 INFO 2022-03-11 16:20:37 AddOrReplaceReadGroups Processed 29,000,000 records. Elapsed time: 00:01:33s. Time for last 1,000,000: 2s. Last read position: NC_035784.1:47,938,274 INFO 2022-03-11 16:20:40 AddOrReplaceReadGroups Processed 30,000,000 records. Elapsed time: 00:01:35s. Time for last 1,000,000: 2s. Last read position: NC_035784.1:52,197,911 INFO 2022-03-11 16:20:42 AddOrReplaceReadGroups Processed 31,000,000 records. Elapsed time: 00:01:38s. Time for last 1,000,000: 2s. Last read position: NC_035784.1:52,216,227 INFO 2022-03-11 16:20:45 AddOrReplaceReadGroups Processed 32,000,000 records. Elapsed time: 00:01:40s. Time for last 1,000,000: 2s. Last read position: NC_035784.1:52,258,826 INFO 2022-03-11 16:20:49 AddOrReplaceReadGroups Processed 33,000,000 records. Elapsed time: 00:01:45s. Time for last 1,000,000: 4s. Last read position: NC_035784.1:52,274,102 INFO 2022-03-11 16:20:52 AddOrReplaceReadGroups Processed 34,000,000 records. Elapsed time: 00:01:48s. Time for last 1,000,000: 3s. Last read position: NC_035784.1:52,280,044 INFO 2022-03-11 16:20:55 AddOrReplaceReadGroups Processed 35,000,000 records. Elapsed time: 00:01:51s. Time for last 1,000,000: 2s. Last read position: NC_035784.1:61,748,920 INFO 2022-03-11 16:20:58 AddOrReplaceReadGroups Processed 36,000,000 records. Elapsed time: 00:01:54s. Time for last 1,000,000: 2s. Last read position: NC_035784.1:72,650,532 INFO 2022-03-11 16:21:01 AddOrReplaceReadGroups Processed 37,000,000 records. Elapsed time: 00:01:57s. Time for last 1,000,000: 2s. Last read position: NC_035784.1:79,771,690 INFO 2022-03-11 16:21:04 AddOrReplaceReadGroups Processed 38,000,000 records. Elapsed time: 00:02:00s. Time for last 1,000,000: 2s. Last read position: NC_035785.1:2,928,795 INFO 2022-03-11 16:21:07 AddOrReplaceReadGroups Processed 39,000,000 records. Elapsed time: 00:02:03s. Time for last 1,000,000: 2s. Last read position: NC_035785.1:32,928,078 INFO 2022-03-11 16:21:10 AddOrReplaceReadGroups Processed 40,000,000 records. Elapsed time: 00:02:06s. Time for last 1,000,000: 3s. Last read position: NC_035786.1:1,430,340 INFO 2022-03-11 16:21:13 AddOrReplaceReadGroups Processed 41,000,000 records. Elapsed time: 00:02:09s. Time for last 1,000,000: 3s. Last read position: NC_035786.1:34,305,637 INFO 2022-03-11 16:21:16 AddOrReplaceReadGroups Processed 42,000,000 records. Elapsed time: 00:02:12s. Time for last 1,000,000: 2s. Last read position: NC_035786.1:56,273,886 INFO 2022-03-11 16:21:19 AddOrReplaceReadGroups Processed 43,000,000 records. Elapsed time: 00:02:15s. Time for last 1,000,000: 3s. Last read position: NC_035787.1:24,929,545 INFO 2022-03-11 16:21:25 AddOrReplaceReadGroups Processed 44,000,000 records. Elapsed time: 00:02:21s. Time for last 1,000,000: 6s. Last read position: NC_035787.1:53,356,894 INFO 2022-03-11 16:21:28 AddOrReplaceReadGroups Processed 45,000,000 records. Elapsed time: 00:02:24s. Time for last 1,000,000: 2s. Last read position: NC_035787.1:69,257,432 INFO 2022-03-11 16:21:31 AddOrReplaceReadGroups Processed 46,000,000 records. Elapsed time: 00:02:27s. Time for last 1,000,000: 3s. Last read position: NC_035788.1:19,221,567 INFO 2022-03-11 16:21:34 AddOrReplaceReadGroups Processed 47,000,000 records. Elapsed time: 00:02:30s. Time for last 1,000,000: 3s. Last read position: NC_035788.1:57,128,141 INFO 2022-03-11 16:21:37 AddOrReplaceReadGroups Processed 48,000,000 records. Elapsed time: 00:02:33s. Time for last 1,000,000: 3s. Last read position: NC_035788.1:78,295,691 INFO 2022-03-11 16:21:40 AddOrReplaceReadGroups Processed 49,000,000 records. Elapsed time: 00:02:36s. Time for last 1,000,000: 3s. Last read position: NC_035789.1:9,891,972 INFO 2022-03-11 16:21:43 AddOrReplaceReadGroups Processed 50,000,000 records. Elapsed time: 00:02:39s. Time for last 1,000,000: 2s. Last read position: NC_007175.2:7,681 INFO 2022-03-11 16:21:46 AddOrReplaceReadGroups Processed 51,000,000 records. Elapsed time: 00:02:42s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 16:21:49 AddOrReplaceReadGroups Processed 52,000,000 records. Elapsed time: 00:02:44s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 16:21:52 AddOrReplaceReadGroups Processed 53,000,000 records. Elapsed time: 00:02:47s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 16:21:55 AddOrReplaceReadGroups Processed 54,000,000 records. Elapsed time: 00:02:50s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 16:22:01 AddOrReplaceReadGroups Processed 55,000,000 records. Elapsed time: 00:02:57s. Time for last 1,000,000: 6s. Last read position: */* INFO 2022-03-11 16:22:04 AddOrReplaceReadGroups Processed 56,000,000 records. Elapsed time: 00:03:00s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 16:22:07 AddOrReplaceReadGroups Processed 57,000,000 records. Elapsed time: 00:03:03s. Time for last 1,000,000: 2s. Last read position: */* [Fri Mar 11 16:22:09 PST 2022] picard.sam.AddOrReplaceReadGroups done. Elapsed time: 3.08 minutes. Runtime.totalMemory()=2885681152 Tool returned: 0 Using GATK jar /home/shared/gatk-4.2.5.0/gatk-package-4.2.5.0-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 /home/shared/gatk-4.2.5.0/gatk-package-4.2.5.0-local.jar AddOrReplaceReadGroups I=S19F.dedup-split.bam O=S19F.dedup-split-RG.bam RGID=1 RGLB=S19F RGPL=ILLUMINA RGPU=unit1 RGSM=S19F INFO 2022-03-11 16:22:10 AddOrReplaceReadGroups ********** NOTE: Picard's command line syntax is changing. ********** ********** For more information, please see: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** ********** The command line looks like this in the new syntax: ********** ********** AddOrReplaceReadGroups -I S19F.dedup-split.bam -O S19F.dedup-split-RG.bam -RGID 1 -RGLB S19F -RGPL ILLUMINA -RGPU unit1 -RGSM S19F ********** 16:22:10.801 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/shared/gatk-4.2.5.0/gatk-package-4.2.5.0-local.jar!/com/intel/gkl/native/libgkl_compression.so [Fri Mar 11 16:22:10 PST 2022] AddOrReplaceReadGroups INPUT=S19F.dedup-split.bam OUTPUT=S19F.dedup-split-RG.bam RGID=1 RGLB=S19F RGPL=ILLUMINA RGPU=unit1 RGSM=S19F VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=2 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Mar 11, 2022 4:22:10 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine INFO: Failed to detect whether we are running on Google Compute Engine. [Fri Mar 11 16:22:10 PST 2022] Executing as sr320@raven on Linux 5.4.0-104-generic amd64; OpenJDK 64-Bit Server VM 11.0.14+9-Ubuntu-0ubuntu2.18.04; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: 4.2.5.0 INFO 2022-03-11 16:22:10 AddOrReplaceReadGroups Created read-group ID=1 PL=ILLUMINA LB=S19F SM=S19F INFO 2022-03-11 16:22:14 AddOrReplaceReadGroups Processed 1,000,000 records. Elapsed time: 00:00:03s. Time for last 1,000,000: 3s. Last read position: NC_035780.1:17,001,169 INFO 2022-03-11 16:22:17 AddOrReplaceReadGroups Processed 2,000,000 records. Elapsed time: 00:00:06s. Time for last 1,000,000: 2s. Last read position: NC_035780.1:32,743,162 INFO 2022-03-11 16:22:19 AddOrReplaceReadGroups Processed 3,000,000 records. Elapsed time: 00:00:09s. Time for last 1,000,000: 2s. Last read position: NC_035780.1:48,181,996 INFO 2022-03-11 16:22:23 AddOrReplaceReadGroups Processed 4,000,000 records. Elapsed time: 00:00:12s. Time for last 1,000,000: 3s. Last read position: NC_035780.1:58,634,172 INFO 2022-03-11 16:22:26 AddOrReplaceReadGroups Processed 5,000,000 records. Elapsed time: 00:00:15s. Time for last 1,000,000: 3s. Last read position: NC_035781.1:2,880,301 INFO 2022-03-11 16:22:29 AddOrReplaceReadGroups Processed 6,000,000 records. Elapsed time: 00:00:18s. Time for last 1,000,000: 3s. Last read position: NC_035781.1:10,624,968 INFO 2022-03-11 16:22:32 AddOrReplaceReadGroups Processed 7,000,000 records. Elapsed time: 00:00:21s. Time for last 1,000,000: 2s. Last read position: NC_035781.1:17,849,534 INFO 2022-03-11 16:22:35 AddOrReplaceReadGroups Processed 8,000,000 records. Elapsed time: 00:00:24s. Time for last 1,000,000: 3s. Last read position: NC_035781.1:29,393,065 INFO 2022-03-11 16:22:38 AddOrReplaceReadGroups Processed 9,000,000 records. Elapsed time: 00:00:27s. Time for last 1,000,000: 3s. Last read position: NC_035781.1:38,943,914 INFO 2022-03-11 16:22:41 AddOrReplaceReadGroups Processed 10,000,000 records. Elapsed time: 00:00:30s. Time for last 1,000,000: 3s. Last read position: NC_035781.1:46,240,532 INFO 2022-03-11 16:22:47 AddOrReplaceReadGroups Processed 11,000,000 records. Elapsed time: 00:00:36s. Time for last 1,000,000: 6s. Last read position: NC_035781.1:53,466,893 INFO 2022-03-11 16:22:50 AddOrReplaceReadGroups Processed 12,000,000 records. Elapsed time: 00:00:39s. Time for last 1,000,000: 3s. Last read position: NC_035782.1:11,776,867 INFO 2022-03-11 16:22:53 AddOrReplaceReadGroups Processed 13,000,000 records. Elapsed time: 00:00:42s. Time for last 1,000,000: 3s. Last read position: NC_035782.1:26,254,329 INFO 2022-03-11 16:22:56 AddOrReplaceReadGroups Processed 14,000,000 records. Elapsed time: 00:00:45s. Time for last 1,000,000: 3s. Last read position: NC_035782.1:35,704,701 INFO 2022-03-11 16:22:59 AddOrReplaceReadGroups Processed 15,000,000 records. Elapsed time: 00:00:48s. Time for last 1,000,000: 3s. Last read position: NC_035782.1:46,755,273 INFO 2022-03-11 16:23:02 AddOrReplaceReadGroups Processed 16,000,000 records. Elapsed time: 00:00:51s. Time for last 1,000,000: 3s. Last read position: NC_035782.1:55,221,460 INFO 2022-03-11 16:23:05 AddOrReplaceReadGroups Processed 17,000,000 records. Elapsed time: 00:00:54s. Time for last 1,000,000: 3s. Last read position: NC_035782.1:62,370,551 INFO 2022-03-11 16:23:08 AddOrReplaceReadGroups Processed 18,000,000 records. Elapsed time: 00:00:57s. Time for last 1,000,000: 3s. Last read position: NC_035782.1:71,440,445 INFO 2022-03-11 16:23:11 AddOrReplaceReadGroups Processed 19,000,000 records. Elapsed time: 00:01:00s. Time for last 1,000,000: 3s. Last read position: NC_035783.1:7,276,543 INFO 2022-03-11 16:23:14 AddOrReplaceReadGroups Processed 20,000,000 records. Elapsed time: 00:01:03s. Time for last 1,000,000: 3s. Last read position: NC_035783.1:18,097,166 INFO 2022-03-11 16:23:20 AddOrReplaceReadGroups Processed 21,000,000 records. Elapsed time: 00:01:09s. Time for last 1,000,000: 6s. Last read position: NC_035783.1:28,151,613 INFO 2022-03-11 16:23:23 AddOrReplaceReadGroups Processed 22,000,000 records. Elapsed time: 00:01:12s. Time for last 1,000,000: 3s. Last read position: NC_035783.1:37,766,875 INFO 2022-03-11 16:23:26 AddOrReplaceReadGroups Processed 23,000,000 records. Elapsed time: 00:01:15s. Time for last 1,000,000: 2s. Last read position: NC_035783.1:46,801,462 INFO 2022-03-11 16:23:29 AddOrReplaceReadGroups Processed 24,000,000 records. Elapsed time: 00:01:18s. Time for last 1,000,000: 3s. Last read position: NC_035784.1:1,550,033 INFO 2022-03-11 16:23:32 AddOrReplaceReadGroups Processed 25,000,000 records. Elapsed time: 00:01:21s. Time for last 1,000,000: 3s. Last read position: NC_035784.1:10,817,813 INFO 2022-03-11 16:23:35 AddOrReplaceReadGroups Processed 26,000,000 records. Elapsed time: 00:01:24s. Time for last 1,000,000: 3s. Last read position: NC_035784.1:19,187,206 INFO 2022-03-11 16:23:38 AddOrReplaceReadGroups Processed 27,000,000 records. Elapsed time: 00:01:28s. Time for last 1,000,000: 3s. Last read position: NC_035784.1:31,121,564 INFO 2022-03-11 16:23:41 AddOrReplaceReadGroups Processed 28,000,000 records. Elapsed time: 00:01:31s. Time for last 1,000,000: 3s. Last read position: NC_035784.1:39,016,090 INFO 2022-03-11 16:23:44 AddOrReplaceReadGroups Processed 29,000,000 records. Elapsed time: 00:01:33s. Time for last 1,000,000: 2s. Last read position: NC_035784.1:47,543,103 INFO 2022-03-11 16:23:47 AddOrReplaceReadGroups Processed 30,000,000 records. Elapsed time: 00:01:36s. Time for last 1,000,000: 2s. Last read position: NC_035784.1:52,142,522 INFO 2022-03-11 16:23:50 AddOrReplaceReadGroups Processed 31,000,000 records. Elapsed time: 00:01:39s. Time for last 1,000,000: 2s. Last read position: NC_035784.1:52,215,711 INFO 2022-03-11 16:23:55 AddOrReplaceReadGroups Processed 32,000,000 records. Elapsed time: 00:01:44s. Time for last 1,000,000: 5s. Last read position: NC_035784.1:52,273,338 INFO 2022-03-11 16:23:58 AddOrReplaceReadGroups Processed 33,000,000 records. Elapsed time: 00:01:47s. Time for last 1,000,000: 2s. Last read position: NC_035784.1:55,355,311 INFO 2022-03-11 16:24:01 AddOrReplaceReadGroups Processed 34,000,000 records. Elapsed time: 00:01:50s. Time for last 1,000,000: 3s. Last read position: NC_035784.1:65,999,296 INFO 2022-03-11 16:24:04 AddOrReplaceReadGroups Processed 35,000,000 records. Elapsed time: 00:01:53s. Time for last 1,000,000: 3s. Last read position: NC_035784.1:79,201,361 INFO 2022-03-11 16:24:07 AddOrReplaceReadGroups Processed 36,000,000 records. Elapsed time: 00:01:56s. Time for last 1,000,000: 3s. Last read position: NC_035785.1:7,238,185 INFO 2022-03-11 16:24:10 AddOrReplaceReadGroups Processed 37,000,000 records. Elapsed time: 00:01:59s. Time for last 1,000,000: 3s. Last read position: NC_035785.1:35,655,579 INFO 2022-03-11 16:24:13 AddOrReplaceReadGroups Processed 38,000,000 records. Elapsed time: 00:02:02s. Time for last 1,000,000: 3s. Last read position: NC_035786.1:5,111,113 INFO 2022-03-11 16:24:16 AddOrReplaceReadGroups Processed 39,000,000 records. Elapsed time: 00:02:05s. Time for last 1,000,000: 3s. Last read position: NC_035786.1:36,455,785 INFO 2022-03-11 16:24:19 AddOrReplaceReadGroups Processed 40,000,000 records. Elapsed time: 00:02:08s. Time for last 1,000,000: 3s. Last read position: NC_035787.1:1,990,661 INFO 2022-03-11 16:24:22 AddOrReplaceReadGroups Processed 41,000,000 records. Elapsed time: 00:02:11s. Time for last 1,000,000: 3s. Last read position: NC_035787.1:35,421,946 INFO 2022-03-11 16:24:28 AddOrReplaceReadGroups Processed 42,000,000 records. Elapsed time: 00:02:17s. Time for last 1,000,000: 5s. Last read position: NC_035787.1:59,788,393 INFO 2022-03-11 16:24:32 AddOrReplaceReadGroups Processed 43,000,000 records. Elapsed time: 00:02:21s. Time for last 1,000,000: 3s. Last read position: NC_035788.1:5,662,421 INFO 2022-03-11 16:24:35 AddOrReplaceReadGroups Processed 44,000,000 records. Elapsed time: 00:02:24s. Time for last 1,000,000: 3s. Last read position: NC_035788.1:42,813,332 INFO 2022-03-11 16:24:38 AddOrReplaceReadGroups Processed 45,000,000 records. Elapsed time: 00:02:27s. Time for last 1,000,000: 3s. Last read position: NC_035788.1:71,672,802 INFO 2022-03-11 16:24:41 AddOrReplaceReadGroups Processed 46,000,000 records. Elapsed time: 00:02:30s. Time for last 1,000,000: 3s. Last read position: NC_035788.1:102,952,757 INFO 2022-03-11 16:24:44 AddOrReplaceReadGroups Processed 47,000,000 records. Elapsed time: 00:02:33s. Time for last 1,000,000: 3s. Last read position: NC_035789.1:20,406,365 INFO 2022-03-11 16:24:47 AddOrReplaceReadGroups Processed 48,000,000 records. Elapsed time: 00:02:36s. Time for last 1,000,000: 2s. Last read position: NC_007175.2:7,441 INFO 2022-03-11 16:24:50 AddOrReplaceReadGroups Processed 49,000,000 records. Elapsed time: 00:02:39s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 16:24:52 AddOrReplaceReadGroups Processed 50,000,000 records. Elapsed time: 00:02:41s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 16:24:55 AddOrReplaceReadGroups Processed 51,000,000 records. Elapsed time: 00:02:44s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 16:24:58 AddOrReplaceReadGroups Processed 52,000,000 records. Elapsed time: 00:02:47s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 16:25:05 AddOrReplaceReadGroups Processed 53,000,000 records. Elapsed time: 00:02:54s. Time for last 1,000,000: 6s. Last read position: */* INFO 2022-03-11 16:25:08 AddOrReplaceReadGroups Processed 54,000,000 records. Elapsed time: 00:02:57s. Time for last 1,000,000: 2s. Last read position: */* [Fri Mar 11 16:25:11 PST 2022] picard.sam.AddOrReplaceReadGroups done. Elapsed time: 3.02 minutes. Runtime.totalMemory()=2755657728 Tool returned: 0 Using GATK jar /home/shared/gatk-4.2.5.0/gatk-package-4.2.5.0-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 /home/shared/gatk-4.2.5.0/gatk-package-4.2.5.0-local.jar AddOrReplaceReadGroups I=S22F.dedup-split.bam O=S22F.dedup-split-RG.bam RGID=1 RGLB=S22F RGPL=ILLUMINA RGPU=unit1 RGSM=S22F INFO 2022-03-11 16:25:13 AddOrReplaceReadGroups ********** NOTE: Picard's command line syntax is changing. ********** ********** For more information, please see: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** ********** The command line looks like this in the new syntax: ********** ********** AddOrReplaceReadGroups -I S22F.dedup-split.bam -O S22F.dedup-split-RG.bam -RGID 1 -RGLB S22F -RGPL ILLUMINA -RGPU unit1 -RGSM S22F ********** 16:25:13.495 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/shared/gatk-4.2.5.0/gatk-package-4.2.5.0-local.jar!/com/intel/gkl/native/libgkl_compression.so [Fri Mar 11 16:25:13 PST 2022] AddOrReplaceReadGroups INPUT=S22F.dedup-split.bam OUTPUT=S22F.dedup-split-RG.bam RGID=1 RGLB=S22F RGPL=ILLUMINA RGPU=unit1 RGSM=S22F VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=2 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Mar 11, 2022 4:25:13 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine INFO: Failed to detect whether we are running on Google Compute Engine. [Fri Mar 11 16:25:13 PST 2022] Executing as sr320@raven on Linux 5.4.0-104-generic amd64; OpenJDK 64-Bit Server VM 11.0.14+9-Ubuntu-0ubuntu2.18.04; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: 4.2.5.0 INFO 2022-03-11 16:25:13 AddOrReplaceReadGroups Created read-group ID=1 PL=ILLUMINA LB=S22F SM=S22F INFO 2022-03-11 16:25:16 AddOrReplaceReadGroups Processed 1,000,000 records. Elapsed time: 00:00:03s. Time for last 1,000,000: 3s. Last read position: NC_035780.1:12,341,363 INFO 2022-03-11 16:25:19 AddOrReplaceReadGroups Processed 2,000,000 records. Elapsed time: 00:00:05s. Time for last 1,000,000: 2s. Last read position: NC_035780.1:27,523,039 INFO 2022-03-11 16:25:22 AddOrReplaceReadGroups Processed 3,000,000 records. Elapsed time: 00:00:08s. Time for last 1,000,000: 2s. Last read position: NC_035780.1:38,990,768 INFO 2022-03-11 16:25:25 AddOrReplaceReadGroups Processed 4,000,000 records. Elapsed time: 00:00:12s. Time for last 1,000,000: 3s. Last read position: NC_035780.1:52,847,262 INFO 2022-03-11 16:25:28 AddOrReplaceReadGroups Processed 5,000,000 records. Elapsed time: 00:00:14s. Time for last 1,000,000: 2s. Last read position: NC_035780.1:58,811,920 INFO 2022-03-11 16:25:31 AddOrReplaceReadGroups Processed 6,000,000 records. Elapsed time: 00:00:17s. Time for last 1,000,000: 2s. Last read position: NC_035781.1:1,853,618 INFO 2022-03-11 16:25:34 AddOrReplaceReadGroups Processed 7,000,000 records. Elapsed time: 00:00:20s. Time for last 1,000,000: 2s. Last read position: NC_035781.1:8,679,981 INFO 2022-03-11 16:25:37 AddOrReplaceReadGroups Processed 8,000,000 records. Elapsed time: 00:00:23s. Time for last 1,000,000: 2s. Last read position: NC_035781.1:14,912,425 INFO 2022-03-11 16:25:40 AddOrReplaceReadGroups Processed 9,000,000 records. Elapsed time: 00:00:26s. Time for last 1,000,000: 2s. Last read position: NC_035781.1:22,336,953 INFO 2022-03-11 16:25:43 AddOrReplaceReadGroups Processed 10,000,000 records. Elapsed time: 00:00:29s. Time for last 1,000,000: 3s. Last read position: NC_035781.1:30,488,934 INFO 2022-03-11 16:25:49 AddOrReplaceReadGroups Processed 11,000,000 records. Elapsed time: 00:00:35s. Time for last 1,000,000: 5s. Last read position: NC_035781.1:40,226,498 INFO 2022-03-11 16:25:52 AddOrReplaceReadGroups Processed 12,000,000 records. Elapsed time: 00:00:38s. Time for last 1,000,000: 3s. Last read position: NC_035781.1:43,968,692 INFO 2022-03-11 16:25:55 AddOrReplaceReadGroups Processed 13,000,000 records. Elapsed time: 00:00:41s. Time for last 1,000,000: 2s. Last read position: NC_035781.1:50,472,485 INFO 2022-03-11 16:25:58 AddOrReplaceReadGroups Processed 14,000,000 records. Elapsed time: 00:00:44s. Time for last 1,000,000: 2s. Last read position: NC_035781.1:61,070,058 INFO 2022-03-11 16:26:01 AddOrReplaceReadGroups Processed 15,000,000 records. Elapsed time: 00:00:47s. Time for last 1,000,000: 3s. Last read position: NC_035782.1:19,372,319 INFO 2022-03-11 16:26:04 AddOrReplaceReadGroups Processed 16,000,000 records. Elapsed time: 00:00:50s. Time for last 1,000,000: 2s. Last read position: NC_035782.1:27,906,182 INFO 2022-03-11 16:26:07 AddOrReplaceReadGroups Processed 17,000,000 records. Elapsed time: 00:00:53s. Time for last 1,000,000: 3s. Last read position: NC_035782.1:37,433,033 INFO 2022-03-11 16:26:10 AddOrReplaceReadGroups Processed 18,000,000 records. Elapsed time: 00:00:56s. Time for last 1,000,000: 3s. Last read position: NC_035782.1:46,881,442 INFO 2022-03-11 16:26:13 AddOrReplaceReadGroups Processed 19,000,000 records. Elapsed time: 00:00:59s. Time for last 1,000,000: 3s. Last read position: NC_035782.1:54,640,754 INFO 2022-03-11 16:26:16 AddOrReplaceReadGroups Processed 20,000,000 records. Elapsed time: 00:01:02s. Time for last 1,000,000: 3s. Last read position: NC_035782.1:61,291,548 INFO 2022-03-11 16:26:19 AddOrReplaceReadGroups Processed 21,000,000 records. Elapsed time: 00:01:05s. Time for last 1,000,000: 2s. Last read position: NC_035782.1:68,385,876 INFO 2022-03-11 16:26:25 AddOrReplaceReadGroups Processed 22,000,000 records. Elapsed time: 00:01:11s. Time for last 1,000,000: 6s. Last read position: NC_035783.1:1,669,723 INFO 2022-03-11 16:26:28 AddOrReplaceReadGroups Processed 23,000,000 records. Elapsed time: 00:01:14s. Time for last 1,000,000: 3s. Last read position: NC_035783.1:11,731,700 INFO 2022-03-11 16:26:31 AddOrReplaceReadGroups Processed 24,000,000 records. Elapsed time: 00:01:18s. Time for last 1,000,000: 3s. Last read position: NC_035783.1:20,411,874 INFO 2022-03-11 16:26:34 AddOrReplaceReadGroups Processed 25,000,000 records. Elapsed time: 00:01:21s. Time for last 1,000,000: 2s. Last read position: NC_035783.1:29,963,687 INFO 2022-03-11 16:26:37 AddOrReplaceReadGroups Processed 26,000,000 records. Elapsed time: 00:01:23s. Time for last 1,000,000: 2s. Last read position: NC_035783.1:34,528,611 INFO 2022-03-11 16:26:40 AddOrReplaceReadGroups Processed 27,000,000 records. Elapsed time: 00:01:26s. Time for last 1,000,000: 2s. Last read position: NC_035783.1:40,342,263 INFO 2022-03-11 16:26:43 AddOrReplaceReadGroups Processed 28,000,000 records. Elapsed time: 00:01:29s. Time for last 1,000,000: 2s. Last read position: NC_035783.1:48,478,559 INFO 2022-03-11 16:26:46 AddOrReplaceReadGroups Processed 29,000,000 records. Elapsed time: 00:01:32s. Time for last 1,000,000: 3s. Last read position: NC_035784.1:499,239 INFO 2022-03-11 16:26:49 AddOrReplaceReadGroups Processed 30,000,000 records. Elapsed time: 00:01:35s. Time for last 1,000,000: 3s. Last read position: NC_035784.1:8,485,403 INFO 2022-03-11 16:26:52 AddOrReplaceReadGroups Processed 31,000,000 records. Elapsed time: 00:01:38s. Time for last 1,000,000: 2s. Last read position: NC_035784.1:16,424,391 INFO 2022-03-11 16:26:56 AddOrReplaceReadGroups Processed 32,000,000 records. Elapsed time: 00:01:42s. Time for last 1,000,000: 4s. Last read position: NC_035784.1:25,498,593 INFO 2022-03-11 16:27:01 AddOrReplaceReadGroups Processed 33,000,000 records. Elapsed time: 00:01:48s. Time for last 1,000,000: 5s. Last read position: NC_035784.1:33,367,666 INFO 2022-03-11 16:27:04 AddOrReplaceReadGroups Processed 34,000,000 records. Elapsed time: 00:01:51s. Time for last 1,000,000: 3s. Last read position: NC_035784.1:41,086,470 INFO 2022-03-11 16:27:07 AddOrReplaceReadGroups Processed 35,000,000 records. Elapsed time: 00:01:53s. Time for last 1,000,000: 2s. Last read position: NC_035784.1:47,752,500 INFO 2022-03-11 16:27:10 AddOrReplaceReadGroups Processed 36,000,000 records. Elapsed time: 00:01:56s. Time for last 1,000,000: 2s. Last read position: NC_035784.1:52,131,632 INFO 2022-03-11 16:27:13 AddOrReplaceReadGroups Processed 37,000,000 records. Elapsed time: 00:01:59s. Time for last 1,000,000: 2s. Last read position: NC_035784.1:52,199,801 INFO 2022-03-11 16:27:15 AddOrReplaceReadGroups Processed 38,000,000 records. Elapsed time: 00:02:01s. Time for last 1,000,000: 2s. Last read position: NC_035784.1:52,259,143 INFO 2022-03-11 16:27:18 AddOrReplaceReadGroups Processed 39,000,000 records. Elapsed time: 00:02:04s. Time for last 1,000,000: 2s. Last read position: NC_035784.1:52,280,397 INFO 2022-03-11 16:27:21 AddOrReplaceReadGroups Processed 40,000,000 records. Elapsed time: 00:02:07s. Time for last 1,000,000: 2s. Last read position: NC_035784.1:61,354,722 INFO 2022-03-11 16:27:24 AddOrReplaceReadGroups Processed 41,000,000 records. Elapsed time: 00:02:10s. Time for last 1,000,000: 3s. Last read position: NC_035784.1:70,378,610 INFO 2022-03-11 16:27:27 AddOrReplaceReadGroups Processed 42,000,000 records. Elapsed time: 00:02:13s. Time for last 1,000,000: 3s. Last read position: NC_035784.1:80,701,499 INFO 2022-03-11 16:27:31 AddOrReplaceReadGroups Processed 43,000,000 records. Elapsed time: 00:02:18s. Time for last 1,000,000: 4s. Last read position: NC_035785.1:8,226,794 INFO 2022-03-11 16:27:36 AddOrReplaceReadGroups Processed 44,000,000 records. Elapsed time: 00:02:22s. Time for last 1,000,000: 4s. Last read position: NC_035785.1:33,638,455 INFO 2022-03-11 16:27:39 AddOrReplaceReadGroups Processed 45,000,000 records. Elapsed time: 00:02:25s. Time for last 1,000,000: 2s. Last read position: NC_035785.1:49,291,030 INFO 2022-03-11 16:27:42 AddOrReplaceReadGroups Processed 46,000,000 records. Elapsed time: 00:02:28s. Time for last 1,000,000: 2s. Last read position: NC_035786.1:21,311,417 INFO 2022-03-11 16:27:45 AddOrReplaceReadGroups Processed 47,000,000 records. Elapsed time: 00:02:31s. Time for last 1,000,000: 3s. Last read position: NC_035786.1:45,069,398 INFO 2022-03-11 16:27:48 AddOrReplaceReadGroups Processed 48,000,000 records. Elapsed time: 00:02:34s. Time for last 1,000,000: 3s. Last read position: NC_035787.1:6,573,210 INFO 2022-03-11 16:27:51 AddOrReplaceReadGroups Processed 49,000,000 records. Elapsed time: 00:02:37s. Time for last 1,000,000: 3s. Last read position: NC_035787.1:31,326,531 INFO 2022-03-11 16:27:54 AddOrReplaceReadGroups Processed 50,000,000 records. Elapsed time: 00:02:40s. Time for last 1,000,000: 3s. Last read position: NC_035787.1:55,422,725 INFO 2022-03-11 16:27:57 AddOrReplaceReadGroups Processed 51,000,000 records. Elapsed time: 00:02:43s. Time for last 1,000,000: 2s. Last read position: NC_035787.1:69,833,634 INFO 2022-03-11 16:28:00 AddOrReplaceReadGroups Processed 52,000,000 records. Elapsed time: 00:02:46s. Time for last 1,000,000: 3s. Last read position: NC_035788.1:19,008,370 INFO 2022-03-11 16:28:03 AddOrReplaceReadGroups Processed 53,000,000 records. Elapsed time: 00:02:49s. Time for last 1,000,000: 3s. Last read position: NC_035788.1:54,311,386 INFO 2022-03-11 16:28:09 AddOrReplaceReadGroups Processed 54,000,000 records. Elapsed time: 00:02:55s. Time for last 1,000,000: 6s. Last read position: NC_035788.1:75,951,493 INFO 2022-03-11 16:28:12 AddOrReplaceReadGroups Processed 55,000,000 records. Elapsed time: 00:02:58s. Time for last 1,000,000: 3s. Last read position: NC_035788.1:103,119,473 INFO 2022-03-11 16:28:15 AddOrReplaceReadGroups Processed 56,000,000 records. Elapsed time: 00:03:01s. Time for last 1,000,000: 3s. Last read position: NC_035789.1:18,251,548 INFO 2022-03-11 16:28:18 AddOrReplaceReadGroups Processed 57,000,000 records. Elapsed time: 00:03:04s. Time for last 1,000,000: 2s. Last read position: NC_007175.2:2,231 INFO 2022-03-11 16:28:21 AddOrReplaceReadGroups Processed 58,000,000 records. Elapsed time: 00:03:07s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 16:28:24 AddOrReplaceReadGroups Processed 59,000,000 records. Elapsed time: 00:03:10s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 16:28:27 AddOrReplaceReadGroups Processed 60,000,000 records. Elapsed time: 00:03:13s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 16:28:30 AddOrReplaceReadGroups Processed 61,000,000 records. Elapsed time: 00:03:16s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 16:28:32 AddOrReplaceReadGroups Processed 62,000,000 records. Elapsed time: 00:03:19s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 16:28:35 AddOrReplaceReadGroups Processed 63,000,000 records. Elapsed time: 00:03:22s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 16:28:40 AddOrReplaceReadGroups Processed 64,000,000 records. Elapsed time: 00:03:26s. Time for last 1,000,000: 4s. Last read position: */* INFO 2022-03-11 16:28:46 AddOrReplaceReadGroups Processed 65,000,000 records. Elapsed time: 00:03:32s. Time for last 1,000,000: 5s. Last read position: */* [Fri Mar 11 16:28:47 PST 2022] picard.sam.AddOrReplaceReadGroups done. Elapsed time: 3.57 minutes. Runtime.totalMemory()=2831155200 Tool returned: 0 Using GATK jar /home/shared/gatk-4.2.5.0/gatk-package-4.2.5.0-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 /home/shared/gatk-4.2.5.0/gatk-package-4.2.5.0-local.jar AddOrReplaceReadGroups I=S23M.dedup-split.bam O=S23M.dedup-split-RG.bam RGID=1 RGLB=S23M RGPL=ILLUMINA RGPU=unit1 RGSM=S23M INFO 2022-03-11 16:28:49 AddOrReplaceReadGroups ********** NOTE: Picard's command line syntax is changing. ********** ********** For more information, please see: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** ********** The command line looks like this in the new syntax: ********** ********** AddOrReplaceReadGroups -I S23M.dedup-split.bam -O S23M.dedup-split-RG.bam -RGID 1 -RGLB S23M -RGPL ILLUMINA -RGPU unit1 -RGSM S23M ********** 16:28:49.037 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/shared/gatk-4.2.5.0/gatk-package-4.2.5.0-local.jar!/com/intel/gkl/native/libgkl_compression.so [Fri Mar 11 16:28:49 PST 2022] AddOrReplaceReadGroups INPUT=S23M.dedup-split.bam OUTPUT=S23M.dedup-split-RG.bam RGID=1 RGLB=S23M RGPL=ILLUMINA RGPU=unit1 RGSM=S23M VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=2 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Mar 11, 2022 4:28:49 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine INFO: Failed to detect whether we are running on Google Compute Engine. [Fri Mar 11 16:28:49 PST 2022] Executing as sr320@raven on Linux 5.4.0-104-generic amd64; OpenJDK 64-Bit Server VM 11.0.14+9-Ubuntu-0ubuntu2.18.04; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: 4.2.5.0 INFO 2022-03-11 16:28:49 AddOrReplaceReadGroups Created read-group ID=1 PL=ILLUMINA LB=S23M SM=S23M INFO 2022-03-11 16:28:52 AddOrReplaceReadGroups Processed 1,000,000 records. Elapsed time: 00:00:02s. Time for last 1,000,000: 2s. Last read position: NC_035780.1:9,124,186 INFO 2022-03-11 16:28:55 AddOrReplaceReadGroups Processed 2,000,000 records. Elapsed time: 00:00:05s. Time for last 1,000,000: 2s. Last read position: NC_035780.1:19,628,382 INFO 2022-03-11 16:28:57 AddOrReplaceReadGroups Processed 3,000,000 records. Elapsed time: 00:00:08s. Time for last 1,000,000: 2s. Last read position: NC_035780.1:28,937,401 INFO 2022-03-11 16:29:00 AddOrReplaceReadGroups Processed 4,000,000 records. Elapsed time: 00:00:11s. Time for last 1,000,000: 3s. Last read position: NC_035780.1:37,862,640 INFO 2022-03-11 16:29:03 AddOrReplaceReadGroups Processed 5,000,000 records. Elapsed time: 00:00:14s. Time for last 1,000,000: 2s. Last read position: NC_035780.1:48,613,003 INFO 2022-03-11 16:29:06 AddOrReplaceReadGroups Processed 6,000,000 records. Elapsed time: 00:00:17s. Time for last 1,000,000: 2s. Last read position: NC_035780.1:59,919,005 INFO 2022-03-11 16:29:09 AddOrReplaceReadGroups Processed 7,000,000 records. Elapsed time: 00:00:20s. Time for last 1,000,000: 2s. Last read position: NC_035781.1:4,214,414 INFO 2022-03-11 16:29:12 AddOrReplaceReadGroups Processed 8,000,000 records. Elapsed time: 00:00:23s. Time for last 1,000,000: 2s. Last read position: NC_035781.1:13,144,743 INFO 2022-03-11 16:29:15 AddOrReplaceReadGroups Processed 9,000,000 records. Elapsed time: 00:00:26s. Time for last 1,000,000: 2s. Last read position: NC_035781.1:21,769,911 INFO 2022-03-11 16:29:18 AddOrReplaceReadGroups Processed 10,000,000 records. Elapsed time: 00:00:29s. Time for last 1,000,000: 2s. Last read position: NC_035781.1:31,506,697 INFO 2022-03-11 16:29:24 AddOrReplaceReadGroups Processed 11,000,000 records. Elapsed time: 00:00:35s. Time for last 1,000,000: 6s. Last read position: NC_035781.1:41,590,637 INFO 2022-03-11 16:29:27 AddOrReplaceReadGroups Processed 12,000,000 records. Elapsed time: 00:00:38s. Time for last 1,000,000: 2s. Last read position: NC_035781.1:52,028,570 INFO 2022-03-11 16:29:30 AddOrReplaceReadGroups Processed 13,000,000 records. Elapsed time: 00:00:41s. Time for last 1,000,000: 2s. Last read position: NC_035781.1:60,953,893 INFO 2022-03-11 16:29:33 AddOrReplaceReadGroups Processed 14,000,000 records. Elapsed time: 00:00:44s. Time for last 1,000,000: 2s. Last read position: NC_035782.1:10,527,167 INFO 2022-03-11 16:29:36 AddOrReplaceReadGroups Processed 15,000,000 records. Elapsed time: 00:00:47s. Time for last 1,000,000: 2s. Last read position: NC_035782.1:21,867,879 INFO 2022-03-11 16:29:39 AddOrReplaceReadGroups Processed 16,000,000 records. Elapsed time: 00:00:50s. Time for last 1,000,000: 2s. Last read position: NC_035782.1:33,106,669 INFO 2022-03-11 16:29:42 AddOrReplaceReadGroups Processed 17,000,000 records. Elapsed time: 00:00:53s. Time for last 1,000,000: 2s. Last read position: NC_035782.1:42,990,301 INFO 2022-03-11 16:29:45 AddOrReplaceReadGroups Processed 18,000,000 records. Elapsed time: 00:00:56s. Time for last 1,000,000: 2s. Last read position: NC_035782.1:53,229,143 INFO 2022-03-11 16:29:48 AddOrReplaceReadGroups Processed 19,000,000 records. Elapsed time: 00:00:59s. Time for last 1,000,000: 2s. Last read position: NC_035782.1:62,284,203 INFO 2022-03-11 16:29:51 AddOrReplaceReadGroups Processed 20,000,000 records. Elapsed time: 00:01:01s. Time for last 1,000,000: 2s. Last read position: NC_035782.1:72,847,183 INFO 2022-03-11 16:29:54 AddOrReplaceReadGroups Processed 21,000,000 records. Elapsed time: 00:01:04s. Time for last 1,000,000: 2s. Last read position: NC_035783.1:6,828,124 INFO 2022-03-11 16:30:00 AddOrReplaceReadGroups Processed 22,000,000 records. Elapsed time: 00:01:11s. Time for last 1,000,000: 6s. Last read position: NC_035783.1:16,303,418 INFO 2022-03-11 16:30:03 AddOrReplaceReadGroups Processed 23,000,000 records. Elapsed time: 00:01:14s. Time for last 1,000,000: 2s. Last read position: NC_035783.1:25,096,303 INFO 2022-03-11 16:30:06 AddOrReplaceReadGroups Processed 24,000,000 records. Elapsed time: 00:01:16s. Time for last 1,000,000: 2s. Last read position: NC_035783.1:35,943,200 INFO 2022-03-11 16:30:09 AddOrReplaceReadGroups Processed 25,000,000 records. Elapsed time: 00:01:19s. Time for last 1,000,000: 2s. Last read position: NC_035783.1:45,322,653 INFO 2022-03-11 16:30:12 AddOrReplaceReadGroups Processed 26,000,000 records. Elapsed time: 00:01:22s. Time for last 1,000,000: 2s. Last read position: NC_035783.1:54,860,620 INFO 2022-03-11 16:30:15 AddOrReplaceReadGroups Processed 27,000,000 records. Elapsed time: 00:01:25s. Time for last 1,000,000: 2s. Last read position: NC_035784.1:5,439,404 INFO 2022-03-11 16:30:17 AddOrReplaceReadGroups Processed 28,000,000 records. Elapsed time: 00:01:28s. Time for last 1,000,000: 2s. Last read position: NC_035784.1:14,946,114 INFO 2022-03-11 16:30:20 AddOrReplaceReadGroups Processed 29,000,000 records. Elapsed time: 00:01:31s. Time for last 1,000,000: 2s. Last read position: NC_035784.1:25,526,676 INFO 2022-03-11 16:30:23 AddOrReplaceReadGroups Processed 30,000,000 records. Elapsed time: 00:01:34s. Time for last 1,000,000: 2s. Last read position: NC_035784.1:35,852,747 INFO 2022-03-11 16:30:26 AddOrReplaceReadGroups Processed 31,000,000 records. Elapsed time: 00:01:37s. Time for last 1,000,000: 2s. Last read position: NC_035784.1:44,485,592 INFO 2022-03-11 16:30:31 AddOrReplaceReadGroups Processed 32,000,000 records. Elapsed time: 00:01:42s. Time for last 1,000,000: 4s. Last read position: NC_035784.1:52,198,069 INFO 2022-03-11 16:30:35 AddOrReplaceReadGroups Processed 33,000,000 records. Elapsed time: 00:01:46s. Time for last 1,000,000: 3s. Last read position: NC_035784.1:55,267,713 INFO 2022-03-11 16:30:38 AddOrReplaceReadGroups Processed 