gravatar for Adriel Rosa

2 hours ago by

Brasil

Hello, I had some problem with gatk haplotypecaller, someone can help me? thats the error:

Error:  Could not find or load main class “-Xmx4g”

my command:

./gatk --java-options “-Xmx4g” HaplotypeCaller -R /home/adriel-rosa/STARteste/referência/Oreochromis_niloticus.O_niloticus_UMD_NMBU.dna.toplevel.fa -I /home/adriel-rosa/STARteste/Alinhamento/T1R2_6H/out/BAM/T1R2_6H.out.bam -O /home/adriel-rosa/STARteste/Gatk/T1R2_6H_out.g.vcf.gz -ERC GVCF

the complete message:

(base) [email protected]:~/gatk-4.1.4.1$ ./gatk --java-options “-Xmx4g” HaplotypeCaller -R /home/adriel-rosa/STARteste/referência/Oreochromis_niloticus.O_niloticus_UMD_NMBU.dna.toplevel.fa -I /home/adriel-rosa/STARteste/Alinhamento/T1R2_6H/out/BAM/T1R2_6H.out.bam -O /home/adriel-rosa/STARteste/Gatk/T1R2_6H_out.g.vcf.gz -ERC GVCF
Using GATK jar /home/adriel-rosa/gatk-4.1.4.1/gatk-package-4.1.4.1-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 “-Xmx4g” -jar /home/adriel-rosa/gatk-4.1.4.1/gatk-package-4.1.4.1-local.jar HaplotypeCaller -R /home/adriel-rosa/STARteste/referência/Oreochromis_niloticus.O_niloticus_UMD_NMBU.dna.toplevel.fa -I /home/adriel-rosa/STARteste/Alinhamento/T1R2_6H/out/BAM/T1R2_6H.out.bam -O /home/adriel-rosa/STARteste/Gatk/T1R2_6H_out.g.vcf.gz -ERC GVCF
Error: Could not find or load main class “-Xmx4g”



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