INFO 2020-03-09 06:14:34 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 8wk_ASNase1_primary_unique.bam -OUTPUT CollectRnaSeqMetrics/8wk_ASNase1_metrics ********** 06:14:35.100 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 06:14:35 EDT 2020] CollectRnaSeqMetrics REF_FLAT=genes_refFlat RIBOSOMAL_INTERVALS=rRNA_intervalList_sorted STRAND_SPECIFICITY=NONE INPUT=8wk_ASNase1_primary_unique.bam OUTPUT=CollectRnaSeqMetrics/8wk_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 06:14:35 EDT 2020] Executing as kkarri@scc-bb6.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 06:14:35 CollectRnaSeqMetrics Loaded 23632 genes. INFO 2020-03-09 06:14:49 SinglePassSamProgram Processed 1,000,000 records. Elapsed time: 00:00:13s. Time for last 1,000,000: 13s. Last read position: chr1:152,227,449 INFO 2020-03-09 06:14:57 SinglePassSamProgram Processed 2,000,000 records. Elapsed time: 00:00:21s. Time for last 1,000,000: 7s. Last read position: chr10:75,398,749 INFO 2020-03-09 06:15:05 SinglePassSamProgram Processed 3,000,000 records. Elapsed time: 00:00:29s. Time for last 1,000,000: 8s. Last read position: chr11:16,895,337 INFO 2020-03-09 06:15:15 SinglePassSamProgram Processed 4,000,000 records. Elapsed time: 00:00:39s. Time for last 1,000,000: 9s. Last read position: chr11:98,636,318 INFO 2020-03-09 06:15:24 SinglePassSamProgram Processed 5,000,000 records. Elapsed time: 00:00:48s. Time for last 1,000,000: 8s. Last read position: chr12:72,060,971 INFO 2020-03-09 06:15:31 SinglePassSamProgram Processed 6,000,000 records. Elapsed time: 00:00:54s. Time for last 1,000,000: 6s. Last read position: chr13:41,280,485 INFO 2020-03-09 06:15:39 SinglePassSamProgram Processed 7,000,000 records. Elapsed time: 00:01:03s. Time for last 1,000,000: 8s. Last read position: chr14:51,448,688 INFO 2020-03-09 06:15:47 SinglePassSamProgram Processed 8,000,000 records. Elapsed time: 00:01:11s. Time for last 1,000,000: 8s. Last read position: chr15:76,010,596 INFO 2020-03-09 06:15:56 SinglePassSamProgram Processed 9,000,000 records. Elapsed time: 00:01:19s. Time for last 1,000,000: 8s. Last read position: chr16:22,898,266 INFO 2020-03-09 06:16:04 SinglePassSamProgram Processed 10,000,000 records. Elapsed time: 00:01:27s. Time for last 1,000,000: 8s. Last read position: chr17:33,960,221 INFO 2020-03-09 06:16:12 SinglePassSamProgram Processed 11,000,000 records. Elapsed time: 00:01:35s. Time for last 1,000,000: 7s. Last read position: chr17:75,059,895 INFO 2020-03-09 06:16:18 SinglePassSamProgram Processed 12,000,000 records. Elapsed time: 00:01:42s. Time for last 1,000,000: 6s. Last read position: chr19:7,289,947 INFO 2020-03-09 06:16:24 SinglePassSamProgram Processed 13,000,000 records. Elapsed time: 00:01:48s. Time for last 1,000,000: 6s. Last read position: chr19:44,471,878 INFO 2020-03-09 06:16:33 SinglePassSamProgram Processed 14,000,000 records. Elapsed time: 00:01:57s. Time for last 1,000,000: 8s. Last read position: chr2:72,094,324 INFO 2020-03-09 06:16:41 SinglePassSamProgram Processed 15,000,000 records. Elapsed time: 00:02:05s. Time for last 1,000,000: 7s. Last read position: chr2:172,980,862 INFO 2020-03-09 06:16:48 SinglePassSamProgram Processed 16,000,000 records. Elapsed time: 00:02:12s. Time for last 1,000,000: 6s. Last read position: chr3:91,884,466 INFO 2020-03-09 06:16:55 SinglePassSamProgram Processed 17,000,000 records. Elapsed time: 00:02:19s. Time for last 1,000,000: 7s. Last read position: chr4:45,391,317 INFO 2020-03-09 06:17:03 SinglePassSamProgram Processed 18,000,000 records. Elapsed time: 00:02:27s. Time for last 1,000,000: 7s. Last read position: chr4:134,481,819 INFO 2020-03-09 06:17:10 SinglePassSamProgram Processed 19,000,000 records. Elapsed time: 00:02:34s. Time for last 1,000,000: 7s. Last read position: chr5:90,889,975 INFO 2020-03-09 06:17:16 SinglePassSamProgram Processed 20,000,000 records. Elapsed time: 00:02:40s. Time for last 1,000,000: 5s. Last read position: chr5:90,896,432 INFO 2020-03-09 06:17:23 SinglePassSamProgram Processed 21,000,000 records. Elapsed time: 00:02:47s. Time for last 1,000,000: 7s. Last read position: chr5:90,901,160 INFO 2020-03-09 06:17:32 SinglePassSamProgram Processed 22,000,000 records. Elapsed time: 00:02:56s. Time for last 1,000,000: 8s. Last read position: chr5:121,899,482 INFO 2020-03-09 06:17:39 SinglePassSamProgram Processed 23,000,000 records. Elapsed time: 00:03:03s. Time for last 1,000,000: 7s. Last read position: chr6:49,025,188 INFO 2020-03-09 06:17:47 SinglePassSamProgram Processed 24,000,000 records. Elapsed time: 00:03:11s. Time for last 1,000,000: 8s. Last read position: chr6:129,374,249 INFO 2020-03-09 06:17:52 SinglePassSamProgram Processed 25,000,000 records. Elapsed time: 00:03:16s. Time for last 1,000,000: 5s. Last read position: chr7:27,621,742 INFO 2020-03-09 06:17:59 SinglePassSamProgram Processed 26,000,000 records. Elapsed time: 00:03:23s. Time for last 1,000,000: 6s. Last read position: chr7:126,805,729 INFO 2020-03-09 06:18:06 SinglePassSamProgram Processed 27,000,000 records. Elapsed time: 00:03:30s. Time for last 1,000,000: 7s. Last read position: chr8:73,898,342 INFO 2020-03-09 06:18:13 SinglePassSamProgram Processed 28,000,000 records. Elapsed time: 00:03:37s. Time for last 1,000,000: 6s. Last read position: chr9:42,060,815 INFO 2020-03-09 06:18:19 SinglePassSamProgram Processed 29,000,000 records. Elapsed time: 00:03:43s. Time for last 1,000,000: 6s. Last read position: chr9:103,118,205 INFO 2020-03-09 06:18:28 SinglePassSamProgram Processed 30,000,000 records. Elapsed time: 00:03:52s. Time for last 1,000,000: 8s. Last read position: chrM:3,235 INFO 2020-03-09 06:18:31 SinglePassSamProgram Processed 31,000,000 records. Elapsed time: 00:03:55s. Time for last 1,000,000: 2s. Last read position: chrM:6,317 INFO 2020-03-09 06:18:34 SinglePassSamProgram Processed 32,000,000 records. Elapsed time: 00:03:58s. Time for last 1,000,000: 3s. Last read position: chrX:34,142,205 [Mon Mar 09 06:18:37 EDT 2020] picard.analysis.CollectRnaSeqMetrics done. Elapsed time: 4.05 minutes. Runtime.totalMemory()=799014912