INFO 2020-03-09 06:13:47 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_PBS1_primary_unique.bam -OUTPUT CollectRnaSeqMetrics/2wk_PBS1_metrics ********** 06:13:47.803 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 06:13:47 EDT 2020] CollectRnaSeqMetrics REF_FLAT=genes_refFlat RIBOSOMAL_INTERVALS=rRNA_intervalList_sorted STRAND_SPECIFICITY=NONE INPUT=2wk_PBS1_primary_unique.bam OUTPUT=CollectRnaSeqMetrics/2wk_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 06:13:47 EDT 2020] Executing as kkarri@scc-bc3.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 06:13:48 CollectRnaSeqMetrics Loaded 23632 genes. INFO 2020-03-09 06:14:01 SinglePassSamProgram Processed 1,000,000 records. Elapsed time: 00:00:12s. Time for last 1,000,000: 12s. Last read position: chr1:166,115,161 INFO 2020-03-09 06:14:09 SinglePassSamProgram Processed 2,000,000 records. Elapsed time: 00:00:20s. Time for last 1,000,000: 7s. Last read position: chr10:96,946,167 INFO 2020-03-09 06:14:17 SinglePassSamProgram Processed 3,000,000 records. Elapsed time: 00:00:28s. Time for last 1,000,000: 7s. Last read position: chr11:78,314,311 INFO 2020-03-09 06:14:25 SinglePassSamProgram Processed 4,000,000 records. Elapsed time: 00:00:36s. Time for last 1,000,000: 8s. Last read position: chr12:73,753,314 INFO 2020-03-09 06:14:32 SinglePassSamProgram Processed 5,000,000 records. Elapsed time: 00:00:43s. Time for last 1,000,000: 6s. Last read position: chr13:62,974,122 INFO 2020-03-09 06:14:39 SinglePassSamProgram Processed 6,000,000 records. Elapsed time: 00:00:50s. Time for last 1,000,000: 7s. Last read position: chr14:70,580,383 INFO 2020-03-09 06:14:47 SinglePassSamProgram Processed 7,000,000 records. Elapsed time: 00:00:58s. Time for last 1,000,000: 7s. Last read position: chr16:4,287,924 INFO 2020-03-09 06:14:56 SinglePassSamProgram Processed 8,000,000 records. Elapsed time: 00:01:07s. Time for last 1,000,000: 8s. Last read position: chr17:12,583,097 INFO 2020-03-09 06:15:03 SinglePassSamProgram Processed 9,000,000 records. Elapsed time: 00:01:14s. Time for last 1,000,000: 7s. Last read position: chr17:57,363,290 INFO 2020-03-09 06:15:10 SinglePassSamProgram Processed 10,000,000 records. Elapsed time: 00:01:21s. Time for last 1,000,000: 7s. Last read position: chr19:12,708,055 INFO 2020-03-09 06:15:18 SinglePassSamProgram Processed 11,000,000 records. Elapsed time: 00:01:29s. Time for last 1,000,000: 7s. Last read position: chr2:50,988,038 INFO 2020-03-09 06:15:26 SinglePassSamProgram Processed 12,000,000 records. Elapsed time: 00:01:37s. Time for last 1,000,000: 7s. Last read position: chr3:5,860,634 INFO 2020-03-09 06:15:33 SinglePassSamProgram Processed 13,000,000 records. Elapsed time: 00:01:44s. Time for last 1,000,000: 7s. Last read position: chr3:122,628,412 INFO 2020-03-09 06:15:39 SinglePassSamProgram Processed 14,000,000 records. Elapsed time: 00:01:51s. Time for last 1,000,000: 6s. Last read position: chr4:117,537,145 INFO 2020-03-09 06:15:47 SinglePassSamProgram Processed 15,000,000 records. Elapsed time: 00:01:58s. Time for last 1,000,000: 7s. Last read position: chr5:90,890,781 INFO 2020-03-09 06:15:52 SinglePassSamProgram Processed 16,000,000 records. Elapsed time: 00:02:04s. Time for last 1,000,000: 5s. Last read position: chr5:90,897,684 INFO 2020-03-09 06:16:00 SinglePassSamProgram Processed 17,000,000 records. Elapsed time: 00:02:11s. Time for last 1,000,000: 7s. Last read position: chr5:90,903,621 INFO 2020-03-09 06:16:08 SinglePassSamProgram Processed 18,000,000 records. Elapsed time: 00:02:19s. Time for last 1,000,000: 7s. Last read position: chr5:146,793,084 INFO 2020-03-09 06:16:15 SinglePassSamProgram Processed 19,000,000 records. Elapsed time: 00:02:26s. Time for last 1,000,000: 7s. Last read position: chr6:128,471,159 INFO 2020-03-09 06:16:21 SinglePassSamProgram Processed 20,000,000 records. Elapsed time: 00:02:32s. Time for last 1,000,000: 5s. Last read position: chr7:52,960,700 INFO 2020-03-09 06:16:28 SinglePassSamProgram Processed 21,000,000 records. Elapsed time: 00:02:39s. Time for last 1,000,000: 6s. Last read position: chr8:41,994,234 INFO 2020-03-09 06:16:35 SinglePassSamProgram Processed 22,000,000 records. Elapsed time: 00:02:46s. Time for last 1,000,000: 7s. Last read position: chr9:42,913,400 INFO 2020-03-09 06:16:41 SinglePassSamProgram Processed 23,000,000 records. Elapsed time: 00:02:52s. Time for last 1,000,000: 6s. Last read position: chr9:103,127,427 INFO 2020-03-09 06:16:49 SinglePassSamProgram Processed 24,000,000 records. Elapsed time: 00:03:00s. Time for last 1,000,000: 7s. Last read position: chrM:5,739 INFO 2020-03-09 06:16:51 SinglePassSamProgram Processed 25,000,000 records. Elapsed time: 00:03:02s. Time for last 1,000,000: 2s. Last read position: chrM:15,021 [Mon Mar 09 06:16:56 EDT 2020] picard.analysis.CollectRnaSeqMetrics done. Elapsed time: 3.14 minutes. Runtime.totalMemory()=1161822208