34,000,000 records. Elapsed time: 00:01:49s. Time for last 1,000,000: 2s. Last read position: NC_035784.1:64,785,273 INFO 2022-03-11 16:30:41 AddOrReplaceReadGroups Processed 35,000,000 records. Elapsed time: 00:01:52s. Time for last 1,000,000: 2s. Last read position: NC_035784.1:74,053,294 INFO 2022-03-11 16:30:44 AddOrReplaceReadGroups Processed 36,000,000 records. Elapsed time: 00:01:55s. Time for last 1,000,000: 2s. Last read position: NC_035784.1:86,140,094 INFO 2022-03-11 16:30:47 AddOrReplaceReadGroups Processed 37,000,000 records. Elapsed time: 00:01:57s. Time for last 1,000,000: 2s. Last read position: NC_035784.1:96,998,305 INFO 2022-03-11 16:30:50 AddOrReplaceReadGroups Processed 38,000,000 records. Elapsed time: 00:02:00s. Time for last 1,000,000: 2s. Last read position: NC_035785.1:8,576,529 INFO 2022-03-11 16:30:52 AddOrReplaceReadGroups Processed 39,000,000 records. Elapsed time: 00:02:03s. Time for last 1,000,000: 2s. Last read position: NC_035785.1:19,917,299 INFO 2022-03-11 16:30:55 AddOrReplaceReadGroups Processed 40,000,000 records. Elapsed time: 00:02:06s. Time for last 1,000,000: 2s. Last read position: NC_035785.1:33,002,757 INFO 2022-03-11 16:30:58 AddOrReplaceReadGroups Processed 41,000,000 records. Elapsed time: 00:02:09s. Time for last 1,000,000: 3s. Last read position: NC_035785.1:42,974,673 INFO 2022-03-11 16:31:01 AddOrReplaceReadGroups Processed 42,000,000 records. Elapsed time: 00:02:12s. Time for last 1,000,000: 2s. Last read position: NC_035786.1:2,199,869 INFO 2022-03-11 16:31:07 AddOrReplaceReadGroups Processed 43,000,000 records. Elapsed time: 00:02:18s. Time for last 1,000,000: 6s. Last read position: NC_035786.1:14,073,133 INFO 2022-03-11 16:31:10 AddOrReplaceReadGroups Processed 44,000,000 records. Elapsed time: 00:02:21s. Time for last 1,000,000: 2s. Last read position: NC_035786.1:28,183,460 INFO 2022-03-11 16:31:13 AddOrReplaceReadGroups Processed 45,000,000 records. Elapsed time: 00:02:24s. Time for last 1,000,000: 2s. Last read position: NC_035786.1:41,403,709 INFO 2022-03-11 16:31:16 AddOrReplaceReadGroups Processed 46,000,000 records. Elapsed time: 00:02:27s. Time for last 1,000,000: 2s. Last read position: NC_035786.1:52,865,862 INFO 2022-03-11 16:31:19 AddOrReplaceReadGroups Processed 47,000,000 records. Elapsed time: 00:02:30s. Time for last 1,000,000: 2s. Last read position: NC_035787.1:6,929,358 INFO 2022-03-11 16:31:22 AddOrReplaceReadGroups Processed 48,000,000 records. Elapsed time: 00:02:33s. Time for last 1,000,000: 2s. Last read position: NC_035787.1:19,156,761 INFO 2022-03-11 16:31:25 AddOrReplaceReadGroups Processed 49,000,000 records. Elapsed time: 00:02:36s. Time for last 1,000,000: 2s. Last read position: NC_035787.1:32,992,303 INFO 2022-03-11 16:31:28 AddOrReplaceReadGroups Processed 50,000,000 records. Elapsed time: 00:02:39s. Time for last 1,000,000: 2s. Last read position: NC_035787.1:44,433,917 INFO 2022-03-11 16:31:31 AddOrReplaceReadGroups Processed 51,000,000 records. Elapsed time: 00:02:42s. Time for last 1,000,000: 2s. Last read position: NC_035787.1:55,059,178 INFO 2022-03-11 16:31:34 AddOrReplaceReadGroups Processed 52,000,000 records. Elapsed time: 00:02:44s. Time for last 1,000,000: 2s. Last read position: NC_035787.1:63,509,490 INFO 2022-03-11 16:31:37 AddOrReplaceReadGroups Processed 53,000,000 records. Elapsed time: 00:02:47s. Time for last 1,000,000: 2s. Last read position: NC_035788.1:1,214,641 INFO 2022-03-11 16:31:43 AddOrReplaceReadGroups Processed 54,000,000 records. Elapsed time: 00:02:54s. Time for last 1,000,000: 6s. Last read position: NC_035788.1:15,147,136 INFO 2022-03-11 16:31:46 AddOrReplaceReadGroups Processed 55,000,000 records. Elapsed time: 00:02:57s. Time for last 1,000,000: 2s. Last read position: NC_035788.1:27,697,608 INFO 2022-03-11 16:31:49 AddOrReplaceReadGroups Processed 56,000,000 records. Elapsed time: 00:03:00s. Time for last 1,000,000: 2s. Last read position: NC_035788.1:42,916,622 INFO 2022-03-11 16:31:52 AddOrReplaceReadGroups Processed 57,000,000 records. Elapsed time: 00:03:02s. Time for last 1,000,000: 2s. Last read position: NC_035788.1:52,229,350 INFO 2022-03-11 16:31:54 AddOrReplaceReadGroups Processed 58,000,000 records. Elapsed time: 00:03:05s. Time for last 1,000,000: 2s. Last read position: NC_035788.1:63,264,750 INFO 2022-03-11 16:31:57 AddOrReplaceReadGroups Processed 59,000,000 records. Elapsed time: 00:03:08s. Time for last 1,000,000: 2s. Last read position: NC_035788.1:73,491,218 INFO 2022-03-11 16:32:00 AddOrReplaceReadGroups Processed 60,000,000 records. Elapsed time: 00:03:11s. Time for last 1,000,000: 2s. Last read position: NC_035788.1:82,867,880 INFO 2022-03-11 16:32:03 AddOrReplaceReadGroups Processed 61,000,000 records. Elapsed time: 00:03:14s. Time for last 1,000,000: 2s. Last read position: NC_035788.1:95,420,996 INFO 2022-03-11 16:32:06 AddOrReplaceReadGroups Processed 62,000,000 records. Elapsed time: 00:03:17s. Time for last 1,000,000: 2s. Last read position: NC_035789.1:3,748,267 INFO 2022-03-11 16:32:09 AddOrReplaceReadGroups Processed 63,000,000 records. Elapsed time: 00:03:20s. Time for last 1,000,000: 2s. Last read position: NC_035789.1:13,635,366 INFO 2022-03-11 16:32:12 AddOrReplaceReadGroups Processed 64,000,000 records. Elapsed time: 00:03:23s. Time for last 1,000,000: 2s. Last read position: NC_035789.1:20,741,890 INFO 2022-03-11 16:32:18 AddOrReplaceReadGroups Processed 65,000,000 records. Elapsed time: 00:03:29s. Time for last 1,000,000: 6s. Last read position: NC_007175.2:209 INFO 2022-03-11 16:32:21 AddOrReplaceReadGroups Processed 66,000,000 records. Elapsed time: 00:03:32s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 16:32:24 AddOrReplaceReadGroups Processed 67,000,000 records. Elapsed time: 00:03:34s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 16:32:26 AddOrReplaceReadGroups Processed 68,000,000 records. Elapsed time: 00:03:37s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 16:32:29 AddOrReplaceReadGroups Processed 69,000,000 records. Elapsed time: 00:03:40s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 16:32:32 AddOrReplaceReadGroups Processed 70,000,000 records. Elapsed time: 00:03:42s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 16:32:34 AddOrReplaceReadGroups Processed 71,000,000 records. Elapsed time: 00:03:45s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 16:32:37 AddOrReplaceReadGroups Processed 72,000,000 records. Elapsed time: 00:03:48s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 16:32:40 AddOrReplaceReadGroups Processed 73,000,000 records. Elapsed time: 00:03:50s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 16:32:42 AddOrReplaceReadGroups Processed 74,000,000 records. Elapsed time: 00:03:53s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 16:32:45 AddOrReplaceReadGroups Processed 75,000,000 records. Elapsed time: 00:03:56s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 16:32:49 AddOrReplaceReadGroups Processed 76,000,000 records. Elapsed time: 00:04:00s. Time for last 1,000,000: 4s. Last read position: */* INFO 2022-03-11 16:32:55 AddOrReplaceReadGroups Processed 77,000,000 records. Elapsed time: 00:04:05s. Time for last 1,000,000: 5s. Last read position: */* INFO 2022-03-11 16:32:57 AddOrReplaceReadGroups Processed 78,000,000 records. Elapsed time: 00:04:08s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 16:33:00 AddOrReplaceReadGroups Processed 79,000,000 records. Elapsed time: 00:04:11s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 16:33:03 AddOrReplaceReadGroups Processed 80,000,000 records. Elapsed time: 00:04:14s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 16:33:06 AddOrReplaceReadGroups Processed 81,000,000 records. Elapsed time: 00:04:16s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 16:33:08 AddOrReplaceReadGroups Processed 82,000,000 records. Elapsed time: 00:04:19s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 16:33:11 AddOrReplaceReadGroups Processed 83,000,000 records. Elapsed time: 00:04:22s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 16:33:14 AddOrReplaceReadGroups Processed 84,000,000 records. Elapsed time: 00:04:24s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 16:33:16 AddOrReplaceReadGroups Processed 85,000,000 records. Elapsed time: 00:04:27s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 16:33:19 AddOrReplaceReadGroups Processed 86,000,000 records. Elapsed time: 00:04:30s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 16:33:22 AddOrReplaceReadGroups Processed 87,000,000 records. Elapsed time: 00:04:33s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 16:33:29 AddOrReplaceReadGroups Processed 88,000,000 records. Elapsed time: 00:04:40s. Time for last 1,000,000: 7s. Last read position: */* INFO 2022-03-11 16:33:32 AddOrReplaceReadGroups Processed 89,000,000 records. Elapsed time: 00:04:43s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 16:33:34 AddOrReplaceReadGroups Processed 90,000,000 records. Elapsed time: 00:04:45s. Time for last 1,000,000: 2s. Last read position: */* [Fri Mar 11 16:33:36 PST 2022] picard.sam.AddOrReplaceReadGroups done. Elapsed time: 4.79 minutes. Runtime.totalMemory()=2797600768 Tool returned: 0 Using GATK jar /home/shared/gatk-4.2.5.0/gatk-package-4.2.5.0-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 /home/shared/gatk-4.2.5.0/gatk-package-4.2.5.0-local.jar AddOrReplaceReadGroups I=S29F.dedup-split.bam O=S29F.dedup-split-RG.bam RGID=1 RGLB=S29F RGPL=ILLUMINA RGPU=unit1 RGSM=S29F INFO 2022-03-11 16:33:38 AddOrReplaceReadGroups ********** NOTE: Picard's command line syntax is changing. ********** ********** For more information, please see: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** ********** The command line looks like this in the new syntax: ********** ********** AddOrReplaceReadGroups -I S29F.dedup-split.bam -O S29F.dedup-split-RG.bam -RGID 1 -RGLB S29F -RGPL ILLUMINA -RGPU unit1 -RGSM S29F ********** 16:33:38.172 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/shared/gatk-4.2.5.0/gatk-package-4.2.5.0-local.jar!/com/intel/gkl/native/libgkl_compression.so [Fri Mar 11 16:33:38 PST 2022] AddOrReplaceReadGroups INPUT=S29F.dedup-split.bam OUTPUT=S29F.dedup-split-RG.bam RGID=1 RGLB=S29F RGPL=ILLUMINA RGPU=unit1 RGSM=S29F VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=2 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Mar 11, 2022 4:33:38 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine INFO: Failed to detect whether we are running on Google Compute Engine. [Fri Mar 11 16:33:38 PST 2022] Executing as sr320@raven on Linux 5.4.0-104-generic amd64; OpenJDK 64-Bit Server VM 11.0.14+9-Ubuntu-0ubuntu2.18.04; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: 4.2.5.0 INFO 2022-03-11 16:33:38 AddOrReplaceReadGroups Created read-group ID=1 PL=ILLUMINA LB=S29F SM=S29F INFO 2022-03-11 16:33:41 AddOrReplaceReadGroups Processed 1,000,000 records. Elapsed time: 00:00:03s. Time for last 1,000,000: 3s. Last read position: NC_035780.1:15,491,084 INFO 2022-03-11 16:33:44 AddOrReplaceReadGroups Processed 2,000,000 records. Elapsed time: 00:00:06s. Time for last 1,000,000: 2s. Last read position: NC_035780.1:31,496,854 INFO 2022-03-11 16:33:47 AddOrReplaceReadGroups Processed 3,000,000 records. Elapsed time: 00:00:09s. Time for last 1,000,000: 2s. Last read position: NC_035780.1:47,233,305 INFO 2022-03-11 16:33:50 AddOrReplaceReadGroups Processed 4,000,000 records. Elapsed time: 00:00:12s. Time for last 1,000,000: 3s. Last read position: NC_035780.1:59,149,954 INFO 2022-03-11 16:33:53 AddOrReplaceReadGroups Processed 5,000,000 records. Elapsed time: 00:00:15s. Time for last 1,000,000: 3s. Last read position: NC_035781.1:5,440,773 INFO 2022-03-11 16:33:56 AddOrReplaceReadGroups Processed 6,000,000 records. Elapsed time: 00:00:18s. Time for last 1,000,000: 2s. Last read position: NC_035781.1:14,027,019 INFO 2022-03-11 16:33:59 AddOrReplaceReadGroups Processed 7,000,000 records. Elapsed time: 00:00:21s. Time for last 1,000,000: 3s. Last read position: NC_035781.1:24,037,649 INFO 2022-03-11 16:34:02 AddOrReplaceReadGroups Processed 8,000,000 records. Elapsed time: 00:00:24s. Time for last 1,000,000: 2s. Last read position: NC_035781.1:36,278,944 INFO 2022-03-11 16:34:05 AddOrReplaceReadGroups Processed 9,000,000 records. Elapsed time: 00:00:27s. Time for last 1,000,000: 3s. Last read position: NC_035781.1:47,191,844 INFO 2022-03-11 16:34:08 AddOrReplaceReadGroups Processed 10,000,000 records. Elapsed time: 00:00:30s. Time for last 1,000,000: 3s. Last read position: NC_035781.1:58,873,681 INFO 2022-03-11 16:34:15 AddOrReplaceReadGroups Processed 11,000,000 records. Elapsed time: 00:00:36s. Time for last 1,000,000: 6s. Last read position: NC_035782.1:19,328,779 INFO 2022-03-11 16:34:18 AddOrReplaceReadGroups Processed 12,000,000 records. Elapsed time: 00:00:39s. Time for last 1,000,000: 2s. Last read position: NC_035782.1:26,225,720 INFO 2022-03-11 16:34:21 AddOrReplaceReadGroups Processed 13,000,000 records. Elapsed time: 00:00:42s. Time for last 1,000,000: 3s. Last read position: NC_035782.1:35,878,855 INFO 2022-03-11 16:34:24 AddOrReplaceReadGroups Processed 14,000,000 records. Elapsed time: 00:00:45s. Time for last 1,000,000: 3s. Last read position: NC_035782.1:48,991,804 INFO 2022-03-11 16:34:27 AddOrReplaceReadGroups Processed 15,000,000 records. Elapsed time: 00:00:48s. Time for last 1,000,000: 3s. Last read position: NC_035782.1:58,698,138 INFO 2022-03-11 16:34:30 AddOrReplaceReadGroups Processed 16,000,000 records. Elapsed time: 00:00:52s. Time for last 1,000,000: 3s. Last read position: NC_035782.1:69,085,757 INFO 2022-03-11 16:34:33 AddOrReplaceReadGroups Processed 17,000,000 records. Elapsed time: 00:00:55s. Time for last 1,000,000: 3s. Last read position: NC_035783.1:6,595,840 INFO 2022-03-11 16:34:36 AddOrReplaceReadGroups Processed 18,000,000 records. Elapsed time: 00:00:58s. Time for last 1,000,000: 3s. Last read position: NC_035783.1:18,397,306 INFO 2022-03-11 16:34:39 AddOrReplaceReadGroups Processed 19,000,000 records. Elapsed time: 00:01:01s. Time for last 1,000,000: 3s. Last read position: NC_035783.1:30,058,304 INFO 2022-03-11 16:34:42 AddOrReplaceReadGroups Processed 20,000,000 records. Elapsed time: 00:01:04s. Time for last 1,000,000: 3s. Last read position: NC_035783.1:37,104,663 INFO 2022-03-11 16:34:49 AddOrReplaceReadGroups Processed 21,000,000 records. Elapsed time: 00:01:10s. Time for last 1,000,000: 6s. Last read position: NC_035783.1:49,910,905 INFO 2022-03-11 16:34:52 AddOrReplaceReadGroups Processed 22,000,000 records. Elapsed time: 00:01:13s. Time for last 1,000,000: 3s. Last read position: NC_035784.1:5,153,683 INFO 2022-03-11 16:34:55 AddOrReplaceReadGroups Processed 23,000,000 records. Elapsed time: 00:01:16s. Time for last 1,000,000: 3s. Last read position: NC_035784.1:16,564,018 INFO 2022-03-11 16:34:58 AddOrReplaceReadGroups Processed 24,000,000 records. Elapsed time: 00:01:19s. Time for last 1,000,000: 3s. Last read position: NC_035784.1:30,205,349 INFO 2022-03-11 16:35:01 AddOrReplaceReadGroups Processed 25,000,000 records. Elapsed time: 00:01:23s. Time for last 1,000,000: 3s. Last read position: NC_035784.1:41,604,815 INFO 2022-03-11 16:35:04 AddOrReplaceReadGroups Processed 26,000,000 records. Elapsed time: 00:01:25s. Time for last 1,000,000: 2s. Last read position: NC_035784.1:50,308,469 INFO 2022-03-11 16:35:07 AddOrReplaceReadGroups Processed 27,000,000 records. Elapsed time: 00:01:28s. Time for last 1,000,000: 2s. Last read position: NC_035784.1:52,213,458 INFO 2022-03-11 16:35:09 AddOrReplaceReadGroups Processed 28,000,000 records. Elapsed time: 00:01:31s. Time for last 1,000,000: 2s. Last read position: NC_035784.1:52,260,315 INFO 2022-03-11 16:35:12 AddOrReplaceReadGroups Processed 29,000,000 records. Elapsed time: 00:01:33s. Time for last 1,000,000: 2s. Last read position: NC_035784.1:52,289,807 INFO 2022-03-11 16:35:15 AddOrReplaceReadGroups Processed 30,000,000 records. Elapsed time: 00:01:36s. Time for last 1,000,000: 3s. Last read position: NC_035784.1:65,924,219 INFO 2022-03-11 16:35:18 AddOrReplaceReadGroups Processed 31,000,000 records. Elapsed time: 00:01:40s. Time for last 1,000,000: 3s. Last read position: NC_035784.1:79,538,982 INFO 2022-03-11 16:35:24 AddOrReplaceReadGroups Processed 32,000,000 records. Elapsed time: 00:01:45s. Time for last 1,000,000: 5s. Last read position: NC_035784.1:94,434,763 INFO 2022-03-11 16:35:27 AddOrReplaceReadGroups Processed 33,000,000 records. Elapsed time: 00:01:49s. Time for last 1,000,000: 3s. Last read position: NC_035785.1:27,958,254 INFO 2022-03-11 16:35:30 AddOrReplaceReadGroups Processed 34,000,000 records. Elapsed time: 00:01:52s. Time for last 1,000,000: 3s. Last read position: NC_035785.1:43,386,867 INFO 2022-03-11 16:35:33 AddOrReplaceReadGroups Processed 35,000,000 records. Elapsed time: 00:01:55s. Time for last 1,000,000: 3s. Last read position: NC_035786.1:19,177,245 INFO 2022-03-11 16:35:36 AddOrReplaceReadGroups Processed 36,000,000 records. Elapsed time: 00:01:58s. Time for last 1,000,000: 3s. Last read position: NC_035786.1:46,361,654 INFO 2022-03-11 16:35:39 AddOrReplaceReadGroups Processed 37,000,000 records. Elapsed time: 00:02:01s. Time for last 1,000,000: 3s. Last read position: NC_035787.1:9,903,344 INFO 2022-03-11 16:35:42 AddOrReplaceReadGroups Processed 38,000,000 records. Elapsed time: 00:02:04s. Time for last 1,000,000: 3s. Last read position: NC_035787.1:38,036,849 INFO 2022-03-11 16:35:46 AddOrReplaceReadGroups Processed 39,000,000 records. Elapsed time: 00:02:07s. Time for last 1,000,000: 3s. Last read position: NC_035787.1:59,211,037 INFO 2022-03-11 16:35:49 AddOrReplaceReadGroups Processed 40,000,000 records. Elapsed time: 00:02:10s. Time for last 1,000,000: 3s. Last read position: NC_035788.1:3,775,165 INFO 2022-03-11 16:35:52 AddOrReplaceReadGroups Processed 41,000,000 records. Elapsed time: 00:02:13s. Time for last 1,000,000: 3s. Last read position: NC_035788.1:38,876,989 INFO 2022-03-11 16:35:58 AddOrReplaceReadGroups Processed 42,000,000 records. Elapsed time: 00:02:20s. Time for last 1,000,000: 6s. Last read position: NC_035788.1:61,815,625 INFO 2022-03-11 16:36:01 AddOrReplaceReadGroups Processed 43,000,000 records. Elapsed time: 00:02:23s. Time for last 1,000,000: 3s. Last read position: NC_035788.1:83,950,059 INFO 2022-03-11 16:36:04 AddOrReplaceReadGroups Processed 44,000,000 records. Elapsed time: 00:02:26s. Time for last 1,000,000: 3s. Last read position: NC_035789.1:11,685,279 INFO 2022-03-11 16:36:07 AddOrReplaceReadGroups Processed 45,000,000 records. Elapsed time: 00:02:29s. Time for last 1,000,000: 3s. Last read position: NC_007175.2:1,900 INFO 2022-03-11 16:36:10 AddOrReplaceReadGroups Processed 46,000,000 records. Elapsed time: 00:02:32s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 16:36:13 AddOrReplaceReadGroups Processed 47,000,000 records. Elapsed time: 00:02:35s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 16:36:16 AddOrReplaceReadGroups Processed 48,000,000 records. Elapsed time: 00:02:38s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 16:36:19 AddOrReplaceReadGroups Processed 49,000,000 records. Elapsed time: 00:02:40s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 16:36:22 AddOrReplaceReadGroups Processed 50,000,000 records. Elapsed time: 00:02:43s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 16:36:25 AddOrReplaceReadGroups Processed 51,000,000 records. Elapsed time: 00:02:46s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 16:36:27 AddOrReplaceReadGroups Processed 52,000,000 records. Elapsed time: 00:02:49s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 16:36:35 AddOrReplaceReadGroups Processed 53,000,000 records. Elapsed time: 00:02:56s. Time for last 1,000,000: 7s. Last read position: */* INFO 2022-03-11 16:36:38 AddOrReplaceReadGroups Processed 54,000,000 records. Elapsed time: 00:02:59s. Time for last 1,000,000: 2s. Last read position: */* [Fri Mar 11 16:36:38 PST 2022] picard.sam.AddOrReplaceReadGroups done. Elapsed time: 3.01 minutes. Runtime.totalMemory()=2743074816 Tool returned: 0 Using GATK jar /home/shared/gatk-4.2.5.0/gatk-package-4.2.5.0-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 /home/shared/gatk-4.2.5.0/gatk-package-4.2.5.0-local.jar AddOrReplaceReadGroups I=S31M.dedup-split.bam O=S31M.dedup-split-RG.bam RGID=1 RGLB=S31M RGPL=ILLUMINA RGPU=unit1 RGSM=S31M INFO 2022-03-11 16:36:40 AddOrReplaceReadGroups ********** NOTE: Picard's command line syntax is changing. ********** ********** For more information, please see: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** ********** The command line looks like this in the new syntax: ********** ********** AddOrReplaceReadGroups -I S31M.dedup-split.bam -O S31M.dedup-split-RG.bam -RGID 1 -RGLB S31M -RGPL ILLUMINA -RGPU unit1 -RGSM S31M ********** 16:36:40.410 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/shared/gatk-4.2.5.0/gatk-package-4.2.5.0-local.jar!/com/intel/gkl/native/libgkl_compression.so [Fri Mar 11 16:36:40 PST 2022] AddOrReplaceReadGroups INPUT=S31M.dedup-split.bam OUTPUT=S31M.dedup-split-RG.bam RGID=1 RGLB=S31M RGPL=ILLUMINA RGPU=unit1 RGSM=S31M VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=2 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Mar 11, 2022 4:36:40 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine INFO: Failed to detect whether we are running on Google Compute Engine. [Fri Mar 11 16:36:40 PST 2022] Executing as sr320@raven on Linux 5.4.0-104-generic amd64; OpenJDK 64-Bit Server VM 11.0.14+9-Ubuntu-0ubuntu2.18.04; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: 4.2.5.0 INFO 2022-03-11 16:36:40 AddOrReplaceReadGroups Created read-group ID=1 PL=ILLUMINA LB=S31M SM=S31M INFO 2022-03-11 16:36:43 AddOrReplaceReadGroups Processed 1,000,000 records. Elapsed time: 00:00:03s. Time for last 1,000,000: 3s. Last read position: NC_035780.1:17,026,472 INFO 2022-03-11 16:36:46 AddOrReplaceReadGroups Processed 2,000,000 records. Elapsed time: 00:00:06s. Time for last 1,000,000: 3s. Last read position: NC_035780.1:33,827,722 INFO 2022-03-11 16:36:49 AddOrReplaceReadGroups Processed 3,000,000 records. Elapsed time: 00:00:09s. Time for last 1,000,000: 3s. Last read position: NC_035780.1:52,059,081 INFO 2022-03-11 16:36:53 AddOrReplaceReadGroups Processed 4,000,000 records. Elapsed time: 00:00:12s. Time for last 1,000,000: 3s. Last read position: NC_035781.1:4,514,589 INFO 2022-03-11 16:36:56 AddOrReplaceReadGroups Processed 5,000,000 records. Elapsed time: 00:00:15s. Time for last 1,000,000: 3s. Last read position: NC_035781.1:21,163,710 INFO 2022-03-11 16:36:59 AddOrReplaceReadGroups Processed 6,000,000 records. Elapsed time: 00:00:18s. Time for last 1,000,000: 3s. Last read position: NC_035781.1:37,545,637 INFO 2022-03-11 16:37:02 AddOrReplaceReadGroups Processed 7,000,000 records. Elapsed time: 00:00:21s. Time for last 1,000,000: 3s. Last read position: NC_035781.1:54,511,199 INFO 2022-03-11 16:37:05 AddOrReplaceReadGroups Processed 8,000,000 records. Elapsed time: 00:00:25s. Time for last 1,000,000: 3s. Last read position: NC_035782.1:12,297,268 INFO 2022-03-11 16:37:08 AddOrReplaceReadGroups Processed 9,000,000 records. Elapsed time: 00:00:28s. Time for last 1,000,000: 3s. Last read position: NC_035782.1:32,545,103 INFO 2022-03-11 16:37:12 AddOrReplaceReadGroups Processed 10,000,000 records. Elapsed time: 00:00:31s. Time for last 1,000,000: 3s. Last read position: NC_035782.1:50,176,374 INFO 2022-03-11 16:37:15 AddOrReplaceReadGroups Processed 11,000,000 records. Elapsed time: 00:00:34s. Time for last 1,000,000: 3s. Last read position: NC_035782.1:66,913,442 INFO 2022-03-11 16:37:22 AddOrReplaceReadGroups Processed 12,000,000 records. Elapsed time: 00:00:41s. Time for last 1,000,000: 7s. Last read position: NC_035783.1:8,534,625 INFO 2022-03-11 16:37:25 AddOrReplaceReadGroups Processed 13,000,000 records. Elapsed time: 00:00:45s. Time for last 1,000,000: 3s. Last read position: NC_035783.1:23,295,887 INFO 2022-03-11 16:37:28 AddOrReplaceReadGroups Processed 14,000,000 records. Elapsed time: 00:00:48s. Time for last 1,000,000: 3s. Last read position: NC_035783.1:41,848,877 INFO 2022-03-11 16:37:32 AddOrReplaceReadGroups Processed 15,000,000 records. Elapsed time: 00:00:51s. Time for last 1,000,000: 3s. Last read position: NC_035783.1:57,315,051 INFO 2022-03-11 16:37:35 AddOrReplaceReadGroups Processed 16,000,000 records. Elapsed time: 00:00:54s. Time for last 1,000,000: 3s. Last read position: NC_035784.1:15,145,373 INFO 2022-03-11 16:37:38 AddOrReplaceReadGroups Processed 17,000,000 records. Elapsed time: 00:00:57s. Time for last 1,000,000: 3s. Last read position: NC_035784.1:32,883,645 INFO 2022-03-11 16:37:41 AddOrReplaceReadGroups Processed 18,000,000 records. Elapsed time: 00:01:00s. Time for last 1,000,000: 3s. Last read position: NC_035784.1:46,445,674 INFO 2022-03-11 16:37:44 AddOrReplaceReadGroups Processed 19,000,000 records. Elapsed time: 00:01:03s. Time for last 1,000,000: 2s. Last read position: NC_035784.1:52,209,321 INFO 2022-03-11 16:37:47 AddOrReplaceReadGroups Processed 20,000,000 records. Elapsed time: 00:01:06s. Time for last 1,000,000: 2s. Last read position: NC_035784.1:52,276,454 INFO 2022-03-11 16:37:50 AddOrReplaceReadGroups Processed 21,000,000 records. Elapsed time: 00:01:09s. Time for last 1,000,000: 3s. Last read position: NC_035784.1:63,922,569 INFO 2022-03-11 16:37:56 AddOrReplaceReadGroups Processed 22,000,000 records. Elapsed time: 00:01:16s. Time for last 1,000,000: 6s. Last read position: NC_035784.1:77,658,623 INFO 2022-03-11 16:37:59 AddOrReplaceReadGroups Processed 23,000,000 records. Elapsed time: 00:01:19s. Time for last 1,000,000: 3s. Last read position: NC_035784.1:90,734,988 INFO 2022-03-11 16:38:02 AddOrReplaceReadGroups Processed 24,000,000 records. Elapsed time: 00:01:22s. Time for last 1,000,000: 3s. Last read position: NC_035785.1:6,749,264 INFO 2022-03-11 16:38:06 AddOrReplaceReadGroups Processed 25,000,000 records. Elapsed time: 00:01:25s. Time for last 1,000,000: 3s. Last read position: NC_035785.1:29,534,941 INFO 2022-03-11 16:38:09 AddOrReplaceReadGroups Processed 26,000,000 records. Elapsed time: 00:01:28s. Time for last 1,000,000: 3s. Last read position: NC_035785.1:44,858,938 INFO 2022-03-11 16:38:12 AddOrReplaceReadGroups Processed 27,000,000 records. Elapsed time: 00:01:31s. Time for last 1,000,000: 3s. Last read position: NC_035786.1:11,681,163 INFO 2022-03-11 16:38:15 AddOrReplaceReadGroups Processed 28,000,000 records. Elapsed time: 00:01:34s. Time for last 1,000,000: 3s. Last read position: NC_035786.1:35,490,563 INFO 2022-03-11 16:38:18 AddOrReplaceReadGroups Processed 29,000,000 records. Elapsed time: 00:01:37s. Time for last 1,000,000: 3s. Last read position: NC_035786.1:56,706,163 INFO 2022-03-11 16:38:21 AddOrReplaceReadGroups Processed 30,000,000 records. Elapsed time: 00:01:41s. Time for last 1,000,000: 3s. Last read position: NC_035787.1:21,361,131 INFO 2022-03-11 16:38:24 AddOrReplaceReadGroups Processed 31,000,000 records. Elapsed time: 00:01:44s. Time for last 1,000,000: 3s. Last read position: NC_035787.1:42,637,417 INFO 2022-03-11 16:38:31 AddOrReplaceReadGroups Processed 32,000,000 records. Elapsed time: 00:01:50s. Time for last 1,000,000: 6s. Last read position: NC_035787.1:59,367,194 INFO 2022-03-11 16:38:34 AddOrReplaceReadGroups Processed 33,000,000 records. Elapsed time: 00:01:53s. Time for last 1,000,000: 3s. Last read position: NC_035787.1:75,317,594 INFO 2022-03-11 16:38:37 AddOrReplaceReadGroups Processed 34,000,000 records. Elapsed time: 00:01:56s. Time for last 1,000,000: 3s. Last read position: NC_035788.1:19,656,867 INFO 2022-03-11 16:38:40 AddOrReplaceReadGroups Processed 35,000,000 records. Elapsed time: 00:01:59s. Time for last 1,000,000: 3s. Last read position: NC_035788.1:47,072,478 INFO 2022-03-11 16:38:43 AddOrReplaceReadGroups Processed 36,000,000 records. Elapsed time: 00:02:03s. Time for last 1,000,000: 3s. Last read position: NC_035788.1:64,111,402 INFO 2022-03-11 16:38:46 AddOrReplaceReadGroups Processed 37,000,000 records. Elapsed time: 00:02:06s. Time for last 1,000,000: 3s. Last read position: NC_035788.1:81,194,605 INFO 2022-03-11 16:38:49 AddOrReplaceReadGroups Processed 38,000,000 records. Elapsed time: 00:02:09s. Time for last 1,000,000: 3s. Last read position: NC_035789.1:1,293,173 INFO 2022-03-11 16:38:53 AddOrReplaceReadGroups Processed 39,000,000 records. Elapsed time: 00:02:12s. Time for last 1,000,000: 3s. Last read position: NC_035789.1:18,596,708 INFO 2022-03-11 16:38:56 AddOrReplaceReadGroups Processed 40,000,000 records. Elapsed time: 00:02:15s. Time for last 1,000,000: 3s. Last read position: */* INFO 2022-03-11 16:38:59 AddOrReplaceReadGroups Processed 41,000,000 records. Elapsed time: 00:02:18s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 16:39:05 AddOrReplaceReadGroups Processed 42,000,000 records. Elapsed time: 00:02:25s. Time for last 1,000,000: 6s. Last read position: */* INFO 2022-03-11 16:39:08 AddOrReplaceReadGroups Processed 43,000,000 records. Elapsed time: 00:02:28s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 16:39:11 AddOrReplaceReadGroups Processed 44,000,000 records. Elapsed time: 00:02:31s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 16:39:14 AddOrReplaceReadGroups Processed 45,000,000 records. Elapsed time: 00:02:34s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 16:39:17 AddOrReplaceReadGroups Processed 46,000,000 records. Elapsed time: 00:02:36s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 16:39:20 AddOrReplaceReadGroups Processed 47,000,000 records. Elapsed time: 00:02:39s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 16:39:23 AddOrReplaceReadGroups Processed 48,000,000 records. Elapsed time: 00:02:42s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 16:39:26 AddOrReplaceReadGroups Processed 49,000,000 records. Elapsed time: 00:02:45s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 16:39:29 AddOrReplaceReadGroups Processed 50,000,000 records. Elapsed time: 00:02:48s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 16:39:32 AddOrReplaceReadGroups Processed 51,000,000 records. Elapsed time: 00:02:51s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 16:39:35 AddOrReplaceReadGroups Processed 52,000,000 records. Elapsed time: 00:02:54s. Time for last 1,000,000: 3s. Last read position: */* [Fri Mar 11 16:39:42 PST 2022] picard.sam.AddOrReplaceReadGroups done. Elapsed time: 3.03 minutes. Runtime.totalMemory()=2709520384 Tool returned: 0 Using GATK jar /home/shared/gatk-4.2.5.0/gatk-package-4.2.5.0-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 /home/shared/gatk-4.2.5.0/gatk-package-4.2.5.0-local.jar AddOrReplaceReadGroups I=S35F.dedup-split.bam O=S35F.dedup-split-RG.bam RGID=1 RGLB=S35F RGPL=ILLUMINA RGPU=unit1 RGSM=S35F INFO 2022-03-11 16:39:43 AddOrReplaceReadGroups ********** NOTE: Picard's command line syntax is changing. ********** ********** For more information, please see: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** ********** The command line looks like this in the new syntax: ********** ********** AddOrReplaceReadGroups -I S35F.dedup-split.bam -O S35F.dedup-split-RG.bam -RGID 1 -RGLB S35F -RGPL ILLUMINA -RGPU unit1 -RGSM S35F ********** 16:39:43.627 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/shared/gatk-4.2.5.0/gatk-package-4.2.5.0-local.jar!