How do I fix the issue "Sequence dictionaries are not the same size (6671, 242)"

I am using 2.18.7-1-gb02e42e-SNAPSHOT and Java HotSpot(TM) 64-Bit Server VM (build 25.45-b02, mixed mode)

I used the CreateSequenceDictionary on my .fasta genome:

java -Xmx2g -jar picard.jar \
CreateSequenceDictionary \
R=.fasta \
O=.dict \

This seemed to work, and made a .dict file. However, when I run CollectMultipleMetrics to get information on my RNAseq alignments done by STAR 2.5.0c:

java -Xmx2g -jar picard.jar \
CollectMultipleMetrics \
R=.fasta \
I=.bam \
O= \
PROGRAM=null \
PROGRAM=CollectAlignmentSummaryMetrics \
PROGRAM=QualityScoreDistribution \
PROGRAM=CollectGcBiasMetrics \
PROGRAM=MeanQualityByCycle \
PROGRAM=CollectInsertSizeMetrics \

There is an exception: "Exception in thread "main" htsjdk.samtools.util.SequenceUtil$SequenceListsDifferException: Sequence dictionaries are not the same size (6671, 242)"

I'd love any help on understanding the problem and how to fix it. Let me know if I can provide any other useful information.


Complete CollectMultipleMetrics output:

14:00:31.203 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file://sw/picard/build/libs/picard.jar!/com/intel/gkl/native/libgkl_compression.so
[Sun Jul 01 14:00:31 GMT-05:00 2018] CollectMultipleMetrics INPUT=.bam OUTPUT= PROGRAM=[CollectAlignmentSummaryMetrics, QualityScoreDistribution, CollectGcBiasMetrics, MeanQualityByCycle, CollectInsertSizeMetrics] REFERENCE_SEQUENCE=.fasta ASSUME_SORTED=true STOP_AFTER=0 METRIC_ACCUMULATION_LEVEL=[ALL_READS] INCLUDE_UNPAIRED=false 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
[Sun Jul 01 14:00:31 GMT-05:00 2018] Executing as on Linux 3.10.0-693.21.1.el7.x86_64 amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_45-b14; Deflater: Intel; Inflater: Intel; Provider GCS is not available; Picard version: 2.18.7-1-gb02e42e-SNAPSHOT
[Sun Jul 01 14:00:31 GMT-05:00 2018] picard.analysis.CollectMultipleMetrics done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=2058354688
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
Exception in thread "main" htsjdk.samtools.util.SequenceUtil$SequenceListsDifferException: Sequence dictionaries are not the same size (6671, 242)
at htsjdk.samtools.util.SequenceUtil.assertSequenceListsEqual(SequenceUtil.java:237)
at htsjdk.samtools.util.SequenceUtil.assertSequenceDictionariesEqual(SequenceUtil.java:320)
at htsjdk.samtools.util.SequenceUtil.assertSequenceDictionariesEqual(SequenceUtil.java:306)
at picard.analysis.SinglePassSamProgram.makeItSo(SinglePassSamProgram.java:107)
at picard.analysis.CollectMultipleMetrics.doWork(CollectMultipleMetrics.java:426)
at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:282)
at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:103)
at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:113)


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