[Thu Jun 15 06:17:20 EDT 2017] picard.analysis.CollectRnaSeqMetrics REF_FLAT=genes_refFlat RIBOSOMAL_INTERVALS=rRNA_intervalList_sorted STRAND_SPECIFICITY=NONE INPUT=TA_IP2_primary_unique.bam OUTPUT=CollectRnaSeqMetrics/TA_IP2_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
[Thu Jun 15 06:17:20 EDT 2017] Executing as kkarri@scc-kb7.scc.bu.edu on Linux 2.6.32-642.13.1.el6.x86_64 amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_21-b11; Picard version: 1.123(286a232caea2fdc8fdd88574c09c460b46386fff_1413818736) IntelDeflater
INFO	2017-06-15 06:17:21	CollectRnaSeqMetrics	Loaded 16744 genes.
WARNING	2017-06-15 06:17:21	IntervalList	Ignoring interval for unknown reference: chrUn_KL568198v1:340-554	-	LSU-rRNA_Hsa
WARNING	2017-06-15 06:17:21	IntervalList	Ignoring interval for unknown reference: chrUn_KL568266v1:1-693	+	SSU-rRNA_Hsa
WARNING	2017-06-15 06:17:21	IntervalList	Ignoring interval for unknown reference: chrUn_KL568266v1:8656-9079	+	LSU-rRNA_Hsa
WARNING	2017-06-15 06:17:21	IntervalList	Ignoring interval for unknown reference: chrUn_KL568271v1:1-456	-	LSU-rRNA_Hsa
WARNING	2017-06-15 06:17:21	IntervalList	Ignoring interval for unknown reference: chrUn_KL568337v1:51050-51814	-	SSU-rRNA_Hsa
WARNING	2017-06-15 06:17:21	IntervalList	Ignoring interval for unknown reference: chrUn_KL568346v1:82780-83467	-	SSU-rRNA_Hsa
WARNING	2017-06-15 06:17:21	IntervalList	Ignoring interval for unknown reference: chrUn_KL568348v1:20080-20133	+	LSU-rRNA_Hsa
WARNING	2017-06-15 06:17:21	IntervalList	Ignoring interval for unknown reference: chrUn_KL568355v1:1276-1573	-	SSU-rRNA_Hsa
WARNING	2017-06-15 06:17:21	IntervalList	Ignoring interval for unknown reference: chrUn_KL568355v1:2048-2812	+	SSU-rRNA_Hsa
WARNING	2017-06-15 06:17:21	IntervalList	Ignoring interval for unknown reference: chrUn_KL568374v1:125331-125437	-	LSU-rRNA_Hsa
WARNING	2017-06-15 06:17:21	IntervalList	Ignoring interval for unknown reference: chrUn_KL568374v1:125475-126132	-	LSU-rRNA_Hsa
WARNING	2017-06-15 06:17:21	IntervalList	Ignoring interval for unknown reference: chrUn_KL568374v1:197093-197399	-	LSU-rRNA_Hsa
WARNING	2017-06-15 06:17:21	IntervalList	Ignoring interval for unknown reference: chrUn_KL568374v1:199759-200396	+	SSU-rRNA_Hsa
WARNING	2017-06-15 06:17:21	IntervalList	Ignoring interval for unknown reference: chrUn_KL568374v1:225478-225779	+	LSU-rRNA_Hsa
WARNING	2017-06-15 06:17:21	IntervalList	Ignoring interval for unknown reference: chrUn_KL568374v1:225902-225960	+	LSU-rRNA_Hsa
WARNING	2017-06-15 06:17:21	IntervalList	Ignoring interval for unknown reference: chrUn_KL568381v1:26642-27424	-	LSU-rRNA_Hsa
WARNING	2017-06-15 06:17:21	IntervalList	Ignoring interval for unknown reference: chrUn_KL568381v1:28825-29580	-	SSU-rRNA_Hsa
WARNING	2017-06-15 06:17:21	IntervalList	Ignoring interval for unknown reference: chrUn_KL568382v1:5520-5681	+	LSU-rRNA_Hsa
WARNING	2017-06-15 06:17:21	IntervalList	Ignoring interval for unknown reference: chrUn_KL568384v1:85-858	+	SSU-rRNA_Hsa
WARNING	2017-06-15 06:17:21	IntervalList	Ignoring interval for unknown reference: chrUn_KL568384v1:2140-2670	+	LSU-rRNA_Hsa