/com/intel/gkl/native/libgkl_compression.so [Fri Mar 11 16:39:43 PST 2022] AddOrReplaceReadGroups INPUT=S35F.dedup-split.bam OUTPUT=S35F.dedup-split-RG.bam RGID=1 RGLB=S35F RGPL=ILLUMINA RGPU=unit1 RGSM=S35F VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=2 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Mar 11, 2022 4:39:43 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine INFO: Failed to detect whether we are running on Google Compute Engine. [Fri Mar 11 16:39:43 PST 2022] Executing as sr320@raven on Linux 5.4.0-104-generic amd64; OpenJDK 64-Bit Server VM 11.0.14+9-Ubuntu-0ubuntu2.18.04; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: 4.2.5.0 INFO 2022-03-11 16:39:43 AddOrReplaceReadGroups Created read-group ID=1 PL=ILLUMINA LB=S35F SM=S35F INFO 2022-03-11 16:39:46 AddOrReplaceReadGroups Processed 1,000,000 records. Elapsed time: 00:00:03s. Time for last 1,000,000: 3s. Last read position: NC_035780.1:17,788,293 INFO 2022-03-11 16:39:49 AddOrReplaceReadGroups Processed 2,000,000 records. Elapsed time: 00:00:05s. Time for last 1,000,000: 2s. Last read position: NC_035780.1:37,242,715 INFO 2022-03-11 16:39:52 AddOrReplaceReadGroups Processed 3,000,000 records. Elapsed time: 00:00:08s. Time for last 1,000,000: 2s. Last read position: NC_035780.1:54,832,396 INFO 2022-03-11 16:39:55 AddOrReplaceReadGroups Processed 4,000,000 records. Elapsed time: 00:00:12s. Time for last 1,000,000: 3s. Last read position: NC_035780.1:63,430,242 INFO 2022-03-11 16:39:58 AddOrReplaceReadGroups Processed 5,000,000 records. Elapsed time: 00:00:15s. Time for last 1,000,000: 2s. Last read position: NC_035781.1:8,527,293 INFO 2022-03-11 16:40:01 AddOrReplaceReadGroups Processed 6,000,000 records. Elapsed time: 00:00:17s. Time for last 1,000,000: 2s. Last read position: NC_035781.1:16,351,618 INFO 2022-03-11 16:40:04 AddOrReplaceReadGroups Processed 7,000,000 records. Elapsed time: 00:00:20s. Time for last 1,000,000: 2s. Last read position: NC_035781.1:29,131,114 INFO 2022-03-11 16:40:07 AddOrReplaceReadGroups Processed 8,000,000 records. Elapsed time: 00:00:23s. Time for last 1,000,000: 2s. Last read position: NC_035781.1:40,242,918 INFO 2022-03-11 16:40:10 AddOrReplaceReadGroups Processed 9,000,000 records. Elapsed time: 00:00:26s. Time for last 1,000,000: 3s. Last read position: NC_035781.1:46,993,328 INFO 2022-03-11 16:40:13 AddOrReplaceReadGroups Processed 10,000,000 records. Elapsed time: 00:00:29s. Time for last 1,000,000: 3s. Last read position: NC_035781.1:58,842,390 INFO 2022-03-11 16:40:16 AddOrReplaceReadGroups Processed 11,000,000 records. Elapsed time: 00:00:32s. Time for last 1,000,000: 3s. Last read position: NC_035782.1:20,973,776 INFO 2022-03-11 16:40:23 AddOrReplaceReadGroups Processed 12,000,000 records. Elapsed time: 00:00:39s. Time for last 1,000,000: 6s. Last read position: NC_035782.1:30,904,511 INFO 2022-03-11 16:40:26 AddOrReplaceReadGroups Processed 13,000,000 records. Elapsed time: 00:00:42s. Time for last 1,000,000: 3s. Last read position: NC_035782.1:45,281,943 INFO 2022-03-11 16:40:29 AddOrReplaceReadGroups Processed 14,000,000 records. Elapsed time: 00:00:45s. Time for last 1,000,000: 2s. Last read position: NC_035782.1:55,307,204 INFO 2022-03-11 16:40:32 AddOrReplaceReadGroups Processed 15,000,000 records. Elapsed time: 00:00:48s. Time for last 1,000,000: 3s. Last read position: NC_035782.1:64,532,206 INFO 2022-03-11 16:40:35 AddOrReplaceReadGroups Processed 16,000,000 records. Elapsed time: 00:00:51s. Time for last 1,000,000: 2s. Last read position: NC_035782.1:74,709,981 INFO 2022-03-11 16:40:38 AddOrReplaceReadGroups Processed 17,000,000 records. Elapsed time: 00:00:54s. Time for last 1,000,000: 3s. Last read position: NC_035783.1:13,424,636 INFO 2022-03-11 16:40:41 AddOrReplaceReadGroups Processed 18,000,000 records. Elapsed time: 00:00:57s. Time for last 1,000,000: 3s. Last read position: NC_035783.1:25,868,774 INFO 2022-03-11 16:40:44 AddOrReplaceReadGroups Processed 19,000,000 records. Elapsed time: 00:01:00s. Time for last 1,000,000: 2s. Last read position: NC_035783.1:34,697,255 INFO 2022-03-11 16:40:46 AddOrReplaceReadGroups Processed 20,000,000 records. Elapsed time: 00:01:03s. Time for last 1,000,000: 2s. Last read position: NC_035783.1:44,406,403 INFO 2022-03-11 16:40:50 AddOrReplaceReadGroups Processed 21,000,000 records. Elapsed time: 00:01:06s. Time for last 1,000,000: 3s. Last read position: NC_035784.1:1,657,903 INFO 2022-03-11 16:40:53 AddOrReplaceReadGroups Processed 22,000,000 records. Elapsed time: 00:01:09s. Time for last 1,000,000: 3s. Last read position: NC_035784.1:12,819,190 INFO 2022-03-11 16:40:59 AddOrReplaceReadGroups Processed 23,000,000 records. Elapsed time: 00:01:15s. Time for last 1,000,000: 5s. Last read position: NC_035784.1:23,658,283 INFO 2022-03-11 16:41:02 AddOrReplaceReadGroups Processed 24,000,000 records. Elapsed time: 00:01:18s. Time for last 1,000,000: 2s. Last read position: NC_035784.1:35,281,530 INFO 2022-03-11 16:41:05 AddOrReplaceReadGroups Processed 25,000,000 records. Elapsed time: 00:01:21s. Time for last 1,000,000: 3s. Last read position: NC_035784.1:46,887,192 INFO 2022-03-11 16:41:08 AddOrReplaceReadGroups Processed 26,000,000 records. Elapsed time: 00:01:24s. Time for last 1,000,000: 2s. Last read position: NC_035784.1:52,151,499 INFO 2022-03-11 16:41:10 AddOrReplaceReadGroups Processed 27,000,000 records. Elapsed time: 00:01:26s. Time for last 1,000,000: 2s. Last read position: NC_035784.1:52,215,657 INFO 2022-03-11 16:41:13 AddOrReplaceReadGroups Processed 28,000,000 records. Elapsed time: 00:01:29s. Time for last 1,000,000: 2s. Last read position: NC_035784.1:52,261,563 INFO 2022-03-11 16:41:15 AddOrReplaceReadGroups Processed 29,000,000 records. Elapsed time: 00:01:31s. Time for last 1,000,000: 2s. Last read position: NC_035784.1:54,373,288 INFO 2022-03-11 16:41:18 AddOrReplaceReadGroups Processed 30,000,000 records. Elapsed time: 00:01:34s. Time for last 1,000,000: 3s. Last read position: NC_035784.1:67,610,829 INFO 2022-03-11 16:41:21 AddOrReplaceReadGroups Processed 31,000,000 records. Elapsed time: 00:01:37s. Time for last 1,000,000: 3s. Last read position: NC_035784.1:81,706,631 INFO 2022-03-11 16:41:24 AddOrReplaceReadGroups Processed 32,000,000 records. Elapsed time: 00:01:41s. Time for last 1,000,000: 3s. Last read position: NC_035785.1:24,978,087 INFO 2022-03-11 16:41:28 AddOrReplaceReadGroups Processed 33,000,000 records. Elapsed time: 00:01:44s. Time for last 1,000,000: 3s. Last read position: NC_035785.1:42,975,008 INFO 2022-03-11 16:41:33 AddOrReplaceReadGroups Processed 34,000,000 records. Elapsed time: 00:01:49s. Time for last 1,000,000: 5s. Last read position: NC_035786.1:28,838,824 INFO 2022-03-11 16:41:36 AddOrReplaceReadGroups Processed 35,000,000 records. Elapsed time: 00:01:52s. Time for last 1,000,000: 3s. Last read position: NC_035786.1:56,273,843 INFO 2022-03-11 16:41:39 AddOrReplaceReadGroups Processed 36,000,000 records. Elapsed time: 00:01:56s. Time for last 1,000,000: 3s. Last read position: NC_035787.1:33,563,037 INFO 2022-03-11 16:41:42 AddOrReplaceReadGroups Processed 37,000,000 records. Elapsed time: 00:01:59s. Time for last 1,000,000: 2s. Last read position: NC_035787.1:61,085,841 INFO 2022-03-11 16:41:45 AddOrReplaceReadGroups Processed 38,000,000 records. Elapsed time: 00:02:02s. Time for last 1,000,000: 2s. Last read position: NC_035788.1:16,834,039 INFO 2022-03-11 16:41:48 AddOrReplaceReadGroups Processed 39,000,000 records. Elapsed time: 00:02:05s. Time for last 1,000,000: 3s. Last read position: NC_035788.1:60,587,020 INFO 2022-03-11 16:41:51 AddOrReplaceReadGroups Processed 40,000,000 records. Elapsed time: 00:02:08s. Time for last 1,000,000: 3s. Last read position: NC_035788.1:90,923,559 INFO 2022-03-11 16:41:54 AddOrReplaceReadGroups Processed 41,000,000 records. Elapsed time: 00:02:11s. Time for last 1,000,000: 3s. Last read position: NC_035789.1:19,942,439 INFO 2022-03-11 16:41:57 AddOrReplaceReadGroups Processed 42,000,000 records. Elapsed time: 00:02:14s. Time for last 1,000,000: 2s. Last read position: NC_007175.2:8,836 INFO 2022-03-11 16:42:00 AddOrReplaceReadGroups Processed 43,000,000 records. Elapsed time: 00:02:16s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 16:42:07 AddOrReplaceReadGroups Processed 44,000,000 records. Elapsed time: 00:02:23s. Time for last 1,000,000: 6s. Last read position: */* INFO 2022-03-11 16:42:10 AddOrReplaceReadGroups Processed 45,000,000 records. Elapsed time: 00:02:26s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 16:42:13 AddOrReplaceReadGroups Processed 46,000,000 records. Elapsed time: 00:02:29s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 16:42:15 AddOrReplaceReadGroups Processed 47,000,000 records. Elapsed time: 00:02:32s. Time for last 1,000,000: 2s. Last read position: */* [Fri Mar 11 16:42:19 PST 2022] picard.sam.AddOrReplaceReadGroups done. Elapsed time: 2.60 minutes. Runtime.totalMemory()=2856321024 Tool returned: 0 Using GATK jar /home/shared/gatk-4.2.5.0/gatk-package-4.2.5.0-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 /home/shared/gatk-4.2.5.0/gatk-package-4.2.5.0-local.jar AddOrReplaceReadGroups I=S36F.dedup-split.bam O=S36F.dedup-split-RG.bam RGID=1 RGLB=S36F RGPL=ILLUMINA RGPU=unit1 RGSM=S36F INFO 2022-03-11 16:42:20 AddOrReplaceReadGroups ********** NOTE: Picard's command line syntax is changing. ********** ********** For more information, please see: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** ********** The command line looks like this in the new syntax: ********** ********** AddOrReplaceReadGroups -I S36F.dedup-split.bam -O S36F.dedup-split-RG.bam -RGID 1 -RGLB S36F -RGPL ILLUMINA -RGPU unit1 -RGSM S36F ********** 16:42:20.994 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/shared/gatk-4.2.5.0/gatk-package-4.2.5.0-local.jar!/com/intel/gkl/native/libgkl_compression.so [Fri Mar 11 16:42:21 PST 2022] AddOrReplaceReadGroups INPUT=S36F.dedup-split.bam OUTPUT=S36F.dedup-split-RG.bam RGID=1 RGLB=S36F RGPL=ILLUMINA RGPU=unit1 RGSM=S36F VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=2 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Mar 11, 2022 4:42:21 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine INFO: Failed to detect whether we are running on Google Compute Engine. [Fri Mar 11 16:42:21 PST 2022] Executing as sr320@raven on Linux 5.4.0-104-generic amd64; OpenJDK 64-Bit Server VM 11.0.14+9-Ubuntu-0ubuntu2.18.04; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: 4.2.5.0 INFO 2022-03-11 16:42:21 AddOrReplaceReadGroups Created read-group ID=1 PL=ILLUMINA LB=S36F SM=S36F INFO 2022-03-11 16:42:24 AddOrReplaceReadGroups Processed 1,000,000 records. Elapsed time: 00:00:03s. Time for last 1,000,000: 3s. Last read position: NC_035780.1:15,828,045 INFO 2022-03-11 16:42:27 AddOrReplaceReadGroups Processed 2,000,000 records. Elapsed time: 00:00:05s. Time for last 1,000,000: 2s. Last read position: NC_035780.1:32,742,260 INFO 2022-03-11 16:42:30 AddOrReplaceReadGroups Processed 3,000,000 records. Elapsed time: 00:00:08s. Time for last 1,000,000: 3s. Last read position: NC_035780.1:49,537,102 INFO 2022-03-11 16:42:33 AddOrReplaceReadGroups Processed 4,000,000 records. Elapsed time: 00:00:11s. Time for last 1,000,000: 2s. Last read position: NC_035780.1:59,129,008 INFO 2022-03-11 16:42:36 AddOrReplaceReadGroups Processed 5,000,000 records. Elapsed time: 00:00:14s. Time for last 1,000,000: 2s. Last read position: NC_035781.1:3,863,447 INFO 2022-03-11 16:42:38 AddOrReplaceReadGroups Processed 6,000,000 records. Elapsed time: 00:00:17s. Time for last 1,000,000: 2s. Last read position: NC_035781.1:13,259,969 INFO 2022-03-11 16:42:41 AddOrReplaceReadGroups Processed 7,000,000 records. Elapsed time: 00:00:20s. Time for last 1,000,000: 2s. Last read position: NC_035781.1:22,800,090 INFO 2022-03-11 16:42:44 AddOrReplaceReadGroups Processed 8,000,000 records. Elapsed time: 00:00:23s. Time for last 1,000,000: 2s. Last read position: NC_035781.1:33,019,113 INFO 2022-03-11 16:42:47 AddOrReplaceReadGroups Processed 9,000,000 records. Elapsed time: 00:00:26s. Time for last 1,000,000: 2s. Last read position: NC_035781.1:40,789,807 INFO 2022-03-11 16:42:50 AddOrReplaceReadGroups Processed 10,000,000 records. Elapsed time: 00:00:29s. Time for last 1,000,000: 2s. Last read position: NC_035781.1:49,477,929 INFO 2022-03-11 16:42:56 AddOrReplaceReadGroups Processed 11,000,000 records. Elapsed time: 00:00:35s. Time for last 1,000,000: 6s. Last read position: NC_035782.1:3,599,033 INFO 2022-03-11 16:43:00 AddOrReplaceReadGroups Processed 12,000,000 records. Elapsed time: 00:00:38s. Time for last 1,000,000: 3s. Last read position: NC_035782.1:24,964,030 INFO 2022-03-11 16:43:02 AddOrReplaceReadGroups Processed 13,000,000 records. Elapsed time: 00:00:41s. Time for last 1,000,000: 2s. Last read position: NC_035782.1:35,484,943 INFO 2022-03-11 16:43:05 AddOrReplaceReadGroups Processed 14,000,000 records. Elapsed time: 00:00:44s. Time for last 1,000,000: 3s. Last read position: NC_035782.1:47,695,795 INFO 2022-03-11 16:43:08 AddOrReplaceReadGroups Processed 15,000,000 records. Elapsed time: 00:00:47s. Time for last 1,000,000: 2s. Last read position: NC_035782.1:56,807,045 INFO 2022-03-11 16:43:11 AddOrReplaceReadGroups Processed 16,000,000 records. Elapsed time: 00:00:50s. Time for last 1,000,000: 2s. Last read position: NC_035782.1:65,570,795 INFO 2022-03-11 16:43:14 AddOrReplaceReadGroups Processed 17,000,000 records. Elapsed time: 00:00:53s. Time for last 1,000,000: 2s. Last read position: NC_035783.1:2,327,080 INFO 2022-03-11 16:43:17 AddOrReplaceReadGroups Processed 18,000,000 records. Elapsed time: 00:00:56s. Time for last 1,000,000: 2s. Last read position: NC_035783.1:15,048,920 INFO 2022-03-11 16:43:20 AddOrReplaceReadGroups Processed 19,000,000 records. Elapsed time: 00:00:59s. Time for last 1,000,000: 3s. Last read position: NC_035783.1:27,007,596 INFO 2022-03-11 16:43:23 AddOrReplaceReadGroups Processed 20,000,000 records. Elapsed time: 00:01:02s. Time for last 1,000,000: 2s. Last read position: NC_035783.1:36,362,092 INFO 2022-03-11 16:43:26 AddOrReplaceReadGroups Processed 21,000,000 records. Elapsed time: 00:01:05s. Time for last 1,000,000: 2s. Last read position: NC_035783.1:46,126,967 INFO 2022-03-11 16:43:33 AddOrReplaceReadGroups Processed 22,000,000 records. Elapsed time: 00:01:12s. Time for last 1,000,000: 6s. Last read position: NC_035784.1:2,159,749 INFO 2022-03-11 16:43:36 AddOrReplaceReadGroups Processed 23,000,000 records. Elapsed time: 00:01:14s. Time for last 1,000,000: 2s. Last read position: NC_035784.1:12,777,139 INFO 2022-03-11 16:43:39 AddOrReplaceReadGroups Processed 24,000,000 records. Elapsed time: 00:01:17s. Time for last 1,000,000: 2s. Last read position: NC_035784.1:23,306,619 INFO 2022-03-11 16:43:42 AddOrReplaceReadGroups Processed 25,000,000 records. Elapsed time: 00:01:20s. Time for last 1,000,000: 2s. Last read position: NC_035784.1:34,162,921 INFO 2022-03-11 16:43:45 AddOrReplaceReadGroups Processed 26,000,000 records. Elapsed time: 00:01:23s. Time for last 1,000,000: 2s. Last read position: NC_035784.1:44,775,912 INFO 2022-03-11 16:43:47 AddOrReplaceReadGroups Processed 27,000,000 records. Elapsed time: 00:01:26s. Time for last 1,000,000: 2s. Last read position: NC_035784.1:50,305,090 INFO 2022-03-11 16:43:50 AddOrReplaceReadGroups Processed 28,000,000 records. Elapsed time: 00:01:29s. Time for last 1,000,000: 2s. Last read position: NC_035784.1:52,197,903 INFO 2022-03-11 16:43:52 AddOrReplaceReadGroups Processed 29,000,000 records. Elapsed time: 00:01:31s. Time for last 1,000,000: 2s. Last read position: NC_035784.1:52,255,933 INFO 2022-03-11 16:43:55 AddOrReplaceReadGroups Processed 30,000,000 records. Elapsed time: 00:01:34s. Time for last 1,000,000: 2s. Last read position: NC_035784.1:52,277,200 INFO 2022-03-11 16:43:57 AddOrReplaceReadGroups Processed 31,000,000 records. Elapsed time: 00:01:36s. Time for last 1,000,000: 2s. Last read position: NC_035784.1:59,797,167 INFO 2022-03-11 16:44:00 AddOrReplaceReadGroups Processed 32,000,000 records. Elapsed time: 00:01:39s. Time for last 1,000,000: 2s. Last read position: NC_035784.1:71,058,932 INFO 2022-03-11 16:44:06 AddOrReplaceReadGroups Processed 33,000,000 records. Elapsed time: 00:01:45s. Time for last 1,000,000: 5s. Last read position: NC_035784.1:86,550,785 INFO 2022-03-11 16:44:09 AddOrReplaceReadGroups Processed 34,000,000 records. Elapsed time: 00:01:48s. Time for last 1,000,000: 3s. Last read position: NC_035785.1:26,938,650 INFO 2022-03-11 16:44:12 AddOrReplaceReadGroups Processed 35,000,000 records. Elapsed time: 00:01:51s. Time for last 1,000,000: 2s. Last read position: NC_035785.1:42,516,402 INFO 2022-03-11 16:44:15 AddOrReplaceReadGroups Processed 36,000,000 records. Elapsed time: 00:01:54s. Time for last 1,000,000: 3s. Last read position: NC_035786.1:21,095,371 INFO 2022-03-11 16:44:18 AddOrReplaceReadGroups Processed 37,000,000 records. Elapsed time: 00:01:57s. Time for last 1,000,000: 3s. Last read position: NC_035786.1:50,498,153 INFO 2022-03-11 16:44:21 AddOrReplaceReadGroups Processed 38,000,000 records. Elapsed time: 00:02:00s. Time for last 1,000,000: 3s. Last read position: NC_035787.1:21,264,561 INFO 2022-03-11 16:44:24 AddOrReplaceReadGroups Processed 39,000,000 records. Elapsed time: 00:02:03s. Time for last 1,000,000: 3s. Last read position: NC_035787.1:54,277,518 INFO 2022-03-11 16:44:27 AddOrReplaceReadGroups Processed 40,000,000 records. Elapsed time: 00:02:06s. Time for last 1,000,000: 2s. Last read position: NC_035787.1:73,912,343 INFO 2022-03-11 16:44:30 AddOrReplaceReadGroups Processed 41,000,000 records. Elapsed time: 00:02:09s. Time for last 1,000,000: 3s. Last read position: NC_035788.1:40,539,608 INFO 2022-03-11 16:44:33 AddOrReplaceReadGroups Processed 42,000,000 records. Elapsed time: 00:02:12s. Time for last 1,000,000: 3s. Last read position: NC_035788.1:70,753,410 INFO 2022-03-11 16:44:36 AddOrReplaceReadGroups Processed 43,000,000 records. Elapsed time: 00:02:15s. Time for last 1,000,000: 3s. Last read position: NC_035788.1:103,017,657 INFO 2022-03-11 16:44:43 AddOrReplaceReadGroups Processed 44,000,000 records. Elapsed time: 00:02:22s. Time for last 1,000,000: 6s. Last read position: NC_035789.1:20,269,602 INFO 2022-03-11 16:44:46 AddOrReplaceReadGroups Processed 45,000,000 records. Elapsed time: 00:02:25s. Time for last 1,000,000: 2s. Last read position: NC_007175.2:8,635 INFO 2022-03-11 16:44:48 AddOrReplaceReadGroups Processed 46,000,000 records. Elapsed time: 00:02:27s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 16:44:51 AddOrReplaceReadGroups Processed 47,000,000 records. Elapsed time: 00:02:30s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 16:44:54 AddOrReplaceReadGroups Processed 48,000,000 records. Elapsed time: 00:02:33s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 16:44:57 AddOrReplaceReadGroups Processed 49,000,000 records. Elapsed time: 00:02:36s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 16:45:00 AddOrReplaceReadGroups Processed 50,000,000 records. Elapsed time: 00:02:39s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 16:45:03 AddOrReplaceReadGroups Processed 51,000,000 records. Elapsed time: 00:02:41s. Time for last 1,000,000: 2s. Last read position: */* [Fri Mar 11 16:45:07 PST 2022] picard.sam.AddOrReplaceReadGroups done. Elapsed time: 2.78 minutes. Runtime.totalMemory()=2755657728 Tool returned: 0 Using GATK jar /home/shared/gatk-4.2.5.0/gatk-package-4.2.5.0-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 /home/shared/gatk-4.2.5.0/gatk-package-4.2.5.0-local.jar AddOrReplaceReadGroups I=S39F.dedup-split.bam O=S39F.dedup-split-RG.bam RGID=1 RGLB=S39F RGPL=ILLUMINA RGPU=unit1 RGSM=S39F INFO 2022-03-11 16:45:09 AddOrReplaceReadGroups ********** NOTE: Picard's command line syntax is changing. ********** ********** For more information, please see: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** ********** The command line looks like this in the new syntax: ********** ********** AddOrReplaceReadGroups -I S39F.dedup-split.bam -O S39F.dedup-split-RG.bam -RGID 1 -RGLB S39F -RGPL ILLUMINA -RGPU unit1 -RGSM S39F ********** 16:45:09.578 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/shared/gatk-4.2.5.0/gatk-package-4.2.5.0-local.jar!/com/intel/gkl/native/libgkl_compression.so [Fri Mar 11 16:45:09 PST 2022] AddOrReplaceReadGroups INPUT=S39F.dedup-split.bam OUTPUT=S39F.dedup-split-RG.bam RGID=1 RGLB=S39F RGPL=ILLUMINA RGPU=unit1 RGSM=S39F VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=2 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Mar 11, 2022 4:45:09 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine INFO: Failed to detect whether we are running on Google Compute Engine. [Fri Mar 11 16:45:09 PST 2022] Executing as sr320@raven on Linux 5.4.0-104-generic amd64; OpenJDK 64-Bit Server VM 11.0.14+9-Ubuntu-0ubuntu2.18.04; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: 4.2.5.0 INFO 2022-03-11 16:45:09 AddOrReplaceReadGroups Created read-group ID=1 PL=ILLUMINA LB=S39F SM=S39F INFO 2022-03-11 16:45:12 AddOrReplaceReadGroups Processed 1,000,000 records. Elapsed time: 00:00:03s. Time for last 1,000,000: 3s. Last read position: NC_035780.1:14,553,373 INFO 2022-03-11 16:45:15 AddOrReplaceReadGroups Processed 2,000,000 records. Elapsed time: 00:00:06s. Time for last 1,000,000: 2s. Last read position: NC_035780.1:31,332,398 INFO 2022-03-11 16:45:18 AddOrReplaceReadGroups Processed 3,000,000 records. Elapsed time: 00:00:09s. Time for last 1,000,000: 3s. Last read position: NC_035780.1:46,822,782 INFO 2022-03-11 16:45:21 AddOrReplaceReadGroups Processed 4,000,000 records. Elapsed time: 00:00:12s. Time for last 1,000,000: 2s. Last read position: NC_035780.1:58,157,699 INFO 2022-03-11 16:45:24 AddOrReplaceReadGroups Processed 5,000,000 records. Elapsed time: 00:00:15s. Time for last 1,000,000: 3s. Last read position: NC_035781.1:2,128,321 INFO 2022-03-11 16:45:27 AddOrReplaceReadGroups Processed 6,000,000 records. Elapsed time: 00:00:18s. Time for last 1,000,000: 2s. Last read position: NC_035781.1:9,580,690 INFO 2022-03-11 16:45:30 AddOrReplaceReadGroups Processed 7,000,000 records. Elapsed time: 00:00:20s. Time for last 1,000,000: 2s. Last read position: NC_035781.1:15,771,771 INFO 2022-03-11 16:45:33 AddOrReplaceReadGroups Processed 8,000,000 records. Elapsed time: 00:00:23s. Time for last 1,000,000: 2s. Last read position: NC_035781.1:25,645,293 INFO 2022-03-11 16:45:36 AddOrReplaceReadGroups Processed 9,000,000 records. Elapsed time: 00:00:26s. Time for last 1,000,000: 3s. Last read position: NC_035781.1:35,304,639 INFO 2022-03-11 16:45:39 AddOrReplaceReadGroups Processed 10,000,000 records. Elapsed time: 00:00:29s. Time for last 1,000,000: 2s. Last read position: NC_035781.1:43,515,546 INFO 2022-03-11 16:45:42 AddOrReplaceReadGroups Processed 11,000,000 records. Elapsed time: 00:00:32s. Time for last 1,000,000: 2s. Last read position: NC_035781.1:50,621,438 INFO 2022-03-11 16:45:49 AddOrReplaceReadGroups Processed 12,000,000 records. Elapsed time: 00:00:39s. Time for last 1,000,000: 6s. Last read position: NC_035782.1:3,563,951 INFO 2022-03-11 16:45:52 AddOrReplaceReadGroups Processed 13,000,000 records. Elapsed time: 00:00:42s. Time for last 1,000,000: 2s. Last read position: NC_035782.1:22,494,857 INFO 2022-03-11 16:45:55 AddOrReplaceReadGroups Processed 14,000,000 records. Elapsed time: 00:00:45s. Time for last 1,000,000: 2s. Last read position: NC_035782.1:30,764,810 INFO 2022-03-11 16:45:58 AddOrReplaceReadGroups Processed 15,000,000 records. Elapsed time: 00:00:48s. Time for last 1,000,000: 2s. Last read position: NC_035782.1:40,813,315 INFO 2022-03-11 16:46:01 AddOrReplaceReadGroups Processed 16,000,000 records. Elapsed time: 00:00:51s. Time for last 1,000,000: 3s. Last read position: NC_035782.1:51,379,088 INFO 2022-03-11 16:46:04 AddOrReplaceReadGroups Processed 17,000,000 records. Elapsed time: 00:00:54s. Time for last 1,000,000: 2s. Last read position: NC_035782.1:58,933,302 INFO 2022-03-11 16:46:06 AddOrReplaceReadGroups Processed 18,000,000 records. Elapsed time: 00:00:57s. Time for last 1,000,000: 2s. Last read position: NC_035782.1:66,749,074 INFO 2022-03-11 16:46:09 AddOrReplaceReadGroups Processed 19,000,000 records. Elapsed time: 00:01:00s. Time for last 1,000,000: 2s. Last read position: NC_035783.1:369,858 INFO 2022-03-11 16:46:12 AddOrReplaceReadGroups Processed 20,000,000 records. Elapsed time: 00:01:03s. Time for last 1,000,000: 2s. Last read position: NC_035783.1:12,518,595 INFO 2022-03-11 16:46:15 AddOrReplaceReadGroups Processed 21,000,000 records. Elapsed time: 00:01:06s. Time for last 1,000,000: 3s. Last read position: NC_035783.1:22,411,398 INFO 2022-03-11 16:46:21 AddOrReplaceReadGroups Processed 22,000,000 records. Elapsed time: 00:01:11s. Time for last 1,000,000: 5s. Last read position: NC_035783.1:32,078,578 INFO 2022-03-11 16:46:25 AddOrReplaceReadGroups Processed 23,000,000 records. Elapsed time: 00:01:15s. Time for last 1,000,000: 3s. Last read position: NC_035783.1:40,342,191 INFO 2022-03-11 16:46:28 AddOrReplaceReadGroups Processed 24,000,000 records. Elapsed time: 00:01:18s. Time for last 1,000,000: 2s. Last read position: NC_035783.1:49,874,388 INFO 2022-03-11 16:46:31 AddOrReplaceReadGroups Processed 25,000,000 records. Elapsed time: 00:01:21s. Time for last 1,000,000: 2s. Last read position: NC_035784.1:3,415,103 INFO 2022-03-11 16:46:34 AddOrReplaceReadGroups Processed 26,000,000 records. Elapsed time: 00:01:24s. Time for last 1,000,000: 2s. Last read position: NC_035784.1:12,498,378 INFO 2022-03-11 16:46:37 AddOrReplaceReadGroups Processed 27,000,000 records. Elapsed time: 00:01:27s. Time for last 1,000,000: 2s. Last read position: NC_035784.1:19,625,177 INFO 2022-03-11 16:46:40 AddOrReplaceReadGroups Processed 28,000,000 records. Elapsed time: 00:01:30s. Time for last 1,000,000: 3s. Last read position: NC_035784.1:31,095,152 INFO 2022-03-11 16:46:43 AddOrReplaceReadGroups Processed 29,000,000 records. Elapsed time: 00:01:33s. Time for last 1,000,000: 2s. Last read position: NC_035784.1:38,053,902 INFO 2022-03-11 16:46:45 AddOrReplaceReadGroups Processed 30,000,000 records. Elapsed time: 00:01:36s. Time for last 1,000,000: 2s. Last read position: NC_035784.1:47,741,805 INFO 2022-03-11 16:46:48 AddOrReplaceReadGroups Processed 31,000,000 records. Elapsed time: 00:01:38s. Time for last 1,000,000: 2s. Last read position: NC_035784.1:52,177,961 INFO 2022-03-11 16:46:51 AddOrReplaceReadGroups Processed 32,000,000 records. Elapsed time: 00:01:41s. Time for last 1,000,000: 2s. Last read position: NC_035784.1:52,233,293 INFO 2022-03-11 16:46:54 AddOrReplaceReadGroups Processed 33,000,000 records. Elapsed time: 00:01:44s. Time for last 1,000,000: 3s. Last read position: NC_035784.1:52,275,364 INFO 2022-03-11 16:46:58 AddOrReplaceReadGroups Processed 34,000,000 records. Elapsed time: 00:01:49s. Time for last 1,000,000: 4s. Last read position: NC_035784.1:57,711,858 INFO 2022-03-11 16:47:01 AddOrReplaceReadGroups Processed 35,000,000 records. Elapsed time: 00:01:52s. Time for last 1,000,000: 2s. Last read position: NC_035784.1:67,212,323 INFO 2022-03-11 16:47:04 AddOrReplaceReadGroups Processed 36,000,000 records. Elapsed time: 00:01:55s. Time for last 1,000,000: 2s. Last read position: NC_035784.1:79,542,554 INFO 2022-03-11 16:47:07 AddOrReplaceReadGroups Processed 37,000,000 records. Elapsed time: 00:01:58s. Time for last 1,000,000: 2s. Last read position: NC_035785.1:7,498,845 INFO 2022-03-11 16:47:10 AddOrReplaceReadGroups Processed 38,000,000 records. Elapsed time: 00:02:01s. Time for last 1,000,000: 3s. Last read position: NC_035785.1:35,142,690 INFO 2022-03-11 16:47:13 AddOrReplaceReadGroups Processed 39,000,000 records. Elapsed time: 00:02:04s. Time for last 1,000,000: 2s. Last read position: NC_035786.1:4,936,879 INFO 2022-03-11 16:47:16 AddOrReplaceReadGroups Processed 40,000,000 records. Elapsed time: 00:02:07s. Time for last 1,000,000: 3s. Last read position: NC_035786.1:35,839,781 INFO 2022-03-11 16:47:19 AddOrReplaceReadGroups Processed 41,000,000 records. Elapsed time: 00:02:10s. Time for last 1,000,000: 3s. Last read position: NC_035787.1:1,321,189 INFO 2022-03-11 16:47:22 AddOrReplaceReadGroups Processed 42,000,000 records. Elapsed time: 00:02:13s. Time for last 1,000,000: 3s. Last read position: NC_035787.1:31,334,546 INFO 2022-03-11 16:47:25 AddOrReplaceReadGroups Processed 43,000,000 records. Elapsed time: 00:02:16s. Time for last 1,000,000: 2s. Last read position: NC_035787.1:57,984,440 INFO 2022-03-11 16:47:31 AddOrReplaceReadGroups Processed 44,000,000 records. Elapsed time: 00:02:22s. Time for last 1,000,000: 6s. Last read position: NC_035788.1:1,134,998 INFO 2022-03-11 16:47:35 AddOrReplaceReadGroups Processed 45,000,000 records. Elapsed time: 00:02:25s. Time for last 1,000,000: 3s. Last read position: NC_035788.1:39,986,046 INFO 2022-03-11 16:47:38 AddOrReplaceReadGroups Processed 46,000,000 records. Elapsed time: 00:02:28s. Time for last 1,000,000: 3s. Last read position: NC_035788.1:70,237,939 INFO 2022-03-11 16:47:41 AddOrReplaceReadGroups Processed 47,000,000 records. Elapsed time: 00:02:31s. Time for last 1,000,000: 2s. Last read position: NC_035788.1:95,158,713 INFO 2022-03-11 16:47:44 AddOrReplaceReadGroups Processed 48,000,000 records. Elapsed time: 00:02:34s. Time for last 1,000,000: 3s. Last read position: NC_035789.1:18,301,677 INFO 2022-03-11 16:47:47 AddOrReplaceReadGroups Processed 49,000,000 records. Elapsed time: 00:02:37s. Time for last 1,000,000: 2s. Last read position: NC_007175.2:5,297 INFO 2022-03-11 16:47:49 AddOrReplaceReadGroups Processed 50,000,000 records. Elapsed time: 00:02:40s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 16:47:52 AddOrReplaceReadGroups Processed 51,000,000 records. Elapsed time: 00:02:42s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 16:47:55 AddOrReplaceReadGroups Processed 52,000,000 records. Elapsed time: 00:02:45s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 16:47:58 AddOrReplaceReadGroups Processed 53,000,000 records. Elapsed time: 00:02:48s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 16:48:01 AddOrReplaceReadGroups Processed 54,000,000 records. Elapsed time: 00:02:51s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 16:48:08 AddOrReplaceReadGroups Processed 55,000,000 records. Elapsed time: 00:02:58s. Time for last 1,000,000: 7s. Last read position: */* [Fri Mar 11 16:48:10 PST 2022] picard.sam.AddOrReplaceReadGroups done. Elapsed time: 3.02 minutes. Runtime.totalMemory()=2772434944 Tool returned: 0 Using GATK jar /home/shared/gatk-4.2.5.0/gatk-package-4.2.5.0-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 /home/shared/gatk-4.2.5.0/gatk-package-4.2.5.0-local.jar AddOrReplaceReadGroups I=S3F.dedup-split.bam O=S3F.dedup-split-RG.bam RGID=1 RGLB=S3F RGPL=ILLUMINA RGPU=unit1 RGSM=S3F INFO 2022-03-11 16:48:12 AddOrReplaceReadGroups ********** NOTE: Picard's command line syntax is changing. ********** ********** For more information, please see: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** ********** The command line looks like this in the new syntax: ********** ********** AddOrReplaceReadGroups -I S3F.dedup-split.bam -O S3F.dedup-split-RG.bam -RGID 1 -RGLB S3F -RGPL ILLUMINA -RGPU unit1 -RGSM S3F ********** 16:48:12.548 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/shared/gatk-4.2.5.0/gatk-package-4.2.5.0-local.jar!/com/intel/gkl/native/libgkl_compression.so [Fri Mar 11 16:48:12 PST 2022] AddOrReplaceReadGroups INPUT=S3F.dedup-split.bam OUTPUT=S3F.dedup-split-RG.bam RGID=1 RGLB=S3F RGPL=ILLUMINA RGPU=unit1 RGSM=S3F VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=2 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Mar 11, 2022 4:48:12 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine INFO: Failed to detect whether we are running on Google Compute Engine. [Fri Mar 11 16:48:12 PST 2022] Executing as sr320@raven on Linux 5.4.0-104-generic amd64; OpenJDK 64-Bit Server VM 11.0.14+9-Ubuntu-0ubuntu2.18.04; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: 4.2.5.0 INFO 2022-03-11 16:48:12 AddOrReplaceReadGroups Created read-group ID=1 PL=ILLUMINA LB=S3F SM=S3F INFO 2022-03-11 16:48:15 AddOrReplaceReadGroups Processed 1,000,000 records. Elapsed time: 00:00:03s. Time for last 1,000,000: 3s. Last read position: NC_035780.1:19,345,154 INFO 2022-03-11 16:48:18 AddOrReplaceReadGroups Processed 2,000,000 records. Elapsed time: 00:00:06s. Time for last 1,000,000: 2s. Last read position: NC_035780.1:36,248,451 INFO 2022-03-11 16:48:21 AddOrReplaceReadGroups Processed 3,000,000 records. Elapsed time: 00:00:09s. Time for last 1,000,000: 3s. Last read position: NC_035780.1:54,165,589 INFO 2022-03-11 16:48:24 AddOrReplaceReadGroups Processed 4,000,000 records. Elapsed time: 00:00:12s. Time for last 1,000,000: 2s. Last read position: NC_035780.1:62,773,486 INFO 2022-03-11 16:48:27 AddOrReplaceReadGroups Processed 5,000,000 records. Elapsed time: 00:00:15s. Time for last 1,000,000: 3s. Last read position: NC_035781.1:7,483,605 INFO 2022-03-11 16:48:30 AddOrReplaceReadGroups Processed 6,000,000 records. Elapsed time: 00:00:18s. Time for last 1,000,000: 2s. Last read position: NC_035781.1:14,194,161 INFO 2022-03-11 16:48:33 AddOrReplaceReadGroups Processed 7,000,000 records. Elapsed time: 00:00:21s. Time for last 1,000,000: 3s. Last read position: NC_035781.1:24,037,822 INFO 2022-03-11 16:48:36 AddOrReplaceReadGroups Processed 8,000,000 records. Elapsed time: 00:00:24s. Time for last 1,000,000: 3s. Last read position: NC_035781.1:34,427,735 INFO 2022-03-11 16:48:39 AddOrReplaceReadGroups Processed 9,000,000 records. Elapsed time: 00:00:27s. Time for last 1,000,000: 3s. Last read position: NC_035781.1:44,116,722 INFO 2022-03-11 16:48:42 AddOrReplaceReadGroups Processed 10,000,000 records. Elapsed time: 00:00:30s. Time for last 1,000,000: 2s. Last read position: NC_035781.1:53,193,790 INFO 2022-03-11 16:48:49 AddOrReplaceReadGroups Processed 11,000,000 records. Elapsed time: 00:00:36s. Time for last 1,000,000: 6s. Last read position: NC_035782.1:14,293,635 INFO 2022-03-11 16:48:52 AddOrReplaceReadGroups Processed 12,000,000 records. Elapsed time: 00:00:39s. Time for last 1,000,000: 2s. Last read position: NC_035782.1:27,242,602 INFO 2022-03-11 16:48:55 AddOrReplaceReadGroups Processed 13,000,000 records. Elapsed time: 00:00:42s. Time for last 1,000,000: 2s. Last read position: NC_035782.1:38,426,126 INFO 2022-03-11 16:48:58 AddOrReplaceReadGroups Processed 14,000,000 records. Elapsed time: 00:00:45s. Time for last 1,000,000: 2s. Last read position: NC_035782.1:50,119,802 INFO 2022-03-11 16:49:01 AddOrReplaceReadGroups Processed 15,000,000 records. Elapsed time: 00:00:48s. Time for last 1,000,000: 2s. Last read position: NC_035782.1:58,746,015 INFO 2022-03-11 16:49:04 AddOrReplaceReadGroups Processed 16,000,000 records. Elapsed time: 00:00:51s. Time for last 1,000,000: 2s. Last read position: NC_035782.1:67,657,645 INFO 2022-03-11 16:49:07 AddOrReplaceReadGroups Processed 17,000,000 records. Elapsed time: 00:00:54s. Time for last 1,000,000: 2s. Last read position: NC_035783.1:4,644,868 INFO 2022-03-11 16:49:10 AddOrReplaceReadGroups Processed 18,000,000 records. Elapsed time: 00:00:57s. Time for last 1,000,000: 3s. Last read position: NC_035783.1:16,830,111 INFO 2022-03-11 16:49:13 AddOrReplaceReadGroups Processed 19,000,000 records. Elapsed time: 00:01:00s. Time for last 1,000,000: 3s. Last read position: NC_035783.1:29,045,778 INFO 2022-03-11 16:49:16 AddOrReplaceReadGroups Processed 20,000,000 records. Elapsed time: 00:01:03s. Time for last 1,000,000: 2s. Last read position: NC_035783.1:36,736,947 INFO 2022-03-11 16:49:18 AddOrReplaceReadGroups Processed 21,000,000 records. Elapsed time: 00:01:06s. Time for last 1,000,000: 2s. Last read position: NC_035783.1:47,769,471 INFO 2022-03-11 16:49:25 AddOrReplaceReadGroups Processed 22,000,000 records. Elapsed time: 00:01:12s. Time for last 1,000,000: 6s. Last read position: NC_035784.1:3,222,208 INFO 2022-03-11 16:49:28 AddOrReplaceReadGroups Processed 23,000,000 records. Elapsed time: 00:01:15s. Time for last 1,000,000: 2s. Last read position: NC_035784.1:13,461,206 INFO 2022-03-11 16:49:31 AddOrReplaceReadGroups Processed 24,000,000 records. Elapsed time: 00:01:18s. Time for last 1,000,000: 2s. Last read position: NC_035784.1:23,906,943 INFO 2022-03-11 16:49:34 AddOrReplaceReadGroups Processed 25,000,000 records. Elapsed time: 00:01:21s. Time for last 1,000,000: 2s. Last read position: NC_035784.1:35,086,298 INFO 2022-03-11 16:49:37 AddOrReplaceReadGroups Processed 26,000,000 records. Elapsed time: 00:01:24s. Time for last 1,000,000: 3s. Last read position: NC_035784.1:46,111,905 INFO 2022-03-11 16:49:40 AddOrReplaceReadGroups Processed 27,000,000 records. Elapsed time: 00:01:27s. Time for last 1,000,000: 2s. Last read position: NC_035784.1:52,173,820 INFO 2022-03-11 16:49:42 AddOrReplaceReadGroups Processed 28,000,000 records. Elapsed time: 00:01:29s. Time for last 1,000,000: 2s. Last read position: NC_035784.1:52,255,716 INFO 2022-03-11 16:49:45 AddOrReplaceReadGroups Processed 29,000,000 records. Elapsed time: 00:01:32s. Time for last 1,000,000: 2s. Last read position: NC_035784.1:52,279,928 INFO 2022-03-11 16:49:47 AddOrReplaceReadGroups Processed 30,000,000 records. Elapsed time: 00:01:35s. Time for last 1,000,000: 2s. Last read position: NC_035784.1:63,155,449 INFO 2022-03-11 16:49:50 AddOrReplaceReadGroups Processed 31,000,000 records. Elapsed time: 00:01:38s. Time for last 1,000,000: 3s. Last read position: NC_035784.1:75,765,638 INFO 2022-03-11 16:49:54 AddOrReplaceReadGroups Processed 32,000,000 records. Elapsed time: 00:01:41s. Time for last 1,000,000: 3s. Last read position: NC_035785.1:8,701 INFO 2022-03-11 16:50:00 AddOrReplaceReadGroups Processed 33,000,000 records. Elapsed time: 00:01:47s. Time for last 1,000,000: 5s. Last read position: NC_035785.1:33,937,077 INFO 2022-03-11 16:50:03 AddOrReplaceReadGroups Processed 34,000,000 records. Elapsed time: 00:01:50s. Time for last 1,000,000: 3s. Last read position: NC_035786.1:4,274,781 INFO 2022-03-11 16:50:06 AddOrReplaceReadGroups Processed 35,000,000 records. Elapsed time: 00:01:53s. Time for last 1,000,000: 3s. Last read position: NC_035786.1:37,679,861 INFO 2022-03-11 16:50:09 AddOrReplaceReadGroups Processed 36,000,000 records. Elapsed time: 00:01:56s. Time for last 1,000,000: 3s. Last read position: NC_035787.1:5,099,049 INFO 2022-03-11 16:50:12 AddOrReplaceReadGroups Processed 37,000,000 records. Elapsed time: 00:01:59s. Time for last 1,000,000: 3s. Last read position: NC_035787.1:43,286,269 INFO 2022-03-11 16:50:15 AddOrReplaceReadGroups Processed 38,000,000 records. Elapsed time: 00:02:02s. Time for last 1,000,000: 2s. Last read position: NC_035787.1:62,018,060 INFO 2022-03-11 16:50:18 AddOrReplaceReadGroups Processed 39,000,000 records. Elapsed time: 00:02:05s. Time for last 1,000,000: 3s. Last read position: NC_035788.1:18,716,471 INFO 2022-03-11 16:50:21 AddOrReplaceReadGroups Processed 40,000,000 records. Elapsed time: 00:02:08s. Time for last 1,000,000: 3s. Last read position: NC_035788.1:61,844,368 INFO 2022-03-11 16:50:24 AddOrReplaceReadGroups Processed 41,000,000 records. Elapsed time: 00:02:11s. Time for last 1,000,000: 3s. Last read position: NC_035788.1:84,739,070 INFO 2022-03-11 16:50:27 AddOrReplaceReadGroups Processed 42,000,000 records. Elapsed time: 00:02:15s. Time for last 1,000,000: 3s. Last read position: NC_035789.1:18,235,945 INFO 2022-03-11 16:50:33 AddOrReplaceReadGroups Processed 43,000,000 records. Elapsed time: 00:02:21s. Time for last 1,000,000: 6s. Last read position: NC_007175.2:7,396 INFO 2022-03-11 16:50:36 AddOrReplaceReadGroups Processed 44,000,000 records. Elapsed time: 00:02:23s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 16:50:39 AddOrReplaceReadGroups Processed 45,000,000 records. Elapsed time: 00:02:26s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 16:50:42 AddOrReplaceReadGroups Processed 46,000,000 records. Elapsed time: 00:02:29s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 16:50:45 AddOrReplaceReadGroups Processed 47,000,000 records. Elapsed time: 00:02:32s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 16:50:48 AddOrReplaceReadGroups Processed 48,000,000 records. Elapsed time: 00:02:35s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 16:50:51 AddOrReplaceReadGroups Processed 49,000,000 records. Elapsed time: 00:02:38s. Time for last 1,000,000: 2s. Last read position: */* [Fri Mar 11 16:50:54 PST 2022] picard.sam.AddOrReplaceReadGroups done. Elapsed time: 2.70 minutes. Runtime.totalMemory()=2923429888 Tool returned: 0 Using GATK jar /home/shared/gatk-4.2.5.0/gatk-package-4.2.5.0-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 /home/shared/gatk-4.2.5.0/gatk-package-4.2.5.0-local.jar AddOrReplaceReadGroups I=S41F.dedup-split.bam O=S41F.dedup-split-RG.bam RGID=1 RGLB=S41F RGPL=ILLUMINA RGPU=unit1 RGSM=S41F INFO 2022-03-11 16:50:56 AddOrReplaceReadGroups ********** NOTE: Picard's command line syntax is changing. ********** ********** For more information, please see: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** ********** The command line looks like this in the new syntax: ********** ********** AddOrReplaceReadGroups -I S41F.dedup-split.bam -O S41F.dedup-split-RG.bam -RGID 1 -RGLB S41F -RGPL ILLUMINA -RGPU unit1 -RGSM S41F ********** 16:50:56.369 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/shared/gatk-4.2.5.0/gatk-package-4.2.5.0-local.jar!