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 16wk_PBS3_primary_unique.bam -OUTPUT CollectRnaSeqMetrics/16wk_PBS3_metrics ********** 06:13:48.637 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=16wk_PBS3_primary_unique.bam OUTPUT=CollectRnaSeqMetrics/16wk_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 06:13:48 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 06:14:10 SinglePassSamProgram Processed 1,000,000 records. Elapsed time: 00:00:18s. Time for last 1,000,000: 18s. Last read position: chr1:173,155,832 INFO 2020-03-09 06:14:18 SinglePassSamProgram Processed 2,000,000 records. Elapsed time: 00:00:27s. Time for last 1,000,000: 8s. Last read position: chr10:128,237,962 INFO 2020-03-09 06:14:28 SinglePassSamProgram Processed 3,000,000 records. Elapsed time: 00:00:37s. Time for last 1,000,000: 10s. Last read position: chr11:110,035,612 INFO 2020-03-09 06:14:36 SinglePassSamProgram Processed 4,000,000 records. Elapsed time: 00:00:45s. Time for last 1,000,000: 7s. Last read position: chr12:105,185,230 INFO 2020-03-09 06:14:43 SinglePassSamProgram Processed 5,000,000 records. Elapsed time: 00:00:51s. Time for last 1,000,000: 6s. Last read position: chr13:96,501,310 INFO 2020-03-09 06:14:52 SinglePassSamProgram Processed 6,000,000 records. Elapsed time: 00:01:00s. Time for last 1,000,000: 9s. Last read position: chr15:27,762,767 INFO 2020-03-09 06:15:01 SinglePassSamProgram Processed 7,000,000 records. Elapsed time: 00:01:10s. Time for last 1,000,000: 9s. Last read position: chr16:23,451,069 INFO 2020-03-09 06:15:09 SinglePassSamProgram Processed 8,000,000 records. Elapsed time: 00:01:17s. Time for last 1,000,000: 7s. Last read position: chr17:57,348,667 INFO 2020-03-09 06:15:17 SinglePassSamProgram Processed 9,000,000 records. Elapsed time: 00:01:26s. Time for last 1,000,000: 8s. Last read position: chr19:12,717,496 INFO 2020-03-09 06:15:26 SinglePassSamProgram Processed 10,000,000 records. Elapsed time: 00:01:34s. Time for last 1,000,000: 8s. Last read position: chr2:69,633,974 INFO 2020-03-09 06:15:34 SinglePassSamProgram Processed 11,000,000 records. Elapsed time: 00:01:43s. Time for last 1,000,000: 8s. Last read position: chr3:23,703,411 INFO 2020-03-09 06:15:42 SinglePassSamProgram Processed 12,000,000 records. Elapsed time: 00:01:51s. Time for last 1,000,000: 8s. Last read position: chr3:146,294,185 INFO 2020-03-09 06:15:50 SinglePassSamProgram Processed 13,000,000 records. Elapsed time: 00:01:58s. Time for last 1,000,000: 7s. Last read position: chr4:61,808,960 INFO 2020-03-09 06:15:59 SinglePassSamProgram Processed 14,000,000 records. Elapsed time: 00:02:07s. Time for last 1,000,000: 8s. Last read position: chr5:77,728,728 INFO 2020-03-09 06:16:05 SinglePassSamProgram Processed 15,000,000 records. Elapsed time: 00:02:14s. Time for last 1,000,000: 6s. Last read position: chr5:90,898,542 INFO 2020-03-09 06:16:14 SinglePassSamProgram Processed 16,000,000 records. Elapsed time: 00:02:23s. Time for last 1,000,000: 8s. Last read position: chr5:130,489,060 INFO 2020-03-09 06:16:22 SinglePassSamProgram Processed 17,000,000 records. Elapsed time: 00:02:30s. Time for last 1,000,000: 7s. Last read position: chr6:121,825,900 INFO 2020-03-09 06:16:29 SinglePassSamProgram Processed 18,000,000 records. Elapsed time: 00:02:38s. Time for last 1,000,000: 7s. Last read position: chr7:27,627,979 INFO 2020-03-09 06:16:38 SinglePassSamProgram Processed 19,000,000 records. Elapsed time: 00:02:46s. Time for last 1,000,000: 8s. Last read position: chr7:148,022,646 INFO 2020-03-09 06:16:46 SinglePassSamProgram Processed 20,000,000 records. Elapsed time: 00:02:54s. Time for last 1,000,000: 8s. Last read position: chr9:7,793,114 INFO 2020-03-09 06:16:54 SinglePassSamProgram Processed 21,000,000 records. Elapsed time: 00:03:02s. Time for last 1,000,000: 7s. Last read position: chr9:103,130,288 INFO 2020-03-09 06:17:04 SinglePassSamProgram Processed 22,000,000 records. Elapsed time: 00:03:12s. Time for last 1,000,000: 9s. Last read position: chrM:6,202 [Mon Mar 09 06:17:10 EDT 2020] picard.analysis.CollectRnaSeqMetrics done. Elapsed time: 3.36 minutes. Runtime.totalMemory()=1167065088