Picard CollectHsMetrics doesn't generate the output file
REQUIRED for all errors and issues:
a) GATK version used: Picard v3.2
b) Exact command used: picard CollectHsMetrics -I /fast/data/raw/SLX-23587/BAM/SLX-23587.C5.markdup.sorted.bam -O SLX23587-C5_HSmetrics.txt -R /fast/data/RefFiles/hg38_noAltHla_UCSC.fa -BAIT_INTERVALS /fast/data/RefFiles/covered_targets_Twist_Methylome_hg38_intervals.bed -TARGET_INTERVALS /fast/data/RefFiles/covered_targets_Twist_Methylome_hg38_intervals.bed -MINIMUM_MAPPING_QUALITY 20 -COVERAGE_CAP 1000 -NEAR_DISTANCE 500
c) Entire program log:
/bin/picard: line 5: warning: setlocale: LC_ALL: cannot change locale (en_US.UTF-8): No such file or directory
12:55:49.997 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/monica.dellarosa/.conda/envs/molpipvenv/share/picard-3.2.0-0/picard.jar!/com/intel/gkl/native/libgkl_compression.so
[Fri Feb 21 12:55:50 UTC 2025] CollectHsMetrics --BAIT_INTERVALS /fast/data/RefFiles/covered_targets_Twist_Methylome_hg38_intervals.bed --TARGET_INTERVALS /fast/data/RefFiles/covered_targets_Twist_Methylome_hg38_intervals.bed --INPUT /fast/data/raw/SLX-23587/BAM/SLX-23587.C5.markdup.sorted.bam --OUTPUT SLX23587-C5_HSmetrics.txt --NEAR_DISTANCE 500 --MINIMUM_MAPPING_QUALITY 20 --COVERAGE_CAP 1000 --REFERENCE_SEQUENCE /fast/data/RefFiles/hg38_noAltHla_UCSC.fa --METRIC_ACCUMULATION_LEVEL ALL_READS --MINIMUM_BASE_QUALITY 20 --CLIP_OVERLAPPING_READS true --INCLUDE_INDELS false --SAMPLE_SIZE 10000 --ALLELE_FRACTION 0.001 --ALLELE_FRACTION 0.005 --ALLELE_FRACTION 0.01 --ALLELE_FRACTION 0.02 --ALLELE_FRACTION 0.05 --ALLELE_FRACTION 0.1 --ALLELE_FRACTION 0.2 --ALLELE_FRACTION 0.3 --ALLELE_FRACTION 0.5 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Fri Feb 21 12:55:50 UTC 2025] Executing as monica.dellarosa@athena on Linux 5.15.0-119-generic amd64; OpenJDK 64-Bit Server VM 17.0.13-internal+0-adhoc..src; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:3.2.0-1-g3948afb6b
INFO 2025-02-21 12:56:04 CollectHsMetrics Processed 1,000,000 records. Elapsed time: 00:00:07s. Time for last 1,000,000: 7s. Last read position: chr1:3,224,644
INFO 2025-02-21 12:56:11 CollectHsMetrics Processed 2,000,000 records. Elapsed time: 00:00:13s. Time for last 1,000,000: 6s. Last read position: chr1:9,700,320
INFO 2025-02-21 12:56:17 CollectHsMetrics Processed 3,000,000 records. Elapsed time: 00:00:20s. Time for last 1,000,000: 6s. Last read position: chr1:17,128,872
INFO 2025-02-21 12:56:24 CollectHsMetrics Processed 4,000,000 records. Elapsed time: 00:00:26s. Time for last 1,000,000: 6s. Last read position: chr1:25,686,327
INFO 2025-02-21 12:56:30 CollectHsMetrics Processed 5,000,000 records. Elapsed time: 00:00:33s. Time for last 1,000,000: 6s. Last read position: chr1:35,031,312
INFO 2025-02-21 12:56:37 CollectHsMetrics Processed 6,000,000 records. Elapsed time: 00:00:40s. Time for last 1,000,000: 6s. Last read position: chr1:44,613,094
INFO 2025-02-21 12:56:44 CollectHsMetrics Processed 7,000,000 records. Elapsed time: 00:00:46s. Time for last 1,000,000: 6s. Last read position: chr1:58,506,931
INFO 2025-02-21 12:56:50 CollectHsMetrics Processed 8,000,000 records. Elapsed time: 00:00:53s. Time for last 1,000,000: 6s. Last read position: chr1:86,357,084
INFO 2025-02-21 12:56:56 CollectHsMetrics Processed 9,000,000 records. Elapsed time: 00:00:59s. Time for last 1,000,000: 6s. Last read position: chr1:110,173,933
INFO 2025-02-21 12:57:02 CollectHsMetrics Processed 10,000,000 records. Elapsed time: 00:01:05s. Time for last 1,000,000: 5s. Last read position: chr1:144,551,100
INFO 2025-02-21 12:57:08 CollectHsMetrics Processed 11,000,000 records. Elapsed time: 00:01:10s. Time for last 1,000,000: 5s. Last read position: chr1:155,032,847
INFO 2025-02-21 12:57:15 CollectHsMetrics Processed 12,000,000 records. Elapsed time: 00:01:17s. Time for last 1,000,000: 6s. Last read position: chr1:165,355,191
INFO 2025-02-21 12:57:21 CollectHsMetrics Processed 13,000,000 records. Elapsed time: 00:01:24s. Time for last 1,000,000: 6s. Last read position: chr1:183,554,699
INFO 2025-02-21 12:57:27 CollectHsMetrics Processed 14,000,000 records. Elapsed time: 00:01:30s. Time for last 1,000,000: 6s. Last read position: chr1:204,981,809