/com/intel/gkl/native/libgkl_compression.so [Fri Mar 11 16:50:56 PST 2022] AddOrReplaceReadGroups INPUT=S41F.dedup-split.bam OUTPUT=S41F.dedup-split-RG.bam RGID=1 RGLB=S41F RGPL=ILLUMINA RGPU=unit1 RGSM=S41F VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=2 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Mar 11, 2022 4:50:56 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine INFO: Failed to detect whether we are running on Google Compute Engine. [Fri Mar 11 16:50:56 PST 2022] Executing as sr320@raven on Linux 5.4.0-104-generic amd64; OpenJDK 64-Bit Server VM 11.0.14+9-Ubuntu-0ubuntu2.18.04; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: 4.2.5.0 INFO 2022-03-11 16:50:56 AddOrReplaceReadGroups Created read-group ID=1 PL=ILLUMINA LB=S41F SM=S41F INFO 2022-03-11 16:50:59 AddOrReplaceReadGroups Processed 1,000,000 records. Elapsed time: 00:00:03s. Time for last 1,000,000: 3s. Last read position: NC_035780.1:14,519,251 INFO 2022-03-11 16:51:02 AddOrReplaceReadGroups Processed 2,000,000 records. Elapsed time: 00:00:06s. Time for last 1,000,000: 3s. Last read position: NC_035780.1:31,097,757 INFO 2022-03-11 16:51:05 AddOrReplaceReadGroups Processed 3,000,000 records. Elapsed time: 00:00:09s. Time for last 1,000,000: 3s. Last read position: NC_035780.1:46,886,977 INFO 2022-03-11 16:51:08 AddOrReplaceReadGroups Processed 4,000,000 records. Elapsed time: 00:00:12s. Time for last 1,000,000: 2s. Last read position: NC_035780.1:59,132,421 INFO 2022-03-11 16:51:11 AddOrReplaceReadGroups Processed 5,000,000 records. Elapsed time: 00:00:15s. Time for last 1,000,000: 3s. Last read position: NC_035781.1:4,103,951 INFO 2022-03-11 16:51:14 AddOrReplaceReadGroups Processed 6,000,000 records. Elapsed time: 00:00:18s. Time for last 1,000,000: 2s. Last read position: NC_035781.1:13,239,772 INFO 2022-03-11 16:51:17 AddOrReplaceReadGroups Processed 7,000,000 records. Elapsed time: 00:00:21s. Time for last 1,000,000: 3s. Last read position: NC_035781.1:22,500,097 INFO 2022-03-11 16:51:20 AddOrReplaceReadGroups Processed 8,000,000 records. Elapsed time: 00:00:24s. Time for last 1,000,000: 2s. Last read position: NC_035781.1:32,819,573 INFO 2022-03-11 16:51:23 AddOrReplaceReadGroups Processed 9,000,000 records. Elapsed time: 00:00:27s. Time for last 1,000,000: 2s. Last read position: NC_035781.1:40,786,550 INFO 2022-03-11 16:51:26 AddOrReplaceReadGroups Processed 10,000,000 records. Elapsed time: 00:00:30s. Time for last 1,000,000: 2s. Last read position: NC_035781.1:50,541,900 INFO 2022-03-11 16:51:30 AddOrReplaceReadGroups Processed 11,000,000 records. Elapsed time: 00:00:33s. Time for last 1,000,000: 3s. Last read position: NC_035782.1:3,602,610 INFO 2022-03-11 16:51:35 AddOrReplaceReadGroups Processed 12,000,000 records. Elapsed time: 00:00:39s. Time for last 1,000,000: 5s. Last read position: NC_035782.1:21,053,719 INFO 2022-03-11 16:51:38 AddOrReplaceReadGroups Processed 13,000,000 records. Elapsed time: 00:00:42s. Time for last 1,000,000: 2s. Last read position: NC_035782.1:30,661,839 INFO 2022-03-11 16:51:41 AddOrReplaceReadGroups Processed 14,000,000 records. Elapsed time: 00:00:45s. Time for last 1,000,000: 3s. Last read position: NC_035782.1:44,253,420 INFO 2022-03-11 16:51:44 AddOrReplaceReadGroups Processed 15,000,000 records. Elapsed time: 00:00:48s. Time for last 1,000,000: 2s. Last read position: NC_035782.1:54,895,340 INFO 2022-03-11 16:51:47 AddOrReplaceReadGroups Processed 16,000,000 records. Elapsed time: 00:00:51s. Time for last 1,000,000: 2s. Last read position: NC_035782.1:64,004,218 INFO 2022-03-11 16:51:50 AddOrReplaceReadGroups Processed 17,000,000 records. Elapsed time: 00:00:54s. Time for last 1,000,000: 3s. Last read position: NC_035782.1:75,648,372 INFO 2022-03-11 16:51:53 AddOrReplaceReadGroups Processed 18,000,000 records. Elapsed time: 00:00:57s. Time for last 1,000,000: 2s. Last read position: NC_035783.1:12,866,136 INFO 2022-03-11 16:51:56 AddOrReplaceReadGroups Processed 19,000,000 records. Elapsed time: 00:01:00s. Time for last 1,000,000: 3s. Last read position: NC_035783.1:24,775,467 INFO 2022-03-11 16:51:59 AddOrReplaceReadGroups Processed 20,000,000 records. Elapsed time: 00:01:03s. Time for last 1,000,000: 2s. Last read position: NC_035783.1:34,435,947 INFO 2022-03-11 16:52:02 AddOrReplaceReadGroups Processed 21,000,000 records. Elapsed time: 00:01:06s. Time for last 1,000,000: 2s. Last read position: NC_035783.1:40,342,893 INFO 2022-03-11 16:52:08 AddOrReplaceReadGroups Processed 22,000,000 records. Elapsed time: 00:01:12s. Time for last 1,000,000: 6s. Last read position: NC_035783.1:52,083,695 INFO 2022-03-11 16:52:12 AddOrReplaceReadGroups Processed 23,000,000 records. Elapsed time: 00:01:15s. Time for last 1,000,000: 3s. Last read position: NC_035784.1:6,833,683 INFO 2022-03-11 16:52:15 AddOrReplaceReadGroups Processed 24,000,000 records. Elapsed time: 00:01:18s. Time for last 1,000,000: 2s. Last read position: NC_035784.1:15,934,159 INFO 2022-03-11 16:52:18 AddOrReplaceReadGroups Processed 25,000,000 records. Elapsed time: 00:01:21s. Time for last 1,000,000: 3s. Last read position: NC_035784.1:28,898,464 INFO 2022-03-11 16:52:21 AddOrReplaceReadGroups Processed 26,000,000 records. Elapsed time: 00:01:24s. Time for last 1,000,000: 2s. Last read position: NC_035784.1:39,496,430 INFO 2022-03-11 16:52:23 AddOrReplaceReadGroups Processed 27,000,000 records. Elapsed time: 00:01:27s. Time for last 1,000,000: 2s. Last read position: NC_035784.1:47,759,521 INFO 2022-03-11 16:52:26 AddOrReplaceReadGroups Processed 28,000,000 records. Elapsed time: 00:01:30s. Time for last 1,000,000: 2s. Last read position: NC_035784.1:52,196,722 INFO 2022-03-11 16:52:29 AddOrReplaceReadGroups Processed 29,000,000 records. Elapsed time: 00:01:32s. Time for last 1,000,000: 2s. Last read position: NC_035784.1:52,231,728 INFO 2022-03-11 16:52:31 AddOrReplaceReadGroups Processed 30,000,000 records. Elapsed time: 00:01:35s. Time for last 1,000,000: 2s. Last read position: NC_035784.1:52,262,069 INFO 2022-03-11 16:52:34 AddOrReplaceReadGroups Processed 31,000,000 records. Elapsed time: 00:01:37s. Time for last 1,000,000: 2s. Last read position: NC_035784.1:52,288,416 INFO 2022-03-11 16:52:37 AddOrReplaceReadGroups Processed 32,000,000 records. Elapsed time: 00:01:40s. Time for last 1,000,000: 2s. Last read position: NC_035784.1:63,720,076 INFO 2022-03-11 16:52:41 AddOrReplaceReadGroups Processed 33,000,000 records. Elapsed time: 00:01:44s. Time for last 1,000,000: 4s. Last read position: NC_035784.1:75,793,048 INFO 2022-03-11 16:52:46 AddOrReplaceReadGroups Processed 34,000,000 records. Elapsed time: 00:01:49s. Time for last 1,000,000: 4s. Last read position: NC_035784.1:94,167,913 INFO 2022-03-11 16:52:49 AddOrReplaceReadGroups Processed 35,000,000 records. Elapsed time: 00:01:52s. Time for last 1,000,000: 3s. Last read position: NC_035785.1:31,845,202 INFO 2022-03-11 16:52:52 AddOrReplaceReadGroups Processed 36,000,000 records. Elapsed time: 00:01:55s. Time for last 1,000,000: 2s. Last read position: NC_035785.1:45,760,465 INFO 2022-03-11 16:52:55 AddOrReplaceReadGroups Processed 37,000,000 records. Elapsed time: 00:01:58s. Time for last 1,000,000: 2s. Last read position: NC_035786.1:20,602,014 INFO 2022-03-11 16:52:58 AddOrReplaceReadGroups Processed 38,000,000 records. Elapsed time: 00:02:01s. Time for last 1,000,000: 3s. Last read position: NC_035786.1:47,696,088 INFO 2022-03-11 16:53:01 AddOrReplaceReadGroups Processed 39,000,000 records. Elapsed time: 00:02:04s. Time for last 1,000,000: 3s. Last read position: NC_035787.1:14,278,013 INFO 2022-03-11 16:53:04 AddOrReplaceReadGroups Processed 40,000,000 records. Elapsed time: 00:02:07s. Time for last 1,000,000: 3s. Last read position: NC_035787.1:47,586,140 INFO 2022-03-11 16:53:07 AddOrReplaceReadGroups Processed 41,000,000 records. Elapsed time: 00:02:10s. Time for last 1,000,000: 2s. Last read position: NC_035787.1:62,984,898 INFO 2022-03-11 16:53:10 AddOrReplaceReadGroups Processed 42,000,000 records. Elapsed time: 00:02:13s. Time for last 1,000,000: 3s. Last read position: NC_035788.1:16,046,985 INFO 2022-03-11 16:53:13 AddOrReplaceReadGroups Processed 43,000,000 records. Elapsed time: 00:02:16s. Time for last 1,000,000: 3s. Last read position: NC_035788.1:51,997,312 INFO 2022-03-11 16:53:19 AddOrReplaceReadGroups Processed 44,000,000 records. Elapsed time: 00:02:23s. Time for last 1,000,000: 6s. Last read position: NC_035788.1:75,723,326 INFO 2022-03-11 16:53:22 AddOrReplaceReadGroups Processed 45,000,000 records. Elapsed time: 00:02:26s. Time for last 1,000,000: 3s. Last read position: NC_035789.1:2,568,175 INFO 2022-03-11 16:53:25 AddOrReplaceReadGroups Processed 46,000,000 records. Elapsed time: 00:02:29s. Time for last 1,000,000: 3s. Last read position: NC_035789.1:29,767,467 INFO 2022-03-11 16:53:28 AddOrReplaceReadGroups Processed 47,000,000 records. Elapsed time: 00:02:32s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 16:53:31 AddOrReplaceReadGroups Processed 48,000,000 records. Elapsed time: 00:02:34s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 16:53:34 AddOrReplaceReadGroups Processed 49,000,000 records. Elapsed time: 00:02:37s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 16:53:37 AddOrReplaceReadGroups Processed 50,000,000 records. Elapsed time: 00:02:40s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 16:53:40 AddOrReplaceReadGroups Processed 51,000,000 records. Elapsed time: 00:02:43s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 16:53:42 AddOrReplaceReadGroups Processed 52,000,000 records. Elapsed time: 00:02:46s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 16:53:45 AddOrReplaceReadGroups Processed 53,000,000 records. Elapsed time: 00:02:49s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 16:53:48 AddOrReplaceReadGroups Processed 54,000,000 records. Elapsed time: 00:02:52s. Time for last 1,000,000: 2s. Last read position: */* [Fri Mar 11 16:53:54 PST 2022] picard.sam.AddOrReplaceReadGroups done. Elapsed time: 2.96 minutes. Runtime.totalMemory()=2717908992 Tool returned: 0 Using GATK jar /home/shared/gatk-4.2.5.0/gatk-package-4.2.5.0-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 /home/shared/gatk-4.2.5.0/gatk-package-4.2.5.0-local.jar AddOrReplaceReadGroups I=S44F.dedup-split.bam O=S44F.dedup-split-RG.bam RGID=1 RGLB=S44F RGPL=ILLUMINA RGPU=unit1 RGSM=S44F INFO 2022-03-11 16:53:55 AddOrReplaceReadGroups ********** NOTE: Picard's command line syntax is changing. ********** ********** For more information, please see: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** ********** The command line looks like this in the new syntax: ********** ********** AddOrReplaceReadGroups -I S44F.dedup-split.bam -O S44F.dedup-split-RG.bam -RGID 1 -RGLB S44F -RGPL ILLUMINA -RGPU unit1 -RGSM S44F ********** 16:53:55.859 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/shared/gatk-4.2.5.0/gatk-package-4.2.5.0-local.jar!/com/intel/gkl/native/libgkl_compression.so [Fri Mar 11 16:53:55 PST 2022] AddOrReplaceReadGroups INPUT=S44F.dedup-split.bam OUTPUT=S44F.dedup-split-RG.bam RGID=1 RGLB=S44F RGPL=ILLUMINA RGPU=unit1 RGSM=S44F VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=2 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Mar 11, 2022 4:53:55 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine INFO: Failed to detect whether we are running on Google Compute Engine. [Fri Mar 11 16:53:55 PST 2022] Executing as sr320@raven on Linux 5.4.0-104-generic amd64; OpenJDK 64-Bit Server VM 11.0.14+9-Ubuntu-0ubuntu2.18.04; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: 4.2.5.0 INFO 2022-03-11 16:53:56 AddOrReplaceReadGroups Created read-group ID=1 PL=ILLUMINA LB=S44F SM=S44F INFO 2022-03-11 16:53:58 AddOrReplaceReadGroups Processed 1,000,000 records. Elapsed time: 00:00:02s. Time for last 1,000,000: 2s. Last read position: NC_035780.1:8,275,188 INFO 2022-03-11 16:54:01 AddOrReplaceReadGroups Processed 2,000,000 records. Elapsed time: 00:00:05s. Time for last 1,000,000: 2s. Last read position: NC_035780.1:24,837,912 INFO 2022-03-11 16:54:05 AddOrReplaceReadGroups Processed 3,000,000 records. Elapsed time: 00:00:09s. Time for last 1,000,000: 3s. Last read position: NC_035780.1:35,886,529 INFO 2022-03-11 16:54:08 AddOrReplaceReadGroups Processed 4,000,000 records. Elapsed time: 00:00:12s. Time for last 1,000,000: 3s. Last read position: NC_035780.1:52,490,138 INFO 2022-03-11 16:54:11 AddOrReplaceReadGroups Processed 5,000,000 records. Elapsed time: 00:00:15s. Time for last 1,000,000: 3s. Last read position: NC_035780.1:60,620,967 INFO 2022-03-11 16:54:14 AddOrReplaceReadGroups Processed 6,000,000 records. Elapsed time: 00:00:18s. Time for last 1,000,000: 2s. Last read position: NC_035781.1:5,229,535 INFO 2022-03-11 16:54:17 AddOrReplaceReadGroups Processed 7,000,000 records. Elapsed time: 00:00:21s. Time for last 1,000,000: 3s. Last read position: NC_035781.1:13,794,245 INFO 2022-03-11 16:54:20 AddOrReplaceReadGroups Processed 8,000,000 records. Elapsed time: 00:00:24s. Time for last 1,000,000: 2s. Last read position: NC_035781.1:23,028,716 INFO 2022-03-11 16:54:23 AddOrReplaceReadGroups Processed 9,000,000 records. Elapsed time: 00:00:27s. Time for last 1,000,000: 3s. Last read position: NC_035781.1:33,300,397 INFO 2022-03-11 16:54:26 AddOrReplaceReadGroups Processed 10,000,000 records. Elapsed time: 00:00:30s. Time for last 1,000,000: 2s. Last read position: NC_035781.1:40,754,608 INFO 2022-03-11 16:54:29 AddOrReplaceReadGroups Processed 11,000,000 records. Elapsed time: 00:00:33s. Time for last 1,000,000: 2s. Last read position: NC_035781.1:48,644,399 INFO 2022-03-11 16:54:35 AddOrReplaceReadGroups Processed 12,000,000 records. Elapsed time: 00:00:39s. Time for last 1,000,000: 6s. Last read position: NC_035781.1:59,239,684 INFO 2022-03-11 16:54:38 AddOrReplaceReadGroups Processed 13,000,000 records. Elapsed time: 00:00:42s. Time for last 1,000,000: 3s. Last read position: NC_035782.1:19,331,126 INFO 2022-03-11 16:54:41 AddOrReplaceReadGroups Processed 14,000,000 records. Elapsed time: 00:00:45s. Time for last 1,000,000: 2s. Last read position: NC_035782.1:21,027,968 INFO 2022-03-11 16:54:44 AddOrReplaceReadGroups Processed 15,000,000 records. Elapsed time: 00:00:48s. Time for last 1,000,000: 2s. Last read position: NC_035782.1:29,976,257 INFO 2022-03-11 16:54:47 AddOrReplaceReadGroups Processed 16,000,000 records. Elapsed time: 00:00:51s. Time for last 1,000,000: 3s. Last read position: NC_035782.1:41,065,105 INFO 2022-03-11 16:54:50 AddOrReplaceReadGroups Processed 17,000,000 records. Elapsed time: 00:00:54s. Time for last 1,000,000: 3s. Last read position: NC_035782.1:53,489,234 INFO 2022-03-11 16:54:53 AddOrReplaceReadGroups Processed 18,000,000 records. Elapsed time: 00:00:57s. Time for last 1,000,000: 2s. Last read position: NC_035782.1:61,687,232 INFO 2022-03-11 16:54:56 AddOrReplaceReadGroups Processed 19,000,000 records. Elapsed time: 00:01:00s. Time for last 1,000,000: 3s. Last read position: NC_035782.1:72,790,082 INFO 2022-03-11 16:54:59 AddOrReplaceReadGroups Processed 20,000,000 records. Elapsed time: 00:01:03s. Time for last 1,000,000: 3s. Last read position: NC_035783.1:9,990,701 INFO 2022-03-11 16:55:02 AddOrReplaceReadGroups Processed 21,000,000 records. Elapsed time: 00:01:06s. Time for last 1,000,000: 3s. Last read position: NC_035783.1:20,813,186 INFO 2022-03-11 16:55:06 AddOrReplaceReadGroups Processed 22,000,000 records. Elapsed time: 00:01:10s. Time for last 1,000,000: 3s. Last read position: NC_035783.1:30,059,992 INFO 2022-03-11 16:55:11 AddOrReplaceReadGroups Processed 23,000,000 records. Elapsed time: 00:01:15s. Time for last 1,000,000: 4s. Last read position: NC_035783.1:34,525,349 INFO 2022-03-11 16:55:14 AddOrReplaceReadGroups Processed 24,000,000 records. Elapsed time: 00:01:18s. Time for last 1,000,000: 2s. Last read position: NC_035783.1:39,446,820 INFO 2022-03-11 16:55:17 AddOrReplaceReadGroups Processed 25,000,000 records. Elapsed time: 00:01:21s. Time for last 1,000,000: 2s. Last read position: NC_035783.1:49,881,127 INFO 2022-03-11 16:55:20 AddOrReplaceReadGroups Processed 26,000,000 records. Elapsed time: 00:01:24s. Time for last 1,000,000: 3s. Last read position: NC_035784.1:3,917,718 INFO 2022-03-11 16:55:23 AddOrReplaceReadGroups Processed 27,000,000 records. Elapsed time: 00:01:27s. Time for last 1,000,000: 3s. Last read position: NC_035784.1:14,320,618 INFO 2022-03-11 16:55:26 AddOrReplaceReadGroups Processed 28,000,000 records. Elapsed time: 00:01:30s. Time for last 1,000,000: 3s. Last read position: NC_035784.1:28,734,081 INFO 2022-03-11 16:55:29 AddOrReplaceReadGroups Processed 29,000,000 records. Elapsed time: 00:01:33s. Time for last 1,000,000: 3s. Last read position: NC_035784.1:39,712,012 INFO 2022-03-11 16:55:32 AddOrReplaceReadGroups Processed 30,000,000 records. Elapsed time: 00:01:36s. Time for last 1,000,000: 2s. Last read position: NC_035784.1:47,758,931 INFO 2022-03-11 16:55:34 AddOrReplaceReadGroups Processed 31,000,000 records. Elapsed time: 00:01:38s. Time for last 1,000,000: 2s. Last read position: NC_035784.1:52,196,413 INFO 2022-03-11 16:55:37 AddOrReplaceReadGroups Processed 32,000,000 records. Elapsed time: 00:01:41s. Time for last 1,000,000: 2s. Last read position: NC_035784.1:52,215,551 INFO 2022-03-11 16:55:40 AddOrReplaceReadGroups Processed 33,000,000 records. Elapsed time: 00:01:44s. Time for last 1,000,000: 2s. Last read position: NC_035784.1:52,257,671 INFO 2022-03-11 16:55:45 AddOrReplaceReadGroups Processed 34,000,000 records. Elapsed time: 00:01:49s. Time for last 1,000,000: 4s. Last read position: NC_035784.1:52,274,021 INFO 2022-03-11 16:55:47 AddOrReplaceReadGroups Processed 35,000,000 records. Elapsed time: 00:01:51s. Time for last 1,000,000: 2s. Last read position: NC_035784.1:52,288,680 INFO 2022-03-11 16:55:50 AddOrReplaceReadGroups Processed 36,000,000 records. Elapsed time: 00:01:54s. Time for last 1,000,000: 2s. Last read position: NC_035784.1:63,148,845 INFO 2022-03-11 16:55:53 AddOrReplaceReadGroups Processed 37,000,000 records. Elapsed time: 00:01:57s. Time for last 1,000,000: 3s. Last read position: NC_035784.1:73,044,593 INFO 2022-03-11 16:55:56 AddOrReplaceReadGroups Processed 38,000,000 records. Elapsed time: 00:02:00s. Time for last 1,000,000: 2s. Last read position: NC_035784.1:85,968,197 INFO 2022-03-11 16:55:59 AddOrReplaceReadGroups Processed 39,000,000 records. Elapsed time: 00:02:03s. Time for last 1,000,000: 3s. Last read position: NC_035785.1:15,115,663 INFO 2022-03-11 16:56:02 AddOrReplaceReadGroups Processed 40,000,000 records. Elapsed time: 00:02:06s. Time for last 1,000,000: 2s. Last read position: NC_035785.1:36,420,056 INFO 2022-03-11 16:56:05 AddOrReplaceReadGroups Processed 41,000,000 records. Elapsed time: 00:02:09s. Time for last 1,000,000: 2s. Last read position: NC_035786.1:5,560,475 INFO 2022-03-11 16:56:08 AddOrReplaceReadGroups Processed 42,000,000 records. Elapsed time: 00:02:12s. Time for last 1,000,000: 3s. Last read position: NC_035786.1:33,803,623 INFO 2022-03-11 16:56:11 AddOrReplaceReadGroups Processed 43,000,000 records. Elapsed time: 00:02:15s. Time for last 1,000,000: 3s. Last read position: NC_035786.1:55,146,139 INFO 2022-03-11 16:56:15 AddOrReplaceReadGroups Processed 44,000,000 records. Elapsed time: 00:02:19s. Time for last 1,000,000: 3s. Last read position: NC_035787.1:21,267,343 INFO 2022-03-11 16:56:20 AddOrReplaceReadGroups Processed 45,000,000 records. Elapsed time: 00:02:24s. Time for last 1,000,000: 5s. Last read position: NC_035787.1:50,750,536 INFO 2022-03-11 16:56:23 AddOrReplaceReadGroups Processed 46,000,000 records. Elapsed time: 00:02:27s. Time for last 1,000,000: 2s. Last read position: NC_035787.1:62,326,174 INFO 2022-03-11 16:56:26 AddOrReplaceReadGroups Processed 47,000,000 records. Elapsed time: 00:02:30s. Time for last 1,000,000: 3s. Last read position: NC_035788.1:9,966,384 INFO 2022-03-11 16:56:29 AddOrReplaceReadGroups Processed 48,000,000 records. Elapsed time: 00:02:33s. Time for last 1,000,000: 3s. Last read position: NC_035788.1:48,527,834 INFO 2022-03-11 16:56:32 AddOrReplaceReadGroups Processed 49,000,000 records. Elapsed time: 00:02:36s. Time for last 1,000,000: 3s. Last read position: NC_035788.1:71,665,891 INFO 2022-03-11 16:56:36 AddOrReplaceReadGroups Processed 50,000,000 records. Elapsed time: 00:02:40s. Time for last 1,000,000: 3s. Last read position: NC_035788.1:98,044,986 INFO 2022-03-11 16:56:39 AddOrReplaceReadGroups Processed 51,000,000 records. Elapsed time: 00:02:43s. Time for last 1,000,000: 3s. Last read position: NC_035789.1:20,033,164 INFO 2022-03-11 16:56:41 AddOrReplaceReadGroups Processed 52,000,000 records. Elapsed time: 00:02:45s. Time for last 1,000,000: 2s. Last read position: NC_007175.2:8,425 INFO 2022-03-11 16:56:44 AddOrReplaceReadGroups Processed 53,000,000 records. Elapsed time: 00:02:48s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 16:56:47 AddOrReplaceReadGroups Processed 54,000,000 records. Elapsed time: 00:02:51s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 16:56:53 AddOrReplaceReadGroups Processed 55,000,000 records. Elapsed time: 00:02:57s. Time for last 1,000,000: 6s. Last read position: */* INFO 2022-03-11 16:56:56 AddOrReplaceReadGroups Processed 56,000,000 records. Elapsed time: 00:03:00s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 16:56:59 AddOrReplaceReadGroups Processed 57,000,000 records. Elapsed time: 00:03:03s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 16:57:02 AddOrReplaceReadGroups Processed 58,000,000 records. Elapsed time: 00:03:06s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 16:57:05 AddOrReplaceReadGroups Processed 59,000,000 records. Elapsed time: 00:03:09s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 16:57:08 AddOrReplaceReadGroups Processed 60,000,000 records. Elapsed time: 00:03:12s. Time for last 1,000,000: 2s. Last read position: */* [Fri Mar 11 16:57:12 PST 2022] picard.sam.AddOrReplaceReadGroups done. Elapsed time: 3.27 minutes. Runtime.totalMemory()=2956984320 Tool returned: 0 Using GATK jar /home/shared/gatk-4.2.5.0/gatk-package-4.2.5.0-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 /home/shared/gatk-4.2.5.0/gatk-package-4.2.5.0-local.jar AddOrReplaceReadGroups I=S48M.dedup-split.bam O=S48M.dedup-split-RG.bam RGID=1 RGLB=S48M RGPL=ILLUMINA RGPU=unit1 RGSM=S48M INFO 2022-03-11 16:57:13 AddOrReplaceReadGroups ********** NOTE: Picard's command line syntax is changing. ********** ********** For more information, please see: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** ********** The command line looks like this in the new syntax: ********** ********** AddOrReplaceReadGroups -I S48M.dedup-split.bam -O S48M.dedup-split-RG.bam -RGID 1 -RGLB S48M -RGPL ILLUMINA -RGPU unit1 -RGSM S48M ********** 16:57:13.851 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/shared/gatk-4.2.5.0/gatk-package-4.2.5.0-local.jar!/com/intel/gkl/native/libgkl_compression.so [Fri Mar 11 16:57:13 PST 2022] AddOrReplaceReadGroups INPUT=S48M.dedup-split.bam OUTPUT=S48M.dedup-split-RG.bam RGID=1 RGLB=S48M RGPL=ILLUMINA RGPU=unit1 RGSM=S48M VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=2 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Mar 11, 2022 4:57:13 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine INFO: Failed to detect whether we are running on Google Compute Engine. [Fri Mar 11 16:57:13 PST 2022] Executing as sr320@raven on Linux 5.4.0-104-generic amd64; OpenJDK 64-Bit Server VM 11.0.14+9-Ubuntu-0ubuntu2.18.04; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: 4.2.5.0 INFO 2022-03-11 16:57:13 AddOrReplaceReadGroups Created read-group ID=1 PL=ILLUMINA LB=S48M SM=S48M INFO 2022-03-11 16:57:16 AddOrReplaceReadGroups Processed 1,000,000 records. Elapsed time: 00:00:02s. Time for last 1,000,000: 2s. Last read position: NC_035780.1:5,144,385 INFO 2022-03-11 16:57:19 AddOrReplaceReadGroups Processed 2,000,000 records. Elapsed time: 00:00:05s. Time for last 1,000,000: 2s. Last read position: NC_035780.1:12,208,181 INFO 2022-03-11 16:57:22 AddOrReplaceReadGroups Processed 3,000,000 records. Elapsed time: 00:00:08s. Time for last 1,000,000: 2s. Last read position: NC_035780.1:19,116,268 INFO 2022-03-11 16:57:25 AddOrReplaceReadGroups Processed 4,000,000 records. Elapsed time: 00:00:11s. Time for last 1,000,000: 2s. Last read position: NC_035780.1:25,226,370 INFO 2022-03-11 16:57:28 AddOrReplaceReadGroups Processed 5,000,000 records. Elapsed time: 00:00:14s. Time for last 1,000,000: 2s. Last read position: NC_035780.1:31,046,859 INFO 2022-03-11 16:57:31 AddOrReplaceReadGroups Processed 6,000,000 records. Elapsed time: 00:00:17s. Time for last 1,000,000: 2s. Last read position: NC_035780.1:37,875,145 INFO 2022-03-11 16:57:34 AddOrReplaceReadGroups Processed 7,000,000 records. Elapsed time: 00:00:20s. Time for last 1,000,000: 2s. Last read position: NC_035780.1:44,354,332 INFO 2022-03-11 16:57:37 AddOrReplaceReadGroups Processed 8,000,000 records. Elapsed time: 00:00:23s. Time for last 1,000,000: 2s. Last read position: NC_035780.1:53,566,608 INFO 2022-03-11 16:57:40 AddOrReplaceReadGroups Processed 9,000,000 records. Elapsed time: 00:00:26s. Time for last 1,000,000: 2s. Last read position: NC_035780.1:60,461,275 INFO 2022-03-11 16:57:43 AddOrReplaceReadGroups Processed 10,000,000 records. Elapsed time: 00:00:29s. Time for last 1,000,000: 2s. Last read position: NC_035781.1:1,207,081 INFO 2022-03-11 16:57:49 AddOrReplaceReadGroups Processed 11,000,000 records. Elapsed time: 00:00:35s. Time for last 1,000,000: 6s. Last read position: NC_035781.1:7,827,404 INFO 2022-03-11 16:57:52 AddOrReplaceReadGroups Processed 12,000,000 records. Elapsed time: 00:00:38s. Time for last 1,000,000: 2s. Last read position: NC_035781.1:13,808,490 INFO 2022-03-11 16:57:55 AddOrReplaceReadGroups Processed 13,000,000 records. Elapsed time: 00:00:41s. Time for last 1,000,000: 2s. Last read position: NC_035781.1:20,750,701 INFO 2022-03-11 16:57:58 AddOrReplaceReadGroups Processed 14,000,000 records. Elapsed time: 00:00:44s. Time for last 1,000,000: 2s. Last read position: NC_035781.1:25,902,507 INFO 2022-03-11 16:58:01 AddOrReplaceReadGroups Processed 15,000,000 records. Elapsed time: 00:00:47s. Time for last 1,000,000: 2s. Last read position: NC_035781.1:33,176,781 INFO 2022-03-11 16:58:04 AddOrReplaceReadGroups Processed 16,000,000 records. Elapsed time: 00:00:50s. Time for last 1,000,000: 2s. Last read position: NC_035781.1:40,049,928 INFO 2022-03-11 16:58:07 AddOrReplaceReadGroups Processed 17,000,000 records. Elapsed time: 00:00:53s. Time for last 1,000,000: 2s. Last read position: NC_035781.1:46,811,600 INFO 2022-03-11 16:58:10 AddOrReplaceReadGroups Processed 18,000,000 records. Elapsed time: 00:00:56s. Time for last 1,000,000: 2s. Last read position: NC_035781.1:53,417,089 INFO 2022-03-11 16:58:12 AddOrReplaceReadGroups Processed 19,000,000 records. Elapsed time: 00:00:58s. Time for last 1,000,000: 2s. Last read position: NC_035781.1:59,882,204 INFO 2022-03-11 16:58:15 AddOrReplaceReadGroups Processed 20,000,000 records. Elapsed time: 00:01:01s. Time for last 1,000,000: 2s. Last read position: NC_035782.1:5,383,074 INFO 2022-03-11 16:58:18 AddOrReplaceReadGroups Processed 21,000,000 records. Elapsed time: 00:01:04s. Time for last 1,000,000: 2s. Last read position: NC_035782.1:13,510,822 INFO 2022-03-11 16:58:24 AddOrReplaceReadGroups Processed 22,000,000 records. Elapsed time: 00:01:11s. Time for last 1,000,000: 6s. Last read position: NC_035782.1:20,894,197 INFO 2022-03-11 16:58:27 AddOrReplaceReadGroups Processed 23,000,000 records. Elapsed time: 00:01:13s. Time for last 1,000,000: 2s. Last read position: NC_035782.1:28,196,935 INFO 2022-03-11 16:58:30 AddOrReplaceReadGroups Processed 24,000,000 records. Elapsed time: 00:01:16s. Time for last 1,000,000: 2s. Last read position: NC_035782.1:34,884,297 INFO 2022-03-11 16:58:33 AddOrReplaceReadGroups Processed 25,000,000 records. Elapsed time: 00:01:19s. Time for last 1,000,000: 2s. Last read position: NC_035782.1:41,986,578 INFO 2022-03-11 16:58:36 AddOrReplaceReadGroups Processed 26,000,000 records. Elapsed time: 00:01:22s. Time for last 1,000,000: 2s. Last read position: NC_035782.1:49,673,651 INFO 2022-03-11 16:58:39 AddOrReplaceReadGroups Processed 27,000,000 records. Elapsed time: 00:01:25s. Time for last 1,000,000: 2s. Last read position: NC_035782.1:55,654,548 INFO 2022-03-11 16:58:42 AddOrReplaceReadGroups Processed 28,000,000 records. Elapsed time: 00:01:28s. Time for last 1,000,000: 3s. Last read position: NC_035782.1:61,870,182 INFO 2022-03-11 16:58:45 AddOrReplaceReadGroups Processed 29,000,000 records. Elapsed time: 00:01:31s. Time for last 1,000,000: 2s. Last read position: NC_035782.1:68,667,287 INFO 2022-03-11 16:58:48 AddOrReplaceReadGroups Processed 30,000,000 records. Elapsed time: 00:01:34s. Time for last 1,000,000: 2s. Last read position: NC_035782.1:75,921,661 INFO 2022-03-11 16:58:51 AddOrReplaceReadGroups Processed 31,000,000 records. Elapsed time: 00:01:37s. Time for last 1,000,000: 2s. Last read position: NC_035783.1:6,022,312 INFO 2022-03-11 16:58:56 AddOrReplaceReadGroups Processed 32,000,000 records. Elapsed time: 00:01:42s. Time for last 1,000,000: 4s. Last read position: NC_035783.1:13,018,513 INFO 2022-03-11 16:59:00 AddOrReplaceReadGroups Processed 33,000,000 records. Elapsed time: 00:01:46s. Time for last 1,000,000: 4s. Last read position: NC_035783.1:18,758,538 INFO 2022-03-11 16:59:03 AddOrReplaceReadGroups Processed 34,000,000 records. Elapsed time: 00:01:49s. Time for last 1,000,000: 2s. Last read position: NC_035783.1:24,375,944 INFO 2022-03-11 16:59:06 AddOrReplaceReadGroups Processed 35,000,000 records. Elapsed time: 00:01:52s. Time for last 1,000,000: 2s. Last read position: NC_035783.1:31,440,544 INFO 2022-03-11 16:59:09 AddOrReplaceReadGroups Processed 36,000,000 records. Elapsed time: 00:01:55s. Time for last 1,000,000: 2s. Last read position: NC_035783.1:38,431,571 INFO 2022-03-11 16:59:12 AddOrReplaceReadGroups Processed 37,000,000 records. Elapsed time: 00:01:58s. Time for last 1,000,000: 2s. Last read position: NC_035783.1:44,898,446 INFO 2022-03-11 16:59:15 AddOrReplaceReadGroups Processed 38,000,000 records. Elapsed time: 00:02:01s. Time for last 1,000,000: 2s. Last read position: NC_035783.1:50,775,184 INFO 2022-03-11 16:59:18 AddOrReplaceReadGroups Processed 39,000,000 records. Elapsed time: 00:02:04s. Time for last 1,000,000: 2s. Last read position: NC_035783.1:58,011,616 INFO 2022-03-11 16:59:21 AddOrReplaceReadGroups Processed 40,000,000 records. Elapsed time: 00:02:07s. Time for last 1,000,000: 2s. Last read position: NC_035784.1:5,244,497 INFO 2022-03-11 16:59:24 AddOrReplaceReadGroups Processed 41,000,000 records. Elapsed time: 00:02:10s. Time for last 1,000,000: 2s. Last read position: NC_035784.1:11,763,951 INFO 2022-03-11 16:59:27 AddOrReplaceReadGroups Processed 42,000,000 records. Elapsed time: 00:02:13s. Time for last 1,000,000: 3s. Last read position: NC_035784.1:17,865,226 INFO 2022-03-11 16:59:33 AddOrReplaceReadGroups Processed 43,000,000 records. Elapsed time: 00:02:19s. Time for last 1,000,000: 6s. Last read position: NC_035784.1:25,068,836 INFO 2022-03-11 16:59:36 AddOrReplaceReadGroups Processed 44,000,000 records. Elapsed time: 00:02:22s. Time for last 1,000,000: 3s. Last read position: NC_035784.1:31,718,118 INFO 2022-03-11 16:59:39 AddOrReplaceReadGroups Processed 45,000,000 records. Elapsed time: 00:02:25s. Time for last 1,000,000: 2s. Last read position: NC_035784.1:38,433,372 INFO 2022-03-11 16:59:42 AddOrReplaceReadGroups Processed 46,000,000 records. Elapsed time: 00:02:28s. Time for last 1,000,000: 2s. Last read position: NC_035784.1:44,299,252 INFO 2022-03-11 16:59:45 AddOrReplaceReadGroups Processed 47,000,000 records. Elapsed time: 00:02:31s. Time for last 1,000,000: 2s. Last read position: NC_035784.1:48,852,775 INFO 2022-03-11 16:59:48 AddOrReplaceReadGroups Processed 48,000,000 records. Elapsed time: 00:02:34s. Time for last 1,000,000: 2s. Last read position: NC_035784.1:52,229,916 INFO 2022-03-11 16:59:50 AddOrReplaceReadGroups Processed 49,000,000 records. Elapsed time: 00:02:36s. Time for last 1,000,000: 2s. Last read position: NC_035784.1:52,279,502 INFO 2022-03-11 16:59:53 AddOrReplaceReadGroups Processed 50,000,000 records. Elapsed time: 00:02:39s. Time for last 1,000,000: 2s. Last read position: NC_035784.1:57,434,613 INFO 2022-03-11 16:59:56 AddOrReplaceReadGroups Processed 51,000,000 records. Elapsed time: 00:02:42s. Time for last 1,000,000: 2s. Last read position: NC_035784.1:63,964,019 INFO 2022-03-11 16:59:59 AddOrReplaceReadGroups Processed 52,000,000 records. Elapsed time: 00:02:45s. Time for last 1,000,000: 2s. Last read position: NC_035784.1:70,597,780 INFO 2022-03-11 17:00:02 AddOrReplaceReadGroups Processed 53,000,000 records. Elapsed time: 00:02:48s. Time for last 1,000,000: 2s. Last read position: NC_035784.1:77,685,534 INFO 2022-03-11 17:00:08 AddOrReplaceReadGroups Processed 54,000,000 records. Elapsed time: 00:02:54s. Time for last 1,000,000: 5s. Last read position: NC_035784.1:86,085,903 INFO 2022-03-11 17:00:11 AddOrReplaceReadGroups Processed 55,000,000 records. Elapsed time: 00:02:57s. Time for last 1,000,000: 2s. Last read position: NC_035784.1:93,564,488 INFO 2022-03-11 17:00:14 AddOrReplaceReadGroups Processed 56,000,000 records. Elapsed time: 00:03:00s. Time for last 1,000,000: 2s. Last read position: NC_035785.1:2,554,026 INFO 2022-03-11 17:00:17 AddOrReplaceReadGroups Processed 57,000,000 records. Elapsed time: 00:03:03s. Time for last 1,000,000: 2s. Last read position: NC_035785.1:10,165,918 INFO 2022-03-11 17:00:20 AddOrReplaceReadGroups Processed 58,000,000 records. Elapsed time: 00:03:06s. Time for last 1,000,000: 2s. Last read position: NC_035785.1:17,732,650 INFO 2022-03-11 17:00:23 AddOrReplaceReadGroups Processed 59,000,000 records. Elapsed time: 00:03:09s. Time for last 1,000,000: 2s. Last read position: NC_035785.1:27,416,611 INFO 2022-03-11 17:00:26 AddOrReplaceReadGroups Processed 60,000,000 records. Elapsed time: 00:03:12s. Time for last 1,000,000: 2s. Last read position: NC_035785.1:35,201,372 INFO 2022-03-11 17:00:29 AddOrReplaceReadGroups Processed 61,000,000 records. Elapsed time: 00:03:15s. Time for last 1,000,000: 2s. Last read position: NC_035785.1:41,895,535 INFO 2022-03-11 17:00:31 AddOrReplaceReadGroups Processed 62,000,000 records. Elapsed time: 00:03:17s. Time for last 1,000,000: 2s. Last read position: NC_035785.1:49,891,590 INFO 2022-03-11 17:00:34 AddOrReplaceReadGroups Processed 63,000,000 records. Elapsed time: 00:03:20s. Time for last 1,000,000: 2s. Last read position: NC_035786.1:3,642,040 INFO 2022-03-11 17:00:37 AddOrReplaceReadGroups Processed 64,000,000 records. Elapsed time: 00:03:23s. Time for last 1,000,000: 2s. Last read position: NC_035786.1:11,762,583 INFO 2022-03-11 17:00:43 AddOrReplaceReadGroups Processed 65,000,000 records. Elapsed time: 00:03:29s. Time for last 1,000,000: 5s. Last read position: NC_035786.1:21,866,061 INFO 2022-03-11 17:00:46 AddOrReplaceReadGroups Processed 66,000,000 records. Elapsed time: 00:03:32s. Time for last 1,000,000: 2s. Last read position: NC_035786.1:31,667,699 INFO 2022-03-11 17:00:49 AddOrReplaceReadGroups Processed 67,000,000 records. Elapsed time: 00:03:35s. Time for last 1,000,000: 2s. Last read position: NC_035786.1:40,353,834 INFO 2022-03-11 17:00:52 AddOrReplaceReadGroups Processed 68,000,000 records. Elapsed time: 00:03:38s. Time for last 1,000,000: 2s. Last read position: NC_035786.1:48,881,411 INFO 2022-03-11 17:00:55 AddOrReplaceReadGroups Processed 69,000,000 records. Elapsed time: 00:03:41s. Time for last 1,000,000: 2s. Last read position: NC_035786.1:55,831,143 INFO 2022-03-11 17:00:58 AddOrReplaceReadGroups Processed 70,000,000 records. Elapsed time: 00:03:44s. Time for last 1,000,000: 2s. Last read position: NC_035787.1:5,690,240 INFO 2022-03-11 17:01:01 