外顯子分析彈錯解決方案:Exception in thread "main" picard.PicardException: New reference sequence does not contain a matching contig for NC_007605
最近從公共數據庫下載了一堆bam文件和reference 基因組文件,重新分析外顯子流程時,跑出了“Exception in thread "main" picard.PicardException: New reference sequence does not contain a matching contig for NC_007605”這個錯誤。
源代碼是這樣的:
java -jar picard.jar ReorderSam I=original.bam O=reordered.bam R=reference.fasta CREATE_INDEX=TRUE
搜了一下,gatk官網給出的解決方式,見鏈接:https://gatkforums.broadinstitute.org/gatk/discussion/10071/question-about-picard-reordersam-new-reference-sequence-does-not-contain-a-matching-contig-for
鏈接給出的解釋是:By default the tool requires an exact match -- to relax that requirement, use ALLOW_INCOMPLETE_DICT_CONCORDANCE
ALLOW_INCOMPLETE_DICT_CONCORDANCE=Boolean,
If true, then allows only a partial overlap of the BAM contigs with the new reference
sequence contigs. By default, this tool requires a corresponding contig in the new
reference for each read contig Default value: false. This option can be set to ‘null‘ to
如果不加ALLOW_INCOMPLETE_DICT_CONCORDANCE這個參數的話,系統默認為FALSE,即精確匹配,如果想放松匹配要求的話,則可以在命令行添加參數ALLOW_INCOMPLETE_DICT_CONCORDANCE=TRUE,這樣就不會報錯了。
見修改後的命令行:
java -jar picard.jar ReorderSam I=original.bam O=reordered.bam R=reference.fasta CREATE_INDEX=TRUE ALLOW_INCOMPLETE_DICT_CONCORDANCE=true
外顯子分析彈錯解決方案:Exception in thread "main" picard.PicardException: New reference sequence does not contain a matching contig for NC_007605