INFO 2025-02-21 12:57:34 CollectHsMetrics Processed 15,000,000 records. Elapsed time: 00:01:37s. Time for last 1,000,000: 6s. Last read position: chr1:221,840,690
INFO 2025-02-21 12:57:40 CollectHsMetrics Processed 16,000,000 records. Elapsed time: 00:01:43s. Time for last 1,000,000: 6s. Last read position: chr1:233,440,268
INFO 2025-02-21 12:57:47 CollectHsMetrics Processed 17,000,000 records. Elapsed time: 00:01:49s. Time for last 1,000,000: 6s. Last read position: chr10:385,820
INFO 2025-02-21 12:57:53 CollectHsMetrics Processed 18,000,000 records. Elapsed time: 00:01:56s. Time for last 1,000,000: 6s. Last read position: chr10:11,573,802
INFO 2025-02-21 12:57:59 CollectHsMetrics Processed 19,000,000 records. Elapsed time: 00:02:02s. Time for last 1,000,000: 6s. Last read position: chr10:31,142,096
INFO 2025-02-21 12:58:05 CollectHsMetrics Processed 20,000,000 records. Elapsed time: 00:02:08s. Time for last 1,000,000: 5s. Last read position: chr10:49,381,519
INFO 2025-02-21 12:58:11 CollectHsMetrics Processed 21,000,000 records. Elapsed time: 00:02:14s. Time for last 1,000,000: 6s. Last read position: chr10:72,222,851
INFO 2025-02-21 12:58:18 CollectHsMetrics Processed 22,000,000 records. Elapsed time: 00:02:20s. Time for last 1,000,000: 6s. Last read position: chr10:89,153,258
INFO 2025-02-21 12:58:24 CollectHsMetrics Processed 23,000,000 records. Elapsed time: 00:02:27s. Time for last 1,000,000: 6s. Last read position: chr10:102,160,299
INFO 2025-02-21 12:58:31 CollectHsMetrics Processed 24,000,000 records. Elapsed time: 00:02:34s. Time for last 1,000,000: 6s. Last read position: chr10:119,819,752
INFO 2025-02-21 12:58:37 CollectHsMetrics Processed 25,000,000 records. Elapsed time: 00:02:40s. Time for last 1,000,000: 6s. Last read position: chr10:131,743,233
INFO 2025-02-21 12:58:44 CollectHsMetrics Processed 26,000,000 records. Elapsed time: 00:02:47s. Time for last 1,000,000: 6s. Last read position: chr11:646,189
INFO 2025-02-21 12:58:51 CollectHsMetrics Processed 27,000,000 records. Elapsed time: 00:02:53s. Time for last 1,000,000: 6s. Last read position: chr11:6,270,476
INFO 2025-02-21 12:58:57 CollectHsMetrics Processed 28,000,000 records. Elapsed time: 00:03:00s. Time for last 1,000,000: 6s. Last read position: chr11:18,634,104
INFO 2025-02-21 12:59:04 CollectHsMetrics Processed 29,000,000 records. Elapsed time: 00:03:07s. Time for last 1,000,000: 6s. Last read position: chr11:44,938,675
INFO 2025-02-21 12:59:11 CollectHsMetrics Processed 30,000,000 records. Elapsed time: 00:03:13s. Time for last 1,000,000: 6s. Last read position: chr11:61,679,784
INFO 2025-02-21 12:59:18 CollectHsMetrics Processed 31,000,000 records. Elapsed time: 00:03:21s. Time for last 1,000,000: 7s. Last read position: chr11:66,719,979
INFO 2025-02-21 12:59:25 CollectHsMetrics Processed 32,000,000 records. Elapsed time: 00:03:27s. Time for last 1,000,000: 6s. Last read position: chr11:72,430,379
INFO 2025-02-21 12:59:31 CollectHsMetrics Processed 33,000,000 records. Elapsed time: 00:03:34s. Time for last 1,000,000: 6s. Last read position: chr11:89,896,507
INFO 2025-02-21 12:59:38 CollectHsMetrics Processed 34,000,000 records. Elapsed time: 00:03:40s. Time for last 1,000,000: 6s. Last read position: chr11:114,678,085
INFO 2025-02-21 12:59:44 CollectHsMetrics Processed 35,000,000 records. Elapsed time: 00:03:47s. Time for last 1,000,000: 6s. Last read position: chr11:125,263,485
INFO 2025-02-21 12:59:51 CollectHsMetrics Processed 36,000,000 records. Elapsed time: 00:03:54s. Time for last 1,000,000: 6s. Last read position: chr12:1,812,807
INFO 2025-02-21 12:59:57 CollectHsMetrics Processed 37,000,000 records. Elapsed time: 00:04:00s. Time for last 1,000,000: 6s. Last read position: chr12:11,751,317
INFO 2025-02-21 13:00:04 CollectHsMetrics Processed 38,000,000 records. Elapsed time: 00:04:06s. Time for last 1,000,000: 6s. Last read position: chr12:38,154,266
INFO 2025-02-21 13:00:10 CollectHsMetrics Processed 39,000,000 records. Elapsed time: 00:04:13s. Time for last 1,000,000: 6s. Last read position: chr12:53,500,479
INFO 2025-02-21 13:00:17 CollectHsMetrics Processed 40,000,000 records. Elapsed time: 00:04:19s. Time for last 1,000,000: 6s. Last read position: chr12:70,839,205
