INFO 2020-03-09 06:13:45 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_PBS1_primary_unique.bam -OUTPUT CollectRnaSeqMetrics/16wk_PBS1_metrics ********** 06:13:46.911 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 06:13:46 EDT 2020] CollectRnaSeqMetrics REF_FLAT=genes_refFlat RIBOSOMAL_INTERVALS=rRNA_intervalList_sorted STRAND_SPECIFICITY=NONE INPUT=16wk_PBS1_primary_unique.bam OUTPUT=CollectRnaSeqMetrics/16wk_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-bb3.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 06:14:10 SinglePassSamProgram Processed 1,000,000 records. Elapsed time: 00:00:21s. Time for last 1,000,000: 21s. Last read position: chr1:163,171,686 INFO 2020-03-09 06:14:20 SinglePassSamProgram Processed 2,000,000 records. Elapsed time: 00:00:31s. Time for last 1,000,000: 10s. Last read position: chr10:89,267,613 INFO 2020-03-09 06:14:33 SinglePassSamProgram Processed 3,000,000 records. Elapsed time: 00:00:43s. Time for last 1,000,000: 12s. Last read position: chr11:78,313,351 INFO 2020-03-09 06:14:44 SinglePassSamProgram Processed 4,000,000 records. Elapsed time: 00:00:55s. Time for last 1,000,000: 11s. Last read position: chr12:52,849,436 INFO 2020-03-09 06:14:53 SinglePassSamProgram Processed 5,000,000 records. Elapsed time: 00:01:04s. Time for last 1,000,000: 9s. Last read position: chr12:113,361,510 INFO 2020-03-09 06:15:04 SinglePassSamProgram Processed 6,000,000 records. Elapsed time: 00:01:15s. Time for last 1,000,000: 11s. Last read position: chr14:41,936,342 INFO 2020-03-09 06:15:17 SinglePassSamProgram Processed 7,000,000 records. Elapsed time: 00:01:28s. Time for last 1,000,000: 12s. Last read position: chr15:78,235,674 INFO 2020-03-09 06:15:29 SinglePassSamProgram Processed 8,000,000 records. Elapsed time: 00:01:40s. Time for last 1,000,000: 12s. Last read position: chr16:23,452,300 INFO 2020-03-09 06:15:39 SinglePassSamProgram Processed 9,000,000 records. Elapsed time: 00:01:50s. Time for last 1,000,000: 9s. Last read position: chr17:39,984,271 INFO 2020-03-09 06:15:49 SinglePassSamProgram Processed 10,000,000 records. Elapsed time: 00:02:00s. Time for last 1,000,000: 10s. Last read position: chr18:62,665,172 INFO 2020-03-09 06:15:59 SinglePassSamProgram Processed 11,000,000 records. Elapsed time: 00:02:10s. Time for last 1,000,000: 9s. Last read position: chr19:46,662,438 INFO 2020-03-09 06:16:10 SinglePassSamProgram Processed 12,000,000 records. Elapsed time: 00:02:21s. Time for last 1,000,000: 11s. Last read position: chr2:122,089,899 INFO 2020-03-09 06:16:21 SinglePassSamProgram Processed 13,000,000 records. Elapsed time: 00:02:31s. Time for last 1,000,000: 10s. Last read position: chr3:82,834,227 INFO 2020-03-09 06:16:31 SinglePassSamProgram Processed 14,000,000 records. Elapsed time: 00:02:41s. Time for last 1,000,000: 10s. Last read position: chr4:45,410,416 INFO 2020-03-09 06:16:41 SinglePassSamProgram Processed 15,000,000 records. Elapsed time: 00:02:52s. Time for last 1,000,000: 10s. Last read position: chr4:140,548,118 INFO 2020-03-09 06:16:51 SinglePassSamProgram Processed 16,000,000 records. Elapsed time: 00:03:01s. Time for last 1,000,000: 9s. Last read position: chr5:90,893,020 INFO 2020-03-09 06:17:01 SinglePassSamProgram Processed 17,000,000 records. Elapsed time: 00:03:12s. Time for last 1,000,000: 10s. Last read position: chr5:90,898,588 INFO 2020-03-09 06:17:13 SinglePassSamProgram Processed 18,000,000 records. Elapsed time: 00:03:24s. Time for last 1,000,000: 11s. Last read position: chr5:90,904,980 INFO 2020-03-09 06:17:22 SinglePassSamProgram Processed 19,000,000 records. Elapsed time: 00:03:33s. Time for last 1,000,000: 9s. Last read position: chr6:57,688,783 INFO 2020-03-09 06:17:33 SinglePassSamProgram Processed 20,000,000 records. Elapsed time: 00:03:44s. Time for last 1,000,000: 10s. Last read position: chr6:148,129,864 INFO 2020-03-09 06:17:43 SinglePassSamProgram Processed 21,000,000 records. Elapsed time: 00:03:53s. Time for last 1,000,000: 9s. Last read position: chr7:91,733,775 INFO 2020-03-09 06:17:53 SinglePassSamProgram Processed 22,000,000 records. Elapsed time: 00:04:03s. Time for last 1,000,000: 10s. Last read position: chr8:47,578,357 INFO 2020-03-09 06:18:02 SinglePassSamProgram Processed 23,000,000 records. Elapsed time: 00:04:13s. Time for last 1,000,000: 9s. Last read position: chr9:46,036,803 INFO 2020-03-09 06:18:11 SinglePassSamProgram Processed 24,000,000 records. Elapsed time: 00:04:22s. Time for last 1,000,000: 8s. Last read position: chr9:103,130,277 INFO 2020-03-09 06:18:19 SinglePassSamProgram Processed 25,000,000 records. Elapsed time: 00:04:30s. Time for last 1,000,000: 8s. Last read position: chrM:6,043 INFO 2020-03-09 06:18:26 SinglePassSamProgram Processed 26,000,000 records. Elapsed time: 00:04:37s. Time for last 1,000,000: 6s. Last read position: chrX:100,669,200 [Mon Mar 09 06:18:29 EDT 2020] picard.analysis.CollectRnaSeqMetrics done. Elapsed time: 4.71 minutes. Runtime.totalMemory()=1154482176