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 16wk_ASNase3_primary_unique.bam -OUTPUT CollectRnaSeqMetrics/16wk_ASNase3_metrics ********** 06:13:47.767 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=16wk_ASNase3_primary_unique.bam OUTPUT=CollectRnaSeqMetrics/16wk_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 06:13:47 EDT 2020] Executing as kkarri@scc-bb5.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: chr1:186,665,232 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: chr11:53,073,621 INFO 2020-03-09 06:14:16 SinglePassSamProgram Processed 3,000,000 records. Elapsed time: 00:00:27s. Time for last 1,000,000: 7s. Last read position: chr12:8,023,136 INFO 2020-03-09 06:14:22 SinglePassSamProgram Processed 4,000,000 records. Elapsed time: 00:00:33s. Time for last 1,000,000: 6s. Last read position: chr13:55,522,956 INFO 2020-03-09 06:14:30 SinglePassSamProgram Processed 5,000,000 records. Elapsed time: 00:00:41s. Time for last 1,000,000: 7s. Last read position: chr15:3,224,778 INFO 2020-03-09 06:14:37 SinglePassSamProgram Processed 6,000,000 records. Elapsed time: 00:00:48s. Time for last 1,000,000: 6s. Last read position: chr16:18,407,990 INFO 2020-03-09 06:14:44 SinglePassSamProgram Processed 7,000,000 records. Elapsed time: 00:00:55s. Time for last 1,000,000: 7s. Last read position: chr17:29,098,529 INFO 2020-03-09 06:14:47 SinglePassSamProgram Processed 8,000,000 records. Elapsed time: 00:00:58s. Time for last 1,000,000: 3s. Last read position: chr17:39,983,991 INFO 2020-03-09 06:14:50 SinglePassSamProgram Processed 9,000,000 records. Elapsed time: 00:01:01s. Time for last 1,000,000: 2s. Last read position: chr17:39,984,805 INFO 2020-03-09 06:14:56 SinglePassSamProgram Processed 10,000,000 records. Elapsed time: 00:01:07s. Time for last 1,000,000: 6s. Last read position: chr18:68,851,719 INFO 2020-03-09 06:15:02 SinglePassSamProgram Processed 11,000,000 records. Elapsed time: 00:01:13s. Time for last 1,000,000: 6s. Last read position: chr2:22,866,643 INFO 2020-03-09 06:15:10 SinglePassSamProgram Processed 12,000,000 records. Elapsed time: 00:01:21s. Time for last 1,000,000: 7s. Last read position: chr2:174,167,370 INFO 2020-03-09 06:15:15 SinglePassSamProgram Processed 13,000,000 records. Elapsed time: 00:01:26s. Time for last 1,000,000: 5s. Last read position: chr3:89,823,249 INFO 2020-03-09 06:15:22 SinglePassSamProgram Processed 14,000,000 records. Elapsed time: 00:01:33s. Time for last 1,000,000: 6s. Last read position: chr4:98,704,089 INFO 2020-03-09 06:15:29 SinglePassSamProgram Processed 15,000,000 records. Elapsed time: 00:01:40s. Time for last 1,000,000: 6s. Last read position: chr5:90,890,027 INFO 2020-03-09 06:15:34 SinglePassSamProgram Processed 16,000,000 records. Elapsed time: 00:01:45s. Time for last 1,000,000: 5s. Last read position: chr5:90,901,090 INFO 2020-03-09 06:15:42 SinglePassSamProgram Processed 17,000,000 records. Elapsed time: 00:01:53s. Time for last 1,000,000: 7s. Last read position: chr5:138,431,273 INFO 2020-03-09 06:15:48 SinglePassSamProgram Processed 18,000,000 records. Elapsed time: 00:01:59s. Time for last 1,000,000: 6s. Last read position: chr6:128,435,652 INFO 2020-03-09 06:15:54 SinglePassSamProgram Processed 19,000,000 records. Elapsed time: 00:02:05s. Time for last 1,000,000: 6s. Last read position: chr7:54,105,686 INFO 2020-03-09 06:16:01 SinglePassSamProgram Processed 20,000,000 records. Elapsed time: 00:02:12s. Time for last 1,000,000: 6s. Last read position: chr8:87,494,479 INFO 2020-03-09 06:16:07 SinglePassSamProgram Processed 21,000,000 records. Elapsed time: 00:02:18s. Time for last 1,000,000: 6s. Last read position: chr9:78,326,455 INFO 2020-03-09 06:16:13 SinglePassSamProgram Processed 22,000,000 records. Elapsed time: 00:02:24s. Time for last 1,000,000: 5s. Last read position: chr9:123,371,169 INFO 2020-03-09 06:16:18 SinglePassSamProgram Processed 23,000,000 records. Elapsed time: 00:02:29s. Time for last 1,000,000: 5s. Last read position: chrM:15,082 [Mon Mar 09 06:16:21 EDT 2020] picard.analysis.CollectRnaSeqMetrics done. Elapsed time: 2.56 minutes. Runtime.totalMemory()=835190784