break_block for GRCh37 assembly: Error --> Floating point exception (core dumped)

[amitgsir]

Hi,

I am Amit Goyal.
I have been using break_block for hg19 version successfully to get the ROI specific break_blocked.vcf or whole_genome.vcf using specific region of interest bed file and hg19 whole genome bed file, respectively.

However, when I tried to use the same tool with GRCh37.p13 assembly, I am getting the error:
Floating point exception (core dumped)

Here is my command line:
~/gvcftools-0.17.0/bin/break_blocks --ref ~/GRCh37.p13/human_g1k_v37_decoy.fasta < Input.gvcf
--region-file ~/GRCh37.p13.bed > output.break_block.vcf

I tried the gvcftools_v0.16 as well as latetst 0.17. But find the same error message.

Any recommendation will be helpful.
Thanks,
Amit

I used the same reference genome to generate the gvcf file.
Below is how the bed file looks like:
1 1 249250621
2 1 243199373
3 1 198022430
4 1 191154276
5 1 180915260
6 1 171115067
7 1 159138663
8 1 146364022
9 1 141213431
10 1 135534747
11 1 135006516
12 1 133851895
13 1 115169878
14 1 107349540
15 1 102531392
16 1 90354753
17 1 81195210
18 1 78077248
19 1 59128983
20 1 63025520
21 1 48129895
22 1 51304566
X 1 155270560
Y 1 59373566
MT 1 16569
GL000207.1 1 4262
GL000226.1 1 15008
GL000229.1 1 19913
GL000231.1 1 27386
GL000210.1 1 27682
GL000239.1 1 33824
GL000235.1 1 34474
GL000201.1 1 36148
GL000247.1 1 36422
GL000245.1 1 36651
GL000197.1 1 37175
GL000203.1 1 37498
GL000246.1 1 38154
GL000249.1 1 38502
GL000196.1 1 38914
GL000248.1 1 39786
GL000244.1 1 39929
GL000238.1 1 39939
GL000202.1 1 40103
GL000234.1 1 40531
GL000232.1 1 40652
GL000206.1 1 41001
GL000240.1 1 41933
GL000236.1 1 41934
GL000241.1 1 42152
GL000243.1 1 43341
GL000242.1 1 43523
GL000230.1 1 43691
GL000237.1 1 45867
GL000233.1 1 45941
GL000204.1 1 81310
GL000198.1 1 90085
GL000208.1 1 92689
GL000191.1 1 106433
GL000227.1 1 128374
GL000228.1 1 129120
GL000214.1 1 137718
GL000221.1 1 155397
GL000209.1 1 159169
GL000218.1 1 161147
GL000220.1 1 161802
GL000213.1 1 164239
GL000211.1 1 166566
GL000199.1 1 169874
GL000217.1 1 172149
GL000216.1 1 172294
GL000215.1 1 172545
GL000205.1 1 174588
GL000219.1 1 179198
GL000224.1 1 179693
GL000223.1 1 180455
GL000195.1 1 182896
GL000212.1 1 186858
GL000222.1 1 186861
GL000200.1 1 187035
GL000193.1 1 189789
GL000194.1 1 191469
GL000225.1 1 211173
GL000192.1 1 547496
NC_007605 1 171823
hs37d5 1 35477943