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zkutalik / ssimp_software

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Assertion `which_build_ref != ssimp:: which_build_t:: unknown' failed #118

Open karanvirsingh99 opened 1 year ago

karanvirsingh99 commented 1 year ago

Hello, I am running into a similar issue as posted previously. I am running version 0.5.6, compiled for macOS (I have tested the linux version as well and run into the same issue).

After running this: ./ssimp --gwas gwas/small.random.txt --ref 1KG/EUR --out output.txt

I get this error code:

file_name:gwas/small.random.txt ... loading the 1.7GB database of positions under three builds. This will take about a minute. Loaded. Estimating which build (hg18/hg19/hg37) of the reference panel and the GWAS file, in case it is necessary to modify the GWAS file to match the reference panel some_records_from_each_chromosome.size():0 (ref) :count_of_hg18_0based,count_of_hg19_0based,count_of_hg20_0based,count_of_hg18_1based,count_of_hg19_1based,count_of_hg20_1based: 0 , 0 , 0 , 0 , 0 , 0 gwas_all_chrpos.size():0 (gwas):count_of_hg18_0based,count_of_hg19_0based,count_of_hg20_0based,count_of_hg18_1based,count_of_hg19_1based,count_of_hg20_1based: 0 , 0 , 0 , 0 , 0 , 0 which_build_gwas,which_build_ref: unknown , unknown ssimp: src/ssimp.cc:877: int main(int, char**): Assertionwhich_build_ref != ssimp:: which_build_t:: unknown' failed. Aborted (core dumped) `

I have checked that the database.of.builds.1kg.uk10k.hrc.2018.01.18.bin file has size 1'789'839'360.

longmanz commented 9 months ago

Hi, To everyone who has encountered this issue: this error happens when we use the wrong v5b 1000Genomes files. Any one who wants to use 1000Genomes as reference, should follow this thread (https://github.com/zkutalik/ssimp_software/issues/117) to download the original v5a files instead. Do NOT use the default ssimp --download.1KG because it will automatically download the updated but incompatible v5b files for SSimp.

But please note that, you will still need the integrated_call_male_samples_v3.20130502.ALL.panel (male-specific) and/or integrated_call_samples_v3.20130502.ALL.panel if you want to restrict your imputation to any subset of individual. So in that case, you will need to download them separately from https://bochet.gcc.biostat.washington.edu/beagle/1000_Genomes_phase3_v5a/sample_info/ . Or you can keep these two files from your SSimp folder if you have already run ssimp --download.1KG.