INFO 2025-02-21 13:00:22 CollectHsMetrics Processed 41,000,000 records. Elapsed time: 00:04:25s. Time for last 1,000,000: 5s. Last read position: chr12:103,571,923
INFO 2025-02-21 13:00:29 CollectHsMetrics Processed 42,000,000 records. Elapsed time: 00:04:31s. Time for last 1,000,000: 6s. Last read position: chr12:116,659,961
INFO 2025-02-21 13:00:35 CollectHsMetrics Processed 43,000,000 records. Elapsed time: 00:04:38s. Time for last 1,000,000: 6s. Last read position: chr12:125,621,838
INFO 2025-02-21 13:00:42 CollectHsMetrics Processed 44,000,000 records. Elapsed time: 00:04:45s. Time for last 1,000,000: 6s. Last read position: chr12:132,953,038
INFO 2025-02-21 13:00:48 CollectHsMetrics Processed 45,000,000 records. Elapsed time: 00:04:51s. Time for last 1,000,000: 6s. Last read position: chr13:32,254,770
INFO 2025-02-21 13:00:55 CollectHsMetrics Processed 46,000,000 records. Elapsed time: 00:04:57s. Time for last 1,000,000: 6s. Last read position: chr13:52,488,631
INFO 2025-02-21 13:01:00 CollectHsMetrics Processed 47,000,000 records. Elapsed time: 00:05:03s. Time for last 1,000,000: 5s. Last read position: chr13:98,959,821
INFO 2025-02-21 13:01:07 CollectHsMetrics Processed 48,000,000 records. Elapsed time: 00:05:09s. Time for last 1,000,000: 6s. Last read position: chr13:112,835,450
INFO 2025-02-21 13:01:13 CollectHsMetrics Processed 49,000,000 records. Elapsed time: 00:05:16s. Time for last 1,000,000: 6s. Last read position: chr14:23,384,588
INFO 2025-02-21 13:01:19 CollectHsMetrics Processed 50,000,000 records. Elapsed time: 00:05:22s. Time for last 1,000,000: 6s. Last read position: chr14:52,790,813
INFO 2025-02-21 13:01:26 CollectHsMetrics Processed 51,000,000 records. Elapsed time: 00:05:28s. Time for last 1,000,000: 6s. Last read position: chr14:69,767,943
INFO 2025-02-21 13:01:32 CollectHsMetrics Processed 52,000,000 records. Elapsed time: 00:05:35s. Time for last 1,000,000: 6s. Last read position: chr14:90,389,633
INFO 2025-02-21 13:01:38 CollectHsMetrics Processed 53,000,000 records. Elapsed time: 00:05:41s. Time for last 1,000,000: 6s. Last read position: chr14:101,198,233
INFO 2025-02-21 13:01:45 CollectHsMetrics Processed 54,000,000 records. Elapsed time: 00:05:47s. Time for last 1,000,000: 6s. Last read position: chr14:106,460,216
INFO 2025-02-21 13:01:49 CollectHsMetrics Processed 55,000,000 records. Elapsed time: 00:05:52s. Time for last 1,000,000: 4s. Last read position: chr15:31,173,391
INFO 2025-02-21 13:01:56 CollectHsMetrics Processed 56,000,000 records. Elapsed time: 00:05:58s. Time for last 1,000,000: 6s. Last read position: chr15:45,645,422
INFO 2025-02-21 13:02:02 CollectHsMetrics Processed 57,000,000 records. Elapsed time: 00:06:04s. Time for last 1,000,000: 6s. Last read position: chr15:65,698,282
INFO 2025-02-21 13:02:08 CollectHsMetrics Processed 58,000,000 records. Elapsed time: 00:06:11s. Time for last 1,000,000: 6s. Last read position: chr15:77,543,381
INFO 2025-02-21 13:02:14 CollectHsMetrics Processed 59,000,000 records. Elapsed time: 00:06:17s. Time for last 1,000,000: 6s. Last read position: chr15:90,594,419
INFO 2025-02-21 13:02:21 CollectHsMetrics Processed 60,000,000 records. Elapsed time: 00:06:24s. Time for last 1,000,000: 6s. Last read position: chr16:569,080
INFO 2025-02-21 13:02:28 CollectHsMetrics Processed 61,000,000 records. Elapsed time: 00:06:31s. Time for last 1,000,000: 7s. Last read position: chr16:3,155,404
INFO 2025-02-21 13:02:34 CollectHsMetrics Processed 62,000,000 records. Elapsed time: 00:06:37s. Time for last 1,000,000: 6s. Last read position: chr16:16,369,604
INFO 2025-02-21 13:02:40 CollectHsMetrics Processed 63,000,000 records. Elapsed time: 00:06:43s. Time for last 1,000,000: 6s. Last read position: chr16:30,205,970
INFO 2025-02-21 13:02:46 CollectHsMetrics Processed 64,000,000 records. Elapsed time: 00:06:49s. Time for last 1,000,000: 6s. Last read position: chr16:54,932,173
INFO 2025-02-21 13:02:53 CollectHsMetrics Processed 65,000,000 records. Elapsed time: 00:06:56s. Time for last 1,000,000: 6s. Last read position: chr16:69,849,250
INFO 2025-02-21 13:03:00 CollectHsMetrics Processed 66,000,000 records. Elapsed time: 00:07:02s. Time for last 1,000,000: 6s. Last read position: chr16:84,832,481