WARNING	2017-06-15 06:17:21	IntervalList	Ignoring interval for unknown reference: chrUn_KL568397v1:3851-3955	-	5S
WARNING	2017-06-15 06:17:21	IntervalList	Ignoring interval for unknown reference: chrUn_KL568409v1:257516-257634	+	LSU-rRNA_Hsa
WARNING	2017-06-15 06:17:21	IntervalList	Ignoring interval for unknown reference: chrUn_KL568488v1:1-679	+	SSU-rRNA_Hsa
WARNING	2017-06-15 06:17:21	IntervalList	Ignoring interval for unknown reference: chrUn_KL568488v1:8612-9035	+	LSU-rRNA_Hsa
WARNING	2017-06-15 06:17:21	IntervalList	Ignoring interval for unknown reference: chrUn_KL568488v1:12943-13029	+	LSU-rRNA_Hsa
WARNING	2017-06-15 06:17:21	IntervalList	Ignoring interval for unknown reference: chrUn_KL568488v1:13334-13451	+	5S
WARNING	2017-06-15 06:17:21	IntervalList	Ignoring interval for unknown reference: chrUn_KL568488v1:22763-22864	+	LSU-rRNA_Hsa
WARNING	2017-06-15 06:17:21	IntervalList	Ignoring interval for unknown reference: chrUn_KL568490v1:3-478	-	LSU-rRNA_Hsa
WARNING	2017-06-15 06:17:21	IntervalList	Ignoring interval for unknown reference: chrUn_AABR07024263v1:15751-15837	+	5S
WARNING	2017-06-15 06:17:21	IntervalList	Ignoring interval for unknown reference: chr8_KL567997v1_random:6314-6532	-	LSU-rRNA_Hsa
WARNING	2017-06-15 06:17:21	IntervalList	Ignoring interval for unknown reference: chr8_KL567997v1_random:6534-6580	-	LSU-rRNA_Hsa
WARNING	2017-06-15 06:17:21	IntervalList	Ignoring interval for unknown reference: chrX_KL568125v1_random:52250-52333	+	5S
WARNING	2017-06-15 06:17:21	IntervalList	Ignoring interval for unknown reference: chr11_KL568025v1_random:3587-3686	+	5S
WARNING	2017-06-15 06:17:21	IntervalList	Ignoring interval for unknown reference: chr1_AABR07046231v1_random:22945-23138	+	LSU-rRNA_Hsa
[Thu Jun 15 06:17:21 EDT 2017] picard.analysis.CollectRnaSeqMetrics done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=2058027008
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
Exception in thread "main" picard.PicardException: Sequence dictionaries differ in /scratch/9332913.1.linga/TA_IP2_primary_unique.bam and /scratch/9332913.1.linga/rRNA_intervalList_sorted
	at picard.analysis.directed.RnaSeqMetricsCollector.makeOverlapDetector(RnaSeqMetricsCollector.java:76)
	at picard.analysis.CollectRnaSeqMetrics.setup(CollectRnaSeqMetrics.java:109)
	at picard.analysis.SinglePassSamProgram.makeItSo(SinglePassSamProgram.java:100)
	at picard.analysis.SinglePassSamProgram.doWork(SinglePassSamProgram.java:53)
	at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:185)
	at picard.cmdline.CommandLineProgram.instanceMainWithExit(CommandLineProgram.java:125)
	at picard.analysis.CollectRnaSeqMetrics.main(CollectRnaSeqMetrics.java:97)
Caused by: htsjdk.samtools.util.SequenceUtil$SequenceListsDifferException: Sequences at index 1 don't match: 1/112626471/chr10 1/266435125/chr2/AS=rn6
	at htsjdk.samtools.util.SequenceUtil.assertSequenceListsEqual(SequenceUtil.java:121)
	at htsjdk.samtools.util.SequenceUtil.assertSequenceDictionariesEqual(SequenceUtil.java:169)
	at picard.analysis.directed.RnaSeqMetricsCollector.makeOverlapDetector(RnaSeqMetricsCollector.java:74)
	... 6 more