INFO 2020-03-09 06:13:48 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_ASNase2_primary_unique.bam -OUTPUT CollectRnaSeqMetrics/8wk_ASNase2_metrics ********** 06:13:49.004 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 06:13:49 EDT 2020] CollectRnaSeqMetrics REF_FLAT=genes_refFlat RIBOSOMAL_INTERVALS=rRNA_intervalList_sorted STRAND_SPECIFICITY=NONE INPUT=8wk_ASNase2_primary_unique.bam OUTPUT=CollectRnaSeqMetrics/8wk_ASNase2_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 06:13:49 EDT 2020] Executing as kkarri@scc-bb1.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 06:13:49 CollectRnaSeqMetrics Loaded 23632 genes. INFO 2020-03-09 06:14:02 SinglePassSamProgram Processed 1,000,000 records. Elapsed time: 00:00:12s. Time for last 1,000,000: 12s. Last read position: chr1:163,171,737 INFO 2020-03-09 06:14:09 SinglePassSamProgram Processed 2,000,000 records. Elapsed time: 00:00:19s. Time for last 1,000,000: 6s. Last read position: chr10:87,936,540 INFO 2020-03-09 06:14:16 SinglePassSamProgram Processed 3,000,000 records. Elapsed time: 00:00:26s. Time for last 1,000,000: 7s. Last read position: chr11:75,517,309 INFO 2020-03-09 06:14:24 SinglePassSamProgram Processed 4,000,000 records. Elapsed time: 00:00:34s. Time for last 1,000,000: 7s. Last read position: chr12:8,022,886 INFO 2020-03-09 06:14:30 SinglePassSamProgram Processed 5,000,000 records. Elapsed time: 00:00:40s. Time for last 1,000,000: 5s. Last read position: chr12:105,583,601 INFO 2020-03-09 06:14:37 SinglePassSamProgram Processed 6,000,000 records. Elapsed time: 00:00:47s. Time for last 1,000,000: 7s. Last read position: chr14:31,826,437 INFO 2020-03-09 06:14:44 SinglePassSamProgram Processed 7,000,000 records. Elapsed time: 00:00:54s. Time for last 1,000,000: 7s. Last read position: chr15:58,788,095 INFO 2020-03-09 06:14:52 SinglePassSamProgram Processed 8,000,000 records. Elapsed time: 00:01:02s. Time for last 1,000,000: 7s. Last read position: chr16:22,986,100 INFO 2020-03-09 06:14:59 SinglePassSamProgram Processed 9,000,000 records. Elapsed time: 00:01:09s. Time for last 1,000,000: 6s. Last read position: chr17:39,984,025 INFO 2020-03-09 06:15:05 SinglePassSamProgram Processed 10,000,000 records. Elapsed time: 00:01:15s. Time for last 1,000,000: 6s. Last read position: chr18:66,140,795 INFO 2020-03-09 06:15:12 SinglePassSamProgram Processed 11,000,000 records. Elapsed time: 00:01:22s. Time for last 1,000,000: 6s. Last read position: chr19:44,469,927 INFO 2020-03-09 06:15:19 SinglePassSamProgram Processed 12,000,000 records. Elapsed time: 00:01:29s. Time for last 1,000,000: 7s. Last read position: chr2:91,468,518 INFO 2020-03-09 06:15:26 SinglePassSamProgram Processed 13,000,000 records. Elapsed time: 00:01:36s. Time for last 1,000,000: 6s. Last read position: chr3:14,888,029 INFO 2020-03-09 06:15:32 SinglePassSamProgram Processed 14,000,000 records. Elapsed time: 00:01:43s. Time for last 1,000,000: 6s. Last read position: chr3:129,575,808 INFO 2020-03-09 06:15:39 SinglePassSamProgram Processed 15,000,000 records. Elapsed time: 00:01:49s. Time for last 1,000,000: 6s. Last read position: chr4:61,746,345 INFO 2020-03-09 06:15:46 SinglePassSamProgram Processed 16,000,000 records. Elapsed time: 00:01:56s. Time for last 1,000,000: 7s. Last read position: chr5:8,958,449 INFO 2020-03-09 06:15:52 SinglePassSamProgram Processed 17,000,000 records. Elapsed time: 00:02:02s. Time for last 1,000,000: 5s. Last read position: chr5:90,894,940 INFO 2020-03-09 06:15:58 SinglePassSamProgram Processed 18,000,000 records. Elapsed time: 00:02:08s. Time for last 1,000,000: 6s. Last read position: chr5:91,791,409 INFO 2020-03-09 06:16:05 SinglePassSamProgram Processed 19,000,000 records. Elapsed time: 00:02:15s. Time for last 1,000,000: 6s. Last read position: chr6:29,108,190 INFO 2020-03-09 06:16:12 SinglePassSamProgram Processed 20,000,000 records. Elapsed time: 00:02:22s. Time for last 1,000,000: 7s. Last read position: chr6:137,699,504 INFO 2020-03-09 06:16:18 SinglePassSamProgram Processed 21,000,000 records. Elapsed time: 00:02:28s. Time for last 1,000,000: 5s. Last read position: chr7:52,713,475 INFO 2020-03-09 06:16:24 SinglePassSamProgram Processed 22,000,000 records. Elapsed time: 00:02:34s. Time for last 1,000,000: 6s. Last read position: chr7:149,566,704 INFO 2020-03-09 06:16:31 SinglePassSamProgram Processed 23,000,000 records. Elapsed time: 00:02:41s. Time for last 1,000,000: 6s. Last read position: chr8:124,439,860 INFO 2020-03-09 06:16:37 SinglePassSamProgram Processed 24,000,000 records. Elapsed time: 00:02:47s. Time for last 1,000,000: 6s. Last read position: chr9:103,112,853 INFO 2020-03-09 06:16:45 SinglePassSamProgram Processed 25,000,000 records. Elapsed time: 00:02:55s. Time for last 1,000,000: 7s. Last read position: chrM:4,626 INFO 2020-03-09 06:16:48 SinglePassSamProgram Processed 26,000,000 records. Elapsed time: 00:02:58s. Time for last 1,000,000: 2s. Last read position: chrM:14,666 [Mon Mar 09 06:16:52 EDT 2020] picard.analysis.CollectRnaSeqMetrics done. Elapsed time: 3.05 minutes. Runtime.totalMemory()=1112539136