INFO 2025-02-21 13:03:06 CollectHsMetrics Processed 67,000,000 records. Elapsed time: 00:07:09s. Time for last 1,000,000: 6s. Last read position: chr16:88,763,255
INFO 2025-02-21 13:03:13 CollectHsMetrics Processed 68,000,000 records. Elapsed time: 00:07:16s. Time for last 1,000,000: 6s. Last read position: chr17:2,373,880
INFO 2025-02-21 13:03:20 CollectHsMetrics Processed 69,000,000 records. Elapsed time: 00:07:23s. Time for last 1,000,000: 6s. Last read position: chr17:10,549,524
INFO 2025-02-21 13:03:26 CollectHsMetrics Processed 70,000,000 records. Elapsed time: 00:07:29s. Time for last 1,000,000: 6s. Last read position: chr17:21,573,454
INFO 2025-02-21 13:03:33 CollectHsMetrics Processed 71,000,000 records. Elapsed time: 00:07:35s. Time for last 1,000,000: 6s. Last read position: chr17:38,135,928
INFO 2025-02-21 13:03:39 CollectHsMetrics Processed 72,000,000 records. Elapsed time: 00:07:42s. Time for last 1,000,000: 6s. Last read position: chr17:45,135,973
INFO 2025-02-21 13:03:46 CollectHsMetrics Processed 73,000,000 records. Elapsed time: 00:07:49s. Time for last 1,000,000: 6s. Last read position: chr17:57,293,300
INFO 2025-02-21 13:03:53 CollectHsMetrics Processed 74,000,000 records. Elapsed time: 00:07:55s. Time for last 1,000,000: 6s. Last read position: chr17:73,515,716
INFO 2025-02-21 13:04:00 CollectHsMetrics Processed 75,000,000 records. Elapsed time: 00:08:02s. Time for last 1,000,000: 6s. Last read position: chr17:79,782,043
INFO 2025-02-21 13:04:07 CollectHsMetrics Processed 76,000,000 records. Elapsed time: 00:08:09s. Time for last 1,000,000: 7s. Last read position: chr17:82,931,238
INFO 2025-02-21 13:04:13 CollectHsMetrics Processed 77,000,000 records. Elapsed time: 00:08:15s. Time for last 1,000,000: 6s. Last read position: chr18:23,312,151
INFO 2025-02-21 13:04:19 CollectHsMetrics Processed 78,000,000 records. Elapsed time: 00:08:22s. Time for last 1,000,000: 6s. Last read position: chr18:55,765,662
INFO 2025-02-21 13:04:25 CollectHsMetrics Processed 79,000,000 records. Elapsed time: 00:08:28s. Time for last 1,000,000: 6s. Last read position: chr18:79,346,407
INFO 2025-02-21 13:04:32 CollectHsMetrics Processed 80,000,000 records. Elapsed time: 00:08:35s. Time for last 1,000,000: 6s. Last read position: chr19:2,644,370
INFO 2025-02-21 13:04:39 CollectHsMetrics Processed 81,000,000 records. Elapsed time: 00:08:42s. Time for last 1,000,000: 6s. Last read position: chr19:8,342,168
INFO 2025-02-21 13:04:46 CollectHsMetrics Processed 82,000,000 records. Elapsed time: 00:08:48s. Time for last 1,000,000: 6s. Last read position: chr19:16,286,482
INFO 2025-02-21 13:04:52 CollectHsMetrics Processed 83,000,000 records. Elapsed time: 00:08:55s. Time for last 1,000,000: 6s. Last read position: chr19:33,124,746
INFO 2025-02-21 13:04:59 CollectHsMetrics Processed 84,000,000 records. Elapsed time: 00:09:01s. Time for last 1,000,000: 6s. Last read position: chr19:39,902,984
INFO 2025-02-21 13:05:05 CollectHsMetrics Processed 85,000,000 records. Elapsed time: 00:09:08s. Time for last 1,000,000: 6s. Last read position: chr19:47,510,043
INFO 2025-02-21 13:05:12 CollectHsMetrics Processed 86,000,000 records. Elapsed time: 00:09:15s. Time for last 1,000,000: 6s. Last read position: chr19:54,305,928
INFO 2025-02-21 13:05:19 CollectHsMetrics Processed 87,000,000 records. Elapsed time: 00:09:22s. Time for last 1,000,000: 6s. Last read position: chr2:1,767,528
INFO 2025-02-21 13:05:25 CollectHsMetrics Processed 88,000,000 records. Elapsed time: 00:09:28s. Time for last 1,000,000: 6s. Last read position: chr2:14,634,958
INFO 2025-02-21 13:05:32 CollectHsMetrics Processed 89,000,000 records. Elapsed time: 00:09:35s. Time for last 1,000,000: 6s. Last read position: chr2:29,224,845
INFO 2025-02-21 13:05:39 CollectHsMetrics Processed 90,000,000 records. Elapsed time: 00:09:41s. Time for last 1,000,000: 6s. Last read position: chr2:47,165,567
INFO 2025-02-21 13:05:45 CollectHsMetrics Processed 91,000,000 records. Elapsed time: 00:09:48s. Time for last 1,000,000: 6s. Last read position: chr2:70,118,944
INFO 2025-02-21 13:05:52 CollectHsMetrics Processed 92,000,000 records. Elapsed time: 00:09:55s. Time for last 1,000,000: 6s. Last read position: chr2:88,609,104
