INFO 2020-03-09 06:13:48 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_ASNase2_primary_unique.bam -OUTPUT CollectRnaSeqMetrics/16wk_ASNase2_metrics ********** 06:13:50.234 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 06:13:50 EDT 2020] CollectRnaSeqMetrics REF_FLAT=genes_refFlat RIBOSOMAL_INTERVALS=rRNA_intervalList_sorted STRAND_SPECIFICITY=NONE INPUT=16wk_ASNase2_primary_unique.bam OUTPUT=CollectRnaSeqMetrics/16wk_ASNase2_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 06:13:50 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 06:13:53 CollectRnaSeqMetrics Loaded 23632 genes. INFO 2020-03-09 06:14:13 SinglePassSamProgram Processed 1,000,000 records. Elapsed time: 00:00:19s. Time for last 1,000,000: 19s. Last read position: chr1:173,066,215 INFO 2020-03-09 06:14:24 SinglePassSamProgram Processed 2,000,000 records. Elapsed time: 00:00:30s. Time for last 1,000,000: 11s. Last read position: chr10:127,006,078 INFO 2020-03-09 06:14:35 SinglePassSamProgram Processed 3,000,000 records. Elapsed time: 00:00:41s. Time for last 1,000,000: 11s. Last read position: chr11:97,250,518 INFO 2020-03-09 06:14:47 SinglePassSamProgram Processed 4,000,000 records. Elapsed time: 00:00:53s. Time for last 1,000,000: 11s. Last read position: chr12:88,790,965 INFO 2020-03-09 06:14:56 SinglePassSamProgram Processed 5,000,000 records. Elapsed time: 00:01:02s. Time for last 1,000,000: 8s. Last read position: chr13:30,905,999 INFO 2020-03-09 06:15:07 SinglePassSamProgram Processed 6,000,000 records. Elapsed time: 00:01:13s. Time for last 1,000,000: 11s. Last read position: chr14:56,358,407 INFO 2020-03-09 06:15:19 SinglePassSamProgram Processed 7,000,000 records. Elapsed time: 00:01:25s. Time for last 1,000,000: 12s. Last read position: chr15:89,389,493 INFO 2020-03-09 06:15:32 SinglePassSamProgram Processed 8,000,000 records. Elapsed time: 00:01:38s. Time for last 1,000,000: 12s. Last read position: chr16:93,610,064 INFO 2020-03-09 06:15:41 SinglePassSamProgram Processed 9,000,000 records. Elapsed time: 00:01:47s. Time for last 1,000,000: 9s. Last read position: chr17:57,356,726 INFO 2020-03-09 06:15:52 SinglePassSamProgram Processed 10,000,000 records. Elapsed time: 00:01:58s. Time for last 1,000,000: 10s. Last read position: chr19:10,058,762 INFO 2020-03-09 06:16:03 SinglePassSamProgram Processed 11,000,000 records. Elapsed time: 00:02:09s. Time for last 1,000,000: 10s. Last read position: chr2:34,631,366 INFO 2020-03-09 06:16:14 SinglePassSamProgram Processed 12,000,000 records. Elapsed time: 00:02:20s. Time for last 1,000,000: 11s. Last read position: chr2:174,253,045 INFO 2020-03-09 06:16:23 SinglePassSamProgram Processed 13,000,000 records. Elapsed time: 00:02:29s. Time for last 1,000,000: 9s. Last read position: chr3:95,700,223 INFO 2020-03-09 06:16:33 SinglePassSamProgram Processed 14,000,000 records. Elapsed time: 00:02:39s. Time for last 1,000,000: 10s. Last read position: chr4:60,593,605 INFO 2020-03-09 06:16:43 SinglePassSamProgram Processed 15,000,000 records. Elapsed time: 00:02:49s. Time for last 1,000,000: 9s. Last read position: chr4:132,048,272 INFO 2020-03-09 06:16:53 SinglePassSamProgram Processed 16,000,000 records. Elapsed time: 00:02:59s. Time for last 1,000,000: 10s. Last read position: chr5:90,893,064 INFO 2020-03-09 06:17:04 SinglePassSamProgram Processed 17,000,000 records. Elapsed time: 00:03:10s. Time for last 1,000,000: 10s. Last read position: chr5:90,903,679 INFO 2020-03-09 06:17:14 SinglePassSamProgram Processed 18,000,000 records. Elapsed time: 00:03:20s. Time for last 1,000,000: 10s. Last read position: chr6:34,724,976 INFO 2020-03-09 06:17:25 SinglePassSamProgram Processed 19,000,000 records. Elapsed time: 00:03:31s. Time for last 1,000,000: 10s. Last read position: chr6:138,104,883 INFO 2020-03-09 06:17:34 SinglePassSamProgram Processed 20,000,000 records. Elapsed time: 00:03:40s. Time for last 1,000,000: 8s. Last read position: chr7:73,194,963 INFO 2020-03-09 06:17:44 SinglePassSamProgram Processed 21,000,000 records. Elapsed time: 00:03:50s. Time for last 1,000,000: 9s. Last read position: chr8:26,133,072 INFO 2020-03-09 06:17:53 SinglePassSamProgram Processed 22,000,000 records. Elapsed time: 00:04:00s. Time for last 1,000,000: 9s. Last read position: chr9:36,551,016 INFO 2020-03-09 06:18:04 SinglePassSamProgram Processed 23,000,000 records. Elapsed time: 00:04:10s. Time for last 1,000,000: 10s. Last read position: chr9:103,130,231 INFO 2020-03-09 06:18:10 SinglePassSamProgram Processed 24,000,000 records. Elapsed time: 00:04:16s. Time for last 1,000,000: 6s. Last read position: chrM:6,150 [Mon Mar 09 06:18:18 EDT 2020] picard.analysis.CollectRnaSeqMetrics done. Elapsed time: 4.48 minutes. Runtime.totalMemory()=1159725056