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 8wk_PBS1_primary_unique.bam -OUTPUT CollectRnaSeqMetrics/8wk_PBS1_metrics ********** 06:14:27.093 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=8wk_PBS1_primary_unique.bam OUTPUT=CollectRnaSeqMetrics/8wk_PBS1_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 06:14:40 SinglePassSamProgram Processed 1,000,000 records. Elapsed time: 00:00:12s. Time for last 1,000,000: 12s. Last read position: chr1:173,155,438 INFO 2020-03-09 06:14:48 SinglePassSamProgram Processed 2,000,000 records. Elapsed time: 00:00:19s. Time for last 1,000,000: 7s. Last read position: chr10:120,829,887 INFO 2020-03-09 06:14:55 SinglePassSamProgram Processed 3,000,000 records. Elapsed time: 00:00:26s. Time for last 1,000,000: 7s. Last read position: chr11:83,562,782 INFO 2020-03-09 06:15:02 SinglePassSamProgram Processed 4,000,000 records. Elapsed time: 00:00:33s. Time for last 1,000,000: 6s. Last read position: chr12:89,679,683 INFO 2020-03-09 06:15:07 SinglePassSamProgram Processed 5,000,000 records. Elapsed time: 00:00:38s. Time for last 1,000,000: 5s. Last read position: chr13:74,317,916 INFO 2020-03-09 06:15:15 SinglePassSamProgram Processed 6,000,000 records. Elapsed time: 00:00:46s. Time for last 1,000,000: 7s. Last read position: chr15:3,225,607 INFO 2020-03-09 06:15:22 SinglePassSamProgram Processed 7,000,000 records. Elapsed time: 00:00:53s. Time for last 1,000,000: 7s. Last read position: chr16:18,411,870 INFO 2020-03-09 06:15:29 SinglePassSamProgram Processed 8,000,000 records. Elapsed time: 00:01:00s. Time for last 1,000,000: 7s. Last read position: chr17:29,431,041 INFO 2020-03-09 06:15:36 SinglePassSamProgram Processed 9,000,000 records. Elapsed time: 00:01:07s. Time for last 1,000,000: 6s. Last read position: chr17:84,238,165 INFO 2020-03-09 06:15:42 SinglePassSamProgram Processed 10,000,000 records. Elapsed time: 00:01:13s. Time for last 1,000,000: 6s. Last read position: chr19:29,202,562 INFO 2020-03-09 06:15:48 SinglePassSamProgram Processed 11,000,000 records. Elapsed time: 00:01:19s. Time for last 1,000,000: 6s. Last read position: chr2:31,332,456 INFO 2020-03-09 06:15:55 SinglePassSamProgram Processed 12,000,000 records. Elapsed time: 00:01:26s. Time for last 1,000,000: 7s. Last read position: chr2:168,009,824 INFO 2020-03-09 06:16:01 SinglePassSamProgram Processed 13,000,000 records. Elapsed time: 00:01:32s. Time for last 1,000,000: 6s. Last read position: chr3:98,106,652 INFO 2020-03-09 06:16:07 SinglePassSamProgram Processed 14,000,000 records. Elapsed time: 00:01:39s. Time for last 1,000,000: 6s. Last read position: chr4:62,804,373 INFO 2020-03-09 06:16:14 SinglePassSamProgram Processed 15,000,000 records. Elapsed time: 00:01:46s. Time for last 1,000,000: 6s. Last read position: chr5:52,541,936 INFO 2020-03-09 06:16:20 SinglePassSamProgram Processed 16,000,000 records. Elapsed time: 00:01:51s. Time for last 1,000,000: 5s. Last read position: chr5:90,896,374 INFO 2020-03-09 06:16:26 SinglePassSamProgram Processed 17,000,000 records. Elapsed time: 00:01:57s. Time for last 1,000,000: 6s. Last read position: chr5:90,901,522 INFO 2020-03-09 06:16:33 SinglePassSamProgram Processed 18,000,000 records. Elapsed time: 00:02:05s. Time for last 1,000,000: 7s. Last read position: chr5:123,622,053 INFO 2020-03-09 06:16:39 SinglePassSamProgram Processed 19,000,000 records. Elapsed time: 00:02:10s. Time for last 1,000,000: 5s. Last read position: chr6:83,603,275 INFO 2020-03-09 06:16:46 SinglePassSamProgram Processed 20,000,000 records. Elapsed time: 00:02:17s. Time for last 1,000,000: 6s. Last read position: chr7:20,281,718 INFO 2020-03-09 06:16:51 SinglePassSamProgram Processed 21,000,000 records. Elapsed time: 00:02:22s. Time for last 1,000,000: 5s. Last read position: chr7:88,489,744 INFO 2020-03-09 06:16:57 SinglePassSamProgram Processed 22,000,000 records. Elapsed time: 00:02:29s. Time for last 1,000,000: 6s. Last read position: chr8:47,619,960 INFO 2020-03-09 06:17:04 SinglePassSamProgram Processed 23,000,000 records. Elapsed time: 00:02:35s. Time for last 1,000,000: 6s. Last read position: chr9:44,782,263 INFO 2020-03-09 06:17:10 SinglePassSamProgram Processed 24,000,000 records. Elapsed time: 00:02:41s. Time for last 1,000,000: 5s. Last read position: chr9:103,130,372 INFO 2020-03-09 06:17:17 SinglePassSamProgram Processed 25,000,000 records. Elapsed time: 00:02:48s. Time for last 1,000,000: 6s. Last read position: chrM:5,910 INFO 2020-03-09 06:17:20 SinglePassSamProgram Processed 26,000,000 records. Elapsed time: 00:02:51s. Time for last 1,000,000: 3s. Last read position: chrX:34,145,813 [Mon Mar 09 06:17:23 EDT 2020] picard.analysis.CollectRnaSeqMetrics done. Elapsed time: 2.94 minutes. Runtime.totalMemory()=779616256