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zkutalik / ssimp_software

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Assertion failed: (crps.pos > 0), function main, file src/ssimp.cc, line 812. #58

Closed sjfandrews closed 6 years ago

sjfandrews commented 6 years ago

Hi, I am encountering an issue that is causing the SSIMP to fail. Seems to be due to lifting the summary stats from hg18 to hg19

 ssimp gwas/ggt_test.txt       ~/reference_panels/1000genomes/ALL.chr{CHRM}.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz       output_ggttest.txt --sample.names ~/reference_panels/1000genomes/integrated_call_samples_v3.20130502.ALL.panel/sample/super_pop=EUR

file_name:gwas/ggt_test.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():2,300 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 , 70 , 36 , 100 , 1,897 , 860 gwas_all_chrpos.size():1,000 count_of_hg18_0based,count_of_hg19_0based,count_of_hg20_0based,count_of_hg18_1based,count_of_hg19_1based,count_of_hg20_1based: 60 , 0 , 1 , 945 , 0 , 0 which_build_gwas,which_build_ref: hg18_1 , hg19_1 builds are different. Need to adjust the positions in the GWAS to match those in the ref panel gwas_old_build_to_new.size():1,000 Assertion failed: (crps.pos > 0), function main, file src/ssimp.cc, line 812. Abort trap: 6

sinarueeger commented 6 years ago

thanks! we will look into this and get pack to you asap.

sjfandrews commented 6 years ago

I performed my own liftOver from hg18 to hg19 and SSIMP successfully ran.

sinarueeger commented 6 years ago

That is good to hear! We will still be working on the fix for our internal liftover.