INFO 2020-03-09 06:13:38 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_ASNase1_primary_unique.bam -OUTPUT CollectRnaSeqMetrics/16wk_ASNase1_metrics ********** 06:13:42.800 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 06:13:42 EDT 2020] CollectRnaSeqMetrics REF_FLAT=genes_refFlat RIBOSOMAL_INTERVALS=rRNA_intervalList_sorted STRAND_SPECIFICITY=NONE INPUT=16wk_ASNase1_primary_unique.bam OUTPUT=CollectRnaSeqMetrics/16wk_ASNase1_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 06:13:42 EDT 2020] Executing as kkarri@scc-bb1.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 06:13:43 CollectRnaSeqMetrics Loaded 23632 genes. INFO 2020-03-09 06:13:56 SinglePassSamProgram Processed 1,000,000 records. Elapsed time: 00:00:12s. Time for last 1,000,000: 12s. Last read position: chr1:182,097,087 INFO 2020-03-09 06:14:03 SinglePassSamProgram Processed 2,000,000 records. Elapsed time: 00:00:20s. Time for last 1,000,000: 7s. Last read position: chr11:22,901,576 INFO 2020-03-09 06:14:10 SinglePassSamProgram Processed 3,000,000 records. Elapsed time: 00:00:27s. Time for last 1,000,000: 7s. Last read position: chr11:120,422,127 INFO 2020-03-09 06:14:17 SinglePassSamProgram Processed 4,000,000 records. Elapsed time: 00:00:34s. Time for last 1,000,000: 6s. Last read position: chr12:105,576,713 INFO 2020-03-09 06:14:23 SinglePassSamProgram Processed 5,000,000 records. Elapsed time: 00:00:40s. Time for last 1,000,000: 6s. Last read position: chr14:30,817,228 INFO 2020-03-09 06:14:32 SinglePassSamProgram Processed 6,000,000 records. Elapsed time: 00:00:48s. Time for last 1,000,000: 8s. Last read position: chr15:75,778,648 INFO 2020-03-09 06:14:39 SinglePassSamProgram Processed 7,000,000 records. Elapsed time: 00:00:56s. Time for last 1,000,000: 7s. Last read position: chr16:29,652,255 INFO 2020-03-09 06:14:45 SinglePassSamProgram Processed 8,000,000 records. Elapsed time: 00:01:01s. Time for last 1,000,000: 5s. Last read position: chr17:39,983,362 INFO 2020-03-09 06:14:47 SinglePassSamProgram Processed 9,000,000 records. Elapsed time: 00:01:03s. Time for last 1,000,000: 2s. Last read position: chr17:39,984,571 INFO 2020-03-09 06:14:53 SinglePassSamProgram Processed 10,000,000 records. Elapsed time: 00:01:09s. Time for last 1,000,000: 5s. Last read position: chr18:20,825,021 INFO 2020-03-09 06:14:59 SinglePassSamProgram Processed 11,000,000 records. Elapsed time: 00:01:15s. Time for last 1,000,000: 6s. Last read position: chr19:42,135,845 INFO 2020-03-09 06:15:06 SinglePassSamProgram Processed 12,000,000 records. Elapsed time: 00:01:23s. Time for last 1,000,000: 7s. Last read position: chr2:126,378,971 INFO 2020-03-09 06:15:12 SinglePassSamProgram Processed 13,000,000 records. Elapsed time: 00:01:28s. Time for last 1,000,000: 5s. Last read position: chr3:82,812,642 INFO 2020-03-09 06:15:18 SinglePassSamProgram Processed 14,000,000 records. Elapsed time: 00:01:35s. Time for last 1,000,000: 6s. Last read position: chr4:19,549,166 INFO 2020-03-09 06:15:25 SinglePassSamProgram Processed 15,000,000 records. Elapsed time: 00:01:41s. Time for last 1,000,000: 6s. Last read position: chr4:107,736,507 INFO 2020-03-09 06:15:32 SinglePassSamProgram Processed 16,000,000 records. Elapsed time: 00:01:48s. Time for last 1,000,000: 6s. Last read position: chr5:90,890,792 INFO 2020-03-09 06:15:38 SinglePassSamProgram Processed 17,000,000 records. Elapsed time: 00:01:54s. Time for last 1,000,000: 6s. Last read position: chr5:90,904,335 INFO 2020-03-09 06:15:44 SinglePassSamProgram Processed 18,000,000 records. Elapsed time: 00:02:01s. Time for last 1,000,000: 6s. Last read position: chr6:71,151,679 INFO 2020-03-09 06:15:51 SinglePassSamProgram Processed 19,000,000 records. Elapsed time: 00:02:08s. Time for last 1,000,000: 7s. Last read position: chr7:20,281,989 INFO 2020-03-09 06:15:58 SinglePassSamProgram Processed 20,000,000 records. Elapsed time: 00:02:14s. Time for last 1,000,000: 6s. Last read position: chr7:134,136,238 INFO 2020-03-09 06:16:04 SinglePassSamProgram Processed 21,000,000 records. Elapsed time: 00:02:21s. Time for last 1,000,000: 6s. Last read position: chr8:112,101,042 INFO 2020-03-09 06:16:11 SinglePassSamProgram Processed 22,000,000 records. Elapsed time: 00:02:27s. Time for last 1,000,000: 6s. Last read position: chr9:103,119,793 INFO 2020-03-09 06:16:18 SinglePassSamProgram Processed 23,000,000 records. Elapsed time: 00:02:34s. Time for last 1,000,000: 7s. Last read position: chrM:4,316 INFO 2020-03-09 06:16:22 SinglePassSamProgram Processed 24,000,000 records. Elapsed time: 00:02:38s. Time for last 1,000,000: 4s. Last read position: chrX:148,438,423 [Mon Mar 09 06:16:23 EDT 2020] picard.analysis.CollectRnaSeqMetrics done. Elapsed time: 2.68 minutes. Runtime.totalMemory()=875036672