AddOrReplaceReadGroups Processed 71,000,000 records. Elapsed time: 00:03:47s. Time for last 1,000,000: 2s. Last read position: NC_035787.1:14,571,347 INFO 2022-03-11 17:01:04 AddOrReplaceReadGroups Processed 72,000,000 records. Elapsed time: 00:03:50s. Time for last 1,000,000: 2s. Last read position: NC_035787.1:23,655,099 INFO 2022-03-11 17:01:07 AddOrReplaceReadGroups Processed 73,000,000 records. Elapsed time: 00:03:53s. Time for last 1,000,000: 2s. Last read position: NC_035787.1:32,882,445 INFO 2022-03-11 17:01:10 AddOrReplaceReadGroups Processed 74,000,000 records. Elapsed time: 00:03:56s. Time for last 1,000,000: 2s. Last read position: NC_035787.1:41,451,061 INFO 2022-03-11 17:01:12 AddOrReplaceReadGroups Processed 75,000,000 records. Elapsed time: 00:03:58s. Time for last 1,000,000: 2s. Last read position: NC_035787.1:47,515,928 INFO 2022-03-11 17:01:18 AddOrReplaceReadGroups Processed 76,000,000 records. Elapsed time: 00:04:04s. Time for last 1,000,000: 5s. Last read position: NC_035787.1:54,663,296 INFO 2022-03-11 17:01:21 AddOrReplaceReadGroups Processed 77,000,000 records. Elapsed time: 00:04:07s. Time for last 1,000,000: 2s. Last read position: NC_035787.1:60,987,755 INFO 2022-03-11 17:01:24 AddOrReplaceReadGroups Processed 78,000,000 records. Elapsed time: 00:04:10s. Time for last 1,000,000: 2s. Last read position: NC_035787.1:67,383,585 INFO 2022-03-11 17:01:27 AddOrReplaceReadGroups Processed 79,000,000 records. Elapsed time: 00:04:13s. Time for last 1,000,000: 2s. Last read position: NC_035788.1:1,579,751 INFO 2022-03-11 17:01:30 AddOrReplaceReadGroups Processed 80,000,000 records. Elapsed time: 00:04:16s. Time for last 1,000,000: 2s. Last read position: NC_035788.1:10,439,613 INFO 2022-03-11 17:01:33 AddOrReplaceReadGroups Processed 81,000,000 records. Elapsed time: 00:04:19s. Time for last 1,000,000: 2s. Last read position: NC_035788.1:18,304,056 INFO 2022-03-11 17:01:36 AddOrReplaceReadGroups Processed 82,000,000 records. Elapsed time: 00:04:22s. Time for last 1,000,000: 2s. Last read position: NC_035788.1:27,663,318 INFO 2022-03-11 17:01:39 AddOrReplaceReadGroups Processed 83,000,000 records. Elapsed time: 00:04:25s. Time for last 1,000,000: 2s. Last read position: NC_035788.1:39,685,114 INFO 2022-03-11 17:01:42 AddOrReplaceReadGroups Processed 84,000,000 records. Elapsed time: 00:04:28s. Time for last 1,000,000: 2s. Last read position: NC_035788.1:46,796,090 INFO 2022-03-11 17:01:45 AddOrReplaceReadGroups Processed 85,000,000 records. Elapsed time: 00:04:31s. Time for last 1,000,000: 2s. Last read position: NC_035788.1:53,453,226 INFO 2022-03-11 17:01:48 AddOrReplaceReadGroups Processed 86,000,000 records. Elapsed time: 00:04:34s. Time for last 1,000,000: 3s. Last read position: NC_035788.1:60,534,200 INFO 2022-03-11 17:01:53 AddOrReplaceReadGroups Processed 87,000,000 records. Elapsed time: 00:04:39s. Time for last 1,000,000: 5s. Last read position: NC_035788.1:67,413,403 INFO 2022-03-11 17:01:56 AddOrReplaceReadGroups Processed 88,000,000 records. Elapsed time: 00:04:42s. Time for last 1,000,000: 2s. Last read position: NC_035788.1:74,167,215 INFO 2022-03-11 17:01:59 AddOrReplaceReadGroups Processed 89,000,000 records. Elapsed time: 00:04:45s. Time for last 1,000,000: 2s. Last read position: NC_035788.1:80,656,981 INFO 2022-03-11 17:02:02 AddOrReplaceReadGroups Processed 90,000,000 records. Elapsed time: 00:04:48s. Time for last 1,000,000: 2s. Last read position: NC_035788.1:89,632,075 INFO 2022-03-11 17:02:05 AddOrReplaceReadGroups Processed 91,000,000 records. Elapsed time: 00:04:51s. Time for last 1,000,000: 2s. Last read position: NC_035788.1:99,550,823 INFO 2022-03-11 17:02:08 AddOrReplaceReadGroups Processed 92,000,000 records. Elapsed time: 00:04:54s. Time for last 1,000,000: 2s. Last read position: NC_035789.1:2,986,822 INFO 2022-03-11 17:02:11 AddOrReplaceReadGroups Processed 93,000,000 records. Elapsed time: 00:04:57s. Time for last 1,000,000: 2s. Last read position: NC_035789.1:10,068,974 INFO 2022-03-11 17:02:14 AddOrReplaceReadGroups Processed 94,000,000 records. Elapsed time: 00:05:00s. Time for last 1,000,000: 2s. Last read position: NC_035789.1:15,991,176 INFO 2022-03-11 17:02:17 AddOrReplaceReadGroups Processed 95,000,000 records. Elapsed time: 00:05:03s. Time for last 1,000,000: 2s. Last read position: NC_035789.1:21,195,880 INFO 2022-03-11 17:02:20 AddOrReplaceReadGroups Processed 96,000,000 records. Elapsed time: 00:05:06s. Time for last 1,000,000: 2s. Last read position: NC_035789.1:30,018,621 INFO 2022-03-11 17:02:26 AddOrReplaceReadGroups Processed 97,000,000 records. Elapsed time: 00:05:12s. Time for last 1,000,000: 6s. Last read position: */* INFO 2022-03-11 17:02:29 AddOrReplaceReadGroups Processed 98,000,000 records. Elapsed time: 00:05:15s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 17:02:31 AddOrReplaceReadGroups Processed 99,000,000 records. Elapsed time: 00:05:17s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 17:02:34 AddOrReplaceReadGroups Processed 100,000,000 records. Elapsed time: 00:05:20s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 17:02:37 AddOrReplaceReadGroups Processed 101,000,000 records. Elapsed time: 00:05:23s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 17:02:40 AddOrReplaceReadGroups Processed 102,000,000 records. Elapsed time: 00:05:26s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 17:02:42 AddOrReplaceReadGroups Processed 103,000,000 records. Elapsed time: 00:05:28s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 17:02:45 AddOrReplaceReadGroups Processed 104,000,000 records. Elapsed time: 00:05:31s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 17:02:48 AddOrReplaceReadGroups Processed 105,000,000 records. Elapsed time: 00:05:34s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 17:02:51 AddOrReplaceReadGroups Processed 106,000,000 records. Elapsed time: 00:05:37s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 17:02:53 AddOrReplaceReadGroups Processed 107,000,000 records. Elapsed time: 00:05:39s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 17:02:56 AddOrReplaceReadGroups Processed 108,000,000 records. Elapsed time: 00:05:42s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 17:03:03 AddOrReplaceReadGroups Processed 109,000,000 records. Elapsed time: 00:05:49s. Time for last 1,000,000: 7s. Last read position: */* INFO 2022-03-11 17:03:06 AddOrReplaceReadGroups Processed 110,000,000 records. Elapsed time: 00:05:52s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 17:03:09 AddOrReplaceReadGroups Processed 111,000,000 records. Elapsed time: 00:05:55s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 17:03:12 AddOrReplaceReadGroups Processed 112,000,000 records. Elapsed time: 00:05:58s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 17:03:14 AddOrReplaceReadGroups Processed 113,000,000 records. Elapsed time: 00:06:00s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 17:03:17 AddOrReplaceReadGroups Processed 114,000,000 records. Elapsed time: 00:06:03s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 17:03:20 AddOrReplaceReadGroups Processed 115,000,000 records. Elapsed time: 00:06:06s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 17:03:23 AddOrReplaceReadGroups Processed 116,000,000 records. Elapsed time: 00:06:09s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 17:03:25 AddOrReplaceReadGroups Processed 117,000,000 records. Elapsed time: 00:06:11s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 17:03:28 AddOrReplaceReadGroups Processed 118,000,000 records. Elapsed time: 00:06:14s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 17:03:31 AddOrReplaceReadGroups Processed 119,000,000 records. Elapsed time: 00:06:17s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 17:03:38 AddOrReplaceReadGroups Processed 120,000,000 records. Elapsed time: 00:06:24s. Time for last 1,000,000: 7s. Last read position: */* INFO 2022-03-11 17:03:41 AddOrReplaceReadGroups Processed 121,000,000 records. Elapsed time: 00:06:27s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 17:03:44 AddOrReplaceReadGroups Processed 122,000,000 records. Elapsed time: 00:06:30s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 17:03:47 AddOrReplaceReadGroups Processed 123,000,000 records. Elapsed time: 00:06:33s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 17:03:49 AddOrReplaceReadGroups Processed 124,000,000 records. Elapsed time: 00:06:35s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 17:03:52 AddOrReplaceReadGroups Processed 125,000,000 records. Elapsed time: 00:06:38s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 17:03:55 AddOrReplaceReadGroups Processed 126,000,000 records. Elapsed time: 00:06:41s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 17:03:58 AddOrReplaceReadGroups Processed 127,000,000 records. Elapsed time: 00:06:44s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 17:04:00 AddOrReplaceReadGroups Processed 128,000,000 records. Elapsed time: 00:06:47s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 17:04:03 AddOrReplaceReadGroups Processed 129,000,000 records. Elapsed time: 00:06:49s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 17:04:06 AddOrReplaceReadGroups Processed 130,000,000 records. Elapsed time: 00:06:52s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 17:04:10 AddOrReplaceReadGroups Processed 131,000,000 records. Elapsed time: 00:06:56s. Time for last 1,000,000: 3s. Last read position: */* INFO 2022-03-11 17:04:16 AddOrReplaceReadGroups Processed 132,000,000 records. Elapsed time: 00:07:02s. Time for last 1,000,000: 6s. Last read position: */* INFO 2022-03-11 17:04:19 AddOrReplaceReadGroups Processed 133,000,000 records. Elapsed time: 00:07:05s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 17:04:22 AddOrReplaceReadGroups Processed 134,000,000 records. Elapsed time: 00:07:08s. Time for last 1,000,000: 2s. Last read position: */* [Fri Mar 11 17:04:23 PST 2022] picard.sam.AddOrReplaceReadGroups done. Elapsed time: 7.17 minutes. Runtime.totalMemory()=2764046336 Tool returned: 0 Using GATK jar /home/shared/gatk-4.2.5.0/gatk-package-4.2.5.0-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 /home/shared/gatk-4.2.5.0/gatk-package-4.2.5.0-local.jar AddOrReplaceReadGroups I=S50F.dedup-split.bam O=S50F.dedup-split-RG.bam RGID=1 RGLB=S50F RGPL=ILLUMINA RGPU=unit1 RGSM=S50F INFO 2022-03-11 17:04:25 AddOrReplaceReadGroups ********** NOTE: Picard's command line syntax is changing. ********** ********** For more information, please see: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** ********** The command line looks like this in the new syntax: ********** ********** AddOrReplaceReadGroups -I S50F.dedup-split.bam -O S50F.dedup-split-RG.bam -RGID 1 -RGLB S50F -RGPL ILLUMINA -RGPU unit1 -RGSM S50F ********** 17:04:25.526 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/shared/gatk-4.2.5.0/gatk-package-4.2.5.0-local.jar!/com/intel/gkl/native/libgkl_compression.so [Fri Mar 11 17:04:25 PST 2022] AddOrReplaceReadGroups INPUT=S50F.dedup-split.bam OUTPUT=S50F.dedup-split-RG.bam RGID=1 RGLB=S50F RGPL=ILLUMINA RGPU=unit1 RGSM=S50F VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=2 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Mar 11, 2022 5:04:25 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine INFO: Failed to detect whether we are running on Google Compute Engine. [Fri Mar 11 17:04:25 PST 2022] Executing as sr320@raven on Linux 5.4.0-104-generic amd64; OpenJDK 64-Bit Server VM 11.0.14+9-Ubuntu-0ubuntu2.18.04; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: 4.2.5.0 INFO 2022-03-11 17:04:25 AddOrReplaceReadGroups Created read-group ID=1 PL=ILLUMINA LB=S50F SM=S50F INFO 2022-03-11 17:04:28 AddOrReplaceReadGroups Processed 1,000,000 records. Elapsed time: 00:00:03s. Time for last 1,000,000: 3s. Last read position: NC_035780.1:15,493,361 INFO 2022-03-11 17:04:32 AddOrReplaceReadGroups Processed 2,000,000 records. Elapsed time: 00:00:06s. Time for last 1,000,000: 3s. Last read position: NC_035780.1:32,743,681 INFO 2022-03-11 17:04:35 AddOrReplaceReadGroups Processed 3,000,000 records. Elapsed time: 00:00:09s. Time for last 1,000,000: 3s. Last read position: NC_035780.1:50,998,152 INFO 2022-03-11 17:04:38 AddOrReplaceReadGroups Processed 4,000,000 records. Elapsed time: 00:00:12s. Time for last 1,000,000: 3s. Last read position: NC_035780.1:61,421,838 INFO 2022-03-11 17:04:41 AddOrReplaceReadGroups Processed 5,000,000 records. Elapsed time: 00:00:15s. Time for last 1,000,000: 3s. Last read position: NC_035781.1:5,945,557 INFO 2022-03-11 17:04:44 AddOrReplaceReadGroups Processed 6,000,000 records. Elapsed time: 00:00:18s. Time for last 1,000,000: 3s. Last read position: NC_035781.1:15,491,235 INFO 2022-03-11 17:04:47 AddOrReplaceReadGroups Processed 7,000,000 records. Elapsed time: 00:00:21s. Time for last 1,000,000: 3s. Last read position: NC_035781.1:26,724,355 INFO 2022-03-11 17:04:50 AddOrReplaceReadGroups Processed 8,000,000 records. Elapsed time: 00:00:24s. Time for last 1,000,000: 3s. Last read position: NC_035781.1:39,266,717 INFO 2022-03-11 17:04:53 AddOrReplaceReadGroups Processed 9,000,000 records. Elapsed time: 00:00:27s. Time for last 1,000,000: 3s. Last read position: NC_035781.1:43,966,587 INFO 2022-03-11 17:04:56 AddOrReplaceReadGroups Processed 10,000,000 records. Elapsed time: 00:00:31s. Time for last 1,000,000: 3s. Last read position: NC_035781.1:53,426,019 INFO 2022-03-11 17:05:00 AddOrReplaceReadGroups Processed 11,000,000 records. Elapsed time: 00:00:34s. Time for last 1,000,000: 3s. Last read position: NC_035782.1:13,800,890 INFO 2022-03-11 17:05:06 AddOrReplaceReadGroups Processed 12,000,000 records. Elapsed time: 00:00:40s. Time for last 1,000,000: 6s. Last read position: NC_035782.1:26,909,611 INFO 2022-03-11 17:05:09 AddOrReplaceReadGroups Processed 13,000,000 records. Elapsed time: 00:00:43s. Time for last 1,000,000: 3s. Last read position: NC_035782.1:38,898,488 INFO 2022-03-11 17:05:12 AddOrReplaceReadGroups Processed 14,000,000 records. Elapsed time: 00:00:46s. Time for last 1,000,000: 3s. Last read position: NC_035782.1:51,587,891 INFO 2022-03-11 17:05:15 AddOrReplaceReadGroups Processed 15,000,000 records. Elapsed time: 00:00:49s. Time for last 1,000,000: 3s. Last read position: NC_035782.1:61,290,913 INFO 2022-03-11 17:05:18 AddOrReplaceReadGroups Processed 16,000,000 records. Elapsed time: 00:00:52s. Time for last 1,000,000: 3s. Last read position: NC_035782.1:72,048,300 INFO 2022-03-11 17:05:21 AddOrReplaceReadGroups Processed 17,000,000 records. Elapsed time: 00:00:55s. Time for last 1,000,000: 3s. Last read position: NC_035783.1:10,059,200 INFO 2022-03-11 17:05:24 AddOrReplaceReadGroups Processed 18,000,000 records. Elapsed time: 00:00:59s. Time for last 1,000,000: 3s. Last read position: NC_035783.1:21,727,766 INFO 2022-03-11 17:05:27 AddOrReplaceReadGroups Processed 19,000,000 records. Elapsed time: 00:01:02s. Time for last 1,000,000: 3s. Last read position: NC_035783.1:32,506,491 INFO 2022-03-11 17:05:30 AddOrReplaceReadGroups Processed 20,000,000 records. Elapsed time: 00:01:05s. Time for last 1,000,000: 3s. Last read position: NC_035783.1:40,343,064 INFO 2022-03-11 17:05:33 AddOrReplaceReadGroups Processed 21,000,000 records. Elapsed time: 00:01:08s. Time for last 1,000,000: 3s. Last read position: NC_035783.1:52,226,168 INFO 2022-03-11 17:05:40 AddOrReplaceReadGroups Processed 22,000,000 records. Elapsed time: 00:01:14s. Time for last 1,000,000: 6s. Last read position: NC_035784.1:7,563,984 INFO 2022-03-11 17:05:43 AddOrReplaceReadGroups Processed 23,000,000 records. Elapsed time: 00:01:17s. Time for last 1,000,000: 3s. Last read position: NC_035784.1:18,067,612 INFO 2022-03-11 17:05:46 AddOrReplaceReadGroups Processed 24,000,000 records. Elapsed time: 00:01:20s. Time for last 1,000,000: 3s. Last read position: NC_035784.1:31,577,513 INFO 2022-03-11 17:05:49 AddOrReplaceReadGroups Processed 25,000,000 records. Elapsed time: 00:01:23s. Time for last 1,000,000: 3s. Last read position: NC_035784.1:41,983,841 INFO 2022-03-11 17:05:52 AddOrReplaceReadGroups Processed 26,000,000 records. Elapsed time: 00:01:26s. Time for last 1,000,000: 2s. Last read position: NC_035784.1:47,913,655 INFO 2022-03-11 17:05:55 AddOrReplaceReadGroups Processed 27,000,000 records. Elapsed time: 00:01:29s. Time for last 1,000,000: 2s. Last read position: NC_035784.1:52,198,100 INFO 2022-03-11 17:05:57 AddOrReplaceReadGroups Processed 28,000,000 records. Elapsed time: 00:01:32s. Time for last 1,000,000: 2s. Last read position: NC_035784.1:52,259,557 INFO 2022-03-11 17:06:00 AddOrReplaceReadGroups Processed 29,000,000 records. Elapsed time: 00:01:34s. Time for last 1,000,000: 2s. Last read position: NC_035784.1:52,781,607 INFO 2022-03-11 17:06:03 AddOrReplaceReadGroups Processed 30,000,000 records. Elapsed time: 00:01:37s. Time for last 1,000,000: 3s. Last read position: NC_035784.1:65,726,517 INFO 2022-03-11 17:06:06 AddOrReplaceReadGroups Processed 31,000,000 records. Elapsed time: 00:01:40s. Time for last 1,000,000: 3s. Last read position: NC_035784.1:79,540,755 INFO 2022-03-11 17:06:09 AddOrReplaceReadGroups Processed 32,000,000 records. Elapsed time: 00:01:43s. Time for last 1,000,000: 3s. Last read position: NC_035785.1:10,012,069 INFO 2022-03-11 17:06:15 AddOrReplaceReadGroups Processed 33,000,000 records. Elapsed time: 00:01:49s. Time for last 1,000,000: 6s. Last read position: NC_035785.1:36,876,973 INFO 2022-03-11 17:06:18 AddOrReplaceReadGroups Processed 34,000,000 records. Elapsed time: 00:01:53s. Time for last 1,000,000: 3s. Last read position: NC_035786.1:14,236,694 INFO 2022-03-11 17:06:21 AddOrReplaceReadGroups Processed 35,000,000 records. Elapsed time: 00:01:56s. Time for last 1,000,000: 3s. Last read position: NC_035786.1:46,688,362 INFO 2022-03-11 17:06:25 AddOrReplaceReadGroups Processed 36,000,000 records. Elapsed time: 00:01:59s. Time for last 1,000,000: 3s. Last read position: NC_035787.1:16,028,085 INFO 2022-03-11 17:06:28 AddOrReplaceReadGroups Processed 37,000,000 records. Elapsed time: 00:02:02s. Time for last 1,000,000: 3s. Last read position: NC_035787.1:53,360,299 INFO 2022-03-11 17:06:31 AddOrReplaceReadGroups Processed 38,000,000 records. Elapsed time: 00:02:05s. Time for last 1,000,000: 3s. Last read position: NC_035787.1:72,446,739 INFO 2022-03-11 17:06:34 AddOrReplaceReadGroups Processed 39,000,000 records. Elapsed time: 00:02:08s. Time for last 1,000,000: 3s. Last read position: NC_035788.1:41,418,068 INFO 2022-03-11 17:06:37 AddOrReplaceReadGroups Processed 40,000,000 records. Elapsed time: 00:02:11s. Time for last 1,000,000: 3s. Last read position: NC_035788.1:71,754,353 INFO 2022-03-11 17:06:40 AddOrReplaceReadGroups Processed 41,000,000 records. Elapsed time: 00:02:14s. Time for last 1,000,000: 3s. Last read position: NC_035789.1:4,917,405 INFO 2022-03-11 17:06:43 AddOrReplaceReadGroups Processed 42,000,000 records. Elapsed time: 00:02:17s. Time for last 1,000,000: 3s. Last read position: NC_035789.1:31,595,962 INFO 2022-03-11 17:06:49 AddOrReplaceReadGroups Processed 43,000,000 records. Elapsed time: 00:02:24s. Time for last 1,000,000: 6s. Last read position: */* INFO 2022-03-11 17:06:52 AddOrReplaceReadGroups Processed 44,000,000 records. Elapsed time: 00:02:26s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 17:06:55 AddOrReplaceReadGroups Processed 45,000,000 records. Elapsed time: 00:02:29s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 17:06:58 AddOrReplaceReadGroups Processed 46,000,000 records. Elapsed time: 00:02:32s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 17:07:01 AddOrReplaceReadGroups Processed 47,000,000 records. Elapsed time: 00:02:35s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 17:07:04 AddOrReplaceReadGroups Processed 48,000,000 records. Elapsed time: 00:02:38s. Time for last 1,000,000: 2s. Last read position: */* [Fri Mar 11 17:07:06 PST 2022] picard.sam.AddOrReplaceReadGroups done. Elapsed time: 2.68 minutes. Runtime.totalMemory()=2772434944 Tool returned: 0 Using GATK jar /home/shared/gatk-4.2.5.0/gatk-package-4.2.5.0-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 /home/shared/gatk-4.2.5.0/gatk-package-4.2.5.0-local.jar AddOrReplaceReadGroups I=S52F.dedup-split.bam O=S52F.dedup-split-RG.bam RGID=1 RGLB=S52F RGPL=ILLUMINA RGPU=unit1 RGSM=S52F INFO 2022-03-11 17:07:08 AddOrReplaceReadGroups ********** NOTE: Picard's command line syntax is changing. ********** ********** For more information, please see: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** ********** The command line looks like this in the new syntax: ********** ********** AddOrReplaceReadGroups -I S52F.dedup-split.bam -O S52F.dedup-split-RG.bam -RGID 1 -RGLB S52F -RGPL ILLUMINA -RGPU unit1 -RGSM S52F ********** 17:07:08.135 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/shared/gatk-4.2.5.0/gatk-package-4.2.5.0-local.jar!/com/intel/gkl/native/libgkl_compression.so [Fri Mar 11 17:07:08 PST 2022] AddOrReplaceReadGroups INPUT=S52F.dedup-split.bam OUTPUT=S52F.dedup-split-RG.bam RGID=1 RGLB=S52F RGPL=ILLUMINA RGPU=unit1 RGSM=S52F VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=2 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Mar 11, 2022 5:07:08 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine INFO: Failed to detect whether we are running on Google Compute Engine. [Fri Mar 11 17:07:08 PST 2022] Executing as sr320@raven on Linux 5.4.0-104-generic amd64; OpenJDK 64-Bit Server VM 11.0.14+9-Ubuntu-0ubuntu2.18.04; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: 4.2.5.0 INFO 2022-03-11 17:07:08 AddOrReplaceReadGroups Created read-group ID=1 PL=ILLUMINA LB=S52F SM=S52F INFO 2022-03-11 17:07:11 AddOrReplaceReadGroups Processed 1,000,000 records. Elapsed time: 00:00:03s. Time for last 1,000,000: 3s. Last read position: NC_035780.1:13,109,970 INFO 2022-03-11 17:07:14 AddOrReplaceReadGroups Processed 2,000,000 records. Elapsed time: 00:00:06s. Time for last 1,000,000: 2s. Last read position: NC_035780.1:25,824,527 INFO 2022-03-11 17:07:17 AddOrReplaceReadGroups Processed 3,000,000 records. Elapsed time: 00:00:09s. Time for last 1,000,000: 2s. Last read position: NC_035780.1:39,289,234 INFO 2022-03-11 17:07:20 AddOrReplaceReadGroups Processed 4,000,000 records. Elapsed time: 00:00:12s. Time for last 1,000,000: 3s. Last read position: NC_035780.1:54,831,872 INFO 2022-03-11 17:07:23 AddOrReplaceReadGroups Processed 5,000,000 records. Elapsed time: 00:00:15s. Time for last 1,000,000: 3s. Last read position: NC_035780.1:64,150,172 INFO 2022-03-11 17:07:26 AddOrReplaceReadGroups Processed 6,000,000 records. Elapsed time: 00:00:18s. Time for last 1,000,000: 3s. Last read position: NC_035781.1:7,578,589 INFO 2022-03-11 17:07:29 AddOrReplaceReadGroups Processed 7,000,000 records. Elapsed time: 00:00:21s. Time for last 1,000,000: 2s. Last read position: NC_035781.1:14,816,160 INFO 2022-03-11 17:07:32 AddOrReplaceReadGroups Processed 8,000,000 records. Elapsed time: 00:00:24s. Time for last 1,000,000: 3s. Last read position: NC_035781.1:23,693,513 INFO 2022-03-11 17:07:36 AddOrReplaceReadGroups Processed 9,000,000 records. Elapsed time: 00:00:27s. Time for last 1,000,000: 3s. Last read position: NC_035781.1:34,641,248 INFO 2022-03-11 17:07:39 AddOrReplaceReadGroups Processed 10,000,000 records. Elapsed time: 00:00:30s. Time for last 1,000,000: 2s. Last read position: NC_035781.1:46,110,321 INFO 2022-03-11 17:07:45 AddOrReplaceReadGroups Processed 11,000,000 records. Elapsed time: 00:00:37s. Time for last 1,000,000: 6s. Last read position: NC_035781.1:55,896,090 INFO 2022-03-11 17:07:48 AddOrReplaceReadGroups Processed 12,000,000 records. Elapsed time: 00:00:40s. Time for last 1,000,000: 3s. Last read position: NC_035782.1:14,692,555 INFO 2022-03-11 17:07:51 AddOrReplaceReadGroups Processed 13,000,000 records. Elapsed time: 00:00:43s. Time for last 1,000,000: 2s. Last read position: NC_035782.1:25,216,494 INFO 2022-03-11 17:07:54 AddOrReplaceReadGroups Processed 14,000,000 records. Elapsed time: 00:00:46s. Time for last 1,000,000: 3s. Last read position: NC_035782.1:36,169,154 INFO 2022-03-11 17:07:57 AddOrReplaceReadGroups Processed 15,000,000 records. Elapsed time: 00:00:49s. Time for last 1,000,000: 3s. Last read position: NC_035782.1:47,499,477 INFO 2022-03-11 17:08:00 AddOrReplaceReadGroups Processed 16,000,000 records. Elapsed time: 00:00:52s. Time for last 1,000,000: 3s. Last read position: NC_035782.1:56,782,837 INFO 2022-03-11 17:08:03 AddOrReplaceReadGroups Processed 17,000,000 records. Elapsed time: 00:00:55s. Time for last 1,000,000: 3s. Last read position: NC_035782.1:65,825,438 INFO 2022-03-11 17:08:06 AddOrReplaceReadGroups Processed 18,000,000 records. Elapsed time: 00:00:58s. Time for last 1,000,000: 3s. Last read position: NC_035783.1:2,331,098 INFO 2022-03-11 17:08:09 AddOrReplaceReadGroups Processed 19,000,000 records. Elapsed time: 00:01:01s. Time for last 1,000,000: 3s. Last read position: NC_035783.1:13,923,883 INFO 2022-03-11 17:08:12 AddOrReplaceReadGroups Processed 20,000,000 records. Elapsed time: 00:01:04s. Time for last 1,000,000: 3s. Last read position: NC_035783.1:25,320,504 INFO 2022-03-11 17:08:15 AddOrReplaceReadGroups Processed 21,000,000 records. Elapsed time: 00:01:07s. Time for last 1,000,000: 2s. Last read position: NC_035783.1:34,448,342 INFO 2022-03-11 17:08:21 AddOrReplaceReadGroups Processed 22,000,000 records. Elapsed time: 00:01:13s. Time for last 1,000,000: 6s. Last read position: NC_035783.1:43,666,157 INFO 2022-03-11 17:08:24 AddOrReplaceReadGroups Processed 23,000,000 records. Elapsed time: 00:01:16s. Time for last 1,000,000: 3s. Last read position: NC_035783.1:57,242,584 INFO 2022-03-11 17:08:27 AddOrReplaceReadGroups Processed 24,000,000 records. Elapsed time: 00:01:19s. Time for last 1,000,000: 3s. Last read position: NC_035784.1:9,397,583 INFO 2022-03-11 17:08:30 AddOrReplaceReadGroups Processed 25,000,000 records. Elapsed time: 00:01:22s. Time for last 1,000,000: 3s. Last read position: NC_035784.1:21,333,227 INFO 2022-03-11 17:08:34 AddOrReplaceReadGroups Processed 26,000,000 records. Elapsed time: 00:01:25s. Time for last 1,000,000: 3s. Last read position: NC_035784.1:33,735,571 INFO 2022-03-11 17:08:37 AddOrReplaceReadGroups Processed 27,000,000 records. Elapsed time: 00:01:28s. Time for last 1,000,000: 3s. Last read position: NC_035784.1:45,263,236 INFO 2022-03-11 17:08:39 AddOrReplaceReadGroups Processed 28,000,000 records. Elapsed time: 00:01:31s. Time for last 1,000,000: 2s. Last read position: NC_035784.1:52,200,755 INFO 2022-03-11 17:08:42 AddOrReplaceReadGroups Processed 29,000,000 records. Elapsed time: 00:01:34s. Time for last 1,000,000: 2s. Last read position: NC_035784.1:52,277,400 INFO 2022-03-11 17:08:45 AddOrReplaceReadGroups Processed 30,000,000 records. Elapsed time: 00:01:36s. Time for last 1,000,000: 2s. Last read position: NC_035784.1:62,034,714 INFO 2022-03-11 17:08:48 AddOrReplaceReadGroups Processed 31,000,000 records. Elapsed time: 00:01:40s. Time for last 1,000,000: 3s. Last read position: NC_035784.1:72,837,088 INFO 2022-03-11 17:08:54 AddOrReplaceReadGroups Processed 32,000,000 records. Elapsed time: 00:01:45s. Time for last 1,000,000: 5s. Last read position: NC_035784.1:81,587,307 INFO 2022-03-11 17:08:57 AddOrReplaceReadGroups Processed 33,000,000 records. Elapsed time: 00:01:49s. Time for last 1,000,000: 3s. Last read position: NC_035785.1:4,019,679 INFO 2022-03-11 17:09:00 AddOrReplaceReadGroups Processed 34,000,000 records. Elapsed time: 00:01:52s. Time for last 1,000,000: 3s. Last read position: NC_035785.1:31,670,007 INFO 2022-03-11 17:09:03 AddOrReplaceReadGroups Processed 35,000,000 records. Elapsed time: 00:01:55s. Time for last 1,000,000: 3s. Last read position: NC_035785.1:43,903,079 INFO 2022-03-11 17:09:06 AddOrReplaceReadGroups Processed 36,000,000 records. Elapsed time: 00:01:58s. Time for last 1,000,000: 3s. Last read position: NC_035786.1:16,982,462 INFO 2022-03-11 17:09:09 AddOrReplaceReadGroups Processed 37,000,000 records. Elapsed time: 00:02:01s. Time for last 1,000,000: 3s. Last read position: NC_035786.1:41,905,805 INFO 2022-03-11 17:09:12 AddOrReplaceReadGroups Processed 38,000,000 records. Elapsed time: 00:02:04s. Time for last 1,000,000: 3s. Last read position: NC_035787.1:1,325,206 INFO 2022-03-11 17:09:16 AddOrReplaceReadGroups Processed 39,000,000 records. Elapsed time: 00:02:07s. Time for last 1,000,000: 3s. Last read position: NC_035787.1:24,983,416 INFO 2022-03-11 17:09:19 AddOrReplaceReadGroups Processed 40,000,000 records. Elapsed time: 00:02:10s. Time for last 1,000,000: 3s. Last read position: NC_035787.1:50,868,817 INFO 2022-03-11 17:09:22 AddOrReplaceReadGroups Processed 41,000,000 records. Elapsed time: 00:02:13s. Time for last 1,000,000: 3s. Last read position: NC_035787.1:63,746,512 INFO 2022-03-11 17:09:25 AddOrReplaceReadGroups Processed 42,000,000 records. Elapsed time: 00:02:16s. Time for last 1,000,000: 3s. Last read position: NC_035788.1:13,850,466 INFO 2022-03-11 17:09:31 AddOrReplaceReadGroups Processed 43,000,000 records. Elapsed time: 00:02:23s. Time for last 1,000,000: 6s. Last read position: NC_035788.1:48,743,814 INFO 2022-03-11 17:09:34 AddOrReplaceReadGroups Processed 44,000,000 records. Elapsed time: 00:02:26s. Time for last 1,000,000: 3s. Last read position: NC_035788.1:65,874,760 INFO 2022-03-11 17:09:37 AddOrReplaceReadGroups Processed 45,000,000 records. Elapsed time: 00:02:29s. Time for last 1,000,000: 3s. Last read position: NC_035788.1:85,395,304 INFO 2022-03-11 17:09:41 AddOrReplaceReadGroups Processed 46,000,000 records. Elapsed time: 00:02:32s. Time for last 1,000,000: 3s. Last read position: NC_035789.1:10,689,065 INFO 2022-03-11 17:09:44 AddOrReplaceReadGroups Processed 47,000,000 records. Elapsed time: 00:02:35s. Time for last 1,000,000: 3s. Last read position: NC_007175.2:5,368 INFO 2022-03-11 17:09:46 AddOrReplaceReadGroups Processed 48,000,000 records. Elapsed time: 00:02:38s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 17:09:49 AddOrReplaceReadGroups Processed 49,000,000 records. Elapsed time: 00:02:41s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 17:09:52 AddOrReplaceReadGroups Processed 50,000,000 records. Elapsed time: 00:02:44s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 17:09:55 AddOrReplaceReadGroups Processed 51,000,000 records. Elapsed time: 00:02:47s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 17:09:58 AddOrReplaceReadGroups Processed 52,000,000 records. Elapsed time: 00:02:50s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 17:10:05 AddOrReplaceReadGroups Processed 53,000,000 records. Elapsed time: 00:02:57s. Time for last 1,000,000: 7s. Last read position: */* INFO 2022-03-11 17:10:08 AddOrReplaceReadGroups Processed 54,000,000 records. Elapsed time: 00:03:00s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 17:10:11 AddOrReplaceReadGroups Processed 55,000,000 records. Elapsed time: 00:03:03s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 17:10:14 AddOrReplaceReadGroups Processed 56,000,000 records. Elapsed time: 00:03:06s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 17:10:17 AddOrReplaceReadGroups Processed 57,000,000 records. Elapsed time: 00:03:09s. Time for last 1,000,000: 2s. Last read position: */* [Fri Mar 11 17:10:21 PST 2022] picard.sam.AddOrReplaceReadGroups done. Elapsed time: 3.23 minutes. Runtime.totalMemory()=2919235584 Tool returned: 0 Using GATK jar /home/shared/gatk-4.2.5.0/gatk-package-4.2.5.0-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 /home/shared/gatk-4.2.5.0/gatk-package-4.2.5.0-local.jar AddOrReplaceReadGroups I=S53F.dedup-split.bam O=S53F.dedup-split-RG.bam RGID=1 RGLB=S53F RGPL=ILLUMINA RGPU=unit1 RGSM=S53F INFO 2022-03-11 17:10:23 AddOrReplaceReadGroups ********** NOTE: Picard's command line syntax is changing. ********** ********** For more information, please see: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** ********** The command line looks like this in the new syntax: ********** ********** AddOrReplaceReadGroups -I S53F.dedup-split.bam -O S53F.dedup-split-RG.bam -RGID 1 -RGLB S53F -RGPL ILLUMINA -RGPU unit1 -RGSM S53F ********** 17:10:23.589 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/shared/gatk-4.2.5.0/gatk-package-4.2.5.0-local.jar!