运行创建索引的命令：

java -jar /share/work/biosoft/picard/picard.jar  CreateSequenceDictionary --REFERENCE Bromus_tectorum.faa --OUTPUT Bromus_tectorum.dict

报错：

10:13:20.679 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/share/work/biosoft/picard/picard-3.0.0/picard.jar!/com/intel/gkl/native/libgkl_compression.so
[Fri Oct 13 10:13:20 CST 2023] CreateSequenceDictionary --OUTPUT Bromus_tectorum.dict --REFERENCE Bromus_tectorum.faa --TRUNCATE_NAMES_AT_WHITESPACE true --NUM_SEQUENCES 2147483647 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Fri Oct 13 10:13:20 CST 2023] Executing as process@cluster.rocks.org on Linux 3.10.0-693.5.2.el7.x86_64 amd64; Java HotSpot(TM) 64-Bit Server VM 19.0.1+10-21; Deflater: Intel; Inflater: Intel; Provider GCS is not available; Picard version: Version:3.0.0
[Fri Oct 13 10:13:20 CST 2023] picard.sam.CreateSequenceDictionary done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2147483648
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
Exception in thread "main" picard.PicardException: Unknown problem. Partial dictionary file was deleted.
        at picard.sam.CreateSequenceDictionary.doWork(CreateSequenceDictionary.java:253)
        at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:289)
        at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:104)
        at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:114)
Caused by: java.lang.IllegalArgumentException: File is not a supported reference file type: Bromus_tectorum.faa
        at htsjdk.samtools.reference.ReferenceSequenceFileFactory.lambda$getFastaExtension$0(ReferenceSequenceFileFactory.java:253)
        at java.base/java.util.Optional.orElseGet(Optional.java:364)
        at htsjdk.samtools.reference.ReferenceSequenceFileFactory.getFastaExtension(ReferenceSequenceFileFactory.java:253)
        at htsjdk.samtools.reference.ReferenceSequenceFileFactory.getReferenceSequenceFile(ReferenceSequenceFileFactory.java:135)
        at htsjdk.samtools.reference.ReferenceSequenceFileFactory.getReferenceSequenceFile(ReferenceSequenceFileFactory.java:100)
        at htsjdk.samtools.reference.ReferenceSequenceFileFactory.getReferenceSequenceFile(ReferenceSequenceFileFactory.java:88)
        at picard.util.SequenceDictionaryUtils$SamSequenceRecordsIterator.<init>(SequenceDictionaryUtils.java:82)
        at picard.sam.CreateSequenceDictionary.lambda$getSamSequenceRecordsIterable$0(CreateSequenceDictionary.java:169)
        at picard.sam.CreateSequenceDictionary.doWork(CreateSequenceDictionary.java:234)
        ... 3 more

解决问题：

报错原因已经提示，就是参考序列文件格式不支持。但文件内容很正常，最后发现是参考序列文件后缀的问题。将.faa后缀改为.fa后缀就解决了。

10:31:43.112 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/share/work/biosoft/picard/picard-3.0.0/picard.jar!/com/intel/gkl/native/libgkl_compression.so
[Fri Oct 13 10:31:43 CST 2023] CreateSequenceDictionary --OUTPUT Bromus_tectorum.dict --REFERENCE Bromus_tectorum.fa --TRUNCATE_NAMES_AT_WHITESPACE true --NUM_SEQUENCES 2147483647 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Fri Oct 13 10:31:43 CST 2023] Executing as process@cluster.rocks.org on Linux 3.10.0-693.5.2.el7.x86_64 amd64; Java HotSpot(TM) 64-Bit Server VM 19.0.1+10-21; Deflater: Intel; Inflater: Intel; Provider GCS is not available; Picard version: Version:3.0.0
[Fri Oct 13 10:32:02 CST 2023] picard.sam.CreateSequenceDictionary done. Elapsed time: 0.33 minutes.
Runtime.totalMemory()=2432696320