Question

Hello bash程序员，我正在使用GATK并尝试遍历我的bam文件并使用我的target_intervals和已知的indel进行本地重新排列。以下是我正在尝试的代码。我希望有人可以帮助解决错误并更正我的代码。

# do the local realignment.
echo "local realignment..."

for file in `ls -d adp/map/*marked_duplicates.bam`
do
java -jar ~/software/GenomeAnalysisTK-3.3-0/GenomeAnalysisTK.jar \
-T IndelRealigner \
-R ~/flybase/fb-r5.57/dmel-all-chromosome-r5.57.fasta \
-I $file \
-known adp/map/*indel_intervals.vcf \
-targetIntervals adp/map/*target_intervals.list \
-o ${file}_realigned_reads.bam
done

wait

# Create a new index file.
echo "indexing the realigned bam file..."

for file in `ls -d adp/map/*realigned_reads.bam`
do
~/software/samtools-1.2/samtools index $file
done

错误：在查看时，它似乎是一个编码问题，我没有看到它。

##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A USER ERROR has occurred (version 3.3-0-g37228af):
##### ERROR
##### ERROR This means that one or more arguments or inputs in your command are incorrect.
##### ERROR The error message below tells you what is the problem.
##### ERROR
##### ERROR If the problem is an invalid argument, please check the online documentation guide
##### ERROR (or rerun your command with --help) to view allowable command-line arguments for this tool.
##### ERROR
##### ERROR Visit our website and forum for extensive documentation and answers to
##### ERROR commonly asked questions http://www.broadinstitute.org/gatk
##### ERROR
##### ERROR Please do NOT post this error to the GATK forum unless you have really tried to fix it yourself.
##### ERROR
##### ERROR MESSAGE: Invalid argument value 'adp/map/360M_F_L002.recal.bam.sorted.bam_marked_duplicates.bam_target_intervals.list' at position 10.
##### ERROR Invalid argument value 'adp/map/517_F_L002.recal.bam.sorted.bam_marked_duplicates.bam_target_intervals.list' at position 11.
##### ERROR Invalid argument value 'adp/map/517M_F_L002.recal.bam.sorted.bam_marked_duplicates.bam_target_intervals.list' at position 12.
##### ERROR Invalid argument value 'adp/map/900_F_L002.recal.bam.sorted.bam_marked_duplicates.bam_target_intervals.list' at position 13.
##### ERROR Invalid argument value 'adp/map/900M_F_L002.recal.bam.sorted.bam_marked_duplicates.bam_target_intervals.list' at position 14

Answer 1

至少部分问题是命令中的*。 GATK不能很好地处理全球问题。要为参数指定多个值，请多次指定参数。

即。而不是

-known adp/map/*indel_intervals.vcf

您需要使用单独的参数指定每个文件

-known adp/map/first_file.indel_intervals.vcf
-known adp/map/second_file.indel_intervals.vcf

也可能存在其他问题。例如，我不确定-targetIntervals可以将多个文件作为输入。此外，这是gatk的旧版本，您可能希望升级到3.8。

得到GATK参数错误，不明白？

1 个答案: