INFO 2020-03-09 06:14:26 CollectRnaSeqMetrics ********** 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: ********** ********** CollectRnaSeqMetrics -REF_FLAT genes_refFlat -RIBOSOMAL_INTERVALS rRNA_intervalList_sorted -STRAND NONE -INPUT 16wk_PBS2_primary_unique.bam -OUTPUT CollectRnaSeqMetrics/16wk_PBS2_metrics ********** 06:14:27.101 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/restricted/projectnb/waxmanlab/environment/.conda/envs/RNAseq/share/picard-2.22.0-0/picard.jar!/com/intel/gkl/native/libgkl_compression.so [Mon Mar 09 06:14:27 EDT 2020] CollectRnaSeqMetrics REF_FLAT=genes_refFlat RIBOSOMAL_INTERVALS=rRNA_intervalList_sorted STRAND_SPECIFICITY=NONE INPUT=16wk_PBS2_primary_unique.bam OUTPUT=CollectRnaSeqMetrics/16wk_PBS2_metrics MINIMUM_LENGTH=500 RRNA_FRAGMENT_PERCENTAGE=0.8 METRIC_ACCUMULATION_LEVEL=[ALL_READS] ASSUME_SORTED=true STOP_AFTER=0 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 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 [Mon Mar 09 06:14:27 EDT 2020] Executing as kkarri@scc-bb6.scc.bu.edu on Linux 3.10.0-1062.12.1.el7.x86_64 amd64; OpenJDK 64-Bit Server VM 1.8.0_152-release-1056-b12; Deflater: Intel; Inflater: Intel; Provider GCS is not available; Picard version: 2.22.0-SNAPSHOT INFO 2020-03-09 06:14:28 CollectRnaSeqMetrics Loaded 23632 genes. INFO 2020-03-09 06:14:43 SinglePassSamProgram Processed 1,000,000 records. Elapsed time: 00:00:14s. Time for last 1,000,000: 14s. Last read position: chr1:162,923,724 INFO 2020-03-09 06:14:50 SinglePassSamProgram Processed 2,000,000 records. Elapsed time: 00:00:21s. Time for last 1,000,000: 7s. Last read position: chr10:87,001,039 INFO 2020-03-09 06:14:58 SinglePassSamProgram Processed 3,000,000 records. Elapsed time: 00:00:29s. Time for last 1,000,000: 8s. Last read position: chr11:74,969,702 INFO 2020-03-09 06:15:06 SinglePassSamProgram Processed 4,000,000 records. Elapsed time: 00:00:37s. Time for last 1,000,000: 7s. Last read position: chr12:8,023,224 INFO 2020-03-09 06:15:12 SinglePassSamProgram Processed 5,000,000 records. Elapsed time: 00:00:43s. Time for last 1,000,000: 6s. Last read position: chr12:105,585,751 INFO 2020-03-09 06:15:19 SinglePassSamProgram Processed 6,000,000 records. Elapsed time: 00:00:50s. Time for last 1,000,000: 7s. Last read position: chr14:31,933,589 INFO 2020-03-09 06:15:27 SinglePassSamProgram Processed 7,000,000 records. Elapsed time: 00:00:58s. Time for last 1,000,000: 7s. Last read position: chr15:31,408,071 INFO 2020-03-09 06:15:34 SinglePassSamProgram Processed 8,000,000 records. Elapsed time: 00:01:05s. Time for last 1,000,000: 7s. Last read position: chr16:22,896,630 INFO 2020-03-09 06:15:42 SinglePassSamProgram Processed 9,000,000 records. Elapsed time: 00:01:13s. Time for last 1,000,000: 7s. Last read position: chr17:34,866,181 INFO 2020-03-09 06:15:48 SinglePassSamProgram Processed 10,000,000 records. Elapsed time: 00:01:19s. Time for last 1,000,000: 6s. Last read position: chr17:80,251,871 INFO 2020-03-09 06:15:55 SinglePassSamProgram Processed 11,000,000 records. Elapsed time: 00:01:26s. Time for last 1,000,000: 6s. Last read position: chr19:25,023,711 INFO 2020-03-09 06:16:02 SinglePassSamProgram Processed 12,000,000 records. Elapsed time: 00:01:33s. Time for last 1,000,000: 7s. Last read position: chr2:34,937,826 INFO 2020-03-09 06:16:09 SinglePassSamProgram Processed 13,000,000 records. Elapsed time: 00:01:40s. Time for last 1,000,000: 7s. Last read position: chr2:172,983,725 INFO 2020-03-09 06:16:16 SinglePassSamProgram Processed 14,000,000 records. Elapsed time: 00:01:47s. Time for last 1,000,000: 6s. Last read position: chr3:102,807,911 INFO 2020-03-09 06:16:22 SinglePassSamProgram Processed 15,000,000 records. Elapsed time: 00:01:53s. Time for last 1,000,000: 6s. Last read position: chr4:62,811,369 INFO 2020-03-09 06:16:30 SinglePassSamProgram Processed 16,000,000 records. Elapsed time: 00:02:01s. Time for last 1,000,000: 7s. Last read position: chr5:53,144,456 INFO 2020-03-09 06:16:35 SinglePassSamProgram Processed 17,000,000 records. Elapsed time: 00:02:06s. Time for last 1,000,000: 5s. Last read position: chr5:90,896,378 INFO 2020-03-09 06:16:42 SinglePassSamProgram Processed 18,000,000 records. Elapsed time: 00:02:13s. Time for last 1,000,000: 6s. Last read position: chr5:90,901,665 INFO 2020-03-09 06:16:49 SinglePassSamProgram Processed 19,000,000 records. Elapsed time: 00:02:20s. Time for last 1,000,000: 7s. Last read position: chr5:146,691,319 INFO 2020-03-09 06:16:56 SinglePassSamProgram Processed 20,000,000 records. Elapsed time: 00:02:27s. Time for last 1,000,000: 6s. Last read position: chr6:127,917,280 INFO 2020-03-09 06:17:02 SinglePassSamProgram Processed 21,000,000 records. Elapsed time: 00:02:33s. Time for last 1,000,000: 6s. Last read position: chr7:27,906,576 INFO 2020-03-09 06:17:09 SinglePassSamProgram Processed 22,000,000 records. Elapsed time: 00:02:40s. Time for last 1,000,000: 6s. Last read position: chr7:147,955,503 INFO 2020-03-09 06:17:16 SinglePassSamProgram Processed 23,000,000 records. Elapsed time: 00:02:47s. Time for last 1,000,000: 6s. Last read position: chr8:108,463,777 INFO 2020-03-09 06:17:22 SinglePassSamProgram Processed 24,000,000 records. Elapsed time: 00:02:53s. Time for last 1,000,000: 6s. Last read position: chr9:78,327,090 INFO 2020-03-09 06:17:29 SinglePassSamProgram Processed 25,000,000 records. Elapsed time: 00:03:00s. Time for last 1,000,000: 6s. Last read position: chrM:685 INFO 2020-03-09 06:17:34 SinglePassSamProgram Processed 26,000,000 records. Elapsed time: 00:03:05s. Time for last 1,000,000: 5s. Last read position: chrM:14,240 [Mon Mar 09 06:17:38 EDT 2020] picard.analysis.CollectRnaSeqMetrics done. Elapsed time: 3.20 minutes. Runtime.totalMemory()=954728448