INFO 2025-02-21 13:05:58 CollectHsMetrics Processed 93,000,000 records. Elapsed time: 00:10:01s. Time for last 1,000,000: 6s. Last read position: chr2:105,641,621
INFO 2025-02-21 13:06:05 CollectHsMetrics Processed 94,000,000 records. Elapsed time: 00:10:07s. Time for last 1,000,000: 6s. Last read position: chr2:122,661,116
INFO 2025-02-21 13:06:11 CollectHsMetrics Processed 95,000,000 records. Elapsed time: 00:10:13s. Time for last 1,000,000: 6s. Last read position: chr2:144,521,008
INFO 2025-02-21 13:06:17 CollectHsMetrics Processed 96,000,000 records. Elapsed time: 00:10:20s. Time for last 1,000,000: 6s. Last read position: chr2:171,784,363
INFO 2025-02-21 13:06:24 CollectHsMetrics Processed 97,000,000 records. Elapsed time: 00:10:27s. Time for last 1,000,000: 6s. Last read position: chr2:196,751,093
INFO 2025-02-21 13:06:30 CollectHsMetrics Processed 98,000,000 records. Elapsed time: 00:10:33s. Time for last 1,000,000: 6s. Last read position: chr2:218,165,486
INFO 2025-02-21 13:06:37 CollectHsMetrics Processed 99,000,000 records. Elapsed time: 00:10:40s. Time for last 1,000,000: 6s. Last read position: chr2:232,772,240
INFO 2025-02-21 13:06:44 CollectHsMetrics Processed 100,000,000 records. Elapsed time: 00:10:47s. Time for last 1,000,000: 6s. Last read position: chr2:240,190,050
INFO 2025-02-21 13:06:51 CollectHsMetrics Processed 101,000,000 records. Elapsed time: 00:10:54s. Time for last 1,000,000: 7s. Last read position: chr20:5,318,337
INFO 2025-02-21 13:06:58 CollectHsMetrics Processed 102,000,000 records. Elapsed time: 00:11:00s. Time for last 1,000,000: 6s. Last read position: chr20:29,876,462
INFO 2025-02-21 13:07:04 CollectHsMetrics Processed 103,000,000 records. Elapsed time: 00:11:07s. Time for last 1,000,000: 6s. Last read position: chr20:43,190,347
INFO 2025-02-21 13:07:11 CollectHsMetrics Processed 104,000,000 records. Elapsed time: 00:11:13s. Time for last 1,000,000: 6s. Last read position: chr20:56,369,832
INFO 2025-02-21 13:07:18 CollectHsMetrics Processed 105,000,000 records. Elapsed time: 00:11:20s. Time for last 1,000,000: 6s. Last read position: chr20:63,461,191
INFO 2025-02-21 13:07:22 CollectHsMetrics Processed 106,000,000 records. Elapsed time: 00:11:24s. Time for last 1,000,000: 4s. Last read position: chr21:10,390,240
INFO 2025-02-21 13:07:28 CollectHsMetrics Processed 107,000,000 records. Elapsed time: 00:11:31s. Time for last 1,000,000: 6s. Last read position: chr21:38,282,853
INFO 2025-02-21 13:07:35 CollectHsMetrics Processed 108,000,000 records. Elapsed time: 00:11:37s. Time for last 1,000,000: 6s. Last read position: chr21:45,544,595
INFO 2025-02-21 13:07:40 CollectHsMetrics Processed 109,000,000 records. Elapsed time: 00:11:43s. Time for last 1,000,000: 5s. Last read position: chr22:20,670,402
INFO 2025-02-21 13:07:47 CollectHsMetrics Processed 110,000,000 records. Elapsed time: 00:11:50s. Time for last 1,000,000: 6s. Last read position: chr22:30,205,650
INFO 2025-02-21 13:07:54 CollectHsMetrics Processed 111,000,000 records. Elapsed time: 00:11:56s. Time for last 1,000,000: 6s. Last read position: chr22:39,483,766
INFO 2025-02-21 13:08:01 CollectHsMetrics Processed 112,000,000 records. Elapsed time: 00:12:03s. Time for last 1,000,000: 6s. Last read position: chr22:46,762,267
INFO 2025-02-21 13:08:06 CollectHsMetrics Processed 113,000,000 records. Elapsed time: 00:12:08s. Time for last 1,000,000: 5s. Last read position: chr3:14,932
INFO 2025-02-21 13:08:12 CollectHsMetrics Processed 114,000,000 records. Elapsed time: 00:12:15s. Time for last 1,000,000: 6s. Last read position: chr3:15,517,221
INFO 2025-02-21 13:08:19 CollectHsMetrics Processed 115,000,000 records. Elapsed time: 00:12:22s. Time for last 1,000,000: 6s. Last read position: chr3:40,613,587
INFO 2025-02-21 13:08:26 CollectHsMetrics Processed 116,000,000 records. Elapsed time: 00:12:29s. Time for last 1,000,000: 7s. Last read position: chr3:50,372,252
INFO 2025-02-21 13:08:33 CollectHsMetrics Processed 117,000,000 records. Elapsed time: 00:12:36s. Time for last 1,000,000: 6s. Last read position: chr3:66,582,650
