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 8wk_ASNase3_primary_unique.bam -OUTPUT CollectRnaSeqMetrics/8wk_ASNase3_metrics ********** 06:13:48.327 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 06:13:48 EDT 2020] CollectRnaSeqMetrics REF_FLAT=genes_refFlat RIBOSOMAL_INTERVALS=rRNA_intervalList_sorted STRAND_SPECIFICITY=NONE INPUT=8wk_ASNase3_primary_unique.bam OUTPUT=CollectRnaSeqMetrics/8wk_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 06:13:48 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 06:13:50 CollectRnaSeqMetrics Loaded 23632 genes. INFO 2020-03-09 06:14:08 SinglePassSamProgram Processed 1,000,000 records. Elapsed time: 00:00:17s. Time for last 1,000,000: 17s. Last read position: chr1:162,927,797 INFO 2020-03-09 06:14:16 SinglePassSamProgram Processed 2,000,000 records. Elapsed time: 00:00:25s. Time for last 1,000,000: 7s. Last read position: chr10:87,000,931 INFO 2020-03-09 06:14:25 SinglePassSamProgram Processed 3,000,000 records. Elapsed time: 00:00:34s. Time for last 1,000,000: 9s. Last read position: chr11:73,017,481 INFO 2020-03-09 06:14:33 SinglePassSamProgram Processed 4,000,000 records. Elapsed time: 00:00:42s. Time for last 1,000,000: 8s. Last read position: chr12:8,018,802 INFO 2020-03-09 06:14:41 SinglePassSamProgram Processed 5,000,000 records. Elapsed time: 00:00:49s. Time for last 1,000,000: 7s. Last read position: chr12:106,278,865 INFO 2020-03-09 06:14:49 SinglePassSamProgram Processed 6,000,000 records. Elapsed time: 00:00:57s. Time for last 1,000,000: 7s. Last read position: chr14:31,750,972 INFO 2020-03-09 06:14:57 SinglePassSamProgram Processed 7,000,000 records. Elapsed time: 00:01:05s. Time for last 1,000,000: 8s. Last read position: chr15:43,339,214 INFO 2020-03-09 06:15:04 SinglePassSamProgram Processed 8,000,000 records. Elapsed time: 00:01:13s. Time for last 1,000,000: 7s. Last read position: chr16:22,892,317 INFO 2020-03-09 06:15:13 SinglePassSamProgram Processed 9,000,000 records. Elapsed time: 00:01:21s. Time for last 1,000,000: 8s. Last read position: chr17:31,749,880 INFO 2020-03-09 06:15:17 SinglePassSamProgram Processed 10,000,000 records. Elapsed time: 00:01:26s. Time for last 1,000,000: 4s. Last read position: chr17:39,984,401 INFO 2020-03-09 06:15:24 SinglePassSamProgram Processed 11,000,000 records. Elapsed time: 00:01:33s. Time for last 1,000,000: 6s. Last read position: chr18:10,104,072 INFO 2020-03-09 06:15:31 SinglePassSamProgram Processed 12,000,000 records. Elapsed time: 00:01:39s. Time for last 1,000,000: 6s. Last read position: chr19:20,685,496 INFO 2020-03-09 06:15:38 SinglePassSamProgram Processed 13,000,000 records. Elapsed time: 00:01:46s. Time for last 1,000,000: 7s. Last read position: chr2:24,939,811 INFO 2020-03-09 06:15:47 SinglePassSamProgram Processed 14,000,000 records. Elapsed time: 00:01:56s. Time for last 1,000,000: 9s. Last read position: chr2:134,323,555 INFO 2020-03-09 06:15:55 SinglePassSamProgram Processed 15,000,000 records. Elapsed time: 00:02:03s. Time for last 1,000,000: 7s. Last read position: chr3:82,818,186 INFO 2020-03-09 06:16:02 SinglePassSamProgram Processed 16,000,000 records. Elapsed time: 00:02:11s. Time for last 1,000,000: 7s. Last read position: chr4:32,072,730 INFO 2020-03-09 06:16:10 SinglePassSamProgram Processed 17,000,000 records. Elapsed time: 00:02:19s. Time for last 1,000,000: 7s. Last read position: chr4:115,193,728 INFO 2020-03-09 06:16:18 SinglePassSamProgram Processed 18,000,000 records. Elapsed time: 00:02:27s. Time for last 1,000,000: 8s. Last read position: chr5:89,867,288 INFO 2020-03-09 06:16:24 SinglePassSamProgram Processed 19,000,000 records. Elapsed time: 00:02:33s. Time for last 1,000,000: 6s. Last read position: chr5:90,897,699 INFO 2020-03-09 06:16:33 SinglePassSamProgram Processed 20,000,000 records. Elapsed time: 00:02:41s. Time for last 1,000,000: 8s. Last read position: chr5:115,691,981 INFO 2020-03-09 06:16:40 SinglePassSamProgram Processed 21,000,000 records. Elapsed time: 00:02:49s. Time for last 1,000,000: 7s. Last read position: chr6:39,093,196 INFO 2020-03-09 06:16:48 SinglePassSamProgram Processed 22,000,000 records. Elapsed time: 00:02:57s. Time for last 1,000,000: 8s. Last read position: chr6:138,105,014 INFO 2020-03-09 06:16:55 SinglePassSamProgram Processed 23,000,000 records. Elapsed time: 00:03:04s. Time for last 1,000,000: 7s. Last read position: chr7:52,714,455 INFO 2020-03-09 06:17:04 SinglePassSamProgram Processed 24,000,000 records. Elapsed time: 00:03:13s. Time for last 1,000,000: 8s. Last read position: chr7:149,762,827 INFO 2020-03-09 06:17:12 SinglePassSamProgram Processed 25,000,000 records. Elapsed time: 00:03:21s. Time for last 1,000,000: 8s. Last read position: chr8:125,413,561 INFO 2020-03-09 06:17:20 SinglePassSamProgram Processed 26,000,000 records. Elapsed time: 00:03:29s. Time for last 1,000,000: 7s. Last read position: chr9:103,112,826 INFO 2020-03-09 06:17:27 SinglePassSamProgram Processed 27,000,000 records. Elapsed time: 00:03:36s. Time for last 1,000,000: 7s. Last read position: chrM:1,475 INFO 2020-03-09 06:17:31 SinglePassSamProgram Processed 28,000,000 records. Elapsed time: 00:03:39s. Time for last 1,000,000: 3s. Last read position: chrM:11,026 [Mon Mar 09 06:17:37 EDT 2020] picard.analysis.CollectRnaSeqMetrics done. Elapsed time: 3.83 minutes. Runtime.totalMemory()=1173356544