INFO 2020-03-09 06:14:30 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_PBS3_primary_unique.bam -OUTPUT CollectRnaSeqMetrics/8wk_PBS3_metrics ********** 06:14:31.154 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 06:14:31 EDT 2020] CollectRnaSeqMetrics REF_FLAT=genes_refFlat RIBOSOMAL_INTERVALS=rRNA_intervalList_sorted STRAND_SPECIFICITY=NONE INPUT=8wk_PBS3_primary_unique.bam OUTPUT=CollectRnaSeqMetrics/8wk_PBS3_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 06:14:31 EDT 2020] Executing as kkarri@scc-bb2.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 06:14:32 CollectRnaSeqMetrics Loaded 23632 genes. INFO 2020-03-09 06:14:47 SinglePassSamProgram Processed 1,000,000 records. Elapsed time: 00:00:15s. Time for last 1,000,000: 15s. Last read position: chr1:159,497,808 INFO 2020-03-09 06:14:54 SinglePassSamProgram Processed 2,000,000 records. Elapsed time: 00:00:22s. Time for last 1,000,000: 7s. Last read position: chr10:80,129,092 INFO 2020-03-09 06:15:02 SinglePassSamProgram Processed 3,000,000 records. Elapsed time: 00:00:30s. Time for last 1,000,000: 7s. Last read position: chr11:57,872,675 INFO 2020-03-09 06:15:10 SinglePassSamProgram Processed 4,000,000 records. Elapsed time: 00:00:38s. Time for last 1,000,000: 7s. Last read position: chr11:115,660,584 INFO 2020-03-09 06:15:18 SinglePassSamProgram Processed 5,000,000 records. Elapsed time: 00:00:45s. Time for last 1,000,000: 7s. Last read position: chr12:105,006,035 INFO 2020-03-09 06:15:24 SinglePassSamProgram Processed 6,000,000 records. Elapsed time: 00:00:52s. Time for last 1,000,000: 6s. Last read position: chr13:91,911,436 INFO 2020-03-09 06:15:32 SinglePassSamProgram Processed 7,000,000 records. Elapsed time: 00:01:00s. Time for last 1,000,000: 7s. Last read position: chr14:77,424,062 INFO 2020-03-09 06:15:40 SinglePassSamProgram Processed 8,000,000 records. Elapsed time: 00:01:08s. Time for last 1,000,000: 8s. Last read position: chr15:101,829,328 INFO 2020-03-09 06:15:49 SinglePassSamProgram Processed 9,000,000 records. Elapsed time: 00:01:17s. Time for last 1,000,000: 8s. Last read position: chr16:87,398,039 INFO 2020-03-09 06:15:56 SinglePassSamProgram Processed 10,000,000 records. Elapsed time: 00:01:23s. Time for last 1,000,000: 6s. Last read position: chr17:47,549,836 INFO 2020-03-09 06:16:03 SinglePassSamProgram Processed 11,000,000 records. Elapsed time: 00:01:30s. Time for last 1,000,000: 7s. Last read position: chr18:73,819,168 INFO 2020-03-09 06:16:10 SinglePassSamProgram Processed 12,000,000 records. Elapsed time: 00:01:37s. Time for last 1,000,000: 6s. Last read position: chr19:44,469,447 INFO 2020-03-09 06:16:17 SinglePassSamProgram Processed 13,000,000 records. Elapsed time: 00:01:44s. Time for last 1,000,000: 7s. Last read position: chr2:69,081,494 INFO 2020-03-09 06:16:25 SinglePassSamProgram Processed 14,000,000 records. Elapsed time: 00:01:53s. Time for last 1,000,000: 8s. Last read position: chr2:177,295,117 INFO 2020-03-09 06:16:32 SinglePassSamProgram Processed 15,000,000 records. Elapsed time: 00:01:59s. Time for last 1,000,000: 6s. Last read position: chr3:98,095,142 INFO 2020-03-09 06:16:38 SinglePassSamProgram Processed 16,000,000 records. Elapsed time: 00:02:06s. Time for last 1,000,000: 6s. Last read position: chr4:61,744,633 INFO 2020-03-09 06:16:46 SinglePassSamProgram Processed 17,000,000 records. Elapsed time: 00:02:13s. Time for last 1,000,000: 7s. Last read position: chr4:154,491,619 INFO 2020-03-09 06:16:52 SinglePassSamProgram Processed 18,000,000 records. Elapsed time: 00:02:19s. Time for last 1,000,000: 6s. Last read position: chr5:90,893,044 INFO 2020-03-09 06:16:58 SinglePassSamProgram Processed 19,000,000 records. Elapsed time: 00:02:25s. Time for last 1,000,000: 5s. Last read position: chr5:90,898,545 INFO 2020-03-09 06:17:06 SinglePassSamProgram Processed 20,000,000 records. Elapsed time: 00:02:33s. Time for last 1,000,000: 7s. Last read position: chr5:90,903,669 INFO 2020-03-09 06:17:13 SinglePassSamProgram Processed 21,000,000 records. Elapsed time: 00:02:40s. Time for last 1,000,000: 7s. Last read position: chr5:146,680,762 INFO 2020-03-09 06:17:20 SinglePassSamProgram Processed 22,000,000 records. Elapsed time: 00:02:47s. Time for last 1,000,000: 6s. Last read position: chr6:121,834,396 INFO 2020-03-09 06:17:27 SinglePassSamProgram Processed 23,000,000 records. Elapsed time: 00:02:54s. Time for last 1,000,000: 6s. Last read position: chr7:20,282,324 INFO 2020-03-09 06:17:33 SinglePassSamProgram Processed 24,000,000 records. Elapsed time: 00:03:01s. Time for last 1,000,000: 6s. Last read position: chr7:117,129,577 INFO 2020-03-09 06:17:41 SinglePassSamProgram Processed 25,000,000 records. Elapsed time: 00:03:08s. Time for last 1,000,000: 7s. Last read position: chr8:83,508,436 INFO 2020-03-09 06:17:48 SinglePassSamProgram Processed 26,000,000 records. Elapsed time: 00:03:15s. Time for last 1,000,000: 7s. Last read position: chr9:45,668,999 INFO 2020-03-09 06:17:54 SinglePassSamProgram Processed 27,000,000 records. Elapsed time: 00:03:21s. Time for last 1,000,000: 6s. Last read position: chr9:103,119,786 INFO 2020-03-09 06:18:02 SinglePassSamProgram Processed 28,000,000 records. Elapsed time: 00:03:30s. Time for last 1,000,000: 8s. Last read position: chrM:4,209 INFO 2020-03-09 06:18:05 SinglePassSamProgram Processed 29,000,000 records. Elapsed time: 00:03:32s. Time for last 1,000,000: 2s. Last read position: chrM:13,766 [Mon Mar 09 06:18:11 EDT 2020] picard.analysis.CollectRnaSeqMetrics done. Elapsed time: 3.67 minutes. Runtime.totalMemory()=1157103616