modkit localise tabix bug

[Sellerzzz]

Hi Modkit,

Thank you for this tool suite, all very useful.

I am having an issue running 'modkit localise'. I've yet to get it to work with my own data and I am unsure why:

`modkit localise ubam_merged/barcode01_pileup.bed --regions resources/CpG_islands_hg38.nochr.noalt.bed --genome-sizes resources/Homo_sapiens.GRCh38.dna.primary_assembly.primary.chromsizes > test/test_localise_CpG.txt`

> loading sequence lengths from "resources/Homo_sapiens.GRCh38.dna.primary_assembly.primary.chromsizes" > Error! invalid tabix index

The chrom-sizes file is a simple tsv as follows: (why is tabix even invoked!?)

1	248956422
10	133797422
11	135086622
...
X	156040895
Y	57227415

All of the contigs mentioned in the bed file are contained within the chrom-sizes file.

1	155188536	155192004	CpG:_361
1	2226773	2229734	CpG:_366
1	36306229	36307408	CpG:_110
...
22	50719958	50721632	CpG:_180
22	50730599	50731304	CpG:_65
22	50783344	50783889	CpG:_63

I'm stumped, any help would be greatly appreciated.

BW, Rob

[Sellerzzz]

My apologies, the issue was the bedmethyl input, slightly confusing error message. However, it does work. Closed.

[ArtRand]

@Sellerzzz Could you tell me the error message? I'd like to make it easier to understand if possible.