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我想從bam文件中提取一些FastQ文件。 Picard可以使用SamToFastq執行此操作，正如它在該工具的文檔中所述，它可以接受bam或sam文件。Picard SamToFastq只提取一個讀取，然後拋出一個錯誤
但是當我運行它時，它只提取一個讀取，然後退出。這是錯誤消息。任何幫助表示讚賞。
[[email protected] picard-tools-1.70]$ java -jar SamToFastq.jar I=/home/davy/xxx_trio_data/xxxx-1.bam F=/home/davy/xxx_trio_data/1005-1.fastq
[Wed Jun 20 14:14:21 BST 2012] net.sf.picard.sam.SamToFastq INPUT=/home/davy/xxx_trio_data/xxxx-1.bam FASTQ=/home/davy/xxxx_trio_data/xxxx-1.fastq OUTPUT_PER_RG=false RE_REVERSE=true INCLUDE_NON_PF_READS=false READ1_TRIM=0 READ2_TRIM=0 INCLUDE_NON_PRIMARY_ALIGNMENTS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false
[Wed Jun 20 14:14:21 BST 2012] Executing as [email protected] on Linux 2.6.34.9-69.fc13.x86_64 amd64; OpenJDK 64-Bit Server VM 1.6.0_18-b18; Picard version: 1.70(1215)
[Wed Jun 20 14:14:21 BST 2012] net.sf.picard.sam.SamToFastq done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2029715456
FAQ: http://sourceforge.net/apps/mediawiki/picard/index.php?title=Main_Page
Exception in thread "main" java.lang.IndexOutOfBoundsException: Index: 1, Size: 1
at java.util.ArrayList.rangeCheck(ArrayList.java:571)
at java.util.ArrayList.get(ArrayList.java:349)
at net.sf.picard.sam.SamToFastq.doWork(SamToFastq.java:156)
at net.sf.picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:177)
at net.sf.picard.sam.SamToFastq.main(SamToFastq.java:118)