dee@dee-Lenovo-V110-15AST:~$ time ./gatk-4.1.3.0/gatk MarkDuplicates -I E_coli_K12.sorted.bam -O E_coli_K12.sorted.markdup.bam.bam -M E_coli_K12.sorted.markdup_metric.txt && "** markdup done**"
Using GATK jar /home/dee/gatk-4.1.3.0/gatk-package-4.1.3.0-local.jar
Running:
java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /home/dee/gatk-4.1.3.0/gatk-package-4.1.3.0-local.jar MarkDuplicates -I E_coli_K12.sorted.bam -O E_coli_K12.sorted.markdup.bam.bam -M E_coli_K12.sorted.markdup_metric.txt
Error: Invalid or corrupt jarfile /home/dee/gatk-4.1.3.0/gatk-package-4.1.3.0-local.jar
real 0m0.054s
user 0m0.038s
sys 0m0.009s
对于这个Error: Invalid or corrupt jarfile的问题，我从网上搜到了解决方案：将gakt script中的ef formatLocalJarCommand(localJar): return ["java"] + PACKAGED_LOCAL……改成def formatLocalJarCommand(localJar): return ["/full/path/to/java"] + PACKAGED_LOCAL……结果"./gatk-4.1.3.0/gatk"和"/usr/lib/python2.7/subprocess.py"都不存在，请问这是怎么回事？谢谢！
Using GATK jar /home/dee/gatk-4.1.3.0/gatk-package-4.1.3.0-local.jar
Running:
java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /home/dee/gatk-4.1.3.0/gatk-package-4.1.3.0-local.jar MarkDuplicates -I E_coli_K12.sorted.bam -O E_coli_K12.sorted.markdup.bam.bam -M E_coli_K12.sorted.markdup_metric.txt
Error: Invalid or corrupt jarfile /home/dee/gatk-4.1.3.0/gatk-package-4.1.3.0-local.jar
real 0m0.054s
user 0m0.038s
sys 0m0.009s
对于这个Error: Invalid or corrupt jarfile的问题，我从网上搜到了解决方案：将gakt script中的ef formatLocalJarCommand(localJar): return ["java"] + PACKAGED_LOCAL……改成def formatLocalJarCommand(localJar): return ["/full/path/to/java"] + PACKAGED_LOCAL……结果"./gatk-4.1.3.0/gatk"和"/usr/lib/python2.7/subprocess.py"都不存在，请问这是怎么回事？谢谢！
