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Assertion failed: (map_of_ref_records_of_tags.size() == tag_its_.size()), function impute_all_the_regions #88

Open sjfandrews opened 6 years ago

sjfandrews commented 6 years ago

Hi I am running into the following error when running SSIMP

Assertion failed: (map_of_ref_records_of_tags.size() == tag_its_.size()), function impute_all_the_regions, file src/ssimp.cc, line 1320. Abort trap: 6

possibly related to issue #64?

The commands I am running are: 

ssimp \
--gwas gwas/ggt_chr20_14to18.txt \
--ref ~/reference_panels/1000genomes/ALL.chr{CHRM}.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz \
--out ggt_ssimp_20:14572321-20:15580397.txt \
--reimpute.tags

using this dataset - example data

it produces the following output: 

file_name:gwas/ggt_chr20_14to18.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 , 50 , 30 , 100 , 2,015 , 949
gwas_all_chrpos.size():5,909
count_of_hg18_0based,count_of_hg19_0based,count_of_hg20_0based,count_of_hg18_1based,count_of_hg19_1based,count_of_hg20_1based:  200 , 289 , 187 , 189 , 5,921 , 186
which_build_gwas,which_build_ref:   hg19_1 , hg19_1
gwas_count_known,gwas_count_unknown:    5,914 , 0
Delete the SNPs with unknown position ...
gwas->number_of_snps():5,914
options:: opt_window_width,options:: opt_flanking_width:    1,000,000 , 250,000
N_reference:2,504

chrm20     13,000,000-14,000,000
     179 # GWAS     SNPs in this window (with 250,000 flanking)
     154 # SNPs in both (i.e. useful as tags)
  27,172 # target SNPs (anything in narrow window, will include some tags)

chrm20     14,000,000-15,000,000
   1,433 # GWAS     SNPs in this window (with 250,000 flanking)
   1,217 # SNPs in both (i.e. useful as tags)
  26,879 # target SNPs (anything in narrow window, will include some tags)

chrm20     15,000,000-16,000,000
   2,563 # GWAS     SNPs in this window (with 250,000 flanking)
   2,153 # SNPs in both (i.e. useful as tags)
  29,635 # target SNPs (anything in narrow window, will include some tags)
Assertion failed: (map_of_ref_records_of_tags.size() == tag_its_.size()), function impute_all_the_regions, file src/ssimp.cc, line 1320.
Abort trap: 6
aaronmcdaid commented 6 years ago

I have a fix for that now

Do you use Linux? If so, you can use the binary file compiled/ssimp-linux-issue88 that is in this unreleased branch.

I described the problem and the solution in pull request #89

If you use Mac, then you could compile it yourself. I don't have access to a Mac myself at the moment. This should be enough to compile the binary on the Mac:

make stu/stu
stu/stu bin/ssimp

and then bin/ssimp is the recompiled binary

sjfandrews commented 5 years ago

Ok, I have finally got around to testing the binary linux-issue88 file and the linux version 0.5.5. The above issue seems to be resolved in the test case.

The OSX 0.5.5 version still encountered the same issue, but using the binary I compiled myself worked.