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 2wk_ASNase3_primary_unique.bam -OUTPUT CollectRnaSeqMetrics/2wk_ASNase3_metrics ********** 06:14:31.129 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=2wk_ASNase3_primary_unique.bam OUTPUT=CollectRnaSeqMetrics/2wk_ASNase3_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 06:14:46 SinglePassSamProgram Processed 1,000,000 records. Elapsed time: 00:00:14s. Time for last 1,000,000: 14s. Last read position: chr1:161,239,054 INFO 2020-03-09 06:14:53 SinglePassSamProgram Processed 2,000,000 records. Elapsed time: 00:00:21s. Time for last 1,000,000: 7s. Last read position: chr10:80,644,689 INFO 2020-03-09 06:15:01 SinglePassSamProgram Processed 3,000,000 records. Elapsed time: 00:00:28s. Time for last 1,000,000: 7s. Last read position: chr11:62,152,517 INFO 2020-03-09 06:15:08 SinglePassSamProgram Processed 4,000,000 records. Elapsed time: 00:00:35s. Time for last 1,000,000: 7s. Last read position: chr11:120,422,295 INFO 2020-03-09 06:15:15 SinglePassSamProgram Processed 5,000,000 records. Elapsed time: 00:00:43s. Time for last 1,000,000: 7s. Last read position: chr12:110,094,351 INFO 2020-03-09 06:15:24 SinglePassSamProgram Processed 6,000,000 records. Elapsed time: 00:00:51s. Time for last 1,000,000: 8s. Last read position: chr14:31,742,990 INFO 2020-03-09 06:15:31 SinglePassSamProgram Processed 7,000,000 records. Elapsed time: 00:00:58s. Time for last 1,000,000: 7s. Last read position: chr15:10,305,028 INFO 2020-03-09 06:15:39 SinglePassSamProgram Processed 8,000,000 records. Elapsed time: 00:01:06s. Time for last 1,000,000: 7s. Last read position: chr16:22,892,419 INFO 2020-03-09 06:15:49 SinglePassSamProgram Processed 9,000,000 records. Elapsed time: 00:01:17s. Time for last 1,000,000: 10s. Last read position: chr16:57,152,808 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: chr17:49,594,597 INFO 2020-03-09 06:16:03 SinglePassSamProgram Processed 11,000,000 records. Elapsed time: 00:01:31s. Time for last 1,000,000: 7s. Last read position: chr19:3,716,663 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: chr2:22,444,706 INFO 2020-03-09 06:16:18 SinglePassSamProgram Processed 13,000,000 records. Elapsed time: 00:01:46s. Time for last 1,000,000: 8s. Last read position: chr2:146,866,585 INFO 2020-03-09 06:16:25 SinglePassSamProgram Processed 14,000,000 records. Elapsed time: 00:01:53s. Time for last 1,000,000: 6s. Last read position: chr3:82,850,578 INFO 2020-03-09 06:16:32 SinglePassSamProgram Processed 15,000,000 records. Elapsed time: 00:02:00s. Time for last 1,000,000: 7s. Last read position: chr4:49,554,130 INFO 2020-03-09 06:16:40 SinglePassSamProgram Processed 16,000,000 records. Elapsed time: 00:02:08s. Time for last 1,000,000: 7s. Last read position: chr5:28,068,818 INFO 2020-03-09 06:16:46 SinglePassSamProgram Processed 17,000,000 records. Elapsed time: 00:02:14s. Time for last 1,000,000: 5s. Last read position: chr5:90,894,917 INFO 2020-03-09 06:16:53 SinglePassSamProgram Processed 18,000,000 records. Elapsed time: 00:02:21s. Time for last 1,000,000: 7s. Last read position: chr5:90,901,588 INFO 2020-03-09 06:17:01 SinglePassSamProgram Processed 19,000,000 records. Elapsed time: 00:02:28s. Time for last 1,000,000: 7s. Last read position: chr5:138,430,998 INFO 2020-03-09 06:17:08 SinglePassSamProgram Processed 20,000,000 records. Elapsed time: 00:02:35s. Time for last 1,000,000: 6s. Last read position: chr6:125,112,669 INFO 2020-03-09 06:17:14 SinglePassSamProgram Processed 21,000,000 records. Elapsed time: 00:02:41s. Time for last 1,000,000: 6s. Last read position: chr7:26,028,753 INFO 2020-03-09 06:17:21 SinglePassSamProgram Processed 22,000,000 records. Elapsed time: 00:02:48s. Time for last 1,000,000: 7s. Last read position: chr7:137,978,012 INFO 2020-03-09 06:17:27 SinglePassSamProgram Processed 23,000,000 records. Elapsed time: 00:02:55s. Time for last 1,000,000: 6s. Last read position: chr8:95,644,257 INFO 2020-03-09 06:17:34 SinglePassSamProgram Processed 24,000,000 records. Elapsed time: 00:03:01s. Time for last 1,000,000: 6s. Last read position: chr9:53,390,456 INFO 2020-03-09 06:17:40 SinglePassSamProgram Processed 25,000,000 records. Elapsed time: 00:03:08s. Time for last 1,000,000: 6s. Last read position: chr9:103,248,165 INFO 2020-03-09 06:17:46 SinglePassSamProgram Processed 26,000,000 records. Elapsed time: 00:03:13s. Time for last 1,000,000: 5s. Last read position: chrM:5,837 INFO 2020-03-09 06:17:48 SinglePassSamProgram Processed 27,000,000 records. Elapsed time: 00:03:16s. Time for last 1,000,000: 2s. Last read position: chrM:14,852 [Mon Mar 09 06:17:52 EDT 2020] picard.analysis.CollectRnaSeqMetrics done. Elapsed time: 3.36 minutes. Runtime.totalMemory()=1028653056