Aborted (core dumped)

[wangtao-prog]

I uese the command like below,but get the errors, I donnot know what is going on, thankyou very much! /rfmix -f sheep1234-1_phased.vcf.gz -r ref_sheep1234-1_phased.vcf.gz -m ref_sheep -g g_map -out out --chromosome=1 Loading genetic map for chromosome 1 ... done Mapping samples ... 291 samples combined Scanning input VCFs for common SNPs on chromosome 1 ... 10528 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 1942419 (31.7%) variant alleles 0 (0.0%) missing alleles Generating internal simulation samples... Internally simulated 0 samples from 0 randomly selected reference parents. 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 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 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) 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) 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) mm::allocate() called at setup_ref_haplotypes():627 (random-forest.cpp) requesting zero or negative size (0) 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) rfmix: random-forest.cpp:248: node_t add_node(tree_t, int, int, int, int, double, mm, int): Assertion `n_ref != 0' failed. rfmix: random-forest.cpp:248: node_t add_node(tree_t, int, int, int, int, double, mm, int): Assertion n_ref != 0' failed. 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 setup_ref_haplotypes():683 (random-forest.cpp) requesting zero or negative size (0) rfmix: random-forest.cpp:248: node_t* add_node(tree_t*, int*, int, int*, int, double, mm*, int): Assertionn_ref != 0' failed. 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) rfmix: random-forest.cpp:248: node_t add_node(tree_t, int, int, int, int, double, mm, int): Assertion `n_ref != 0' failed. 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) rfmix: random-forest.cpp:248: node_t add_node(tree_t, int, int, int, int, double, mm, int): Assertion n_ref != 0' failed. 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) rfmix: random-forest.cpp:248: node_t* add_node(tree_t*, int*, int, int*, int, double, mm*, int): Assertionn_ref != 0' failed. 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) rfmix: random-forest.cpp:248: node_t add_node(tree_t, int, int, int, int, double, mm*, int): Assertion `n_ref != 0' failed. Aborted (core dumped)

I don't know what's wrong with me? In fact, I have two questions: How is the reference file in "- R < reference VCF / BCF File >" generated? If there are five groups in my "query" file, and each group has 30 individuals, can I randomly select 10 individuals from each group to form a "reference" file? If this is not possible, where should I get my < reference VCF / BCF File >?

I see "internally simulated 0 samples from 0 randomly selected reference parents." on my screen, I feel that there may be a problem with < sample map file >. I want to know what the first two columns in < sample map file > represent? For example, my five groups are a, B, C, D, e, and each group has 30 individuals. How to set the first two columns in < sample map file >?

[Zhang-Rui-2018]

Use '\t' as the separator in the sample file may solve this problem.