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_ASNase2_primary_unique.bam -OUTPUT CollectRnaSeqMetrics/2wk_ASNase2_metrics ********** 06:14:31.145 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_ASNase2_primary_unique.bam OUTPUT=CollectRnaSeqMetrics/2wk_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 06:14:31 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 06:14:48 SinglePassSamProgram Processed 1,000,000 records. Elapsed time: 00:00:15s. Time for last 1,000,000: 15s. Last read position: chr1:162,919,871 INFO 2020-03-09 06:14:56 SinglePassSamProgram Processed 2,000,000 records. Elapsed time: 00:00:23s. Time for last 1,000,000: 8s. Last read position: chr10:87,046,725 INFO 2020-03-09 06:15:04 SinglePassSamProgram Processed 3,000,000 records. Elapsed time: 00:00:31s. Time for last 1,000,000: 7s. Last read position: chr11:75,223,726 INFO 2020-03-09 06:15:12 SinglePassSamProgram Processed 4,000,000 records. Elapsed time: 00:00:39s. Time for last 1,000,000: 8s. Last read position: chr12:8,799,262 INFO 2020-03-09 06:15:18 SinglePassSamProgram Processed 5,000,000 records. Elapsed time: 00:00:45s. Time for last 1,000,000: 6s. Last read position: chr13:44,964,949 INFO 2020-03-09 06:15:26 SinglePassSamProgram Processed 6,000,000 records. Elapsed time: 00:00:54s. Time for last 1,000,000: 8s. Last read position: chr14:41,975,860 INFO 2020-03-09 06:15:34 SinglePassSamProgram Processed 7,000,000 records. Elapsed time: 00:01:01s. Time for last 1,000,000: 7s. Last read position: chr15:82,204,742 INFO 2020-03-09 06:15:43 SinglePassSamProgram Processed 8,000,000 records. Elapsed time: 00:01:10s. Time for last 1,000,000: 8s. Last read position: chr16:22,898,248 INFO 2020-03-09 06:15:53 SinglePassSamProgram Processed 9,000,000 records. Elapsed time: 00:01:20s. Time for last 1,000,000: 9s. Last read position: chr17:21,164,664 INFO 2020-03-09 06:16:00 SinglePassSamProgram Processed 10,000,000 records. Elapsed time: 00:01:28s. Time for last 1,000,000: 7s. Last read position: chr18:9,996,191 INFO 2020-03-09 06:16:07 SinglePassSamProgram Processed 11,000,000 records. Elapsed time: 00:01:34s. Time for last 1,000,000: 6s. Last read position: chr19:38,198,897 INFO 2020-03-09 06:16:15 SinglePassSamProgram Processed 12,000,000 records. Elapsed time: 00:01:42s. Time for last 1,000,000: 7s. Last read position: chr2:91,468,865 INFO 2020-03-09 06:16:23 SinglePassSamProgram Processed 13,000,000 records. Elapsed time: 00:01:50s. Time for last 1,000,000: 7s. Last read position: chr3:67,406,738 INFO 2020-03-09 06:16:30 SinglePassSamProgram Processed 14,000,000 records. Elapsed time: 00:01:57s. Time for last 1,000,000: 7s. Last read position: chr4:11,091,607 INFO 2020-03-09 06:16:38 SinglePassSamProgram Processed 15,000,000 records. Elapsed time: 00:02:05s. Time for last 1,000,000: 8s. Last read position: chr4:150,230,357 INFO 2020-03-09 06:16:44 SinglePassSamProgram Processed 16,000,000 records. Elapsed time: 00:02:11s. Time for last 1,000,000: 6s. Last read position: chr5:90,893,149 INFO 2020-03-09 06:16:50 SinglePassSamProgram Processed 17,000,000 records. Elapsed time: 00:02:17s. Time for last 1,000,000: 6s. Last read position: chr5:90,899,830 INFO 2020-03-09 06:16:58 SinglePassSamProgram Processed 18,000,000 records. Elapsed time: 00:02:25s. Time for last 1,000,000: 7s. Last read position: chr5:110,650,762 INFO 2020-03-09 06:17:05 SinglePassSamProgram Processed 19,000,000 records. Elapsed time: 00:02:32s. Time for last 1,000,000: 6s. Last read position: chr6:86,597,375 INFO 2020-03-09 06:17:12 SinglePassSamProgram Processed 20,000,000 records. Elapsed time: 00:02:39s. Time for last 1,000,000: 6s. Last read position: chr7:20,282,229 INFO 2020-03-09 06:17:19 SinglePassSamProgram Processed 21,000,000 records. Elapsed time: 00:02:46s. Time for last 1,000,000: 6s. Last read position: chr7:126,808,349 INFO 2020-03-09 06:17:25 SinglePassSamProgram Processed 22,000,000 records. Elapsed time: 00:02:52s. Time for last 1,000,000: 6s. Last read position: chr8:87,588,302 INFO 2020-03-09 06:17:31 SinglePassSamProgram Processed 23,000,000 records. Elapsed time: 00:02:59s. Time for last 1,000,000: 6s. Last read position: chr9:46,038,300 INFO 2020-03-09 06:17:38 SinglePassSamProgram Processed 24,000,000 records. Elapsed time: 00:03:05s. Time for last 1,000,000: 6s. Last read position: chr9:103,127,452 INFO 2020-03-09 06:17:45 SinglePassSamProgram Processed 25,000,000 records. Elapsed time: 00:03:12s. Time for last 1,000,000: 7s. Last read position: chrM:5,875 INFO 2020-03-09 06:17:48 SinglePassSamProgram Processed 26,000,000 records. Elapsed time: 00:03:15s. Time for last 1,000,000: 2s. Last read position: chrM:15,062 [Mon Mar 09 06:17:52 EDT 2020] picard.analysis.CollectRnaSeqMetrics done. Elapsed time: 3.36 minutes. Runtime.totalMemory()=1103101952