INFO 2025-02-21 13:08:39 CollectHsMetrics Processed 118,000,000 records. Elapsed time: 00:12:41s. Time for last 1,000,000: 5s. Last read position: chr3:105,447,647
INFO 2025-02-21 13:08:45 CollectHsMetrics Processed 119,000,000 records. Elapsed time: 00:12:48s. Time for last 1,000,000: 6s. Last read position: chr3:126,158,911
INFO 2025-02-21 13:08:52 CollectHsMetrics Processed 120,000,000 records. Elapsed time: 00:12:55s. Time for last 1,000,000: 6s. Last read position: chr3:139,018,506
INFO 2025-02-21 13:08:59 CollectHsMetrics Processed 121,000,000 records. Elapsed time: 00:13:02s. Time for last 1,000,000: 6s. Last read position: chr3:161,000,006
INFO 2025-02-21 13:09:05 CollectHsMetrics Processed 122,000,000 records. Elapsed time: 00:13:08s. Time for last 1,000,000: 6s. Last read position: chr3:185,517,012
INFO 2025-02-21 13:09:12 CollectHsMetrics Processed 123,000,000 records. Elapsed time: 00:13:15s. Time for last 1,000,000: 6s. Last read position: chr3:197,620,403
INFO 2025-02-21 13:09:19 CollectHsMetrics Processed 124,000,000 records. Elapsed time: 00:13:22s. Time for last 1,000,000: 7s. Last read position: chr4:3,512,786
INFO 2025-02-21 13:09:25 CollectHsMetrics Processed 125,000,000 records. Elapsed time: 00:13:28s. Time for last 1,000,000: 6s. Last read position: chr4:11,650,811
INFO 2025-02-21 13:09:32 CollectHsMetrics Processed 126,000,000 records. Elapsed time: 00:13:35s. Time for last 1,000,000: 6s. Last read position: chr4:42,657,403
INFO 2025-02-21 13:09:38 CollectHsMetrics Processed 127,000,000 records. Elapsed time: 00:13:41s. Time for last 1,000,000: 6s. Last read position: chr4:76,591,281
INFO 2025-02-21 13:09:45 CollectHsMetrics Processed 128,000,000 records. Elapsed time: 00:13:47s. Time for last 1,000,000: 6s. Last read position: chr4:107,034,875
INFO 2025-02-21 13:09:51 CollectHsMetrics Processed 129,000,000 records. Elapsed time: 00:13:54s. Time for last 1,000,000: 6s. Last read position: chr4:139,654,120
INFO 2025-02-21 13:09:58 CollectHsMetrics Processed 130,000,000 records. Elapsed time: 00:14:00s. Time for last 1,000,000: 6s. Last read position: chr4:168,126,953
INFO 2025-02-21 13:10:04 CollectHsMetrics Processed 131,000,000 records. Elapsed time: 00:14:07s. Time for last 1,000,000: 6s. Last read position: chr4:190,061,632
INFO 2025-02-21 13:10:11 CollectHsMetrics Processed 132,000,000 records. Elapsed time: 00:14:13s. Time for last 1,000,000: 6s. Last read position: chr5:3,828,983
INFO 2025-02-21 13:10:17 CollectHsMetrics Processed 133,000,000 records. Elapsed time: 00:14:19s. Time for last 1,000,000: 5s. Last read position: chr5:31,825,890
INFO 2025-02-21 13:10:23 CollectHsMetrics Processed 134,000,000 records. Elapsed time: 00:14:26s. Time for last 1,000,000: 6s. Last read position: chr5:57,501,686
INFO 2025-02-21 13:10:30 CollectHsMetrics Processed 135,000,000 records. Elapsed time: 00:14:32s. Time for last 1,000,000: 6s. Last read position: chr5:79,430,747
INFO 2025-02-21 13:10:36 CollectHsMetrics Processed 136,000,000 records. Elapsed time: 00:14:39s. Time for last 1,000,000: 6s. Last read position: chr5:111,562,393
INFO 2025-02-21 13:10:43 CollectHsMetrics Processed 137,000,000 records. Elapsed time: 00:14:45s. Time for last 1,000,000: 6s. Last read position: chr5:134,561,914
INFO 2025-02-21 13:10:50 CollectHsMetrics Processed 138,000,000 records. Elapsed time: 00:14:52s. Time for last 1,000,000: 7s. Last read position: chr5:143,679,616
INFO 2025-02-21 13:10:57 CollectHsMetrics Processed 139,000,000 records. Elapsed time: 00:14:59s. Time for last 1,000,000: 6s. Last read position: chr5:163,459,471
INFO 2025-02-21 13:11:03 CollectHsMetrics Processed 140,000,000 records. Elapsed time: 00:15:06s. Time for last 1,000,000: 6s. Last read position: chr5:177,603,613
INFO 2025-02-21 13:11:10 CollectHsMetrics Processed 141,000,000 records. Elapsed time: 00:15:13s. Time for last 1,000,000: 6s. Last read position: chr6:3,423,661
INFO 2025-02-21 13:11:17 CollectHsMetrics Processed 142,000,000 records. Elapsed time: 00:15:19s. Time for last 1,000,000: 6s. Last read position: chr6:20,907,664
INFO 2025-02-21 13:11:24 CollectHsMetrics Processed 143,000,000 records. Elapsed time: 00:15:27s. Time for last 1,000,000: 7s. Last read position: chr6:31,271,923