/com/intel/gkl/native/libgkl_compression.so [Fri Mar 11 17:10:23 PST 2022] AddOrReplaceReadGroups INPUT=S53F.dedup-split.bam OUTPUT=S53F.dedup-split-RG.bam RGID=1 RGLB=S53F RGPL=ILLUMINA RGPU=unit1 RGSM=S53F VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=2 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Mar 11, 2022 5:10:23 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine INFO: Failed to detect whether we are running on Google Compute Engine. [Fri Mar 11 17:10:23 PST 2022] Executing as sr320@raven on Linux 5.4.0-104-generic amd64; OpenJDK 64-Bit Server VM 11.0.14+9-Ubuntu-0ubuntu2.18.04; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: 4.2.5.0 INFO 2022-03-11 17:10:23 AddOrReplaceReadGroups Created read-group ID=1 PL=ILLUMINA LB=S53F SM=S53F INFO 2022-03-11 17:10:26 AddOrReplaceReadGroups Processed 1,000,000 records. Elapsed time: 00:00:03s. Time for last 1,000,000: 3s. Last read position: NC_035780.1:13,581,171 INFO 2022-03-11 17:10:29 AddOrReplaceReadGroups Processed 2,000,000 records. Elapsed time: 00:00:06s. Time for last 1,000,000: 3s. Last read position: NC_035780.1:29,885,957 INFO 2022-03-11 17:10:32 AddOrReplaceReadGroups Processed 3,000,000 records. Elapsed time: 00:00:09s. Time for last 1,000,000: 3s. Last read position: NC_035780.1:45,451,316 INFO 2022-03-11 17:10:35 AddOrReplaceReadGroups Processed 4,000,000 records. Elapsed time: 00:00:12s. Time for last 1,000,000: 3s. Last read position: NC_035780.1:57,916,234 INFO 2022-03-11 17:10:39 AddOrReplaceReadGroups Processed 5,000,000 records. Elapsed time: 00:00:15s. Time for last 1,000,000: 3s. Last read position: NC_035781.1:3,060,417 INFO 2022-03-11 17:10:42 AddOrReplaceReadGroups Processed 6,000,000 records. Elapsed time: 00:00:18s. Time for last 1,000,000: 2s. Last read position: NC_035781.1:10,992,044 INFO 2022-03-11 17:10:44 AddOrReplaceReadGroups Processed 7,000,000 records. Elapsed time: 00:00:21s. Time for last 1,000,000: 2s. Last read position: NC_035781.1:19,155,069 INFO 2022-03-11 17:10:47 AddOrReplaceReadGroups Processed 8,000,000 records. Elapsed time: 00:00:24s. Time for last 1,000,000: 3s. Last read position: NC_035781.1:29,995,317 INFO 2022-03-11 17:10:51 AddOrReplaceReadGroups Processed 9,000,000 records. Elapsed time: 00:00:27s. Time for last 1,000,000: 3s. Last read position: NC_035781.1:40,272,078 INFO 2022-03-11 17:10:53 AddOrReplaceReadGroups Processed 10,000,000 records. Elapsed time: 00:00:30s. Time for last 1,000,000: 2s. Last read position: NC_035781.1:43,065,536 INFO 2022-03-11 17:10:58 AddOrReplaceReadGroups Processed 11,000,000 records. Elapsed time: 00:00:35s. Time for last 1,000,000: 4s. Last read position: NC_035781.1:52,319,910 INFO 2022-03-11 17:11:03 AddOrReplaceReadGroups Processed 12,000,000 records. Elapsed time: 00:00:39s. Time for last 1,000,000: 4s. Last read position: NC_035782.1:8,149,045 INFO 2022-03-11 17:11:06 AddOrReplaceReadGroups Processed 13,000,000 records. Elapsed time: 00:00:42s. Time for last 1,000,000: 2s. Last read position: NC_035782.1:21,015,360 INFO 2022-03-11 17:11:09 AddOrReplaceReadGroups Processed 14,000,000 records. Elapsed time: 00:00:45s. Time for last 1,000,000: 2s. Last read position: NC_035782.1:30,541,603 INFO 2022-03-11 17:11:12 AddOrReplaceReadGroups Processed 15,000,000 records. Elapsed time: 00:00:48s. Time for last 1,000,000: 3s. Last read position: NC_035782.1:42,824,270 INFO 2022-03-11 17:11:15 AddOrReplaceReadGroups Processed 16,000,000 records. Elapsed time: 00:00:51s. Time for last 1,000,000: 3s. Last read position: NC_035782.1:53,781,740 INFO 2022-03-11 17:11:18 AddOrReplaceReadGroups Processed 17,000,000 records. Elapsed time: 00:00:54s. Time for last 1,000,000: 3s. Last read position: NC_035782.1:61,963,702 INFO 2022-03-11 17:11:21 AddOrReplaceReadGroups Processed 18,000,000 records. Elapsed time: 00:00:57s. Time for last 1,000,000: 3s. Last read position: NC_035782.1:72,355,060 INFO 2022-03-11 17:11:24 AddOrReplaceReadGroups Processed 19,000,000 records. Elapsed time: 00:01:00s. Time for last 1,000,000: 3s. Last read position: NC_035783.1:9,220,259 INFO 2022-03-11 17:11:27 AddOrReplaceReadGroups Processed 20,000,000 records. Elapsed time: 00:01:03s. Time for last 1,000,000: 3s. Last read position: NC_035783.1:20,069,131 INFO 2022-03-11 17:11:30 AddOrReplaceReadGroups Processed 21,000,000 records. Elapsed time: 00:01:06s. Time for last 1,000,000: 2s. Last read position: NC_035783.1:30,669,116 INFO 2022-03-11 17:11:36 AddOrReplaceReadGroups Processed 22,000,000 records. Elapsed time: 00:01:12s. Time for last 1,000,000: 6s. Last read position: NC_035783.1:35,651,632 INFO 2022-03-11 17:11:39 AddOrReplaceReadGroups Processed 23,000,000 records. Elapsed time: 00:01:15s. Time for last 1,000,000: 2s. Last read position: NC_035783.1:44,514,254 INFO 2022-03-11 17:11:42 AddOrReplaceReadGroups Processed 24,000,000 records. Elapsed time: 00:01:19s. Time for last 1,000,000: 3s. Last read position: NC_035783.1:59,245,854 INFO 2022-03-11 17:11:45 AddOrReplaceReadGroups Processed 25,000,000 records. Elapsed time: 00:01:22s. Time for last 1,000,000: 3s. Last read position: NC_035784.1:9,400,491 INFO 2022-03-11 17:11:48 AddOrReplaceReadGroups Processed 26,000,000 records. Elapsed time: 00:01:25s. Time for last 1,000,000: 3s. Last read position: NC_035784.1:20,135,258 INFO 2022-03-11 17:11:51 AddOrReplaceReadGroups Processed 27,000,000 records. Elapsed time: 00:01:28s. Time for last 1,000,000: 3s. Last read position: NC_035784.1:32,259,745 INFO 2022-03-11 17:11:54 AddOrReplaceReadGroups Processed 28,000,000 records. Elapsed time: 00:01:31s. Time for last 1,000,000: 3s. Last read position: NC_035784.1:42,049,158 INFO 2022-03-11 17:11:57 AddOrReplaceReadGroups Processed 29,000,000 records. Elapsed time: 00:01:34s. Time for last 1,000,000: 2s. Last read position: NC_035784.1:48,534,854 INFO 2022-03-11 17:12:00 AddOrReplaceReadGroups Processed 30,000,000 records. Elapsed time: 00:01:36s. Time for last 1,000,000: 2s. Last read position: NC_035784.1:52,197,910 INFO 2022-03-11 17:12:03 AddOrReplaceReadGroups Processed 31,000,000 records. Elapsed time: 00:01:39s. Time for last 1,000,000: 2s. Last read position: NC_035784.1:52,258,950 INFO 2022-03-11 17:12:05 AddOrReplaceReadGroups Processed 32,000,000 records. Elapsed time: 00:01:41s. Time for last 1,000,000: 2s. Last read position: NC_035784.1:52,289,249 INFO 2022-03-11 17:12:11 AddOrReplaceReadGroups Processed 33,000,000 records. Elapsed time: 00:01:47s. Time for last 1,000,000: 6s. Last read position: NC_035784.1:64,630,683 INFO 2022-03-11 17:12:14 AddOrReplaceReadGroups Processed 34,000,000 records. Elapsed time: 00:01:50s. Time for last 1,000,000: 3s. Last read position: NC_035784.1:76,643,096 INFO 2022-03-11 17:12:17 AddOrReplaceReadGroups Processed 35,000,000 records. Elapsed time: 00:01:53s. Time for last 1,000,000: 3s. Last read position: NC_035784.1:96,350,719 INFO 2022-03-11 17:12:20 AddOrReplaceReadGroups Processed 36,000,000 records. Elapsed time: 00:01:57s. Time for last 1,000,000: 3s. Last read position: NC_035785.1:32,899,691 INFO 2022-03-11 17:12:23 AddOrReplaceReadGroups Processed 37,000,000 records. Elapsed time: 00:02:00s. Time for last 1,000,000: 3s. Last read position: NC_035786.1:850,499 INFO 2022-03-11 17:12:27 AddOrReplaceReadGroups Processed 38,000,000 records. Elapsed time: 00:02:03s. Time for last 1,000,000: 3s. Last read position: NC_035786.1:30,097,171 INFO 2022-03-11 17:12:30 AddOrReplaceReadGroups Processed 39,000,000 records. Elapsed time: 00:02:06s. Time for last 1,000,000: 3s. Last read position: NC_035786.1:54,842,216 INFO 2022-03-11 17:12:33 AddOrReplaceReadGroups Processed 40,000,000 records. Elapsed time: 00:02:09s. Time for last 1,000,000: 3s. Last read position: NC_035787.1:25,764,971 INFO 2022-03-11 17:12:36 AddOrReplaceReadGroups Processed 41,000,000 records. Elapsed time: 00:02:12s. Time for last 1,000,000: 3s. Last read position: NC_035787.1:55,423,087 INFO 2022-03-11 17:12:39 AddOrReplaceReadGroups Processed 42,000,000 records. Elapsed time: 00:02:15s. Time for last 1,000,000: 3s. Last read position: NC_035787.1:73,505,990 INFO 2022-03-11 17:12:45 AddOrReplaceReadGroups Processed 43,000,000 records. Elapsed time: 00:02:21s. Time for last 1,000,000: 6s. Last read position: NC_035788.1:40,543,007 INFO 2022-03-11 17:12:48 AddOrReplaceReadGroups Processed 44,000,000 records. Elapsed time: 00:02:24s. Time for last 1,000,000: 3s. Last read position: NC_035788.1:70,600,799 INFO 2022-03-11 17:12:51 AddOrReplaceReadGroups Processed 45,000,000 records. Elapsed time: 00:02:27s. Time for last 1,000,000: 3s. Last read position: NC_035788.1:100,356,880 INFO 2022-03-11 17:12:54 AddOrReplaceReadGroups Processed 46,000,000 records. Elapsed time: 00:02:31s. Time for last 1,000,000: 3s. Last read position: NC_035789.1:20,609,247 INFO 2022-03-11 17:12:57 AddOrReplaceReadGroups Processed 47,000,000 records. Elapsed time: 00:02:34s. Time for last 1,000,000: 2s. Last read position: NC_007175.2:8,763 INFO 2022-03-11 17:13:00 AddOrReplaceReadGroups Processed 48,000,000 records. Elapsed time: 00:02:36s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 17:13:03 AddOrReplaceReadGroups Processed 49,000,000 records. Elapsed time: 00:02:39s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 17:13:06 AddOrReplaceReadGroups Processed 50,000,000 records. Elapsed time: 00:02:42s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 17:13:09 AddOrReplaceReadGroups Processed 51,000,000 records. Elapsed time: 00:02:45s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 17:13:12 AddOrReplaceReadGroups Processed 52,000,000 records. Elapsed time: 00:02:48s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 17:13:14 AddOrReplaceReadGroups Processed 53,000,000 records. Elapsed time: 00:02:51s. Time for last 1,000,000: 2s. Last read position: */* [Fri Mar 11 17:13:21 PST 2022] picard.sam.AddOrReplaceReadGroups done. Elapsed time: 2.96 minutes. Runtime.totalMemory()=2709520384 Tool returned: 0 Using GATK jar /home/shared/gatk-4.2.5.0/gatk-package-4.2.5.0-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 /home/shared/gatk-4.2.5.0/gatk-package-4.2.5.0-local.jar AddOrReplaceReadGroups I=S54F.dedup-split.bam O=S54F.dedup-split-RG.bam RGID=1 RGLB=S54F RGPL=ILLUMINA RGPU=unit1 RGSM=S54F INFO 2022-03-11 17:13:22 AddOrReplaceReadGroups ********** NOTE: Picard's command line syntax is changing. ********** ********** For more information, please see: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** ********** The command line looks like this in the new syntax: ********** ********** AddOrReplaceReadGroups -I S54F.dedup-split.bam -O S54F.dedup-split-RG.bam -RGID 1 -RGLB S54F -RGPL ILLUMINA -RGPU unit1 -RGSM S54F ********** 17:13:22.723 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/shared/gatk-4.2.5.0/gatk-package-4.2.5.0-local.jar!/com/intel/gkl/native/libgkl_compression.so [Fri Mar 11 17:13:22 PST 2022] AddOrReplaceReadGroups INPUT=S54F.dedup-split.bam OUTPUT=S54F.dedup-split-RG.bam RGID=1 RGLB=S54F RGPL=ILLUMINA RGPU=unit1 RGSM=S54F VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=2 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Mar 11, 2022 5:13:22 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine INFO: Failed to detect whether we are running on Google Compute Engine. [Fri Mar 11 17:13:22 PST 2022] Executing as sr320@raven on Linux 5.4.0-104-generic amd64; OpenJDK 64-Bit Server VM 11.0.14+9-Ubuntu-0ubuntu2.18.04; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: 4.2.5.0 INFO 2022-03-11 17:13:22 AddOrReplaceReadGroups Created read-group ID=1 PL=ILLUMINA LB=S54F SM=S54F INFO 2022-03-11 17:13:26 AddOrReplaceReadGroups Processed 1,000,000 records. Elapsed time: 00:00:03s. Time for last 1,000,000: 3s. Last read position: NC_035780.1:15,443,903 INFO 2022-03-11 17:13:29 AddOrReplaceReadGroups Processed 2,000,000 records. Elapsed time: 00:00:06s. Time for last 1,000,000: 3s. Last read position: NC_035780.1:30,519,447 INFO 2022-03-11 17:13:32 AddOrReplaceReadGroups Processed 3,000,000 records. Elapsed time: 00:00:09s. Time for last 1,000,000: 3s. Last read position: NC_035780.1:45,292,190 INFO 2022-03-11 17:13:35 AddOrReplaceReadGroups Processed 4,000,000 records. Elapsed time: 00:00:12s. Time for last 1,000,000: 3s. Last read position: NC_035780.1:57,635,776 INFO 2022-03-11 17:13:38 AddOrReplaceReadGroups Processed 5,000,000 records. Elapsed time: 00:00:15s. Time for last 1,000,000: 3s. Last read position: NC_035781.1:2,828,521 INFO 2022-03-11 17:13:41 AddOrReplaceReadGroups Processed 6,000,000 records. Elapsed time: 00:00:18s. Time for last 1,000,000: 3s. Last read position: NC_035781.1:10,992,151 INFO 2022-03-11 17:13:44 AddOrReplaceReadGroups Processed 7,000,000 records. Elapsed time: 00:00:21s. Time for last 1,000,000: 3s. Last read position: NC_035781.1:19,969,967 INFO 2022-03-11 17:13:47 AddOrReplaceReadGroups Processed 8,000,000 records. Elapsed time: 00:00:24s. Time for last 1,000,000: 3s. Last read position: NC_035781.1:30,209,298 INFO 2022-03-11 17:13:50 AddOrReplaceReadGroups Processed 9,000,000 records. Elapsed time: 00:00:28s. Time for last 1,000,000: 3s. Last read position: NC_035781.1:40,741,922 INFO 2022-03-11 17:13:54 AddOrReplaceReadGroups Processed 10,000,000 records. Elapsed time: 00:00:31s. Time for last 1,000,000: 3s. Last read position: NC_035781.1:49,477,354 INFO 2022-03-11 17:14:00 AddOrReplaceReadGroups Processed 11,000,000 records. Elapsed time: 00:00:37s. Time for last 1,000,000: 6s. Last read position: NC_035782.1:778,228 INFO 2022-03-11 17:14:03 AddOrReplaceReadGroups Processed 12,000,000 records. Elapsed time: 00:00:40s. Time for last 1,000,000: 3s. Last read position: NC_035782.1:20,941,581 INFO 2022-03-11 17:14:06 AddOrReplaceReadGroups Processed 13,000,000 records. Elapsed time: 00:00:43s. Time for last 1,000,000: 2s. Last read position: NC_035782.1:26,955,094 INFO 2022-03-11 17:14:09 AddOrReplaceReadGroups Processed 14,000,000 records. Elapsed time: 00:00:46s. Time for last 1,000,000: 3s. Last read position: NC_035782.1:38,336,927 INFO 2022-03-11 17:14:12 AddOrReplaceReadGroups Processed 15,000,000 records. Elapsed time: 00:00:49s. Time for last 1,000,000: 3s. Last read position: NC_035782.1:50,119,528 INFO 2022-03-11 17:14:15 AddOrReplaceReadGroups Processed 16,000,000 records. Elapsed time: 00:00:52s. Time for last 1,000,000: 3s. Last read position: NC_035782.1:58,782,292 INFO 2022-03-11 17:14:18 AddOrReplaceReadGroups Processed 17,000,000 records. Elapsed time: 00:00:55s. Time for last 1,000,000: 3s. Last read position: NC_035782.1:69,753,445 INFO 2022-03-11 17:14:21 AddOrReplaceReadGroups Processed 18,000,000 records. Elapsed time: 00:00:58s. Time for last 1,000,000: 3s. Last read position: NC_035783.1:6,246,190 INFO 2022-03-11 17:14:24 AddOrReplaceReadGroups Processed 19,000,000 records. Elapsed time: 00:01:01s. Time for last 1,000,000: 3s. Last read position: NC_035783.1:18,129,969 INFO 2022-03-11 17:14:27 AddOrReplaceReadGroups Processed 20,000,000 records. Elapsed time: 00:01:04s. Time for last 1,000,000: 3s. Last read position: NC_035783.1:29,202,309 INFO 2022-03-11 17:14:31 AddOrReplaceReadGroups Processed 21,000,000 records. Elapsed time: 00:01:08s. Time for last 1,000,000: 3s. Last read position: NC_035783.1:34,538,597 INFO 2022-03-11 17:14:36 AddOrReplaceReadGroups Processed 22,000,000 records. Elapsed time: 00:01:13s. Time for last 1,000,000: 5s. Last read position: NC_035783.1:44,223,697 INFO 2022-03-11 17:14:40 AddOrReplaceReadGroups Processed 23,000,000 records. Elapsed time: 00:01:17s. Time for last 1,000,000: 3s. Last read position: NC_035783.1:58,607,250 INFO 2022-03-11 17:14:43 AddOrReplaceReadGroups Processed 24,000,000 records. Elapsed time: 00:01:20s. Time for last 1,000,000: 3s. Last read position: NC_035784.1:9,460,647 INFO 2022-03-11 17:14:46 AddOrReplaceReadGroups Processed 25,000,000 records. Elapsed time: 00:01:23s. Time for last 1,000,000: 3s. Last read position: NC_035784.1:21,406,182 INFO 2022-03-11 17:14:49 AddOrReplaceReadGroups Processed 26,000,000 records. Elapsed time: 00:01:26s. Time for last 1,000,000: 3s. Last read position: NC_035784.1:33,628,033 INFO 2022-03-11 17:14:52 AddOrReplaceReadGroups Processed 27,000,000 records. Elapsed time: 00:01:29s. Time for last 1,000,000: 3s. Last read position: NC_035784.1:44,322,980 INFO 2022-03-11 17:14:55 AddOrReplaceReadGroups Processed 28,000,000 records. Elapsed time: 00:01:32s. Time for last 1,000,000: 2s. Last read position: NC_035784.1:47,771,175 INFO 2022-03-11 17:14:58 AddOrReplaceReadGroups Processed 29,000,000 records. Elapsed time: 00:01:35s. Time for last 1,000,000: 2s. Last read position: NC_035784.1:52,198,119 INFO 2022-03-11 17:15:00 AddOrReplaceReadGroups Processed 30,000,000 records. Elapsed time: 00:01:37s. Time for last 1,000,000: 2s. Last read position: NC_035784.1:52,258,930 INFO 2022-03-11 17:15:03 AddOrReplaceReadGroups Processed 31,000,000 records. Elapsed time: 00:01:40s. Time for last 1,000,000: 2s. Last read position: NC_035784.1:52,281,017 INFO 2022-03-11 17:15:09 AddOrReplaceReadGroups Processed 32,000,000 records. Elapsed time: 00:01:46s. Time for last 1,000,000: 5s. Last read position: NC_035784.1:63,443,757 INFO 2022-03-11 17:15:12 AddOrReplaceReadGroups Processed 33,000,000 records. Elapsed time: 00:01:49s. Time for last 1,000,000: 3s. Last read position: NC_035784.1:74,233,092 INFO 2022-03-11 17:15:15 AddOrReplaceReadGroups Processed 34,000,000 records. Elapsed time: 00:01:52s. Time for last 1,000,000: 3s. Last read position: NC_035784.1:92,370,286 INFO 2022-03-11 17:15:18 AddOrReplaceReadGroups Processed 35,000,000 records. Elapsed time: 00:01:55s. Time for last 1,000,000: 3s. Last read position: NC_035785.1:29,774,498 INFO 2022-03-11 17:15:21 AddOrReplaceReadGroups Processed 36,000,000 records. Elapsed time: 00:01:58s. Time for last 1,000,000: 3s. Last read position: NC_035785.1:43,388,829 INFO 2022-03-11 17:15:24 AddOrReplaceReadGroups Processed 37,000,000 records. Elapsed time: 00:02:01s. Time for last 1,000,000: 3s. Last read position: NC_035786.1:17,292,380 INFO 2022-03-11 17:15:27 AddOrReplaceReadGroups Processed 38,000,000 records. Elapsed time: 00:02:04s. Time for last 1,000,000: 3s. Last read position: NC_035786.1:46,224,520 INFO 2022-03-11 17:15:31 AddOrReplaceReadGroups Processed 39,000,000 records. Elapsed time: 00:02:08s. Time for last 1,000,000: 3s. Last read position: NC_035787.1:10,614,833 INFO 2022-03-11 17:15:34 AddOrReplaceReadGroups Processed 40,000,000 records. Elapsed time: 00:02:11s. Time for last 1,000,000: 3s. Last read position: NC_035787.1:42,627,954 INFO 2022-03-11 17:15:37 AddOrReplaceReadGroups Processed 41,000,000 records. Elapsed time: 00:02:14s. Time for last 1,000,000: 3s. Last read position: NC_035787.1:60,041,636 INFO 2022-03-11 17:15:41 AddOrReplaceReadGroups Processed 42,000,000 records. Elapsed time: 00:02:18s. Time for last 1,000,000: 4s. Last read position: NC_035788.1:5,960,308 INFO 2022-03-11 17:15:47 AddOrReplaceReadGroups Processed 43,000,000 records. Elapsed time: 00:02:24s. Time for last 1,000,000: 5s. Last read position: NC_035788.1:43,658,294 INFO 2022-03-11 17:15:50 AddOrReplaceReadGroups Processed 44,000,000 records. Elapsed time: 00:02:27s. Time for last 1,000,000: 3s. Last read position: NC_035788.1:70,221,126 INFO 2022-03-11 17:15:53 AddOrReplaceReadGroups Processed 45,000,000 records. Elapsed time: 00:02:30s. Time for last 1,000,000: 3s. Last read position: NC_035788.1:93,819,959 INFO 2022-03-11 17:15:56 AddOrReplaceReadGroups Processed 46,000,000 records. Elapsed time: 00:02:33s. Time for last 1,000,000: 3s. Last read position: NC_035789.1:17,572,001 INFO 2022-03-11 17:15:59 AddOrReplaceReadGroups Processed 47,000,000 records. Elapsed time: 00:02:36s. Time for last 1,000,000: 2s. Last read position: NC_007175.2:7,252 INFO 2022-03-11 17:16:02 AddOrReplaceReadGroups Processed 48,000,000 records. Elapsed time: 00:02:39s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 17:16:05 AddOrReplaceReadGroups Processed 49,000,000 records. Elapsed time: 00:02:42s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 17:16:08 AddOrReplaceReadGroups Processed 50,000,000 records. Elapsed time: 00:02:45s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 17:16:11 AddOrReplaceReadGroups Processed 51,000,000 records. Elapsed time: 00:02:48s. Time for last 1,000,000: 3s. Last read position: */* INFO 2022-03-11 17:16:14 AddOrReplaceReadGroups Processed 52,000,000 records. Elapsed time: 00:02:51s. Time for last 1,000,000: 3s. Last read position: */* INFO 2022-03-11 17:16:21 AddOrReplaceReadGroups Processed 53,000,000 records. Elapsed time: 00:02:58s. Time for last 1,000,000: 7s. Last read position: */* INFO 2022-03-11 17:16:24 AddOrReplaceReadGroups Processed 54,000,000 records. Elapsed time: 00:03:01s. Time for last 1,000,000: 3s. Last read position: */* INFO 2022-03-11 17:16:27 AddOrReplaceReadGroups Processed 55,000,000 records. Elapsed time: 00:03:04s. Time for last 1,000,000: 3s. Last read position: */* [Fri Mar 11 17:16:29 PST 2022] picard.sam.AddOrReplaceReadGroups done. Elapsed time: 3.11 minutes. Runtime.totalMemory()=2730491904 Tool returned: 0 Using GATK jar /home/shared/gatk-4.2.5.0/gatk-package-4.2.5.0-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 /home/shared/gatk-4.2.5.0/gatk-package-4.2.5.0-local.jar AddOrReplaceReadGroups I=S59M.dedup-split.bam O=S59M.dedup-split-RG.bam RGID=1 RGLB=S59M RGPL=ILLUMINA RGPU=unit1 RGSM=S59M INFO 2022-03-11 17:16:30 AddOrReplaceReadGroups ********** NOTE: Picard's command line syntax is changing. ********** ********** For more information, please see: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** ********** The command line looks like this in the new syntax: ********** ********** AddOrReplaceReadGroups -I S59M.dedup-split.bam -O S59M.dedup-split-RG.bam -RGID 1 -RGLB S59M -RGPL ILLUMINA -RGPU unit1 -RGSM S59M ********** 17:16:30.811 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/shared/gatk-4.2.5.0/gatk-package-4.2.5.0-local.jar!/com/intel/gkl/native/libgkl_compression.so [Fri Mar 11 17:16:30 PST 2022] AddOrReplaceReadGroups INPUT=S59M.dedup-split.bam OUTPUT=S59M.dedup-split-RG.bam RGID=1 RGLB=S59M RGPL=ILLUMINA RGPU=unit1 RGSM=S59M VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=2 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Mar 11, 2022 5:16:30 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine INFO: Failed to detect whether we are running on Google Compute Engine. [Fri Mar 11 17:16:30 PST 2022] Executing as sr320@raven on Linux 5.4.0-104-generic amd64; OpenJDK 64-Bit Server VM 11.0.14+9-Ubuntu-0ubuntu2.18.04; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: 4.2.5.0 INFO 2022-03-11 17:16:30 AddOrReplaceReadGroups Created read-group ID=1 PL=ILLUMINA LB=S59M SM=S59M INFO 2022-03-11 17:16:34 AddOrReplaceReadGroups Processed 1,000,000 records. Elapsed time: 00:00:03s. Time for last 1,000,000: 3s. Last read position: NC_035780.1:16,293,682 INFO 2022-03-11 17:16:36 AddOrReplaceReadGroups Processed 2,000,000 records. Elapsed time: 00:00:06s. Time for last 1,000,000: 2s. Last read position: NC_035780.1:32,679,873 INFO 2022-03-11 17:16:39 AddOrReplaceReadGroups Processed 3,000,000 records. Elapsed time: 00:00:08s. Time for last 1,000,000: 2s. Last read position: NC_035780.1:52,780,707 INFO 2022-03-11 17:16:43 AddOrReplaceReadGroups Processed 4,000,000 records. Elapsed time: 00:00:12s. Time for last 1,000,000: 3s. Last read position: NC_035781.1:1,198,755 INFO 2022-03-11 17:16:46 AddOrReplaceReadGroups Processed 5,000,000 records. Elapsed time: 00:00:15s. Time for last 1,000,000: 3s. Last read position: NC_035781.1:12,133,241 INFO 2022-03-11 17:16:49 AddOrReplaceReadGroups Processed 6,000,000 records. Elapsed time: 00:00:18s. Time for last 1,000,000: 2s. Last read position: NC_035781.1:22,707,194 INFO 2022-03-11 17:16:53 AddOrReplaceReadGroups Processed 7,000,000 records. Elapsed time: 00:00:22s. Time for last 1,000,000: 4s. Last read position: NC_035781.1:36,281,175 INFO 2022-03-11 17:16:56 AddOrReplaceReadGroups Processed 8,000,000 records. Elapsed time: 00:00:25s. Time for last 1,000,000: 3s. Last read position: NC_035781.1:51,875,241 INFO 2022-03-11 17:16:59 AddOrReplaceReadGroups Processed 9,000,000 records. Elapsed time: 00:00:28s. Time for last 1,000,000: 3s. Last read position: NC_035782.1:7,875,802 INFO 2022-03-11 17:17:02 AddOrReplaceReadGroups Processed 10,000,000 records. Elapsed time: 00:00:31s. Time for last 1,000,000: 3s. Last read position: NC_035782.1:26,166,132 INFO 2022-03-11 17:17:08 AddOrReplaceReadGroups Processed 11,000,000 records. Elapsed time: 00:00:37s. Time for last 1,000,000: 6s. Last read position: NC_035782.1:36,382,600 INFO 2022-03-11 17:17:12 AddOrReplaceReadGroups Processed 12,000,000 records. Elapsed time: 00:00:41s. Time for last 1,000,000: 3s. Last read position: NC_035782.1:51,244,503 INFO 2022-03-11 17:17:15 AddOrReplaceReadGroups Processed 13,000,000 records. Elapsed time: 00:00:44s. Time for last 1,000,000: 3s. Last read position: NC_035782.1:61,964,893 INFO 2022-03-11 17:17:18 AddOrReplaceReadGroups Processed 14,000,000 records. Elapsed time: 00:00:47s. Time for last 1,000,000: 3s. Last read position: NC_035783.1:189,905 INFO 2022-03-11 17:17:21 AddOrReplaceReadGroups Processed 15,000,000 records. Elapsed time: 00:00:50s. Time for last 1,000,000: 3s. Last read position: NC_035783.1:15,802,327 INFO 2022-03-11 17:17:24 AddOrReplaceReadGroups Processed 16,000,000 records. Elapsed time: 00:00:53s. Time for last 1,000,000: 3s. Last read position: NC_035783.1:27,812,620 INFO 2022-03-11 17:17:27 AddOrReplaceReadGroups Processed 17,000,000 records. Elapsed time: 00:00:56s. Time for last 1,000,000: 3s. Last read position: NC_035783.1:41,682,094 INFO 2022-03-11 17:17:30 AddOrReplaceReadGroups Processed 18,000,000 records. Elapsed time: 00:00:59s. Time for last 1,000,000: 3s. Last read position: NC_035783.1:55,323,464 INFO 2022-03-11 17:17:33 AddOrReplaceReadGroups Processed 19,000,000 records. Elapsed time: 00:01:02s. Time for last 1,000,000: 3s. Last read position: NC_035784.1:12,269,247 INFO 2022-03-11 17:17:36 AddOrReplaceReadGroups Processed 20,000,000 records. Elapsed time: 00:01:05s. Time for last 1,000,000: 3s. Last read position: NC_035784.1:25,051,983 INFO 2022-03-11 17:17:42 AddOrReplaceReadGroups Processed 21,000,000 records. Elapsed time: 00:01:11s. Time for last 1,000,000: 6s. Last read position: NC_035784.1:37,004,859 INFO 2022-03-11 17:17:45 AddOrReplaceReadGroups Processed 22,000,000 records. Elapsed time: 00:01:14s. Time for last 1,000,000: 3s. Last read position: NC_035784.1:49,265,465 INFO 2022-03-11 17:17:48 AddOrReplaceReadGroups Processed 23,000,000 records. Elapsed time: 00:01:17s. Time for last 1,000,000: 2s. Last read position: NC_035784.1:52,261,375 INFO 2022-03-11 17:17:51 AddOrReplaceReadGroups Processed 24,000,000 records. Elapsed time: 00:01:20s. Time for last 1,000,000: 2s. Last read position: NC_035784.1:62,987,584 INFO 2022-03-11 17:17:54 AddOrReplaceReadGroups Processed 25,000,000 records. Elapsed time: 00:01:23s. Time for last 1,000,000: 3s. Last read position: NC_035784.1:74,060,384 INFO 2022-03-11 17:17:57 AddOrReplaceReadGroups Processed 26,000,000 records. Elapsed time: 00:01:26s. Time for last 1,000,000: 3s. Last read position: NC_035784.1:92,038,530 INFO 2022-03-11 17:18:00 AddOrReplaceReadGroups Processed 27,000,000 records. Elapsed time: 00:01:29s. Time for last 1,000,000: 3s. Last read position: NC_035785.1:14,797,650 INFO 2022-03-11 17:18:03 AddOrReplaceReadGroups Processed 28,000,000 records. Elapsed time: 00:01:32s. Time for last 1,000,000: 3s. Last read position: NC_035785.1:36,423,048 INFO 2022-03-11 17:18:06 AddOrReplaceReadGroups Processed 29,000,000 records. Elapsed time: 00:01:35s. Time for last 1,000,000: 3s. Last read position: NC_035786.1:5,259,926 INFO 2022-03-11 17:18:09 AddOrReplaceReadGroups Processed 30,000,000 records. Elapsed time: 00:01:38s. Time for last 1,000,000: 3s. Last read position: NC_035786.1:28,979,442 INFO 2022-03-11 17:18:12 AddOrReplaceReadGroups Processed 31,000,000 records. Elapsed time: 00:01:41s. Time for last 1,000,000: 3s. Last read position: NC_035786.1:49,122,930 INFO 2022-03-11 17:18:19 AddOrReplaceReadGroups Processed 32,000,000 records. Elapsed time: 00:01:48s. Time for last 1,000,000: 6s. Last read position: NC_035787.1:13,488,094 INFO 2022-03-11 17:18:22 AddOrReplaceReadGroups Processed 33,000,000 records. Elapsed time: 00:01:51s. Time for last 1,000,000: 3s. Last read position: NC_035787.1:36,350,975 INFO 2022-03-11 17:18:25 AddOrReplaceReadGroups Processed 34,000,000 records. Elapsed time: 00:01:54s. Time for last 1,000,000: 3s. Last read position: NC_035787.1:56,611,519 INFO 2022-03-11 17:18:28 AddOrReplaceReadGroups Processed 35,000,000 records. Elapsed time: 00:01:57s. Time for last 1,000,000: 2s. Last read position: NC_035787.1:73,875,085 INFO 2022-03-11 17:18:31 AddOrReplaceReadGroups Processed 36,000,000 records. Elapsed time: 00:02:00s. Time for last 1,000,000: 3s. Last read position: NC_035788.1:25,788,207 INFO 2022-03-11 17:18:34 AddOrReplaceReadGroups Processed 37,000,000 records. Elapsed time: 00:02:03s. Time for last 1,000,000: 3s. Last read position: NC_035788.1:54,330,564 INFO 2022-03-11 17:18:37 AddOrReplaceReadGroups Processed 38,000,000 records. Elapsed time: 00:02:06s. Time for last 1,000,000: 3s. Last read position: NC_035788.1:70,608,763 INFO 2022-03-11 17:18:40 AddOrReplaceReadGroups Processed 39,000,000 records. Elapsed time: 00:02:09s. Time for last 1,000,000: 3s. Last read position: NC_035788.1:91,887,821 INFO 2022-03-11 17:18:43 AddOrReplaceReadGroups Processed 40,000,000 records. Elapsed time: 00:02:12s. Time for last 1,000,000: 3s. Last read position: NC_035789.1:13,585,548 INFO 2022-03-11 17:18:46 AddOrReplaceReadGroups Processed 41,000,000 records. Elapsed time: 00:02:15s. Time for last 1,000,000: 2s. Last read position: NC_007175.2:7,095 INFO 2022-03-11 17:18:52 AddOrReplaceReadGroups Processed 42,000,000 records. Elapsed time: 00:02:21s. Time for last 1,000,000: 6s. Last read position: */* INFO 2022-03-11 17:18:55 AddOrReplaceReadGroups Processed 43,000,000 records. Elapsed time: 00:02:24s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 17:18:58 AddOrReplaceReadGroups Processed 44,000,000 records. Elapsed time: 00:02:27s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 17:19:00 AddOrReplaceReadGroups Processed 45,000,000 records. Elapsed time: 00:02:29s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 17:19:03 AddOrReplaceReadGroups Processed 46,000,000 records. Elapsed time: 00:02:32s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 17:19:06 AddOrReplaceReadGroups Processed 47,000,000 records. Elapsed time: 00:02:35s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 17:19:08 AddOrReplaceReadGroups Processed 48,000,000 records. Elapsed time: 00:02:37s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 17:19:11 AddOrReplaceReadGroups Processed 49,000,000 records. Elapsed time: 00:02:40s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 17:19:14 AddOrReplaceReadGroups Processed 50,000,000 records. Elapsed time: 00:02:43s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 17:19:17 AddOrReplaceReadGroups Processed 51,000,000 records. Elapsed time: 00:02:46s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 17:19:20 AddOrReplaceReadGroups Processed 52,000,000 records. Elapsed time: 00:02:49s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 17:19:26 AddOrReplaceReadGroups Processed 53,000,000 records. Elapsed time: 00:02:55s. Time for last 1,000,000: 6s. Last read position: */* [Fri Mar 11 17:19:28 PST 2022] picard.sam.AddOrReplaceReadGroups done. Elapsed time: 2.97 minutes. Runtime.totalMemory()=2843738112 Tool returned: 0 Using GATK jar /home/shared/gatk-4.2.5.0/gatk-package-4.2.5.0-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 /home/shared/gatk-4.2.5.0/gatk-package-4.2.5.0-local.jar AddOrReplaceReadGroups I=S64M.dedup-split.bam O=S64M.dedup-split-RG.bam RGID=1 RGLB=S64M RGPL=ILLUMINA RGPU=unit1 RGSM=S64M INFO 2022-03-11 17:19:30 AddOrReplaceReadGroups ********** NOTE: Picard's command line syntax is changing. ********** ********** For more information, please see: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** ********** The command line looks like this in the new syntax: ********** ********** AddOrReplaceReadGroups -I S64M.dedup-split.bam -O S64M.dedup-split-RG.bam -RGID 1 -RGLB S64M -RGPL ILLUMINA -RGPU unit1 -RGSM S64M ********** 17:19:30.391 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/shared/gatk-4.2.5.0/gatk-package-4.2.5.0-local.jar!/com/intel/gkl/native/libgkl_compression.so [Fri Mar 11 17:19:30 PST 2022] AddOrReplaceReadGroups INPUT=S64M.dedup-split.bam OUTPUT=S64M.dedup-split-RG.bam RGID=1 RGLB=S64M RGPL=ILLUMINA RGPU=unit1 RGSM=S64M VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=2 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Mar 11, 2022 5:19:30 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine INFO: Failed to detect whether we are running on Google Compute Engine. [Fri Mar 11 17:19:30 PST 2022] Executing as sr320@raven on Linux 5.4.0-104-generic amd64; OpenJDK 64-Bit Server VM 11.0.14+9-Ubuntu-0ubuntu2.18.04; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: 4.2.5.0 INFO 2022-03-11 17:19:30 AddOrReplaceReadGroups Created read-group ID=1 PL=ILLUMINA LB=S64M SM=S64M INFO 2022-03-11 17:19:33 AddOrReplaceReadGroups Processed 1,000,000 records. Elapsed time: 00:00:03s. Time for last 1,000,000: 3s. Last read position: NC_035780.1:18,543,528 INFO 2022-03-11 17:19:36 AddOrReplaceReadGroups Processed 2,000,000 records. Elapsed time: 00:00:06s. Time for last 1,000,000: 3s. Last read position: NC_035780.1:35,790,707 INFO 2022-03-11 17:19:39 AddOrReplaceReadGroups Processed 3,000,000 records. Elapsed time: 00:00:09s. Time for last 1,000,000: 3s. Last read position: NC_035780.1:55,182,744 INFO 2022-03-11 17:19:43 AddOrReplaceReadGroups Processed 4,000,000 records. Elapsed time: 00:00:12s. Time for last 1,000,000: 3s. Last read position: NC_035781.1:5,849,698 INFO 2022-03-11 17:19:46 AddOrReplaceReadGroups Processed 5,000,000 records. Elapsed time: 00:00:15s. Time for last 1,000,000: 3s. Last read position: NC_035781.1:17,525,824 INFO 2022-03-11 17:19:49 AddOrReplaceReadGroups Processed 6,000,000 records. Elapsed time: 00:00:18s. Time for last 1,000,000: 3s. Last read position: NC_035781.1:32,323,100 INFO 2022-03-11 17:19:52 AddOrReplaceReadGroups Processed 7,000,000 records. Elapsed time: 00:00:21s. Time for last 1,000,000: 3s. Last read position: NC_035781.1:49,739,294 INFO 2022-03-11 17:19:55 AddOrReplaceReadGroups Processed 8,000,000 records. Elapsed time: 00:00:25s. Time for last 1,000,000: 3s. Last read position: NC_035782.1:3,622,309 INFO 2022-03-11 17:19:58 AddOrReplaceReadGroups Processed 9,000,000 records. Elapsed time: 00:00:28s. Time for last 1,000,000: 3s. Last read position: NC_035782.1:23,823,354 INFO 2022-03-11 17:20:02 AddOrReplaceReadGroups Processed 10,000,000 records. Elapsed time: 00:00:31s. Time for last 1,000,000: 3s. Last read position: NC_035782.1:38,336,125 INFO 2022-03-11 17:20:08 AddOrReplaceReadGroups Processed 11,000,000 records. Elapsed time: 00:00:38s. Time for last 1,000,000: 6s. Last read position: NC_035782.1:54,929,962 INFO 2022-03-11 17:20:11 AddOrReplaceReadGroups Processed 12,000,000 records. Elapsed time: 00:00:41s. Time for last 1,000,000: 3s. Last read position: NC_035782.1:68,937,233 INFO 2022-03-11 17:20:15 AddOrReplaceReadGroups Processed 13,000,000 records. Elapsed time: 00:00:44s. Time for last 1,000,000: 3s. Last read position: NC_035783.1:10,474,270 INFO 2022-03-11 17:20:18 AddOrReplaceReadGroups Processed 14,000,000 records. Elapsed time: 00:00:47s. Time for last 1,000,000: 3s. Last read position: NC_035783.1:25,552,127 INFO 2022-03-11 17:20:21 AddOrReplaceReadGroups Processed 15,000,000 records. Elapsed time: 00:00:50s. Time for last 1,000,000: 3s. Last read position: NC_035783.1:41,361,041 INFO 2022-03-11 17:20:24 AddOrReplaceReadGroups Processed 16,000,000 records. Elapsed time: 00:00:53s. Time for last 1,000,000: 3s. Last read position: NC_035783.1:57,392,076 INFO 2022-03-11 17:20:27 AddOrReplaceReadGroups Processed 17,000,000 records. Elapsed time: 00:00:57s. Time for last 1,000,000: 3s. Last read position: NC_035784.1:14,782,129 INFO 2022-03-11 17:20:30 AddOrReplaceReadGroups Processed 18,000,000 records. Elapsed time: 00:01:00s. Time for last 1,000,000: 3s. Last read position: NC_035784.1:31,631,480 INFO 2022-03-11 17:20:33 AddOrReplaceReadGroups Processed 19,000,000 records. Elapsed time: 00:01:03s. Time for last 1,000,000: 3s. Last read position: NC_035784.1:45,010,017 INFO 2022-03-11 17:20:36 AddOrReplaceReadGroups Processed 20,000,000 records. Elapsed time: 00:01:06s. Time for last 1,000,000: 2s. Last read position: NC_035784.1:52,194,322 INFO 2022-03-11 17:20:41 AddOrReplaceReadGroups Processed 21,000,000 records. Elapsed time: 00:01:10s. Time for last 1,000,000: 4s. Last read position: NC_035784.1:52,194,878 INFO 2022-03-11 17:20:44 AddOrReplaceReadGroups Processed 22,000,000 records. Elapsed time: 00:01:13s. Time for last 1,000,000: 2s. Last read position: NC_035784.1:52,197,657 INFO 2022-03-11 17:20:46 AddOrReplaceReadGroups Processed 23,000,000 records. Elapsed time: 00:01:16s. Time for last 1,000,000: 2s. Last read position: NC_035784.1:52,199,272 INFO 2022-03-11 17:20:49 AddOrReplaceReadGroups Processed 24,000,000 records. Elapsed time: 00:01:18s. Time for last 1,000,000: 2s. Last read position: NC_035784.1:52,199,808 INFO 2022-03-11 17:20:51 AddOrReplaceReadGroups Processed 25,000,000 records. Elapsed time: 00:01:21s. Time for last 1,000,000: 2s. Last read position: NC_035784.1:52,200,382 INFO 2022-03-11 17:20:54 AddOrReplaceReadGroups Processed 26,000,000 records. Elapsed time: 00:01:23s. Time for last 1,000,000: 2s. Last read position: NC_035784.1:52,213,476 INFO 2022-03-11 17:20:57 AddOrReplaceReadGroups Processed 27,000,000 records. Elapsed time: 00:01:26s. Time for last 1,000,000: 2s. Last read position: NC_035784.1:52,217,717 INFO 2022-03-11 17:20:59 AddOrReplaceReadGroups Processed 28,000,000 records. Elapsed time: 00:01:29s. Time for last 1,000,000: 2s. Last read position: NC_035784.1:52,231,278 INFO 2022-03-11 17:21:02 AddOrReplaceReadGroups Processed 29,000,000 records. Elapsed time: 00:01:31s. Time for last 1,000,000: 2s. Last read position: NC_035784.1:52,255,229 INFO 2022-03-11 17:21:04 AddOrReplaceReadGroups Processed 30,000,000 records. Elapsed time: 00:01:34s. Time for last 1,000,000: 2s. Last read position: NC_035784.1:52,255,853 INFO 2022-03-11 17:21:07 AddOrReplaceReadGroups Processed 31,000,000 records. Elapsed time: 00:01:36s. Time for last 1,000,000: 2s. Last read position: NC_035784.1:52,258,019 INFO 2022-03-11 17:21:09 AddOrReplaceReadGroups Processed 32,000,000 records. Elapsed time: 00:01:39s. Time for last 1,000,000: 2s. Last read position: NC_035784.1:52,260,272 INFO 2022-03-11 17:21:12 AddOrReplaceReadGroups Processed 33,000,000 records. Elapsed time: 00:01:41s. Time for last 1,000,000: 2s. Last read position: NC_035784.1:52,260,849 INFO 2022-03-11 17:21:17 AddOrReplaceReadGroups Processed 34,000,000 records. Elapsed time: 00:01:46s. Time for last 1,000,000: 4s. Last read position: NC_035784.1:52,261,379 INFO 2022-03-11 17:21:19 AddOrReplaceReadGroups Processed 35,000,000 records. Elapsed time: 00:01:49s. Time for last 1,000,000: 2s. Last read position: NC_035784.1:52,273,602 INFO 2022-03-11 17:21:22 AddOrReplaceReadGroups Processed 36,000,000 records. Elapsed time: 00:01:51s. Time for last 1,000,000: 2s. Last read position: NC_035784.1:52,274,173 INFO 2022-03-11 17:21:24 AddOrReplaceReadGroups Processed 37,000,000 records. Elapsed time: 00:01:54s. Time for last 1,000,000: 2s. Last read position: NC_035784.1:52,276,785 INFO 2022-03-11 17:21:27 AddOrReplaceReadGroups Processed 38,000,000 records. Elapsed time: 00:01:56s. Time for last 1,000,000: 2s. Last read position: NC_035784.1:52,278,557 INFO 2022-03-11 17:21:29 AddOrReplaceReadGroups Processed 39,000,000 records. Elapsed time: 00:01:59s. Time for last 1,000,000: 2s. Last read position: NC_035784.1:52,279,139 INFO 2022-03-11 17:21:32 AddOrReplaceReadGroups Processed 40,000,000 records. Elapsed time: 00:02:01s. Time for last 1,000,000: 2s. Last