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 8wk_PBS2_primary_unique.bam -OUTPUT CollectRnaSeqMetrics/8wk_PBS2_metrics ********** 06:14:27.098 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=8wk_PBS2_primary_unique.bam OUTPUT=CollectRnaSeqMetrics/8wk_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 06:14:27 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: 00:00:13s. Time for last 1,000,000: 13s. Last read position: chr1:173,147,566 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: chr10:127,089,046 INFO 2020-03-09 06:14:58 SinglePassSamProgram Processed 3,000,000 records. Elapsed time: 00:00:29s. Time for last 1,000,000: 8s. Last read position: chr11:98,903,075 INFO 2020-03-09 06:15:07 SinglePassSamProgram Processed 4,000,000 records. Elapsed time: 00:00:38s. Time for last 1,000,000: 8s. Last read position: chr12:104,968,721 INFO 2020-03-09 06:15:13 SinglePassSamProgram Processed 5,000,000 records. Elapsed time: 00:00:44s. Time for last 1,000,000: 5s. Last read position: chr13:62,989,308 INFO 2020-03-09 06:15:21 SinglePassSamProgram Processed 6,000,000 records. Elapsed time: 00:00:52s. Time for last 1,000,000: 7s. Last read position: chr15:3,225,713 INFO 2020-03-09 06:15:29 SinglePassSamProgram Processed 7,000,000 records. Elapsed time: 00:01:00s. Time for last 1,000,000: 8s. Last read position: chr16:22,817,984 INFO 2020-03-09 06:15:37 SinglePassSamProgram Processed 8,000,000 records. Elapsed time: 00:01:08s. Time for last 1,000,000: 8s. Last read position: chr17:39,983,377 INFO 2020-03-09 06:15:44 SinglePassSamProgram Processed 9,000,000 records. Elapsed time: 00:01:16s. Time for last 1,000,000: 7s. Last read position: chr18:78,020,046 INFO 2020-03-09 06:15:51 SinglePassSamProgram Processed 10,000,000 records. Elapsed time: 00:01:22s. Time for last 1,000,000: 6s. Last read position: chr19:55,369,390 INFO 2020-03-09 06:16:00 SinglePassSamProgram Processed 11,000,000 records. Elapsed time: 00:01:31s. Time for last 1,000,000: 8s. Last read position: chr2:126,400,897 INFO 2020-03-09 06:16:07 SinglePassSamProgram Processed 12,000,000 records. Elapsed time: 00:01:38s. Time for last 1,000,000: 7s. Last read position: chr3:82,847,713 INFO 2020-03-09 06:16:14 SinglePassSamProgram Processed 13,000,000 records. Elapsed time: 00:01:45s. Time for last 1,000,000: 7s. Last read position: chr4:53,043,910 INFO 2020-03-09 06:16:21 SinglePassSamProgram Processed 14,000,000 records. Elapsed time: 00:01:52s. Time for last 1,000,000: 6s. Last read position: chr4:116,371,945 INFO 2020-03-09 06:16:28 SinglePassSamProgram Processed 15,000,000 records. Elapsed time: 00:01:59s. Time for last 1,000,000: 7s. Last read position: chr5:90,891,756 INFO 2020-03-09 06:16:35 SinglePassSamProgram Processed 16,000,000 records. Elapsed time: 00:02:06s. Time for last 1,000,000: 6s. Last read position: chr5:90,901,611 INFO 2020-03-09 06:16:42 SinglePassSamProgram Processed 17,000,000 records. Elapsed time: 00:02:13s. Time for last 1,000,000: 7s. Last read position: chr5:151,374,463 INFO 2020-03-09 06:16:50 SinglePassSamProgram Processed 18,000,000 records. Elapsed time: 00:02:21s. Time for last 1,000,000: 8s. Last read position: chr6:129,487,566 INFO 2020-03-09 06:16:56 SinglePassSamProgram Processed 19,000,000 records. Elapsed time: 00:02:27s. Time for last 1,000,000: 6s. Last read position: chr7:52,714,997 INFO 2020-03-09 06:17:04 SinglePassSamProgram Processed 20,000,000 records. Elapsed time: 00:02:35s. Time for last 1,000,000: 7s. Last read position: chr8:42,004,934 INFO 2020-03-09 06:17:11 SinglePassSamProgram Processed 21,000,000 records. Elapsed time: 00:02:42s. Time for last 1,000,000: 7s. Last read position: chr9:44,291,506 INFO 2020-03-09 06:17:18 SinglePassSamProgram Processed 22,000,000 records. Elapsed time: 00:02:49s. Time for last 1,000,000: 6s. Last read position: chr9:107,560,335 INFO 2020-03-09 06:17:24 SinglePassSamProgram Processed 23,000,000 records. Elapsed time: 00:02:55s. Time for last 1,000,000: 6s. Last read position: chrM:6,211 INFO 2020-03-09 06:17:29 SinglePassSamProgram Processed 24,000,000 records. Elapsed time: 00:03:00s. Time for last 1,000,000: 4s. Last read position: chrX:148,348,810 [Mon Mar 09 06:17:30 EDT 2020] picard.analysis.CollectRnaSeqMetrics done. Elapsed time: 3.06 minutes. Runtime.totalMemory()=808976384