现象：
./gatk --list
Using GATK jar/software/gatk-4.1.3.0/gatk-package-4.1.3.0-local.jar
Running:
/usr/java/latest/bin/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/software/gatk-4.1.3.0/gatk-package-4.1.3.0-local.jar --help
描述：
When I run
./gatk --help
it seems to be working fine. However, running anything else such as
./gatk --list
produces an error:
Error: Invalid or corrupt jarfile /path/to/gatk/gatk-4.0.0.0/gatk-package-4.0.0.0-local.jar
What's going on? Sorry this might be noob question.
可能的原因：
- 文件没下全
+java版本不对（1.8）
改：
def formatLocalJarCommand(localJar):
return ["java"] + PACKAGED_LOCAL$
to
def formatLocalJarCommand(localJar):
return ["/full/path/to/java1.8"] + PACKAGED_LOCAL$
可以了：
./gatk --list
Using GATK jar /software/gatk-4.1.3.0/gatk-package-4.1.3.0-local.jar
Running:
/jre1.8.0_25/bin/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 /software/gatk-4.1.3.0/gatk-package-4.1.3.0-local.jar --help
USAGE: <program name> [-h]
Available Programs:
--------------------------------------------------------------------------------------
Base Calling: Tools that process sequencing machine data, e.g. Illumina base calls, and detect sequencing level attributes, e.g. adapters
CheckIlluminaDirectory (Picard) Asserts the validity for specified Illumina basecalling data.
CollectIlluminaBasecallingMetrics (Picard) Collects Illumina Basecalling metrics for a sequencing run.
CollectIlluminaLaneMetrics (Picard) Collects Illumina lane metrics for the given BaseCalling analysis directory.
ExtractIlluminaBarcodes (Picard) Tool determines the barcode for each read in an Illumina lane.
IlluminaBasecallsToFastq (Picard) Generate FASTQ file(s) from Illumina basecall read data.
IlluminaBasecallsToSam (Picard) Transforms raw Illumina sequencing data into an unmapped SAM or BAM file.
MarkIlluminaAdapters (Picard) Reads a SAM or BAM file and rewrites it with new adapter-trimming tags.
--------------------------------------------------------------------------------------
Copy Number Variant Discovery: Tools that analyze read coverage to detect copy number variants.
