INFO 2020-03-09 06:14:23 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_PBS2_primary_unique.bam -OUTPUT CollectRnaSeqMetrics/2wk_PBS2_metrics ********** 06:14:25.576 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 06:14:25 EDT 2020] CollectRnaSeqMetrics REF_FLAT=genes_refFlat RIBOSOMAL_INTERVALS=rRNA_intervalList_sorted STRAND_SPECIFICITY=NONE INPUT=2wk_PBS2_primary_unique.bam OUTPUT=CollectRnaSeqMetrics/2wk_PBS2_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 06:14:25 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 06:14:26 CollectRnaSeqMetrics Loaded 23632 genes. INFO 2020-03-09 06:14:40 SinglePassSamProgram Processed 1,000,000 records. Elapsed time: 00:00:14s. Time for last 1,000,000: 14s. Last read position: chr1:157,639,359 INFO 2020-03-09 06:14:49 SinglePassSamProgram Processed 2,000,000 records. Elapsed time: 00:00:22s. Time for last 1,000,000: 8s. Last read position: chr10:81,028,706 INFO 2020-03-09 06:14:56 SinglePassSamProgram Processed 3,000,000 records. Elapsed time: 00:00:29s. Time for last 1,000,000: 7s. Last read position: chr11:69,730,762 INFO 2020-03-09 06:15:03 SinglePassSamProgram Processed 4,000,000 records. Elapsed time: 00:00:36s. Time for last 1,000,000: 7s. Last read position: chr12:8,017,990 INFO 2020-03-09 06:15:10 SinglePassSamProgram Processed 5,000,000 records. Elapsed time: 00:00:44s. Time for last 1,000,000: 7s. Last read position: chr13:25,087,269 INFO 2020-03-09 06:15:18 SinglePassSamProgram Processed 6,000,000 records. Elapsed time: 00:00:51s. Time for last 1,000,000: 7s. Last read position: chr14:41,937,294 INFO 2020-03-09 06:15:25 SinglePassSamProgram Processed 7,000,000 records. Elapsed time: 00:00:58s. Time for last 1,000,000: 7s. Last read position: chr15:81,651,848 INFO 2020-03-09 06:15:34 SinglePassSamProgram Processed 8,000,000 records. Elapsed time: 00:01:07s. Time for last 1,000,000: 8s. Last read position: chr16:22,899,155 INFO 2020-03-09 06:15:42 SinglePassSamProgram Processed 9,000,000 records. Elapsed time: 00:01:15s. Time for last 1,000,000: 7s. Last read position: chr17:34,996,979 INFO 2020-03-09 06:15:49 SinglePassSamProgram Processed 10,000,000 records. Elapsed time: 00:01:22s. Time for last 1,000,000: 6s. Last read position: chr18:34,766,988 INFO 2020-03-09 06:15:55 SinglePassSamProgram Processed 11,000,000 records. Elapsed time: 00:01:29s. Time for last 1,000,000: 6s. Last read position: chr19:40,261,639 INFO 2020-03-09 06:16:04 SinglePassSamProgram Processed 12,000,000 records. Elapsed time: 00:01:37s. Time for last 1,000,000: 8s. Last read position: chr2:103,900,637 INFO 2020-03-09 06:16:11 SinglePassSamProgram Processed 13,000,000 records. Elapsed time: 00:01:44s. Time for last 1,000,000: 7s. Last read position: chr3:82,198,936 INFO 2020-03-09 06:16:17 SinglePassSamProgram Processed 14,000,000 records. Elapsed time: 00:01:51s. Time for last 1,000,000: 6s. Last read position: chr4:12,061,917 INFO 2020-03-09 06:16:25 SinglePassSamProgram Processed 15,000,000 records. Elapsed time: 00:01:58s. Time for last 1,000,000: 7s. Last read position: chr4:148,939,565 INFO 2020-03-09 06:16:31 SinglePassSamProgram Processed 16,000,000 records. Elapsed time: 00:02:04s. Time for last 1,000,000: 6s. Last read position: chr5:90,893,101 INFO 2020-03-09 06:16:37 SinglePassSamProgram Processed 17,000,000 records. Elapsed time: 00:02:10s. Time for last 1,000,000: 5s. Last read position: chr5:90,898,598 INFO 2020-03-09 06:16:44 SinglePassSamProgram Processed 18,000,000 records. Elapsed time: 00:02:17s. Time for last 1,000,000: 7s. Last read position: chr5:90,904,301 INFO 2020-03-09 06:16:51 SinglePassSamProgram Processed 19,000,000 records. Elapsed time: 00:02:24s. Time for last 1,000,000: 6s. Last read position: chr6:35,459,551 INFO 2020-03-09 06:16:58 SinglePassSamProgram Processed 20,000,000 records. Elapsed time: 00:02:31s. Time for last 1,000,000: 7s. Last read position: chr7:14,227,062 INFO 2020-03-09 06:17:04 SinglePassSamProgram Processed 21,000,000 records. Elapsed time: 00:02:37s. Time for last 1,000,000: 5s. Last read position: chr7:91,737,452 INFO 2020-03-09 06:17:10 SinglePassSamProgram Processed 22,000,000 records. Elapsed time: 00:02:44s. Time for last 1,000,000: 6s. Last read position: chr8:35,895,736 INFO 2020-03-09 06:17:17 SinglePassSamProgram Processed 23,000,000 records. Elapsed time: 00:02:51s. Time for last 1,000,000: 6s. Last read position: chr9:42,222,550 INFO 2020-03-09 06:17:23 SinglePassSamProgram Processed 24,000,000 records. Elapsed time: 00:02:56s. Time for last 1,000,000: 5s. Last read position: chr9:103,118,245 INFO 2020-03-09 06:17:31 SinglePassSamProgram Processed 25,000,000 records. Elapsed time: 00:03:04s. Time for last 1,000,000: 8s. Last read position: chrM:3,792 INFO 2020-03-09 06:17:34 SinglePassSamProgram Processed 26,000,000 records. Elapsed time: 00:03:07s. Time for last 1,000,000: 2s. Last read position: chrM:12,596 [Mon Mar 09 06:17:39 EDT 2020] picard.analysis.CollectRnaSeqMetrics done. Elapsed time: 3.23 minutes. Runtime.totalMemory()=757071872