INFO 2020-03-09 06:14:26 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 2wk_ASNase1_primary_unique.bam -OUTPUT CollectRnaSeqMetrics/2wk_ASNase1_metrics ********** 06:14:26.699 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 06:14:27 EDT 2020] CollectRnaSeqMetrics REF_FLAT=genes_refFlat RIBOSOMAL_INTERVALS=rRNA_intervalList_sorted STRAND_SPECIFICITY=NONE INPUT=2wk_ASNase1_primary_unique.bam OUTPUT=CollectRnaSeqMetrics/2wk_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 06:14:27 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 06:14:28 CollectRnaSeqMetrics Loaded 23632 genes. INFO 2020-03-09 06:14:42 SinglePassSamProgram Processed 1,000,000 records. Elapsed time: 00:00:14s. Time for last 1,000,000: 14s. Last read position: chr1:155,755,942 INFO 2020-03-09 06:14:50 SinglePassSamProgram Processed 2,000,000 records. Elapsed time: 00:00:21s. Time for last 1,000,000: 7s. Last read position: chr10:79,798,902 INFO 2020-03-09 06:14:57 SinglePassSamProgram Processed 3,000,000 records. Elapsed time: 00:00:29s. Time for last 1,000,000: 7s. Last read position: chr11:51,798,340 INFO 2020-03-09 06:15:05 SinglePassSamProgram Processed 4,000,000 records. Elapsed time: 00:00:36s. Time for last 1,000,000: 7s. Last read position: chr11:109,833,005 INFO 2020-03-09 06:15:12 SinglePassSamProgram Processed 5,000,000 records. Elapsed time: 00:00:43s. Time for last 1,000,000: 7s. Last read position: chr12:105,003,003 INFO 2020-03-09 06:15:18 SinglePassSamProgram Processed 6,000,000 records. Elapsed time: 00:00:49s. Time for last 1,000,000: 6s. Last read position: chr13:113,368,408 INFO 2020-03-09 06:15:26 SinglePassSamProgram Processed 7,000,000 records. Elapsed time: 00:00:57s. Time for last 1,000,000: 8s. Last read position: chr14:100,266,008 INFO 2020-03-09 06:15:34 SinglePassSamProgram Processed 8,000,000 records. Elapsed time: 00:01:05s. Time for last 1,000,000: 7s. Last read position: chr15:102,360,073 INFO 2020-03-09 06:15:44 SinglePassSamProgram Processed 9,000,000 records. Elapsed time: 00:01:15s. Time for last 1,000,000: 9s. Last read position: chr16:22,899,364 INFO 2020-03-09 06:15:51 SinglePassSamProgram Processed 10,000,000 records. Elapsed time: 00:01:22s. Time for last 1,000,000: 7s. Last read position: chr17:35,141,740 INFO 2020-03-09 06:15:58 SinglePassSamProgram Processed 11,000,000 records. Elapsed time: 00:01:29s. Time for last 1,000,000: 6s. Last read position: chr18:38,428,076 INFO 2020-03-09 06:16:04 SinglePassSamProgram Processed 12,000,000 records. Elapsed time: 00:01:35s. Time for last 1,000,000: 6s. Last read position: chr19:40,086,576 INFO 2020-03-09 06:16:12 SinglePassSamProgram Processed 13,000,000 records. Elapsed time: 00:01:43s. Time for last 1,000,000: 7s. Last read position: chr2:91,116,054 INFO 2020-03-09 06:16:19 SinglePassSamProgram Processed 14,000,000 records. Elapsed time: 00:01:50s. Time for last 1,000,000: 7s. Last read position: chr3:28,618,276 INFO 2020-03-09 06:16:26 SinglePassSamProgram Processed 15,000,000 records. Elapsed time: 00:01:57s. Time for last 1,000,000: 6s. Last read position: chr3:137,529,488 INFO 2020-03-09 06:16:33 SinglePassSamProgram Processed 16,000,000 records. Elapsed time: 00:02:04s. Time for last 1,000,000: 7s. Last read position: chr4:116,371,814 INFO 2020-03-09 06:16:40 SinglePassSamProgram Processed 17,000,000 records. Elapsed time: 00:02:11s. Time for last 1,000,000: 7s. Last read position: chr5:90,889,946 INFO 2020-03-09 06:16:46 SinglePassSamProgram Processed 18,000,000 records. Elapsed time: 00:02:17s. Time for last 1,000,000: 5s. Last read position: chr5:90,901,164 INFO 2020-03-09 06:16:53 SinglePassSamProgram Processed 19,000,000 records. Elapsed time: 00:02:24s. Time for last 1,000,000: 7s. Last read position: chr5:138,426,355 INFO 2020-03-09 06:17:00 SinglePassSamProgram Processed 20,000,000 records. Elapsed time: 00:02:31s. Time for last 1,000,000: 6s. Last read position: chr6:124,664,147 INFO 2020-03-09 06:17:06 SinglePassSamProgram Processed 21,000,000 records. Elapsed time: 00:02:37s. Time for last 1,000,000: 6s. Last read position: chr7:20,282,981 INFO 2020-03-09 06:17:13 SinglePassSamProgram Processed 22,000,000 records. Elapsed time: 00:02:44s. Time for last 1,000,000: 6s. Last read position: chr7:133,767,051 INFO 2020-03-09 06:17:19 SinglePassSamProgram Processed 23,000,000 records. Elapsed time: 00:02:50s. Time for last 1,000,000: 6s. Last read position: chr8:95,630,592 INFO 2020-03-09 06:17:25 SinglePassSamProgram Processed 24,000,000 records. Elapsed time: 00:02:56s. Time for last 1,000,000: 6s. Last read position: chr9:46,077,898 INFO 2020-03-09 06:17:32 SinglePassSamProgram Processed 25,000,000 records. Elapsed time: 00:03:03s. Time for last 1,000,000: 6s. Last read position: chr9:107,436,836 INFO 2020-03-09 06:17:38 SinglePassSamProgram Processed 26,000,000 records. Elapsed time: 00:03:09s. Time for last 1,000,000: 6s. Last read position: chrM:6,151 INFO 2020-03-09 06:17:41 SinglePassSamProgram Processed 27,000,000 records. Elapsed time: 00:03:12s. Time for last 1,000,000: 3s. Last read position: chrX:34,622,621 [Mon Mar 09 06:17:44 EDT 2020] picard.analysis.CollectRnaSeqMetrics done. Elapsed time: 3.30 minutes. Runtime.totalMemory()=808452096