read position: NC_035784.1:52,279,730 INFO 2022-03-11 17:21:34 AddOrReplaceReadGroups Processed 41,000,000 records. Elapsed time: 00:02:04s. Time for last 1,000,000: 2s. Last read position: NC_035784.1:52,288,739 INFO 2022-03-11 17:21:37 AddOrReplaceReadGroups Processed 42,000,000 records. Elapsed time: 00:02:06s. Time for last 1,000,000: 2s. Last read position: NC_035784.1:55,262,157 INFO 2022-03-11 17:21:40 AddOrReplaceReadGroups Processed 43,000,000 records. Elapsed time: 00:02:09s. Time for last 1,000,000: 3s. Last read position: NC_035784.1:70,726,314 INFO 2022-03-11 17:21:43 AddOrReplaceReadGroups Processed 44,000,000 records. Elapsed time: 00:02:13s. Time for last 1,000,000: 3s. Last read position: NC_035784.1:88,724,293 INFO 2022-03-11 17:21:48 AddOrReplaceReadGroups Processed 45,000,000 records. Elapsed time: 00:02:18s. Time for last 1,000,000: 5s. Last read position: NC_035785.1:13,911,455 INFO 2022-03-11 17:21:52 AddOrReplaceReadGroups Processed 46,000,000 records. Elapsed time: 00:02:21s. Time for last 1,000,000: 3s. Last read position: NC_035785.1:35,916,699 INFO 2022-03-11 17:21:55 AddOrReplaceReadGroups Processed 47,000,000 records. Elapsed time: 00:02:24s. Time for last 1,000,000: 3s. Last read position: NC_035786.1:3,266,880 INFO 2022-03-11 17:21:58 AddOrReplaceReadGroups Processed 48,000,000 records. Elapsed time: 00:02:27s. Time for last 1,000,000: 3s. Last read position: NC_035786.1:28,315,990 INFO 2022-03-11 17:22:01 AddOrReplaceReadGroups Processed 49,000,000 records. Elapsed time: 00:02:31s. Time for last 1,000,000: 3s. Last read position: NC_035786.1:50,334,808 INFO 2022-03-11 17:22:04 AddOrReplaceReadGroups Processed 50,000,000 records. Elapsed time: 00:02:34s. Time for last 1,000,000: 3s. Last read position: NC_035787.1:15,854,822 INFO 2022-03-11 17:22:07 AddOrReplaceReadGroups Processed 51,000,000 records. Elapsed time: 00:02:37s. Time for last 1,000,000: 3s. Last read position: NC_035787.1:42,241,050 INFO 2022-03-11 17:22:11 AddOrReplaceReadGroups Processed 52,000,000 records. Elapsed time: 00:02:40s. Time for last 1,000,000: 3s. Last read position: NC_035787.1:61,194,195 INFO 2022-03-11 17:22:14 AddOrReplaceReadGroups Processed 53,000,000 records. Elapsed time: 00:02:43s. Time for last 1,000,000: 3s. Last read position: NC_035788.1:10,069,838 INFO 2022-03-11 17:22:17 AddOrReplaceReadGroups Processed 54,000,000 records. Elapsed time: 00:02:46s. Time for last 1,000,000: 3s. Last read position: NC_035788.1:43,096,951 INFO 2022-03-11 17:22:22 AddOrReplaceReadGroups Processed 55,000,000 records. Elapsed time: 00:02:52s. Time for last 1,000,000: 5s. Last read position: NC_035788.1:63,777,845 INFO 2022-03-11 17:22:27 AddOrReplaceReadGroups Processed 56,000,000 records. Elapsed time: 00:02:56s. Time for last 1,000,000: 4s. Last read position: NC_035788.1:84,507,651 INFO 2022-03-11 17:22:30 AddOrReplaceReadGroups Processed 57,000,000 records. Elapsed time: 00:02:59s. Time for last 1,000,000: 3s. Last read position: NC_035789.1:5,966,318 INFO 2022-03-11 17:22:33 AddOrReplaceReadGroups Processed 58,000,000 records. Elapsed time: 00:03:02s. Time for last 1,000,000: 3s. Last read position: NC_035789.1:28,077,384 INFO 2022-03-11 17:22:36 AddOrReplaceReadGroups Processed 59,000,000 records. Elapsed time: 00:03:05s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 17:22:39 AddOrReplaceReadGroups Processed 60,000,000 records. Elapsed time: 00:03:08s. Time for last 1,000,000: 3s. Last read position: */* INFO 2022-03-11 17:22:42 AddOrReplaceReadGroups Processed 61,000,000 records. Elapsed time: 00:03:11s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 17:22:45 AddOrReplaceReadGroups Processed 62,000,000 records. Elapsed time: 00:03:14s. Time for last 1,000,000: 3s. Last read position: */* INFO 2022-03-11 17:22:48 AddOrReplaceReadGroups Processed 63,000,000 records. Elapsed time: 00:03:17s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 17:22:51 AddOrReplaceReadGroups Processed 64,000,000 records. Elapsed time: 00:03:20s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 17:22:54 AddOrReplaceReadGroups Processed 65,000,000 records. Elapsed time: 00:03:23s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 17:23:01 AddOrReplaceReadGroups Processed 66,000,000 records. Elapsed time: 00:03:30s. Time for last 1,000,000: 7s. Last read position: */* INFO 2022-03-11 17:23:04 AddOrReplaceReadGroups Processed 67,000,000 records. Elapsed time: 00:03:33s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 17:23:07 AddOrReplaceReadGroups Processed 68,000,000 records. Elapsed time: 00:03:36s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 17:23:10 AddOrReplaceReadGroups Processed 69,000,000 records. Elapsed time: 00:03:39s. Time for last 1,000,000: 2s. Last read position: */* [Fri Mar 11 17:23:12 PST 2022] picard.sam.AddOrReplaceReadGroups done. Elapsed time: 3.70 minutes. Runtime.totalMemory()=2864709632 Tool returned: 0 Using GATK jar /home/shared/gatk-4.2.5.0/gatk-package-4.2.5.0-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 /home/shared/gatk-4.2.5.0/gatk-package-4.2.5.0-local.jar AddOrReplaceReadGroups I=S6M.dedup-split.bam O=S6M.dedup-split-RG.bam RGID=1 RGLB=S6M RGPL=ILLUMINA RGPU=unit1 RGSM=S6M INFO 2022-03-11 17:23:13 AddOrReplaceReadGroups ********** NOTE: Picard's command line syntax is changing. ********** ********** For more information, please see: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** ********** The command line looks like this in the new syntax: ********** ********** AddOrReplaceReadGroups -I S6M.dedup-split.bam -O S6M.dedup-split-RG.bam -RGID 1 -RGLB S6M -RGPL ILLUMINA -RGPU unit1 -RGSM S6M ********** 17:23:13.743 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/shared/gatk-4.2.5.0/gatk-package-4.2.5.0-local.jar!/com/intel/gkl/native/libgkl_compression.so [Fri Mar 11 17:23:13 PST 2022] AddOrReplaceReadGroups INPUT=S6M.dedup-split.bam OUTPUT=S6M.dedup-split-RG.bam RGID=1 RGLB=S6M RGPL=ILLUMINA RGPU=unit1 RGSM=S6M VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=2 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Mar 11, 2022 5:23:13 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine INFO: Failed to detect whether we are running on Google Compute Engine. [Fri Mar 11 17:23:13 PST 2022] Executing as sr320@raven on Linux 5.4.0-104-generic amd64; OpenJDK 64-Bit Server VM 11.0.14+9-Ubuntu-0ubuntu2.18.04; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: 4.2.5.0 INFO 2022-03-11 17:23:13 AddOrReplaceReadGroups Created read-group ID=1 PL=ILLUMINA LB=S6M SM=S6M INFO 2022-03-11 17:23:16 AddOrReplaceReadGroups Processed 1,000,000 records. Elapsed time: 00:00:03s. Time for last 1,000,000: 3s. Last read position: NC_035780.1:8,618,774 INFO 2022-03-11 17:23:19 AddOrReplaceReadGroups Processed 2,000,000 records. Elapsed time: 00:00:06s. Time for last 1,000,000: 2s. Last read position: NC_035780.1:19,156,136 INFO 2022-03-11 17:23:22 AddOrReplaceReadGroups Processed 3,000,000 records. Elapsed time: 00:00:08s. Time for last 1,000,000: 2s. Last read position: NC_035780.1:28,425,665 INFO 2022-03-11 17:23:25 AddOrReplaceReadGroups Processed 4,000,000 records. Elapsed time: 00:00:11s. Time for last 1,000,000: 3s. Last read position: NC_035780.1:37,885,672 INFO 2022-03-11 17:23:28 AddOrReplaceReadGroups Processed 5,000,000 records. Elapsed time: 00:00:15s. Time for last 1,000,000: 3s. Last read position: NC_035780.1:49,559,523 INFO 2022-03-11 17:23:33 AddOrReplaceReadGroups Processed 6,000,000 records. Elapsed time: 00:00:19s. Time for last 1,000,000: 4s. Last read position: NC_035780.1:60,694,872 INFO 2022-03-11 17:23:36 AddOrReplaceReadGroups Processed 7,000,000 records. Elapsed time: 00:00:22s. Time for last 1,000,000: 2s. Last read position: NC_035781.1:5,120,565 INFO 2022-03-11 17:23:39 AddOrReplaceReadGroups Processed 8,000,000 records. Elapsed time: 00:00:25s. Time for last 1,000,000: 2s. Last read position: NC_035781.1:14,606,584 INFO 2022-03-11 17:23:42 AddOrReplaceReadGroups Processed 9,000,000 records. Elapsed time: 00:00:28s. Time for last 1,000,000: 2s. Last read position: NC_035781.1:24,169,695 INFO 2022-03-11 17:23:45 AddOrReplaceReadGroups Processed 10,000,000 records. Elapsed time: 00:00:31s. Time for last 1,000,000: 2s. Last read position: NC_035781.1:35,102,722 INFO 2022-03-11 17:23:52 AddOrReplaceReadGroups Processed 11,000,000 records. Elapsed time: 00:00:38s. Time for last 1,000,000: 6s. Last read position: NC_035781.1:45,745,499 INFO 2022-03-11 17:23:55 AddOrReplaceReadGroups Processed 12,000,000 records. Elapsed time: 00:00:41s. Time for last 1,000,000: 2s. Last read position: NC_035781.1:55,160,692 INFO 2022-03-11 17:23:58 AddOrReplaceReadGroups Processed 13,000,000 records. Elapsed time: 00:00:44s. Time for last 1,000,000: 2s. Last read position: NC_035782.1:4,657,664 INFO 2022-03-11 17:24:01 AddOrReplaceReadGroups Processed 14,000,000 records. Elapsed time: 00:00:47s. Time for last 1,000,000: 3s. Last read position: NC_035782.1:17,264,191 INFO 2022-03-11 17:24:04 AddOrReplaceReadGroups Processed 15,000,000 records. Elapsed time: 00:00:50s. Time for last 1,000,000: 2s. Last read position: NC_035782.1:28,607,759 INFO 2022-03-11 17:24:07 AddOrReplaceReadGroups Processed 16,000,000 records. Elapsed time: 00:00:53s. Time for last 1,000,000: 2s. Last read position: NC_035782.1:39,060,162 INFO 2022-03-11 17:24:09 AddOrReplaceReadGroups Processed 17,000,000 records. Elapsed time: 00:00:56s. Time for last 1,000,000: 2s. Last read position: NC_035782.1:50,625,824 INFO 2022-03-11 17:24:12 AddOrReplaceReadGroups Processed 18,000,000 records. Elapsed time: 00:00:59s. Time for last 1,000,000: 2s. Last read position: NC_035782.1:59,499,684 INFO 2022-03-11 17:24:15 AddOrReplaceReadGroups Processed 19,000,000 records. Elapsed time: 00:01:01s. Time for last 1,000,000: 2s. Last read position: NC_035782.1:69,742,113 INFO 2022-03-11 17:24:18 AddOrReplaceReadGroups Processed 20,000,000 records. Elapsed time: 00:01:04s. Time for last 1,000,000: 2s. Last read position: NC_035783.1:4,070,092 INFO 2022-03-11 17:24:21 AddOrReplaceReadGroups Processed 21,000,000 records. Elapsed time: 00:01:07s. Time for last 1,000,000: 2s. Last read position: NC_035783.1:14,444,473 INFO 2022-03-11 17:24:28 AddOrReplaceReadGroups Processed 22,000,000 records. Elapsed time: 00:01:14s. Time for last 1,000,000: 6s. Last read position: NC_035783.1:22,909,984 INFO 2022-03-11 17:24:31 AddOrReplaceReadGroups Processed 23,000,000 records. Elapsed time: 00:01:17s. Time for last 1,000,000: 2s. Last read position: NC_035783.1:33,177,431 INFO 2022-03-11 17:24:34 AddOrReplaceReadGroups Processed 24,000,000 records. Elapsed time: 00:01:20s. Time for last 1,000,000: 3s. Last read position: NC_035783.1:43,526,757 INFO 2022-03-11 17:24:37 AddOrReplaceReadGroups Processed 25,000,000 records. Elapsed time: 00:01:23s. Time for last 1,000,000: 2s. Last read position: NC_035783.1:52,892,819 INFO 2022-03-11 17:24:40 AddOrReplaceReadGroups Processed 26,000,000 records. Elapsed time: 00:01:26s. Time for last 1,000,000: 3s. Last read position: NC_035784.1:3,559,758 INFO 2022-03-11 17:24:43 AddOrReplaceReadGroups Processed 27,000,000 records. Elapsed time: 00:01:29s. Time for last 1,000,000: 2s. Last read position: NC_035784.1:13,262,565 INFO 2022-03-11 17:24:46 AddOrReplaceReadGroups Processed 28,000,000 records. Elapsed time: 00:01:32s. Time for last 1,000,000: 2s. Last read position: NC_035784.1:23,366,250 INFO 2022-03-11 17:24:49 AddOrReplaceReadGroups Processed 29,000,000 records. Elapsed time: 00:01:35s. Time for last 1,000,000: 2s. Last read position: NC_035784.1:33,826,473 INFO 2022-03-11 17:24:52 AddOrReplaceReadGroups Processed 30,000,000 records. Elapsed time: 00:01:38s. Time for last 1,000,000: 2s. Last read position: NC_035784.1:44,224,952 INFO 2022-03-11 17:24:55 AddOrReplaceReadGroups Processed 31,000,000 records. Elapsed time: 00:01:41s. Time for last 1,000,000: 2s. Last read position: NC_035784.1:51,958,096 INFO 2022-03-11 17:24:57 AddOrReplaceReadGroups Processed 32,000,000 records. Elapsed time: 00:01:43s. Time for last 1,000,000: 2s. Last read position: NC_035784.1:53,105,813 INFO 2022-03-11 17:25:03 AddOrReplaceReadGroups Processed 33,000,000 records. Elapsed time: 00:01:50s. Time for last 1,000,000: 6s. Last read position: NC_035784.1:63,246,216 INFO 2022-03-11 17:25:06 AddOrReplaceReadGroups Processed 34,000,000 records. Elapsed time: 00:01:52s. Time for last 1,000,000: 2s. Last read position: NC_035784.1:72,884,824 INFO 2022-03-11 17:25:09 AddOrReplaceReadGroups Processed 35,000,000 records. Elapsed time: 00:01:56s. Time for last 1,000,000: 3s. Last read position: NC_035784.1:85,250,446 INFO 2022-03-11 17:25:12 AddOrReplaceReadGroups Processed 36,000,000 records. Elapsed time: 00:01:58s. Time for last 1,000,000: 2s. Last read position: NC_035784.1:96,542,758 INFO 2022-03-11 17:25:15 AddOrReplaceReadGroups Processed 37,000,000 records. Elapsed time: 00:02:01s. Time for last 1,000,000: 2s. Last read position: NC_035785.1:9,873,690 INFO 2022-03-11 17:25:18 AddOrReplaceReadGroups Processed 38,000,000 records. Elapsed time: 00:02:04s. Time for last 1,000,000: 2s. Last read position: NC_035785.1:20,618,953 INFO 2022-03-11 17:25:21 AddOrReplaceReadGroups Processed 39,000,000 records. Elapsed time: 00:02:07s. Time for last 1,000,000: 2s. Last read position: NC_035785.1:34,939,637 INFO 2022-03-11 17:25:24 AddOrReplaceReadGroups Processed 40,000,000 records. Elapsed time: 00:02:10s. Time for last 1,000,000: 2s. Last read position: NC_035785.1:45,459,718 INFO 2022-03-11 17:25:27 AddOrReplaceReadGroups Processed 41,000,000 records. Elapsed time: 00:02:13s. Time for last 1,000,000: 2s. Last read position: NC_035786.1:5,829,273 INFO 2022-03-11 17:25:30 AddOrReplaceReadGroups Processed 42,000,000 records. Elapsed time: 00:02:16s. Time for last 1,000,000: 2s. Last read position: NC_035786.1:20,425,686 INFO 2022-03-11 17:25:37 AddOrReplaceReadGroups Processed 43,000,000 records. Elapsed time: 00:02:23s. Time for last 1,000,000: 6s. Last read position: NC_035786.1:34,887,575 INFO 2022-03-11 17:25:39 AddOrReplaceReadGroups Processed 44,000,000 records. Elapsed time: 00:02:26s. Time for last 1,000,000: 2s. Last read position: NC_035786.1:47,831,373 INFO 2022-03-11 17:25:42 AddOrReplaceReadGroups Processed 45,000,000 records. Elapsed time: 00:02:28s. Time for last 1,000,000: 2s. Last read position: NC_035787.1:507,374 INFO 2022-03-11 17:25:45 AddOrReplaceReadGroups Processed 46,000,000 records. Elapsed time: 00:02:31s. Time for last 1,000,000: 2s. Last read position: NC_035787.1:14,343,657 INFO 2022-03-11 17:25:48 AddOrReplaceReadGroups Processed 47,000,000 records. Elapsed time: 00:02:34s. Time for last 1,000,000: 2s. Last read position: NC_035787.1:28,614,392 INFO 2022-03-11 17:25:51 AddOrReplaceReadGroups Processed 48,000,000 records. Elapsed time: 00:02:37s. Time for last 1,000,000: 2s. Last read position: NC_035787.1:42,880,776 INFO 2022-03-11 17:25:54 AddOrReplaceReadGroups Processed 49,000,000 records. Elapsed time: 00:02:40s. Time for last 1,000,000: 2s. Last read position: NC_035787.1:52,896,428 INFO 2022-03-11 17:25:57 AddOrReplaceReadGroups Processed 50,000,000 records. Elapsed time: 00:02:43s. Time for last 1,000,000: 2s. Last read position: NC_035787.1:62,898,921 INFO 2022-03-11 17:26:00 AddOrReplaceReadGroups Processed 51,000,000 records. Elapsed time: 00:02:46s. Time for last 1,000,000: 2s. Last read position: NC_035788.1:591,447 INFO 2022-03-11 17:26:03 AddOrReplaceReadGroups Processed 52,000,000 records. Elapsed time: 00:02:49s. Time for last 1,000,000: 2s. Last read position: NC_035788.1:14,081,997 INFO 2022-03-11 17:26:06 AddOrReplaceReadGroups Processed 53,000,000 records. Elapsed time: 00:02:52s. Time for last 1,000,000: 2s. Last read position: NC_035788.1:25,289,607 INFO 2022-03-11 17:26:12 AddOrReplaceReadGroups Processed 54,000,000 records. Elapsed time: 00:02:58s. Time for last 1,000,000: 6s. Last read position: NC_035788.1:41,542,469 INFO 2022-03-11 17:26:15 AddOrReplaceReadGroups Processed 55,000,000 records. Elapsed time: 00:03:01s. Time for last 1,000,000: 2s. Last read position: NC_035788.1:52,240,098 INFO 2022-03-11 17:26:18 AddOrReplaceReadGroups Processed 56,000,000 records. Elapsed time: 00:03:04s. Time for last 1,000,000: 2s. Last read position: NC_035788.1:63,075,459 INFO 2022-03-11 17:26:21 AddOrReplaceReadGroups Processed 57,000,000 records. Elapsed time: 00:03:07s. Time for last 1,000,000: 2s. Last read position: NC_035788.1:74,021,574 INFO 2022-03-11 17:26:24 AddOrReplaceReadGroups Processed 58,000,000 records. Elapsed time: 00:03:10s. Time for last 1,000,000: 2s. Last read position: NC_035788.1:84,821,396 INFO 2022-03-11 17:26:27 AddOrReplaceReadGroups Processed 59,000,000 records. Elapsed time: 00:03:13s. Time for last 1,000,000: 2s. Last read position: NC_035788.1:97,716,965 INFO 2022-03-11 17:26:30 AddOrReplaceReadGroups Processed 60,000,000 records. Elapsed time: 00:03:16s. Time for last 1,000,000: 2s. Last read position: NC_035789.1:5,813,123 INFO 2022-03-11 17:26:33 AddOrReplaceReadGroups Processed 61,000,000 records. Elapsed time: 00:03:19s. Time for last 1,000,000: 2s. Last read position: NC_035789.1:15,908,725 INFO 2022-03-11 17:26:36 AddOrReplaceReadGroups Processed 62,000,000 records. Elapsed time: 00:03:22s. Time for last 1,000,000: 2s. Last read position: NC_035789.1:26,260,816 INFO 2022-03-11 17:26:39 AddOrReplaceReadGroups Processed 63,000,000 records. Elapsed time: 00:03:25s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 17:26:42 AddOrReplaceReadGroups Processed 64,000,000 records. Elapsed time: 00:03:28s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 17:26:48 AddOrReplaceReadGroups Processed 65,000,000 records. Elapsed time: 00:03:34s. Time for last 1,000,000: 6s. Last read position: */* INFO 2022-03-11 17:26:51 AddOrReplaceReadGroups Processed 66,000,000 records. Elapsed time: 00:03:37s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 17:26:54 AddOrReplaceReadGroups Processed 67,000,000 records. Elapsed time: 00:03:40s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 17:26:56 AddOrReplaceReadGroups Processed 68,000,000 records. Elapsed time: 00:03:42s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 17:26:59 AddOrReplaceReadGroups Processed 69,000,000 records. Elapsed time: 00:03:45s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 17:27:02 AddOrReplaceReadGroups Processed 70,000,000 records. Elapsed time: 00:03:48s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 17:27:05 AddOrReplaceReadGroups Processed 71,000,000 records. Elapsed time: 00:03:51s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 17:27:08 AddOrReplaceReadGroups Processed 72,000,000 records. Elapsed time: 00:03:54s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 17:27:10 AddOrReplaceReadGroups Processed 73,000,000 records. Elapsed time: 00:03:56s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 17:27:13 AddOrReplaceReadGroups Processed 74,000,000 records. Elapsed time: 00:03:59s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 17:27:16 AddOrReplaceReadGroups Processed 75,000,000 records. Elapsed time: 00:04:02s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 17:27:23 AddOrReplaceReadGroups Processed 76,000,000 records. Elapsed time: 00:04:09s. Time for last 1,000,000: 7s. Last read position: */* INFO 2022-03-11 17:27:26 AddOrReplaceReadGroups Processed 77,000,000 records. Elapsed time: 00:04:12s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 17:27:29 AddOrReplaceReadGroups Processed 78,000,000 records. Elapsed time: 00:04:15s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 17:27:32 AddOrReplaceReadGroups Processed 79,000,000 records. Elapsed time: 00:04:18s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 17:27:34 AddOrReplaceReadGroups Processed 80,000,000 records. Elapsed time: 00:04:20s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 17:27:37 AddOrReplaceReadGroups Processed 81,000,000 records. Elapsed time: 00:04:23s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 17:27:40 AddOrReplaceReadGroups Processed 82,000,000 records. Elapsed time: 00:04:26s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 17:27:43 AddOrReplaceReadGroups Processed 83,000,000 records. Elapsed time: 00:04:29s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 17:27:46 AddOrReplaceReadGroups Processed 84,000,000 records. Elapsed time: 00:04:32s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 17:27:49 AddOrReplaceReadGroups Processed 85,000,000 records. Elapsed time: 00:04:35s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 17:27:51 AddOrReplaceReadGroups Processed 86,000,000 records. Elapsed time: 00:04:37s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 17:27:59 AddOrReplaceReadGroups Processed 87,000,000 records. Elapsed time: 00:04:45s. Time for last 1,000,000: 7s. Last read position: */* [Fri Mar 11 17:28:00 PST 2022] picard.sam.AddOrReplaceReadGroups done. Elapsed time: 4.78 minutes. Runtime.totalMemory()=2910846976 Tool returned: 0 Using GATK jar /home/shared/gatk-4.2.5.0/gatk-package-4.2.5.0-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 /home/shared/gatk-4.2.5.0/gatk-package-4.2.5.0-local.jar AddOrReplaceReadGroups I=S76F.dedup-split.bam O=S76F.dedup-split-RG.bam RGID=1 RGLB=S76F RGPL=ILLUMINA RGPU=unit1 RGSM=S76F INFO 2022-03-11 17:28:02 AddOrReplaceReadGroups ********** NOTE: Picard's command line syntax is changing. ********** ********** For more information, please see: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** ********** The command line looks like this in the new syntax: ********** ********** AddOrReplaceReadGroups -I S76F.dedup-split.bam -O S76F.dedup-split-RG.bam -RGID 1 -RGLB S76F -RGPL ILLUMINA -RGPU unit1 -RGSM S76F ********** 17:28:02.341 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/shared/gatk-4.2.5.0/gatk-package-4.2.5.0-local.jar!/com/intel/gkl/native/libgkl_compression.so [Fri Mar 11 17:28:02 PST 2022] AddOrReplaceReadGroups INPUT=S76F.dedup-split.bam OUTPUT=S76F.dedup-split-RG.bam RGID=1 RGLB=S76F RGPL=ILLUMINA RGPU=unit1 RGSM=S76F VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=2 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Mar 11, 2022 5:28:02 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine INFO: Failed to detect whether we are running on Google Compute Engine. [Fri Mar 11 17:28:02 PST 2022] Executing as sr320@raven on Linux 5.4.0-104-generic amd64; OpenJDK 64-Bit Server VM 11.0.14+9-Ubuntu-0ubuntu2.18.04; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: 4.2.5.0 INFO 2022-03-11 17:28:02 AddOrReplaceReadGroups Created read-group ID=1 PL=ILLUMINA LB=S76F SM=S76F INFO 2022-03-11 17:28:05 AddOrReplaceReadGroups Processed 1,000,000 records. Elapsed time: 00:00:03s. Time for last 1,000,000: 3s. Last read position: NC_035780.1:13,562,273 INFO 2022-03-11 17:28:08 AddOrReplaceReadGroups Processed 2,000,000 records. Elapsed time: 00:00:06s. Time for last 1,000,000: 2s. Last read position: NC_035780.1:29,080,191 INFO 2022-03-11 17:28:11 AddOrReplaceReadGroups Processed 3,000,000 records. Elapsed time: 00:00:09s. Time for last 1,000,000: 3s. Last read position: NC_035780.1:43,316,211 INFO 2022-03-11 17:28:14 AddOrReplaceReadGroups Processed 4,000,000 records. Elapsed time: 00:00:12s. Time for last 1,000,000: 3s. Last read position: NC_035780.1:57,287,572 INFO 2022-03-11 17:28:17 AddOrReplaceReadGroups Processed 5,000,000 records. Elapsed time: 00:00:15s. Time for last 1,000,000: 2s. Last read position: NC_035781.1:316,493 INFO 2022-03-11 17:28:20 AddOrReplaceReadGroups Processed 6,000,000 records. Elapsed time: 00:00:18s. Time for last 1,000,000: 3s. Last read position: NC_035781.1:7,949,605 INFO 2022-03-11 17:28:23 AddOrReplaceReadGroups Processed 7,000,000 records. Elapsed time: 00:00:21s. Time for last 1,000,000: 2s. Last read position: NC_035781.1:15,194,486 INFO 2022-03-11 17:28:26 AddOrReplaceReadGroups Processed 8,000,000 records. Elapsed time: 00:00:24s. Time for last 1,000,000: 3s. Last read position: NC_035781.1:24,392,299 INFO 2022-03-11 17:28:29 AddOrReplaceReadGroups Processed 9,000,000 records. Elapsed time: 00:00:27s. Time for last 1,000,000: 3s. Last read position: NC_035781.1:33,050,679 INFO 2022-03-11 17:28:32 AddOrReplaceReadGroups Processed 10,000,000 records. Elapsed time: 00:00:30s. Time for last 1,000,000: 3s. Last read position: NC_035781.1:40,788,321 INFO 2022-03-11 17:28:38 AddOrReplaceReadGroups Processed 11,000,000 records. Elapsed time: 00:00:35s. Time for last 1,000,000: 5s. Last read position: NC_035781.1:49,080,061 INFO 2022-03-11 17:28:42 AddOrReplaceReadGroups Processed 12,000,000 records. Elapsed time: 00:00:39s. Time for last 1,000,000: 4s. Last read position: NC_035781.1:59,059,475 INFO 2022-03-11 17:28:45 AddOrReplaceReadGroups Processed 13,000,000 records. Elapsed time: 00:00:42s. Time for last 1,000,000: 3s. Last read position: NC_035782.1:18,289,446 INFO 2022-03-11 17:28:48 AddOrReplaceReadGroups Processed 14,000,000 records. Elapsed time: 00:00:45s. Time for last 1,000,000: 3s. Last read position: NC_035782.1:27,078,864 INFO 2022-03-11 17:28:51 AddOrReplaceReadGroups Processed 15,000,000 records. Elapsed time: 00:00:48s. Time for last 1,000,000: 3s. Last read position: NC_035782.1:37,473,633 INFO 2022-03-11 17:28:54 AddOrReplaceReadGroups Processed 16,000,000 records. Elapsed time: 00:00:52s. Time for last 1,000,000: 3s. Last read position: NC_035782.1:48,183,678 INFO 2022-03-11 17:28:57 AddOrReplaceReadGroups Processed 17,000,000 records. Elapsed time: 00:00:55s. Time for last 1,000,000: 3s. Last read position: NC_035782.1:56,674,196 INFO 2022-03-11 17:29:00 AddOrReplaceReadGroups Processed 18,000,000 records. Elapsed time: 00:00:58s. Time for last 1,000,000: 3s. Last read position: NC_035782.1:64,758,997 INFO 2022-03-11 17:29:03 AddOrReplaceReadGroups Processed 19,000,000 records. Elapsed time: 00:01:01s. Time for last 1,000,000: 3s. Last read position: NC_035782.1:73,044,614 INFO 2022-03-11 17:29:06 AddOrReplaceReadGroups Processed 20,000,000 records. Elapsed time: 00:01:04s. Time for last 1,000,000: 3s. Last read position: NC_035783.1:10,537,429 INFO 2022-03-11 17:29:09 AddOrReplaceReadGroups Processed 21,000,000 records. Elapsed time: 00:01:07s. Time for last 1,000,000: 3s. Last read position: NC_035783.1:19,841,186 INFO 2022-03-11 17:29:15 AddOrReplaceReadGroups Processed 22,000,000 records. Elapsed time: 00:01:13s. Time for last 1,000,000: 6s. Last read position: NC_035783.1:30,059,212 INFO 2022-03-11 17:29:19 AddOrReplaceReadGroups Processed 23,000,000 records. Elapsed time: 00:01:16s. Time for last 1,000,000: 3s. Last read position: NC_035783.1:38,117,904 INFO 2022-03-11 17:29:22 AddOrReplaceReadGroups Processed 24,000,000 records. Elapsed time: 00:01:19s. Time for last 1,000,000: 3s. Last read position: NC_035783.1:48,070,217 INFO 2022-03-11 17:29:25 AddOrReplaceReadGroups Processed 25,000,000 records. Elapsed time: 00:01:22s. Time for last 1,000,000: 3s. Last read position: NC_035784.1:2,245,299 INFO 2022-03-11 17:29:28 AddOrReplaceReadGroups Processed 26,000,000 records. Elapsed time: 00:01:25s. Time for last 1,000,000: 3s. Last read position: NC_035784.1:10,925,107 INFO 2022-03-11 17:29:31 AddOrReplaceReadGroups Processed 27,000,000 records. Elapsed time: 00:01:28s. Time for last 1,000,000: 3s. Last read position: NC_035784.1:20,966,165 INFO 2022-03-11 17:29:34 AddOrReplaceReadGroups Processed 28,000,000 records. Elapsed time: 00:01:31s. Time for last 1,000,000: 3s. Last read position: NC_035784.1:32,011,305 INFO 2022-03-11 17:29:37 AddOrReplaceReadGroups Processed 29,000,000 records. Elapsed time: 00:01:34s. Time for last 1,000,000: 3s. Last read position: NC_035784.1:41,039,419 INFO 2022-03-11 17:29:40 AddOrReplaceReadGroups Processed 30,000,000 records. Elapsed time: 00:01:37s. Time for last 1,000,000: 2s. Last read position: NC_035784.1:46,891,542 INFO 2022-03-11 17:29:43 AddOrReplaceReadGroups Processed 31,000,000 records. Elapsed time: 00:01:40s. Time for last 1,000,000: 2s. Last read position: NC_035784.1:49,892,810 INFO 2022-03-11 17:29:48 AddOrReplaceReadGroups Processed 32,000,000 records. Elapsed time: 00:01:45s. Time for last 1,000,000: 5s. Last read position: NC_035784.1:52,201,072 INFO 2022-03-11 17:29:51 AddOrReplaceReadGroups Processed 33,000,000 records. Elapsed time: 00:01:48s. Time for last 1,000,000: 2s. Last read position: NC_035784.1:52,260,835 INFO 2022-03-11 17:29:53 AddOrReplaceReadGroups Processed 34,000,000 records. Elapsed time: 00:01:51s. Time for last 1,000,000: 2s. Last read position: NC_035784.1:52,653,745 INFO 2022-03-11 17:29:56 AddOrReplaceReadGroups Processed 35,000,000 records. Elapsed time: 00:01:54s. Time for last 1,000,000: 3s. Last read position: NC_035784.1:62,989,575 INFO 2022-03-11 17:29:59 AddOrReplaceReadGroups Processed 36,000,000 records. Elapsed time: 00:01:57s. Time for last 1,000,000: 3s. Last read position: NC_035784.1:73,205,717 INFO 2022-03-11 17:30:02 AddOrReplaceReadGroups Processed 37,000,000 records. Elapsed time: 00:02:00s. Time for last 1,000,000: 3s. Last read position: NC_035784.1:90,572,209 INFO 2022-03-11 17:30:06 AddOrReplaceReadGroups Processed 38,000,000 records. Elapsed time: 00:02:03s. Time for last 1,000,000: 3s. Last read position: NC_035785.1:30,502,305 INFO 2022-03-11 17:30:09 AddOrReplaceReadGroups Processed 39,000,000 records. Elapsed time: 00:02:06s. Time for last 1,000,000: 3s. Last read position: NC_035785.1:41,720,947 INFO 2022-03-11 17:30:12 AddOrReplaceReadGroups Processed 40,000,000 records. Elapsed time: 00:02:09s. Time for last 1,000,000: 3s. Last read position: NC_035786.1:13,746,369 INFO 2022-03-11 17:30:15 AddOrReplaceReadGroups Processed 41,000,000 records. Elapsed time: 00:02:12s. Time for last 1,000,000: 3s. Last read position: NC_035786.1:42,344,710 INFO 2022-03-11 17:30:18 AddOrReplaceReadGroups Processed 42,000,000 records. Elapsed time: 00:02:15s. Time for last 1,000,000: 3s. Last read position: NC_035787.1:4,650,557 INFO 2022-03-11 17:30:24 AddOrReplaceReadGroups Processed 43,000,000 records. Elapsed time: 00:02:22s. Time for last 1,000,000: 6s. Last read position: NC_035787.1:35,403,370 INFO 2022-03-11 17:30:27 AddOrReplaceReadGroups Processed 44,000,000 records. Elapsed time: 00:02:25s. Time for last 1,000,000: 3s. Last read position: NC_035787.1:57,983,836 INFO 2022-03-11 17:30:30 AddOrReplaceReadGroups Processed 45,000,000 records. Elapsed time: 00:02:28s. Time for last 1,000,000: 2s. Last read position: NC_035787.1:66,097,099 INFO 2022-03-11 17:30:33 AddOrReplaceReadGroups Processed 46,000,000 records. Elapsed time: 00:02:31s. Time for last 1,000,000: 3s. Last read position: NC_035788.1:18,951,935 INFO 2022-03-11 17:30:37 AddOrReplaceReadGroups Processed 47,000,000 records. Elapsed time: 00:02:34s. Time for last 1,000,000: 3s. Last read position: NC_035788.1:57,715,208 INFO 2022-03-11 17:30:40 AddOrReplaceReadGroups Processed 48,000,000 records. Elapsed time: 00:02:37s. Time for last 1,000,000: 3s. Last read position: NC_035788.1:80,617,949 INFO 2022-03-11 17:30:43 AddOrReplaceReadGroups Processed 49,000,000 records. Elapsed time: 00:02:40s. Time for last 1,000,000: 3s. Last read position: NC_035789.1:8,694,091 INFO 2022-03-11 17:30:46 AddOrReplaceReadGroups Processed 50,000,000 records. Elapsed time: 00:02:43s. Time for last 1,000,000: 3s. Last read position: NC_007175.2:969 INFO 2022-03-11 17:30:49 AddOrReplaceReadGroups Processed 51,000,000 records. Elapsed time: 00:02:46s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 17:30:52 AddOrReplaceReadGroups Processed 52,000,000 records. Elapsed time: 00:02:49s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 17:30:58 AddOrReplaceReadGroups Processed 53,000,000 records. Elapsed time: 00:02:56s. Time for last 1,000,000: 6s. Last read position: */* INFO 2022-03-11 17:31:01 AddOrReplaceReadGroups Processed 54,000,000 records. Elapsed time: 00:02:59s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 17:31:04 AddOrReplaceReadGroups Processed 55,000,000 records. Elapsed time: 00:03:02s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 17:31:07 AddOrReplaceReadGroups Processed 56,000,000 records. Elapsed time: 00:03:05s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 17:31:10 AddOrReplaceReadGroups Processed 57,000,000 records. Elapsed time: 00:03:08s. Time for last 1,000,000: 2s. Last read position: */* [Fri Mar 11 17:31:12 PST 2022] picard.sam.AddOrReplaceReadGroups done. Elapsed time: 3.17 minutes. Runtime.totalMemory()=2902458368 Tool returned: 0 Using GATK jar /home/shared/gatk-4.2.5.0/gatk-package-4.2.5.0-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 /home/shared/gatk-4.2.5.0/gatk-package-4.2.5.0-local.jar AddOrReplaceReadGroups I=S77F.dedup-split.bam O=S77F.dedup-split-RG.bam RGID=1 RGLB=S77F RGPL=ILLUMINA RGPU=unit1 RGSM=S77F INFO 2022-03-11 17:31:14 AddOrReplaceReadGroups ********** NOTE: Picard's command line syntax is changing. ********** ********** For more information, please see: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** ********** The command line looks like this in the new syntax: ********** ********** AddOrReplaceReadGroups -I S77F.dedup-split.bam -O S77F.dedup-split-RG.bam -RGID 1 -RGLB S77F -RGPL ILLUMINA -RGPU unit1 -RGSM S77F ********** 17:31:14.291 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/shared/gatk-4.2.5.0/gatk-package-4.2.5.0-local.jar!