INFO 2025-02-21 13:11:31 CollectHsMetrics Processed 144,000,000 records. Elapsed time: 00:15:34s. Time for last 1,000,000: 7s. Last read position: chr6:37,597,987
INFO 2025-02-21 13:11:38 CollectHsMetrics Processed 145,000,000 records. Elapsed time: 00:15:41s. Time for last 1,000,000: 6s. Last read position: chr6:52,962,836
INFO 2025-02-21 13:11:45 CollectHsMetrics Processed 146,000,000 records. Elapsed time: 00:15:47s. Time for last 1,000,000: 6s. Last read position: chr6:89,352,204
INFO 2025-02-21 13:11:51 CollectHsMetrics Processed 147,000,000 records. Elapsed time: 00:15:54s. Time for last 1,000,000: 6s. Last read position: chr6:116,571,588
INFO 2025-02-21 13:11:58 CollectHsMetrics Processed 148,000,000 records. Elapsed time: 00:16:00s. Time for last 1,000,000: 6s. Last read position: chr6:142,302,046
INFO 2025-02-21 13:12:04 CollectHsMetrics Processed 149,000,000 records. Elapsed time: 00:16:07s. Time for last 1,000,000: 6s. Last read position: chr6:159,982,070
INFO 2025-02-21 13:12:11 CollectHsMetrics Processed 150,000,000 records. Elapsed time: 00:16:14s. Time for last 1,000,000: 6s. Last read position: chr6:170,030,669
INFO 2025-02-21 13:12:18 CollectHsMetrics Processed 151,000,000 records. Elapsed time: 00:16:21s. Time for last 1,000,000: 7s. Last read position: chr7:2,231,592
INFO 2025-02-21 13:12:25 CollectHsMetrics Processed 152,000,000 records. Elapsed time: 00:16:28s. Time for last 1,000,000: 6s. Last read position: chr7:16,652,248
INFO 2025-02-21 13:12:32 CollectHsMetrics Processed 153,000,000 records. Elapsed time: 00:16:35s. Time for last 1,000,000: 6s. Last read position: chr7:33,156,569
INFO 2025-02-21 13:12:39 CollectHsMetrics Processed 154,000,000 records. Elapsed time: 00:16:41s. Time for last 1,000,000: 6s. Last read position: chr7:50,450,897
INFO 2025-02-21 13:12:44 CollectHsMetrics Processed 155,000,000 records. Elapsed time: 00:16:47s. Time for last 1,000,000: 5s. Last read position: chr7:73,005,194
INFO 2025-02-21 13:12:50 CollectHsMetrics Processed 156,000,000 records. Elapsed time: 00:16:53s. Time for last 1,000,000: 6s. Last read position: chr7:94,879,497
INFO 2025-02-21 13:12:57 CollectHsMetrics Processed 157,000,000 records. Elapsed time: 00:17:00s. Time for last 1,000,000: 6s. Last read position: chr7:106,582,988
INFO 2025-02-21 13:13:04 CollectHsMetrics Processed 158,000,000 records. Elapsed time: 00:17:07s. Time for last 1,000,000: 6s. Last read position: chr7:130,994,481
INFO 2025-02-21 13:13:10 CollectHsMetrics Processed 159,000,000 records. Elapsed time: 00:17:13s. Time for last 1,000,000: 6s. Last read position: chr7:149,640,664
INFO 2025-02-21 13:13:17 CollectHsMetrics Processed 160,000,000 records. Elapsed time: 00:17:20s. Time for last 1,000,000: 7s. Last read position: chr7:157,541,696
INFO 2025-02-21 13:13:24 CollectHsMetrics Processed 161,000,000 records. Elapsed time: 00:17:27s. Time for last 1,000,000: 6s. Last read position: chr8:1,830,795
INFO 2025-02-21 13:13:30 CollectHsMetrics Processed 162,000,000 records. Elapsed time: 00:17:32s. Time for last 1,000,000: 5s. Last read position: chr8:12,427,837
INFO 2025-02-21 13:13:37 CollectHsMetrics Processed 163,000,000 records. Elapsed time: 00:17:39s. Time for last 1,000,000: 6s. Last read position: chr8:27,903,820
INFO 2025-02-21 13:13:43 CollectHsMetrics Processed 164,000,000 records. Elapsed time: 00:17:46s. Time for last 1,000,000: 6s. Last read position: chr8:47,990,862
INFO 2025-02-21 13:13:50 CollectHsMetrics Processed 165,000,000 records. Elapsed time: 00:17:53s. Time for last 1,000,000: 6s. Last read position: chr8:70,485,000
INFO 2025-02-21 13:13:56 CollectHsMetrics Processed 166,000,000 records. Elapsed time: 00:17:59s. Time for last 1,000,000: 6s. Last read position: chr8:97,830,796
INFO 2025-02-21 13:14:03 CollectHsMetrics Processed 167,000,000 records. Elapsed time: 00:18:05s. Time for last 1,000,000: 6s. Last read position: chr8:123,241,418
INFO 2025-02-21 13:14:09 CollectHsMetrics Processed 168,000,000 records. Elapsed time: 00:18:12s. Time for last 1,000,000: 6s. Last read position: chr8:141,020,384
INFO 2025-02-21 13:14:16 CollectHsMetrics Processed 169,000,000 records. Elapsed time: 00:18:19s. Time for last 1,000,000: 7s. Last read position: chr8:144,625,755
