core dump random-forest.cpp:248

[indapa]

Hi RFmix developers,

I am getting a consistently getting a core dump error:

I'm not sure if my reference panel sample population classification map is ill formatted, but it seems maybe rfmix is thinking I have zero ref popluations?

mm::allocate() called at setup_ref_haplotypes():627 (random-forest.cpp) requesting zero or negative size (0)
mm::allocate() called at setup_ref_haplotypes():683 (random-forest.cpp) requesting zero or negative size (0)
mm::allocate() called at bootstrap_haplotypes():462 (random-forest.cpp) requesting zero or negative size (0)
mm::allocate() called at bootstrap_haplotypes():463 (random-forest.cpp) requesting zero or negative size (0)
mm::allocate() called at build_tree():495 (random-forest.cpp) requesting zero or negative size (0)
current: random-forest.cpp:248: node_t* add_node(tree_t*, int*, int, int*, int, double, mm*, int): Assertion `n_ref != 0' failed.
.command.sh: line 2: 35195 Aborted                 (core dumped) /seq/vgb/dd/ancestry/bin/rfmix/current -f 31019073908671.all_chroms.phased.vcf.gz -r AncestryReferencePanel_GlobalAncestry_plus-coyote_plus-alaskan_sled_dog.phased.reheader.fixed.liftOver.canFam4.vcf.gz -m 31019073908671.refpops.tsv -g AncestryReferencePanel_GlobalAncestry_plus-coyote_plus-alaskan_sled_dog.phased.reheader.fixed.liftOver.canFam4.genetic_map.tsv --chromosome=chr38 --n-threads=4 -w 1.0 -s 250 -c 500 -o 31019073908671_chr38

My command line:

#!/bin/bash -ue
/seq/vgb/dd/ancestry/bin/rfmix/current -f 31019073908671.all_chroms.phased.vcf.gz  -r AncestryReferencePanel_GlobalAncestry_plus-coyote_plus-alaskan_sled_dog.phased.reheader.fixed.liftOver.canFam4.vcf.gz -m 31019073908671.refpops.tsv -g AncestryReferencePanel_GlobalAncestry_plus-coyote_plus-alaskan_sled_dog.phased.reheader.fixed.liftOver.canFam4.genetic_map.tsv --chromosome=chr38 --n-threads=4 -w 1.0 -s 250 -c 500 -o 31019073908671_chr38

My ref panel pop file. I've tried both space and tab delmited versions, and I get the same error.

31001602030828 bernese_mountain_dog
31001602110100 bernese_mountain_dog
31001602111888 bernese_mountain_dog
31001806033814 bernese_mountain_dog
BerneseMountainDog01 bernese_mountain_dog
BerneseMountainDog02 bernese_mountain_dog
BerneseMountainDog04 bernese_mountain_dog
BerneseMountainDog11 bernese_mountain_dog
BerneseMountainDog12 bernese_mountain_dog
BerneseMountainDog14 bernese_mountain_dog

My error:

--- For use in scientific publications please cite original publication ---
Brian Maples, Simon Gravel, Eimear E. Kenny, and Carlos D. Bustamante (2013).
RFMix: A Discriminative Modeling Approach for Rapid and Robust Local-Ancestry
Inference. Am. J. Hum. Genet. 93, 278-288


Loading genetic map for chromosome chr38 ...  done
Mapping samples ... 1 samples combined
Scanning input VCFs for common SNPs on chromosome chr38 ...   2158 SNPs
Loading haplotypes... done
Defining and initializing conditional random field...
   setting up CRF points and random forest windows...
   computing random forest window spacing overlay...
   initializing apriori reference subpop across CRF...
   setting up random forest probability estimation arrays... done
Defining and initializing conditional random field...   done
792 (18.4%) variant alleles	0 (0.0%) missing alleles


mm::allocate() called at setup_ref_haplotypes():627 (random-forest.cpp) requesting zero or negative size (0)
mm::allocate() called at setup_ref_haplotypes():683 (random-forest.cpp) requesting zero or negative size (0)
mm::allocate() called at bootstrap_haplotypes():462 (random-forest.cpp) requesting zero or negative size (0)
mm::allocate() called at bootstrap_haplotypes():463 (random-forest.cpp) requesting zero or negative size (0)
mm::allocate() called at build_tree():495 (random-forest.cpp) requesting zero or negative size (0)
current: random-forest.cpp:248: node_t* add_node(tree_t*, int*, int, int*, int, double, mm*, int): Assertion `n_ref != 0' failed.
.command.sh: line 2: 37538 Aborted                 (core dumped) /seq/vgb/dd/ancestry/bin/rfmix/current -f 31019073908671.all_chroms.phased.vcf.gz -r AncestryReferencePanel_GlobalAncestry_plus-coyote_plus-alaskan_sled_dog.phased.reheader.fixed.liftOver.canFam4.vcf.gz -m 31019073908671.refpops.tsv -g AncestryReferencePanel_GlobalAncestry_plus-coyote_plus-alaskan_sled_dog.phased.reheader.fixed.liftOver.canFam4.genetic_map.tsv --chromosome=chr38 --n-threads=4 -w 1.0 -s 250 -c 500 -o 31019073908671_chr38

Any help would be appreciated.