INFO 2020-03-09 06:14:30 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_PBS3_primary_unique.bam -OUTPUT CollectRnaSeqMetrics/2wk_PBS3_metrics ********** 06:14:31.153 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 06:14:31 EDT 2020] CollectRnaSeqMetrics REF_FLAT=genes_refFlat RIBOSOMAL_INTERVALS=rRNA_intervalList_sorted STRAND_SPECIFICITY=NONE INPUT=2wk_PBS3_primary_unique.bam OUTPUT=CollectRnaSeqMetrics/2wk_PBS3_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 06:14:31 EDT 2020] Executing as kkarri@scc-bb2.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 06:14:32 CollectRnaSeqMetrics Loaded 23632 genes. INFO 2020-03-09 06:14:47 SinglePassSamProgram Processed 1,000,000 records. Elapsed time: 00:00:14s. Time for last 1,000,000: 14s. Last read position: chr1:162,927,747 INFO 2020-03-09 06:14:54 SinglePassSamProgram Processed 2,000,000 records. Elapsed time: 00:00:22s. Time for last 1,000,000: 7s. Last read position: chr10:90,579,622 INFO 2020-03-09 06:15:02 SinglePassSamProgram Processed 3,000,000 records. Elapsed time: 00:00:29s. Time for last 1,000,000: 7s. Last read position: chr11:75,284,074 INFO 2020-03-09 06:15:09 SinglePassSamProgram Processed 4,000,000 records. Elapsed time: 00:00:37s. Time for last 1,000,000: 7s. Last read position: chr12:36,182,981 INFO 2020-03-09 06:15:16 SinglePassSamProgram Processed 5,000,000 records. Elapsed time: 00:00:43s. Time for last 1,000,000: 6s. Last read position: chr13:58,496,624 INFO 2020-03-09 06:15:24 SinglePassSamProgram Processed 6,000,000 records. Elapsed time: 00:00:51s. Time for last 1,000,000: 7s. Last read position: chr14:56,358,050 INFO 2020-03-09 06:15:31 SinglePassSamProgram Processed 7,000,000 records. Elapsed time: 00:00:58s. Time for last 1,000,000: 7s. Last read position: chr15:98,481,374 INFO 2020-03-09 06:15:41 SinglePassSamProgram Processed 8,000,000 records. Elapsed time: 00:01:09s. Time for last 1,000,000: 10s. Last read position: chr16:22,899,274 INFO 2020-03-09 06:15:49 SinglePassSamProgram Processed 9,000,000 records. Elapsed time: 00:01:17s. Time for last 1,000,000: 7s. Last read position: chr17:35,610,256 INFO 2020-03-09 06:15:56 SinglePassSamProgram Processed 10,000,000 records. Elapsed time: 00:01:23s. Time for last 1,000,000: 6s. Last read position: chr18:56,692,168 INFO 2020-03-09 06:16:03 SinglePassSamProgram Processed 11,000,000 records. Elapsed time: 00:01:30s. Time for last 1,000,000: 6s. Last read position: chr2:10,016,453 INFO 2020-03-09 06:16:11 SinglePassSamProgram Processed 12,000,000 records. Elapsed time: 00:01:38s. Time for last 1,000,000: 8s. Last read position: chr2:143,778,996 INFO 2020-03-09 06:16:18 SinglePassSamProgram Processed 13,000,000 records. Elapsed time: 00:01:45s. Time for last 1,000,000: 7s. Last read position: chr3:89,673,276 INFO 2020-03-09 06:16:25 SinglePassSamProgram Processed 14,000,000 records. Elapsed time: 00:01:52s. Time for last 1,000,000: 6s. Last read position: chr4:87,751,405 INFO 2020-03-09 06:16:32 SinglePassSamProgram Processed 15,000,000 records. Elapsed time: 00:02:00s. Time for last 1,000,000: 7s. Last read position: chr5:87,754,720 INFO 2020-03-09 06:16:38 SinglePassSamProgram Processed 16,000,000 records. Elapsed time: 00:02:05s. Time for last 1,000,000: 5s. Last read position: chr5:90,896,403 INFO 2020-03-09 06:16:45 SinglePassSamProgram Processed 17,000,000 records. Elapsed time: 00:02:12s. Time for last 1,000,000: 6s. Last read position: chr5:90,901,151 INFO 2020-03-09 06:16:53 SinglePassSamProgram Processed 18,000,000 records. Elapsed time: 00:02:20s. Time for last 1,000,000: 7s. Last read position: chr5:110,712,721 INFO 2020-03-09 06:16:59 SinglePassSamProgram Processed 19,000,000 records. Elapsed time: 00:02:27s. Time for last 1,000,000: 6s. Last read position: chr6:87,739,269 INFO 2020-03-09 06:17:06 SinglePassSamProgram Processed 20,000,000 records. Elapsed time: 00:02:33s. Time for last 1,000,000: 6s. Last read position: chr7:20,282,244 INFO 2020-03-09 06:17:12 SinglePassSamProgram Processed 21,000,000 records. Elapsed time: 00:02:40s. Time for last 1,000,000: 6s. Last read position: chr7:134,167,991 INFO 2020-03-09 06:17:19 SinglePassSamProgram Processed 22,000,000 records. Elapsed time: 00:02:46s. Time for last 1,000,000: 6s. Last read position: chr8:95,631,498 INFO 2020-03-09 06:17:25 SinglePassSamProgram Processed 23,000,000 records. Elapsed time: 00:02:52s. Time for last 1,000,000: 6s. Last read position: chr9:53,390,658 INFO 2020-03-09 06:17:31 SinglePassSamProgram Processed 24,000,000 records. Elapsed time: 00:02:58s. Time for last 1,000,000: 6s. Last read position: chr9:103,128,396 INFO 2020-03-09 06:17:38 SinglePassSamProgram Processed 25,000,000 records. Elapsed time: 00:03:05s. Time for last 1,000,000: 6s. Last read position: chrM:5,846 INFO 2020-03-09 06:17:41 SinglePassSamProgram Processed 26,000,000 records. Elapsed time: 00:03:08s. Time for last 1,000,000: 2s. Last read position: chrX:9,231,825 [Mon Mar 09 06:17:45 EDT 2020] picard.analysis.CollectRnaSeqMetrics done. Elapsed time: 3.23 minutes. Runtime.totalMemory()=936378368