INFO 2025-02-21 13:14:23 CollectHsMetrics Processed 170,000,000 records. Elapsed time: 00:18:26s. Time for last 1,000,000: 6s. Last read position: chr9:33,473,808
INFO 2025-02-21 13:14:29 CollectHsMetrics Processed 171,000,000 records. Elapsed time: 00:18:31s. Time for last 1,000,000: 5s. Last read position: chr9:72,209,786
INFO 2025-02-21 13:14:35 CollectHsMetrics Processed 172,000,000 records. Elapsed time: 00:18:38s. Time for last 1,000,000: 6s. Last read position: chr9:94,782,599
INFO 2025-02-21 13:14:42 CollectHsMetrics Processed 173,000,000 records. Elapsed time: 00:18:44s. Time for last 1,000,000: 6s. Last read position: chr9:114,329,847
INFO 2025-02-21 13:14:48 CollectHsMetrics Processed 174,000,000 records. Elapsed time: 00:18:51s. Time for last 1,000,000: 6s. Last read position: chr9:128,323,336
INFO 2025-02-21 13:14:55 CollectHsMetrics Processed 175,000,000 records. Elapsed time: 00:18:58s. Time for last 1,000,000: 6s. Last read position: chr9:134,635,663
INFO 2025-02-21 13:15:02 CollectHsMetrics Processed 176,000,000 records. Elapsed time: 00:19:05s. Time for last 1,000,000: 6s. Last read position: chrM:3,424
INFO 2025-02-21 13:15:06 CollectHsMetrics Processed 177,000,000 records. Elapsed time: 00:19:08s. Time for last 1,000,000: 3s. Last read position: chrUn_GL000214v1:136,559
INFO 2025-02-21 13:15:12 CollectHsMetrics Processed 178,000,000 records. Elapsed time: 00:19:14s. Time for last 1,000,000: 6s. Last read position: chrX:50,011,971
INFO 2025-02-21 13:15:18 CollectHsMetrics Processed 179,000,000 records. Elapsed time: 00:19:21s. Time for last 1,000,000: 6s. Last read position: chrX:130,672,198
INFO 2025-02-21 13:15:24 CollectHsMetrics Processed 180,000,000 records. Elapsed time: 00:19:26s. Time for last 1,000,000: 5s. Last read position: chrY:56,884,501
INFO 2025-02-21 13:15:31 TheoreticalSensitivity Creating Roulette Wheel
INFO 2025-02-21 13:15:31 TheoreticalSensitivity Calculating quality sums from quality sampler
INFO 2025-02-21 13:15:31 TheoreticalSensitivity 0 sampling iterations completed
INFO 2025-02-21 13:15:33 TheoreticalSensitivity 1000 sampling iterations completed
INFO 2025-02-21 13:15:35 TheoreticalSensitivity 2000 sampling iterations completed
INFO 2025-02-21 13:15:36 TheoreticalSensitivity 3000 sampling iterations completed
INFO 2025-02-21 13:15:38 TheoreticalSensitivity 4000 sampling iterations completed
INFO 2025-02-21 13:15:42 TheoreticalSensitivity 5000 sampling iterations completed
[Fri Feb 21 13:15:46 UTC 2025] picard.analysis.directed.CollectHsMetrics done. Elapsed time: 19.94 minutes.
Runtime.totalMemory()=536870912
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
Exception in thread "main" java.lang.OutOfMemoryError: Java heap space
at java.base/java.lang.Integer.valueOf(Integer.java:1081)
at picard.analysis.TheoreticalSensitivity$RouletteWheel.sampleCumulativeSums(TheoreticalSensitivity.java:190)
at picard.analysis.TheoreticalSensitivity.hetSNPSensitivity(TheoreticalSensitivity.java:82)
at picard.analysis.TheoreticalSensitivity.hetSNPSensitivity(TheoreticalSensitivity.java:62)
at picard.analysis.directed.TargetMetricsCollector$PerUnitTargetMetricCollector.calculateTheoreticalHetSensitivity(TargetMetricsCollector.java:816)
at picard.analysis.directed.TargetMetricsCollector$PerUnitTargetMetricCollector.finish(TargetMetricsCollector.java:702)
at picard.metrics.MultiLevelCollector$AllReadsDistributor.finish(MultiLevelCollector.java:208)
at picard.metrics.MultiLevelCollector.finish(MultiLevelCollector.java:324)
at picard.analysis.directed.CollectTargetedMetrics.doWork(CollectTargetedMetrics.java:168)
at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:281)
at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:105)
at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:115)
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Looks like you are hitting an out of memory error. How much memory did you allocate for the picard tool? You may be able to run picard with increased heap size which may solve your issues. Make sure that the system you are running this on also has that much memory to cover.
java -jar -Xmx8G picard.jar...
I hope this helps.
Regards.
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