Segmentation fault when run gt-pro build

[alienzj]

Hi, @zjshi ,

Below was what I did when followed your protocol paper: "Identifying species-specific k-mers for fast and accurate metagenotyping with Maast and GTPro":

1. maast genomes

   ➤ maast genomes \
   --fna-dir s__Bifidobacterium_longum/genomes/ \
   --out-dir s__Bifidobacterium_longum/maast_out/ \
   --min-prev 0.9 \
   --snp-freq 0.01 \
   --threads 64 \
   > logs/s__Bifidobacterium_longum/s__Bifidobacterium_longum.maast_genomes.log 2>&1

2. gt-pro build

   ➤ GT_Pro build \
   --in s__Bifidobacterium_longum.gtpro_build.list \
   --out s__Bifidobacterium_longum_gtpro_db \
   --threads 32 \
   --overwrite \
   >logs/s__Bifidobacterium_longum/s__Bifidobacterium_longum.gtpro_build.log 2>&1

Then when take a look on "logs/s__Bifidobacterium_longum/s__Bifidobacterium_longum.gtpro_build.log":

610 genomes sequences will be used for database building
[OK] /home/jiezhu/projects/Child-Virome/assay/07.variation/metagenotyping/s__Bifidobacterium_longum/reference.fna found.
[OK] /home/jiezhu/projects/Child-Virome/assay/07.variation/metagenotyping/s__Bifidobacterium_longum/msa.fa found.
[OK] /home/jiezhu/projects/Child-Virome/assay/07.variation/metagenotyping/s__Bifidobacterium_longum/core_snps.vcf found.
[load] loading core-genome consensus sequence from /home/jiezhu/projects/Child-Virome/assay/07.variation/metagenotyping/s__Bifidobacterium_longum/reference.fna
    the loaded core-genome has a consensus sequence of 2105028 bases
[load] loading core snps from /home/jiezhu/projects/Child-Virome/assay/07.variation/metagenotyping/s__Bifidobacterium_longum/core_snps.vcf
    a total of 283 core bi-allelic snps was found
[load] loading key coordinates on core-genome from /home/jiezhu/projects/Child-Virome/assay/07.variation/metagenotyping/s__Bifidobacterium_longum/coords.tsv
    a total of 13 divisions was found
[searching] start to search 31-mers
    a total of 7441 kmer records was found

Error: the following returned non-zero status: 'db_val -d s__Bifidobacterium_longum_gtpro_db/temp/extract/100001-snp-kmer.tsv -n 100001 -t 32 -L s__Bifidobacterium_longum_gtpro_db/temp/inspec_eval/100001.list 1> s__Bifidobacterium_longum_gtpro_db/temp/inspec_eval/100001_kmer_profiles.tsv 2> s__Bifidobacterium_longum_gtpro_db/temp/inspec_eval/100001_kmer_profiles.log':

b'/bin/sh: line 1: 251717 Segmentation fault      (core dumped) db_val -d s__Bifidobacterium_longum_gtpro_db/temp/extract/100001-snp-kmer.tsv -n 100001 -t 32 -L s__Bifidobacterium_longum_gtpro_db/temp/inspec_eval/100001.list > s__Bifidobacterium_longum_gtpro_db/temp/inspec_eval/100001_kmer_profiles.tsv 2> s__Bifidobacterium_longum_gtpro_db/temp/inspec_eval/100001_kmer_profiles.log\n'

May I know any suggestions?

[alienzj]

➤ cat -p s__Bifidobacterium_longum_gtpro_db/temp/inspec_eval/100001_kmer_profiles.log                                                                                                                                    (metagenotyping-env)

db_val  s__Bifidobacterium_longum_gtpro_db/temp/extract/100001-snp-kmer.tsv 32
program reads a list of kmer pools for checking kmer uniqueness: s__Bifidobacterium_longum_gtpro_db/temp/inspec_eval/100001.list
DB loading OK!