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mkirsche / Jasmine

Jasmine: SV Merging Across Samples
MIT License
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a sequence name but not an actual sequence #45

Open aojielian opened 1 year ago

aojielian commented 1 year ago

Hi, when i run Jasmine, i got an error Outputting original deletion for GL000009.2:20426:DEL:Sniffles2.DEL.1DS1A (time = 00:00:01:25.032) Exception in thread "main" java.lang.Exception: samtools faidx produced a sequence name but not an actual sequence: samtools faidx /home/a1lian/hg38.fa GL000009.2:20427-20488 at IrisGenomeQuery.genomeSubstring(IrisGenomeQuery.java:62) at VcfEditor.run(VcfEditor.java:227) at Iris.runIris(Iris.java:21) at PipelineManager.runIris(PipelineManager.java:129) at Main.preprocess(Main.java:47) at Main.main(Main.java:17)

noorsmal commented 1 year ago

I had the same issue. For me it was caused by the --normalize-chrs option that changed the chromosome names from chr1 -> 1. This then caused the chromosome names not to be present in my reference genome fasta file. It was solved by removing that option.