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hartwigmedical / hmftools

Various algorithms for analysing genomics data
GNU General Public License v3.0
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GRIPSS: missing sample names error #441

Closed diljotgrewal closed 1 year ago

diljotgrewal commented 1 year ago

Hi, I'm trying to run gridss and am getting the following error

14:17:28.935 [INFO ] Gripss version: 2.3.4
14:17:28.938 [INFO ] loading reference data
14:17:39.427 [INFO ] loaded 8508747 germline SV PON records from file(reference/sv/sv_pon.37.bedpe.gz)
14:17:41.283 [INFO ] loaded 2546492 germline SGL PON records from file(reference/sv/sgl_pon.37.bed.gz)
14:17:41.292 [INFO ] loaded 458 known hotspot records from file
14:18:02.977 [INFO ] loaded 5295850 repeat-mask entries from file(reference/sv/repeat_mask_data.37.fa.gz)
14:18:03.102 [INFO ] sample(SAMPLE_T) processing VCF(gridss.vcf)
14:18:03.103 [ERROR] missing sample names(ref=SAMPLE_N tumor=SAMPLE_T) in VCF: [SAMPLE_T, SAMPLE_N]

Would appreciate any help figuring this out. Thank you so much Diljot

charlesshale commented 1 year ago

Can you share the command you ran?

If you specify 'reference' and 'sample' config, then the input VCF must contain both those genotype names in that order.

diljotgrewal commented 1 year ago

I'll try to provide a reproducible example with data soon.

In the mean time, I switched to v2.2 and that fixed the problem, without making any changes to vcf or arguments.