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hartwigmedical / hmftools

Various algorithms for analysing genomics data
GNU General Public License v3.0
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SAGE run error #456

Closed xdgene closed 1 year ago

xdgene commented 1 year ago

when i run sage with command： java -jar sage_v3.2.5.jar -reference Normal -reference_bam COLO829R.bam -tumor tumor -tumor_bam COLO829T.bam -ref_genome_version 37 -ref_genome hg19.fasta -hotspots $PWD/variants/KnownHotspots.somatic.37.vcf.gz -panel_bed 2021.bed -panel_only -panel_min_tumor_vaf 0.01 -ensembl_data_dir $PWD/common/ensembl_data -out $PWD/2021.sage.vcf.gz

I got error： 17:23:28.832 [INFO ] Sage version: 3.2.5 17:23:28.840 [INFO ] Using non default panel_only flag 17:23:31.049 [INFO ] read 7964 panel entries from bed file: 2021.bed 17:23:31.303 [INFO ] read 9452 hotspots from vcf: KnownHotspots.somatic.37.vcf.gz Exception in thread "main" java.lang.NullPointerException at com.hartwig.hmftools.sage.vcf.VariantVCF.(VariantVCF.java:104) at com.hartwig.hmftools.sage.vcf.VcfWriter.(VcfWriter.java:22) at com.hartwig.hmftools.sage.SageApplication.(SageApplication.java:66) at com.hartwig.hmftools.sage.SageApplication.main(SageApplication.java:148)

How can i fix this，all files are fine，i dont know what happen with the (VariantVCF.java:104) ：mConsumer = enrichment;