PURPLE ERROR

[YuP9934]

I'm using PURPLE.I know I need to use amber and cobalt before I use them. I make sure the reference samples I use are consistent. But I received the following error message. I don't know what's wrong. Could you help me?

15:34:59.630 [INFO ] Purple version: 3.8.1 15:34:59.640 [INFO ] output directory: /test/PURPLE/ 15:34:59.643 [INFO ] reference(A375M2_gDNA) tumor(A375M2_Exos) 15:34:59.837 [INFO ] using ref genome: V38 15:35:00.512 [ERROR] invalid reference data, exiting

[charlesshale]

Could you paste the command you're running into the ticket? Does it match the one on Purple's read-me and use all HMF required resource files?

thanks.

[YuP9934]

I used amber: java -Xmx32G -cp amber-3.9.jar com.hartwig.hmftools.amber.AmberApplication -reference normal -reference_bam test/projectdir/normal.bam -tumor TUMOR -tumor_bam test/projectdir/TUMOR.bam -output_dir test/amber -ref_genome_version V38 -threads 16 -loci GermlineHetPon.38.vcf.gz It executed successfully. Then I used coblat: java -jar -Xmx8G cobalt_v1.14.jar -reference normal -reference_bam test/projectdir/normal.bam -tumor TUMOR -tumor_bam test/projectdir/TUMOR.bam -output_dir test/cobalt -threads 16 -gc_profile GC_profile.1000bp.38.cnp It executed successfully too. I use the command PURPLE: java -jar purple_v3.8.1.jar -reference normal -tumor TUMOR -amber test/amber -cobalt test/cobalt -gc_profile GC_profile.1000bp.38.cnp -ref_genome_version 38 -ref_genome hg38.fa -ensembl_data_dir test/PURPLE -output_dir test/PURPLE At this time, there is an error. I don't know which step is wrong

[charlesshale]

That Purple command looks ok. Could you try the latest version of Purple (v3.8.4)? It should give more information about which reference file path is invalid.

[AlexanderKotyurgin]

I have exactly the same error while using v3.8.4, no change in logs.>

UPDATE: checked again, found that here was an error in ensembl_data_dir