/com/intel/gkl/native/libgkl_compression.so [Fri Mar 11 17:31:14 PST 2022] AddOrReplaceReadGroups INPUT=S77F.dedup-split.bam OUTPUT=S77F.dedup-split-RG.bam RGID=1 RGLB=S77F RGPL=ILLUMINA RGPU=unit1 RGSM=S77F VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=2 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Mar 11, 2022 5:31:14 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine INFO: Failed to detect whether we are running on Google Compute Engine. [Fri Mar 11 17:31:14 PST 2022] Executing as sr320@raven on Linux 5.4.0-104-generic amd64; OpenJDK 64-Bit Server VM 11.0.14+9-Ubuntu-0ubuntu2.18.04; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: 4.2.5.0 INFO 2022-03-11 17:31:14 AddOrReplaceReadGroups Created read-group ID=1 PL=ILLUMINA LB=S77F SM=S77F INFO 2022-03-11 17:31:17 AddOrReplaceReadGroups Processed 1,000,000 records. Elapsed time: 00:00:03s. Time for last 1,000,000: 3s. Last read position: NC_035780.1:12,582,317 INFO 2022-03-11 17:31:20 AddOrReplaceReadGroups Processed 2,000,000 records. Elapsed time: 00:00:05s. Time for last 1,000,000: 2s. Last read position: NC_035780.1:27,668,543 INFO 2022-03-11 17:31:23 AddOrReplaceReadGroups Processed 3,000,000 records. Elapsed time: 00:00:08s. Time for last 1,000,000: 2s. Last read position: NC_035780.1:39,880,816 INFO 2022-03-11 17:31:26 AddOrReplaceReadGroups Processed 4,000,000 records. Elapsed time: 00:00:12s. Time for last 1,000,000: 3s. Last read position: NC_035780.1:54,193,227 INFO 2022-03-11 17:31:30 AddOrReplaceReadGroups Processed 5,000,000 records. Elapsed time: 00:00:16s. Time for last 1,000,000: 4s. Last read position: NC_035780.1:60,056,976 INFO 2022-03-11 17:31:34 AddOrReplaceReadGroups Processed 6,000,000 records. Elapsed time: 00:00:20s. Time for last 1,000,000: 3s. Last read position: NC_035781.1:3,057,262 INFO 2022-03-11 17:31:37 AddOrReplaceReadGroups Processed 7,000,000 records. Elapsed time: 00:00:23s. Time for last 1,000,000: 2s. Last read position: NC_035781.1:9,561,720 INFO 2022-03-11 17:31:40 AddOrReplaceReadGroups Processed 8,000,000 records. Elapsed time: 00:00:25s. Time for last 1,000,000: 2s. Last read position: NC_035781.1:15,771,736 INFO 2022-03-11 17:31:43 AddOrReplaceReadGroups Processed 9,000,000 records. Elapsed time: 00:00:29s. Time for last 1,000,000: 3s. Last read position: NC_035781.1:24,155,651 INFO 2022-03-11 17:31:46 AddOrReplaceReadGroups Processed 10,000,000 records. Elapsed time: 00:00:32s. Time for last 1,000,000: 2s. Last read position: NC_035781.1:30,923,837 INFO 2022-03-11 17:31:52 AddOrReplaceReadGroups Processed 11,000,000 records. Elapsed time: 00:00:38s. Time for last 1,000,000: 6s. Last read position: NC_035781.1:40,509,760 INFO 2022-03-11 17:31:55 AddOrReplaceReadGroups Processed 12,000,000 records. Elapsed time: 00:00:41s. Time for last 1,000,000: 3s. Last read position: NC_035781.1:47,009,285 INFO 2022-03-11 17:31:58 AddOrReplaceReadGroups Processed 13,000,000 records. Elapsed time: 00:00:44s. Time for last 1,000,000: 3s. Last read position: NC_035781.1:53,643,155 INFO 2022-03-11 17:32:01 AddOrReplaceReadGroups Processed 14,000,000 records. Elapsed time: 00:00:47s. Time for last 1,000,000: 3s. Last read position: NC_035782.1:9,837,757 INFO 2022-03-11 17:32:04 AddOrReplaceReadGroups Processed 15,000,000 records. Elapsed time: 00:00:50s. Time for last 1,000,000: 3s. Last read position: NC_035782.1:24,481,466 INFO 2022-03-11 17:32:07 AddOrReplaceReadGroups Processed 16,000,000 records. Elapsed time: 00:00:53s. Time for last 1,000,000: 2s. Last read position: NC_035782.1:30,158,869 INFO 2022-03-11 17:32:10 AddOrReplaceReadGroups Processed 17,000,000 records. Elapsed time: 00:00:56s. Time for last 1,000,000: 3s. Last read position: NC_035782.1:39,284,179 INFO 2022-03-11 17:32:13 AddOrReplaceReadGroups Processed 18,000,000 records. Elapsed time: 00:00:59s. Time for last 1,000,000: 3s. Last read position: NC_035782.1:50,117,093 INFO 2022-03-11 17:32:17 AddOrReplaceReadGroups Processed 19,000,000 records. Elapsed time: 00:01:02s. Time for last 1,000,000: 3s. Last read position: NC_035782.1:56,806,959 INFO 2022-03-11 17:32:20 AddOrReplaceReadGroups Processed 20,000,000 records. Elapsed time: 00:01:05s. Time for last 1,000,000: 3s. Last read position: NC_035782.1:64,568,918 INFO 2022-03-11 17:32:26 AddOrReplaceReadGroups Processed 21,000,000 records. Elapsed time: 00:01:11s. Time for last 1,000,000: 6s. Last read position: NC_035782.1:72,448,349 INFO 2022-03-11 17:32:29 AddOrReplaceReadGroups Processed 22,000,000 records. Elapsed time: 00:01:14s. Time for last 1,000,000: 3s. Last read position: NC_035783.1:6,883,685 INFO 2022-03-11 17:32:32 AddOrReplaceReadGroups Processed 23,000,000 records. Elapsed time: 00:01:17s. Time for last 1,000,000: 3s. Last read position: NC_035783.1:16,199,650 INFO 2022-03-11 17:32:35 AddOrReplaceReadGroups Processed 24,000,000 records. Elapsed time: 00:01:20s. Time for last 1,000,000: 3s. Last read position: NC_035783.1:25,255,332 INFO 2022-03-11 17:32:38 AddOrReplaceReadGroups Processed 25,000,000 records. Elapsed time: 00:01:23s. Time for last 1,000,000: 3s. Last read position: NC_035783.1:32,386,946 INFO 2022-03-11 17:32:41 AddOrReplaceReadGroups Processed 26,000,000 records. Elapsed time: 00:01:26s. Time for last 1,000,000: 3s. Last read position: NC_035783.1:40,340,811 INFO 2022-03-11 17:32:44 AddOrReplaceReadGroups Processed 27,000,000 records. Elapsed time: 00:01:30s. Time for last 1,000,000: 3s. Last read position: NC_035783.1:49,431,926 INFO 2022-03-11 17:32:47 AddOrReplaceReadGroups Processed 28,000,000 records. Elapsed time: 00:01:33s. Time for last 1,000,000: 3s. Last read position: NC_035784.1:1,967,399 INFO 2022-03-11 17:32:50 AddOrReplaceReadGroups Processed 29,000,000 records. Elapsed time: 00:01:36s. Time for last 1,000,000: 3s. Last read position: NC_035784.1:8,960,770 INFO 2022-03-11 17:32:53 AddOrReplaceReadGroups Processed 30,000,000 records. Elapsed time: 00:01:39s. Time for last 1,000,000: 3s. Last read position: NC_035784.1:17,995,099 INFO 2022-03-11 17:32:58 AddOrReplaceReadGroups Processed 31,000,000 records. Elapsed time: 00:01:44s. Time for last 1,000,000: 4s. Last read position: NC_035784.1:28,732,959 INFO 2022-03-11 17:33:02 AddOrReplaceReadGroups Processed 32,000,000 records. Elapsed time: 00:01:48s. Time for last 1,000,000: 4s. Last read position: NC_035784.1:36,280,208 INFO 2022-03-11 17:33:05 AddOrReplaceReadGroups Processed 33,000,000 records. Elapsed time: 00:01:51s. Time for last 1,000,000: 3s. Last read position: NC_035784.1:44,246,443 INFO 2022-03-11 17:33:08 AddOrReplaceReadGroups Processed 34,000,000 records. Elapsed time: 00:01:54s. Time for last 1,000,000: 2s. Last read position: NC_035784.1:47,758,247 INFO 2022-03-11 17:33:11 AddOrReplaceReadGroups Processed 35,000,000 records. Elapsed time: 00:01:57s. Time for last 1,000,000: 2s. Last read position: NC_035784.1:52,120,666 INFO 2022-03-11 17:33:14 AddOrReplaceReadGroups Processed 36,000,000 records. Elapsed time: 00:01:59s. Time for last 1,000,000: 2s. Last read position: NC_035784.1:52,200,294 INFO 2022-03-11 17:33:16 AddOrReplaceReadGroups Processed 37,000,000 records. Elapsed time: 00:02:02s. Time for last 1,000,000: 2s. Last read position: NC_035784.1:52,258,666 INFO 2022-03-11 17:33:19 AddOrReplaceReadGroups Processed 38,000,000 records. Elapsed time: 00:02:05s. Time for last 1,000,000: 2s. Last read position: NC_035784.1:52,276,779 INFO 2022-03-11 17:33:22 AddOrReplaceReadGroups Processed 39,000,000 records. Elapsed time: 00:02:07s. Time for last 1,000,000: 2s. Last read position: NC_035784.1:54,235,009 INFO 2022-03-11 17:33:25 AddOrReplaceReadGroups Processed 40,000,000 records. Elapsed time: 00:02:10s. Time for last 1,000,000: 3s. Last read position: NC_035784.1:64,780,191 INFO 2022-03-11 17:33:28 AddOrReplaceReadGroups Processed 41,000,000 records. Elapsed time: 00:02:13s. Time for last 1,000,000: 3s. Last read position: NC_035784.1:73,284,990 INFO 2022-03-11 17:33:34 AddOrReplaceReadGroups Processed 42,000,000 records. Elapsed time: 00:02:19s. Time for last 1,000,000: 5s. Last read position: NC_035784.1:88,803,817 INFO 2022-03-11 17:33:37 AddOrReplaceReadGroups Processed 43,000,000 records. Elapsed time: 00:02:22s. Time for last 1,000,000: 3s. Last read position: NC_035785.1:28,423,283 INFO 2022-03-11 17:33:40 AddOrReplaceReadGroups Processed 44,000,000 records. Elapsed time: 00:02:25s. Time for last 1,000,000: 3s. Last read position: NC_035785.1:37,349,400 INFO 2022-03-11 17:33:43 AddOrReplaceReadGroups Processed 45,000,000 records. Elapsed time: 00:02:28s. Time for last 1,000,000: 3s. Last read position: NC_035786.1:9,297,407 INFO 2022-03-11 17:33:46 AddOrReplaceReadGroups Processed 46,000,000 records. Elapsed time: 00:02:31s. Time for last 1,000,000: 3s. Last read position: NC_035786.1:38,965,393 INFO 2022-03-11 17:33:49 AddOrReplaceReadGroups Processed 47,000,000 records. Elapsed time: 00:02:35s. Time for last 1,000,000: 3s. Last read position: NC_035787.1:514,197 INFO 2022-03-11 17:33:52 AddOrReplaceReadGroups Processed 48,000,000 records. Elapsed time: 00:02:38s. Time for last 1,000,000: 3s. Last read position: NC_035787.1:27,240,005 INFO 2022-03-11 17:33:55 AddOrReplaceReadGroups Processed 49,000,000 records. Elapsed time: 00:02:41s. Time for last 1,000,000: 3s. Last read position: NC_035787.1:54,278,802 INFO 2022-03-11 17:33:58 AddOrReplaceReadGroups Processed 50,000,000 records. Elapsed time: 00:02:44s. Time for last 1,000,000: 3s. Last read position: NC_035787.1:65,515,945 INFO 2022-03-11 17:34:01 AddOrReplaceReadGroups Processed 51,000,000 records. Elapsed time: 00:02:47s. Time for last 1,000,000: 3s. Last read position: NC_035788.1:19,042,473 INFO 2022-03-11 17:34:05 AddOrReplaceReadGroups Processed 52,000,000 records. Elapsed time: 00:02:51s. Time for last 1,000,000: 3s. Last read position: NC_035788.1:59,071,066 INFO 2022-03-11 17:34:11 AddOrReplaceReadGroups Processed 53,000,000 records. Elapsed time: 00:02:56s. Time for last 1,000,000: 5s. Last read position: NC_035788.1:79,473,164 INFO 2022-03-11 17:34:14 AddOrReplaceReadGroups Processed 54,000,000 records. Elapsed time: 00:02:59s. Time for last 1,000,000: 3s. Last read position: NC_035789.1:7,522,984 INFO 2022-03-11 17:34:17 AddOrReplaceReadGroups Processed 55,000,000 records. Elapsed time: 00:03:02s. Time for last 1,000,000: 3s. Last read position: NC_035789.1:31,363,294 INFO 2022-03-11 17:34:20 AddOrReplaceReadGroups Processed 56,000,000 records. Elapsed time: 00:03:05s. Time for last 1,000,000: 2s. Last read position: NC_007175.2:13,738 INFO 2022-03-11 17:34:23 AddOrReplaceReadGroups Processed 57,000,000 records. Elapsed time: 00:03:08s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 17:34:26 AddOrReplaceReadGroups Processed 58,000,000 records. Elapsed time: 00:03:11s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 17:34:29 AddOrReplaceReadGroups Processed 59,000,000 records. Elapsed time: 00:03:14s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 17:34:31 AddOrReplaceReadGroups Processed 60,000,000 records. Elapsed time: 00:03:17s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 17:34:34 AddOrReplaceReadGroups Processed 61,000,000 records. Elapsed time: 00:03:20s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 17:34:37 AddOrReplaceReadGroups Processed 62,000,000 records. Elapsed time: 00:03:23s. Time for last 1,000,000: 2s. Last read position: */* [Fri Mar 11 17:34:39 PST 2022] picard.sam.AddOrReplaceReadGroups done. Elapsed time: 3.42 minutes. Runtime.totalMemory()=2881486848 Tool returned: 0 Using GATK jar /home/shared/gatk-4.2.5.0/gatk-package-4.2.5.0-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 /home/shared/gatk-4.2.5.0/gatk-package-4.2.5.0-local.jar AddOrReplaceReadGroups I=S7M.dedup-split.bam O=S7M.dedup-split-RG.bam RGID=1 RGLB=S7M RGPL=ILLUMINA RGPU=unit1 RGSM=S7M INFO 2022-03-11 17:34:40 AddOrReplaceReadGroups ********** NOTE: Picard's command line syntax is changing. ********** ********** For more information, please see: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** ********** The command line looks like this in the new syntax: ********** ********** AddOrReplaceReadGroups -I S7M.dedup-split.bam -O S7M.dedup-split-RG.bam -RGID 1 -RGLB S7M -RGPL ILLUMINA -RGPU unit1 -RGSM S7M ********** 17:34:41.011 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/shared/gatk-4.2.5.0/gatk-package-4.2.5.0-local.jar!/com/intel/gkl/native/libgkl_compression.so [Fri Mar 11 17:34:41 PST 2022] AddOrReplaceReadGroups INPUT=S7M.dedup-split.bam OUTPUT=S7M.dedup-split-RG.bam RGID=1 RGLB=S7M RGPL=ILLUMINA RGPU=unit1 RGSM=S7M VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=2 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Mar 11, 2022 5:34:41 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine INFO: Failed to detect whether we are running on Google Compute Engine. [Fri Mar 11 17:34:41 PST 2022] Executing as sr320@raven on Linux 5.4.0-104-generic amd64; OpenJDK 64-Bit Server VM 11.0.14+9-Ubuntu-0ubuntu2.18.04; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: 4.2.5.0 INFO 2022-03-11 17:34:41 AddOrReplaceReadGroups Created read-group ID=1 PL=ILLUMINA LB=S7M SM=S7M INFO 2022-03-11 17:34:46 AddOrReplaceReadGroups Processed 1,000,000 records. Elapsed time: 00:00:04s. Time for last 1,000,000: 4s. Last read position: NC_035780.1:12,264,470 INFO 2022-03-11 17:34:49 AddOrReplaceReadGroups Processed 2,000,000 records. Elapsed time: 00:00:07s. Time for last 1,000,000: 2s. Last read position: NC_035780.1:24,629,039 INFO 2022-03-11 17:34:52 AddOrReplaceReadGroups Processed 3,000,000 records. Elapsed time: 00:00:10s. Time for last 1,000,000: 2s. Last read position: NC_035780.1:36,347,487 INFO 2022-03-11 17:34:55 AddOrReplaceReadGroups Processed 4,000,000 records. Elapsed time: 00:00:13s. Time for last 1,000,000: 3s. Last read position: NC_035780.1:51,381,024 INFO 2022-03-11 17:34:58 AddOrReplaceReadGroups Processed 5,000,000 records. Elapsed time: 00:00:16s. Time for last 1,000,000: 3s. Last read position: NC_035780.1:65,354,231 INFO 2022-03-11 17:35:01 AddOrReplaceReadGroups Processed 6,000,000 records. Elapsed time: 00:00:19s. Time for last 1,000,000: 3s. Last read position: NC_035781.1:12,730,512 INFO 2022-03-11 17:35:04 AddOrReplaceReadGroups Processed 7,000,000 records. Elapsed time: 00:00:22s. Time for last 1,000,000: 3s. Last read position: NC_035781.1:24,158,662 INFO 2022-03-11 17:35:07 AddOrReplaceReadGroups Processed 8,000,000 records. Elapsed time: 00:00:25s. Time for last 1,000,000: 3s. Last read position: NC_035781.1:38,225,049 INFO 2022-03-11 17:35:10 AddOrReplaceReadGroups Processed 9,000,000 records. Elapsed time: 00:00:28s. Time for last 1,000,000: 3s. Last read position: NC_035781.1:52,406,782 INFO 2022-03-11 17:35:13 AddOrReplaceReadGroups Processed 10,000,000 records. Elapsed time: 00:00:31s. Time for last 1,000,000: 2s. Last read position: NC_035782.1:3,329,472 INFO 2022-03-11 17:35:20 AddOrReplaceReadGroups Processed 11,000,000 records. Elapsed time: 00:00:38s. Time for last 1,000,000: 6s. Last read position: NC_035782.1:19,013,227 INFO 2022-03-11 17:35:23 AddOrReplaceReadGroups Processed 12,000,000 records. Elapsed time: 00:00:41s. Time for last 1,000,000: 3s. Last read position: NC_035782.1:33,977,569 INFO 2022-03-11 17:35:26 AddOrReplaceReadGroups Processed 13,000,000 records. Elapsed time: 00:00:44s. Time for last 1,000,000: 3s. Last read position: NC_035782.1:48,676,028 INFO 2022-03-11 17:35:29 AddOrReplaceReadGroups Processed 14,000,000 records. Elapsed time: 00:00:47s. Time for last 1,000,000: 3s. Last read position: NC_035782.1:60,200,485 INFO 2022-03-11 17:35:32 AddOrReplaceReadGroups Processed 15,000,000 records. Elapsed time: 00:00:50s. Time for last 1,000,000: 3s. Last read position: NC_035782.1:73,818,406 INFO 2022-03-11 17:35:35 AddOrReplaceReadGroups Processed 16,000,000 records. Elapsed time: 00:00:53s. Time for last 1,000,000: 3s. Last read position: NC_035783.1:11,556,366 INFO 2022-03-11 17:35:38 AddOrReplaceReadGroups Processed 17,000,000 records. Elapsed time: 00:00:56s. Time for last 1,000,000: 3s. Last read position: NC_035783.1:22,376,999 INFO 2022-03-11 17:35:41 AddOrReplaceReadGroups Processed 18,000,000 records. Elapsed time: 00:00:59s. Time for last 1,000,000: 3s. Last read position: NC_035783.1:36,499,790 INFO 2022-03-11 17:35:44 AddOrReplaceReadGroups Processed 19,000,000 records. Elapsed time: 00:01:02s. Time for last 1,000,000: 2s. Last read position: NC_035783.1:48,430,497 INFO 2022-03-11 17:35:47 AddOrReplaceReadGroups Processed 20,000,000 records. Elapsed time: 00:01:05s. Time for last 1,000,000: 3s. Last read position: NC_035784.1:2,460,465 INFO 2022-03-11 17:35:53 AddOrReplaceReadGroups Processed 21,000,000 records. Elapsed time: 00:01:12s. Time for last 1,000,000: 6s. Last read position: NC_035784.1:15,121,098 INFO 2022-03-11 17:35:56 AddOrReplaceReadGroups Processed 22,000,000 records. Elapsed time: 00:01:15s. Time for last 1,000,000: 3s. Last read position: NC_035784.1:29,149,971 INFO 2022-03-11 17:36:00 AddOrReplaceReadGroups Processed 23,000,000 records. Elapsed time: 00:01:18s. Time for last 1,000,000: 3s. Last read position: NC_035784.1:42,979,206 INFO 2022-03-11 17:36:02 AddOrReplaceReadGroups Processed 24,000,000 records. Elapsed time: 00:01:21s. Time for last 1,000,000: 2s. Last read position: NC_035784.1:52,055,411 INFO 2022-03-11 17:36:05 AddOrReplaceReadGroups Processed 25,000,000 records. Elapsed time: 00:01:24s. Time for last 1,000,000: 2s. Last read position: NC_035784.1:52,257,132 INFO 2022-03-11 17:36:08 AddOrReplaceReadGroups Processed 26,000,000 records. Elapsed time: 00:01:26s. Time for last 1,000,000: 2s. Last read position: NC_035784.1:53,221,537 INFO 2022-03-11 17:36:11 AddOrReplaceReadGroups Processed 27,000,000 records. Elapsed time: 00:01:29s. Time for last 1,000,000: 3s. Last read position: NC_035784.1:66,062,986 INFO 2022-03-11 17:36:14 AddOrReplaceReadGroups Processed 28,000,000 records. Elapsed time: 00:01:32s. Time for last 1,000,000: 3s. Last read position: NC_035784.1:79,904,558 INFO 2022-03-11 17:36:17 AddOrReplaceReadGroups Processed 29,000,000 records. Elapsed time: 00:01:35s. Time for last 1,000,000: 3s. Last read position: NC_035784.1:95,100,980 INFO 2022-03-11 17:36:20 AddOrReplaceReadGroups Processed 30,000,000 records. Elapsed time: 00:01:38s. Time for last 1,000,000: 2s. Last read position: NC_035785.1:11,645,299 INFO 2022-03-11 17:36:23 AddOrReplaceReadGroups Processed 31,000,000 records. Elapsed time: 00:01:41s. Time for last 1,000,000: 2s. Last read position: NC_035785.1:28,878,523 INFO 2022-03-11 17:36:29 AddOrReplaceReadGroups Processed 32,000,000 records. Elapsed time: 00:01:48s. Time for last 1,000,000: 6s. Last read position: NC_035785.1:41,734,988 INFO 2022-03-11 17:36:32 AddOrReplaceReadGroups Processed 33,000,000 records. Elapsed time: 00:01:51s. Time for last 1,000,000: 2s. Last read position: NC_035786.1:3,438,286 INFO 2022-03-11 17:36:35 AddOrReplaceReadGroups Processed 34,000,000 records. Elapsed time: 00:01:53s. Time for last 1,000,000: 2s. Last read position: NC_035786.1:21,147,085 INFO 2022-03-11 17:36:38 AddOrReplaceReadGroups Processed 35,000,000 records. Elapsed time: 00:01:56s. Time for last 1,000,000: 2s. Last read position: NC_035786.1:39,451,972 INFO 2022-03-11 17:36:41 AddOrReplaceReadGroups Processed 36,000,000 records. Elapsed time: 00:01:59s. Time for last 1,000,000: 3s. Last read position: NC_035786.1:55,374,250 INFO 2022-03-11 17:36:44 AddOrReplaceReadGroups Processed 37,000,000 records. Elapsed time: 00:02:03s. Time for last 1,000,000: 3s. Last read position: NC_035787.1:15,124,656 INFO 2022-03-11 17:36:47 AddOrReplaceReadGroups Processed 38,000,000 records. Elapsed time: 00:02:06s. Time for last 1,000,000: 3s. Last read position: NC_035787.1:33,500,012 INFO 2022-03-11 17:36:50 AddOrReplaceReadGroups Processed 39,000,000 records. Elapsed time: 00:02:09s. Time for last 1,000,000: 3s. Last read position: NC_035787.1:48,349,843 INFO 2022-03-11 17:36:53 AddOrReplaceReadGroups Processed 40,000,000 records. Elapsed time: 00:02:12s. Time for last 1,000,000: 3s. Last read position: NC_035787.1:61,243,798 INFO 2022-03-11 17:36:56 AddOrReplaceReadGroups Processed 41,000,000 records. Elapsed time: 00:02:15s. Time for last 1,000,000: 3s. Last read position: NC_035788.1:1,280,539 INFO 2022-03-11 17:37:02 AddOrReplaceReadGroups Processed 42,000,000 records. Elapsed time: 00:02:21s. Time for last 1,000,000: 6s. Last read position: NC_035788.1:18,365,271 INFO 2022-03-11 17:37:06 AddOrReplaceReadGroups Processed 43,000,000 records. Elapsed time: 00:02:24s. Time for last 1,000,000: 3s. Last read position: NC_035788.1:40,534,944 INFO 2022-03-11 17:37:09 AddOrReplaceReadGroups Processed 44,000,000 records. Elapsed time: 00:02:27s. Time for last 1,000,000: 3s. Last read position: NC_035788.1:55,099,787 INFO 2022-03-11 17:37:12 AddOrReplaceReadGroups Processed 45,000,000 records. Elapsed time: 00:02:30s. Time for last 1,000,000: 3s. Last read position: NC_035788.1:68,840,800 INFO 2022-03-11 17:37:15 AddOrReplaceReadGroups Processed 46,000,000 records. Elapsed time: 00:02:33s. Time for last 1,000,000: 3s. Last read position: NC_035788.1:82,263,015 INFO 2022-03-11 17:37:18 AddOrReplaceReadGroups Processed 47,000,000 records. Elapsed time: 00:02:36s. Time for last 1,000,000: 3s. Last read position: NC_035788.1:101,704,438 INFO 2022-03-11 17:37:21 AddOrReplaceReadGroups Processed 48,000,000 records. Elapsed time: 00:02:39s. Time for last 1,000,000: 3s. Last read position: NC_035789.1:12,535,971 INFO 2022-03-11 17:37:24 AddOrReplaceReadGroups Processed 49,000,000 records. Elapsed time: 00:02:42s. Time for last 1,000,000: 3s. Last read position: NC_035789.1:23,442,181 INFO 2022-03-11 17:37:27 AddOrReplaceReadGroups Processed 50,000,000 records. Elapsed time: 00:02:45s. Time for last 1,000,000: 3s. Last read position: */* INFO 2022-03-11 17:37:30 AddOrReplaceReadGroups Processed 51,000,000 records. Elapsed time: 00:02:48s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 17:37:33 AddOrReplaceReadGroups Processed 52,000,000 records. Elapsed time: 00:02:51s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 17:37:39 AddOrReplaceReadGroups Processed 53,000,000 records. Elapsed time: 00:02:57s. Time for last 1,000,000: 6s. Last read position: */* INFO 2022-03-11 17:37:42 AddOrReplaceReadGroups Processed 54,000,000 records. Elapsed time: 00:03:00s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 17:37:45 AddOrReplaceReadGroups Processed 55,000,000 records. Elapsed time: 00:03:03s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 17:37:48 AddOrReplaceReadGroups Processed 56,000,000 records. Elapsed time: 00:03:06s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 17:37:50 AddOrReplaceReadGroups Processed 57,000,000 records. Elapsed time: 00:03:09s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 17:37:53 AddOrReplaceReadGroups Processed 58,000,000 records. Elapsed time: 00:03:12s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 17:37:56 AddOrReplaceReadGroups Processed 59,000,000 records. Elapsed time: 00:03:14s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 17:37:59 AddOrReplaceReadGroups Processed 60,000,000 records. Elapsed time: 00:03:17s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 17:38:02 AddOrReplaceReadGroups Processed 61,000,000 records. Elapsed time: 00:03:20s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 17:38:05 AddOrReplaceReadGroups Processed 62,000,000 records. Elapsed time: 00:03:23s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 17:38:07 AddOrReplaceReadGroups Processed 63,000,000 records. Elapsed time: 00:03:26s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 17:38:15 AddOrReplaceReadGroups Processed 64,000,000 records. Elapsed time: 00:03:33s. Time for last 1,000,000: 7s. Last read position: */* INFO 2022-03-11 17:38:18 AddOrReplaceReadGroups Processed 65,000,000 records. Elapsed time: 00:03:36s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 17:38:20 AddOrReplaceReadGroups Processed 66,000,000 records. Elapsed time: 00:03:39s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 17:38:23 AddOrReplaceReadGroups Processed 67,000,000 records. Elapsed time: 00:03:42s. Time for last 1,000,000: 2s. Last read position: */* [Fri Mar 11 17:38:25 PST 2022] picard.sam.AddOrReplaceReadGroups done. Elapsed time: 3.74 minutes. Runtime.totalMemory()=2805989376 Tool returned: 0 Using GATK jar /home/shared/gatk-4.2.5.0/gatk-package-4.2.5.0-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 /home/shared/gatk-4.2.5.0/gatk-package-4.2.5.0-local.jar AddOrReplaceReadGroups I=S9M.dedup-split.bam O=S9M.dedup-split-RG.bam RGID=1 RGLB=S9M RGPL=ILLUMINA RGPU=unit1 RGSM=S9M INFO 2022-03-11 17:38:27 AddOrReplaceReadGroups ********** NOTE: Picard's command line syntax is changing. ********** ********** For more information, please see: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** ********** The command line looks like this in the new syntax: ********** ********** AddOrReplaceReadGroups -I S9M.dedup-split.bam -O S9M.dedup-split-RG.bam -RGID 1 -RGLB S9M -RGPL ILLUMINA -RGPU unit1 -RGSM S9M ********** 17:38:27.344 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/shared/gatk-4.2.5.0/gatk-package-4.2.5.0-local.jar!/com/intel/gkl/native/libgkl_compression.so [Fri Mar 11 17:38:27 PST 2022] AddOrReplaceReadGroups INPUT=S9M.dedup-split.bam OUTPUT=S9M.dedup-split-RG.bam RGID=1 RGLB=S9M RGPL=ILLUMINA RGPU=unit1 RGSM=S9M VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=2 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Mar 11, 2022 5:38:27 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine INFO: Failed to detect whether we are running on Google Compute Engine. [Fri Mar 11 17:38:27 PST 2022] Executing as sr320@raven on Linux 5.4.0-104-generic amd64; OpenJDK 64-Bit Server VM 11.0.14+9-Ubuntu-0ubuntu2.18.04; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: 4.2.5.0 INFO 2022-03-11 17:38:27 AddOrReplaceReadGroups Created read-group ID=1 PL=ILLUMINA LB=S9M SM=S9M INFO 2022-03-11 17:38:30 AddOrReplaceReadGroups Processed 1,000,000 records. Elapsed time: 00:00:03s. Time for last 1,000,000: 3s. Last read position: NC_035780.1:10,072,983 INFO 2022-03-11 17:38:33 AddOrReplaceReadGroups Processed 2,000,000 records. Elapsed time: 00:00:05s. Time for last 1,000,000: 2s. Last read position: NC_035780.1:21,872,046 INFO 2022-03-11 17:38:36 AddOrReplaceReadGroups Processed 3,000,000 records. Elapsed time: 00:00:08s. Time for last 1,000,000: 2s. Last read position: NC_035780.1:31,415,361 INFO 2022-03-11 17:38:39 AddOrReplaceReadGroups Processed 4,000,000 records. Elapsed time: 00:00:11s. Time for last 1,000,000: 3s. Last read position: NC_035780.1:41,987,142 INFO 2022-03-11 17:38:42 AddOrReplaceReadGroups Processed 5,000,000 records. Elapsed time: 00:00:14s. Time for last 1,000,000: 3s. Last read position: NC_035780.1:56,091,134 INFO 2022-03-11 17:38:46 AddOrReplaceReadGroups Processed 6,000,000 records. Elapsed time: 00:00:19s. Time for last 1,000,000: 4s. Last read position: NC_035781.1:1,736,966 INFO 2022-03-11 17:38:49 AddOrReplaceReadGroups Processed 7,000,000 records. Elapsed time: 00:00:22s. Time for last 1,000,000: 2s. Last read position: NC_035781.1:12,717,055 INFO 2022-03-11 17:38:52 AddOrReplaceReadGroups Processed 8,000,000 records. Elapsed time: 00:00:25s. Time for last 1,000,000: 2s. Last read position: NC_035781.1:22,275,105 INFO 2022-03-11 17:38:55 AddOrReplaceReadGroups Processed 9,000,000 records. Elapsed time: 00:00:28s. Time for last 1,000,000: 3s. Last read position: NC_035781.1:33,522,227 INFO 2022-03-11 17:38:58 AddOrReplaceReadGroups Processed 10,000,000 records. Elapsed time: 00:00:31s. Time for last 1,000,000: 3s. Last read position: NC_035781.1:45,010,015 INFO 2022-03-11 17:39:02 AddOrReplaceReadGroups Processed 11,000,000 records. Elapsed time: 00:00:34s. Time for last 1,000,000: 3s. Last read position: NC_035781.1:55,236,271 INFO 2022-03-11 17:39:08 AddOrReplaceReadGroups Processed 12,000,000 records. Elapsed time: 00:00:40s. Time for last 1,000,000: 6s. Last read position: NC_035782.1:4,934,604 INFO 2022-03-11 17:39:11 AddOrReplaceReadGroups Processed 13,000,000 records. Elapsed time: 00:00:43s. Time for last 1,000,000: 3s. Last read position: NC_035782.1:18,062,781 INFO 2022-03-11 17:39:14 AddOrReplaceReadGroups Processed 14,000,000 records. Elapsed time: 00:00:46s. Time for last 1,000,000: 3s. Last read position: NC_035782.1:30,576,808 INFO 2022-03-11 17:39:17 AddOrReplaceReadGroups Processed 15,000,000 records. Elapsed time: 00:00:50s. Time for last 1,000,000: 3s. Last read position: NC_035782.1:41,946,157 INFO 2022-03-11 17:39:20 AddOrReplaceReadGroups Processed 16,000,000 records. Elapsed time: 00:00:53s. Time for last 1,000,000: 3s. Last read position: NC_035782.1:53,390,166 INFO 2022-03-11 17:39:23 AddOrReplaceReadGroups Processed 17,000,000 records. Elapsed time: 00:00:56s. Time for last 1,000,000: 3s. Last read position: NC_035782.1:62,861,252 INFO 2022-03-11 17:39:26 AddOrReplaceReadGroups Processed 18,000,000 records. Elapsed time: 00:00:59s. Time for last 1,000,000: 3s. Last read position: NC_035782.1:74,739,958 INFO 2022-03-11 17:39:29 AddOrReplaceReadGroups Processed 19,000,000 records. Elapsed time: 00:01:02s. Time for last 1,000,000: 3s. Last read position: NC_035783.1:9,846,773 INFO 2022-03-11 17:39:32 AddOrReplaceReadGroups Processed 20,000,000 records. Elapsed time: 00:01:05s. Time for last 1,000,000: 3s. Last read position: NC_035783.1:19,578,010 INFO 2022-03-11 17:39:35 AddOrReplaceReadGroups Processed 21,000,000 records. Elapsed time: 00:01:08s. Time for last 1,000,000: 3s. Last read position: NC_035783.1:30,455,412 INFO 2022-03-11 17:39:42 AddOrReplaceReadGroups Processed 22,000,000 records. Elapsed time: 00:01:14s. Time for last 1,000,000: 6s. Last read position: NC_035783.1:41,872,151 INFO 2022-03-11 17:39:45 AddOrReplaceReadGroups Processed 23,000,000 records. Elapsed time: 00:01:17s. Time for last 1,000,000: 3s. Last read position: NC_035783.1:51,869,141 INFO 2022-03-11 17:39:48 AddOrReplaceReadGroups Processed 24,000,000 records. Elapsed time: 00:01:20s. Time for last 1,000,000: 3s. Last read position: NC_035784.1:3,533,828 INFO 2022-03-11 17:39:51 AddOrReplaceReadGroups Processed 25,000,000 records. Elapsed time: 00:01:23s. Time for last 1,000,000: 3s. Last read position: NC_035784.1:14,439,396 INFO 2022-03-11 17:39:54 AddOrReplaceReadGroups Processed 26,000,000 records. Elapsed time: 00:01:26s. Time for last 1,000,000: 3s. Last read position: NC_035784.1:25,821,696 INFO 2022-03-11 17:39:57 AddOrReplaceReadGroups Processed 27,000,000 records. Elapsed time: 00:01:29s. Time for last 1,000,000: 3s. Last read position: NC_035784.1:37,083,961 INFO 2022-03-11 17:40:00 AddOrReplaceReadGroups Processed 28,000,000 records. Elapsed time: 00:01:32s. Time for last 1,000,000: 2s. Last read position: NC_035784.1:45,971,369 INFO 2022-03-11 17:40:03 AddOrReplaceReadGroups Processed 29,000,000 records. Elapsed time: 00:01:35s. Time for last 1,000,000: 2s. Last read position: NC_035784.1:52,256,691 INFO 2022-03-11 17:40:06 AddOrReplaceReadGroups Processed 30,000,000 records. Elapsed time: 00:01:38s. Time for last 1,000,000: 2s. Last read position: NC_035784.1:59,077,849 INFO 2022-03-11 17:40:09 AddOrReplaceReadGroups Processed 31,000,000 records. Elapsed time: 00:01:41s. Time for last 1,000,000: 3s. Last read position: NC_035784.1:69,476,122 INFO 2022-03-11 17:40:13 AddOrReplaceReadGroups Processed 32,000,000 records. Elapsed time: 00:01:46s. Time for last 1,000,000: 4s. Last read position: NC_035784.1:82,068,634 INFO 2022-03-11 17:40:18 AddOrReplaceReadGroups Processed 33,000,000 records. Elapsed time: 00:01:51s. Time for last 1,000,000: 4s. Last read position: NC_035784.1:94,148,737 INFO 2022-03-11 17:40:21 AddOrReplaceReadGroups Processed 34,000,000 records. Elapsed time: 00:01:54s. Time for last 1,000,000: 2s. Last read position: NC_035785.1:5,642,498 INFO 2022-03-11 17:40:24 AddOrReplaceReadGroups Processed 35,000,000 records. Elapsed time: 00:01:57s. Time for last 1,000,000: 2s. Last read position: NC_035785.1:17,749,861 INFO 2022-03-11 17:40:27 AddOrReplaceReadGroups Processed 36,000,000 records. Elapsed time: 00:02:00s. Time for last 1,000,000: 3s. Last read position: NC_035785.1:32,917,375 INFO 2022-03-11 17:40:30 AddOrReplaceReadGroups Processed 37,000,000 records. Elapsed time: 00:02:03s. Time for last 1,000,000: 3s. Last read position: NC_035785.1:43,479,765 INFO 2022-03-11 17:40:33 AddOrReplaceReadGroups Processed 38,000,000 records. Elapsed time: 00:02:05s. Time for last 1,000,000: 2s. Last read position: NC_035786.1:4,192,226 INFO 2022-03-11 17:40:36 AddOrReplaceReadGroups Processed 39,000,000 records. Elapsed time: 00:02:09s. Time for last 1,000,000: 3s. Last read position: NC_035786.1:17,479,057 INFO 2022-03-11 17:40:39 AddOrReplaceReadGroups Processed 40,000,000 records. Elapsed time: 00:02:12s. Time for last 1,000,000: 3s. Last read position: NC_035786.1:34,041,504 INFO 2022-03-11 17:40:42 AddOrReplaceReadGroups Processed 41,000,000 records. Elapsed time: 00:02:15s. Time for last 1,000,000: 3s. Last read position: NC_035786.1:48,426,884 INFO 2022-03-11 17:40:45 AddOrReplaceReadGroups Processed 42,000,000 records. Elapsed time: 00:02:18s. Time for last 1,000,000: 2s. Last read position: NC_035787.1:2,840,644 INFO 2022-03-11 17:40:52 AddOrReplaceReadGroups Processed 43,000,000 records. Elapsed time: 00:02:24s. Time for last 1,000,000: 6s. Last read position: NC_035787.1:17,679,141 INFO 2022-03-11 17:40:55 AddOrReplaceReadGroups Processed 44,000,000 records. Elapsed time: 00:02:27s. Time for last 1,000,000: 3s. Last read position: NC_035787.1:33,155,883 INFO 2022-03-11 17:40:58 AddOrReplaceReadGroups Processed 45,000,000 records. Elapsed time: 00:02:30s. Time for last 1,000,000: 2s. Last read position: NC_035787.1:46,276,639 INFO 2022-03-11 17:41:01 AddOrReplaceReadGroups Processed 46,000,000 records. Elapsed time: 00:02:33s. Time for last 1,000,000: 2s. Last read position: NC_035787.1:58,590,076 INFO 2022-03-11 17:41:04 AddOrReplaceReadGroups Processed 47,000,000 records. Elapsed time: 00:02:36s. Time for last 1,000,000: 2s. Last read position: NC_035787.1:68,448,189 INFO 2022-03-11 17:41:07 AddOrReplaceReadGroups Processed 48,000,000 records. Elapsed time: 00:02:39s. Time for last 1,000,000: 3s. Last read position: NC_035788.1:8,786,726 INFO 2022-03-11 17:41:10 AddOrReplaceReadGroups Processed 49,000,000 records. Elapsed time: 00:02:42s. Time for last 1,000,000: 3s. Last read position: NC_035788.1:22,581,022 INFO 2022-03-11 17:41:13 AddOrReplaceReadGroups Processed 50,000,000 records. Elapsed time: 00:02:45s. Time for last 1,000,000: 3s. Last read position: NC_035788.1:41,367,470 INFO 2022-03-11 17:41:16 AddOrReplaceReadGroups Processed 51,000,000 records. Elapsed time: 00:02:48s. Time for last 1,000,000: 2s. Last read position: NC_035788.1:53,789,422 INFO 2022-03-11 17:41:19 AddOrReplaceReadGroups Processed 52,000,000 records. Elapsed time: 00:02:51s. Time for last 1,000,000: 3s. Last read position: NC_035788.1:66,762,894 INFO 2022-03-11 17:41:25 AddOrReplaceReadGroups Processed 53,000,000 records. Elapsed time: 00:02:57s. Time for last 1,000,000: 6s. Last read position: NC_035788.1:78,309,100 INFO 2022-03-11 17:41:28 AddOrReplaceReadGroups Processed 54,000,000 records. Elapsed time: 00:03:00s. Time for last 1,000,000: 3s. Last read position: NC_035788.1:91,714,728 INFO 2022-03-11 17:41:31 AddOrReplaceReadGroups Processed 55,000,000 records. Elapsed time: 00:03:03s. Time for last 1,000,000: 2s. Last read position: NC_035789.1:2,333,023 INFO 2022-03-11 17:41:34 AddOrReplaceReadGroups Processed 56,000,000 records. Elapsed time: 00:03:06s. Time for last 1,000,000: 2s. Last read position: NC_035789.1:13,779,393 INFO 2022-03-11 17:41:37 AddOrReplaceReadGroups Processed 57,000,000 records. Elapsed time: 00:03:09s. Time for last 1,000,000: 2s. Last read position: NC_035789.1:27,130,137 INFO 2022-03-11 17:41:40 AddOrReplaceReadGroups Processed 58,000,000 records. Elapsed time: 00:03:12s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 17:41:43 AddOrReplaceReadGroups Processed 59,000,000 records. Elapsed time: 00:03:15s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 17:41:45 AddOrReplaceReadGroups Processed 60,000,000 records. Elapsed time: 00:03:18s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 17:41:48 AddOrReplaceReadGroups Processed 61,000,000 records. Elapsed time: 00:03:21s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 17:41:51 AddOrReplaceReadGroups Processed 62,000,000 records. Elapsed time: 00:03:24s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 17:41:54 AddOrReplaceReadGroups Processed 63,000,000 records. Elapsed time: 00:03:26s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 17:42:01 AddOrReplaceReadGroups Processed 64,000,000 records. Elapsed time: 00:03:33s. Time for last 1,000,000: 6s. Last read position: */* INFO 2022-03-11 17:42:04 AddOrReplaceReadGroups Processed 65,000,000 records. Elapsed time: 00:03:36s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 17:42:07 AddOrReplaceReadGroups Processed 66,000,000 records. Elapsed time: 00:03:39s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 17:42:09 AddOrReplaceReadGroups Processed 67,000,000 records. Elapsed time: 00:03:42s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 17:42:12 AddOrReplaceReadGroups Processed 68,000,000 records. Elapsed time: 00:03:45s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 17:42:15 AddOrReplaceReadGroups Processed 69,000,000 records. Elapsed time: 00:03:48s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 17:42:18 AddOrReplaceReadGroups Processed 70,000,000 records. Elapsed time: 00:03:50s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 17:42:21 AddOrReplaceReadGroups Processed 71,000,000 records. Elapsed time: 00:03:53s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 17:42:24 AddOrReplaceReadGroups Processed 72,000,000 records. Elapsed time: 00:03:56s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 17:42:27 AddOrReplaceReadGroups Processed 73,000,000 records. Elapsed time: 00:03:59s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 17:42:29 AddOrReplaceReadGroups Processed 74,000,000 records. Elapsed time: 00:04:02s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 17:42:37 AddOrReplaceReadGroups Processed 75,000,000 records. Elapsed time: 00:04:10s. Time for last 1,000,000: 7s. Last read position: */* INFO 2022-03-11 17:42:40 AddOrReplaceReadGroups Processed 76,000,000 records. Elapsed time: 00:04:12s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 17:42:43 AddOrReplaceReadGroups Processed 77,000,000 records. Elapsed time: 00:04:15s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 17:42:46 AddOrReplaceReadGroups Processed 78,000,000 records. Elapsed time: 00:04:18s. Time for last 1,000,000: 2s. Last read position: */* INFO 2022-03-11 17:42:48 AddOrReplaceReadGroups Processed 79,000,000 records. Elapsed time: 00:04:21s. Time for last 1,000,000: 2s. Last read position: */* [Fri Mar 11 17:42:50 PST 2022] picard.sam.AddOrReplaceReadGroups done. Elapsed time: 4.39 minutes. Runtime.totalMemory()=2780823552 Tool returned: 0