Another segmentation fault

[blarison]

In this case I have successfully run lcmlkin on one vcf while a segmentation fault was produced when running another vcf. The two vcfs were produced in exactly the same way from fasta to vcf and both produce using the python program you provide. The only difference is that the one that ran had more snps and few individuals than the one that didn't (34 vs 44 individuals). I don't know much about segmentation faults but I did run GDB and got the following output. A head and tail of both the vcfs is below.

Thanks!

###GDB OUTPUT
[blarison@login02 maximum-likelihood-relatedness-estimation]$ gdb lcmlkin ~/lowcov/kinship/core.36347
GNU gdb (GDB) Red Hat Enterprise Linux 7.6.1-94.el7
Copyright (C) 2013 Free Software Foundation, Inc.
License GPLv3+: GNU GPL version 3 or later http://gnu.org/licenses/gpl.html
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law. Type "show copying"
and "show warranty" for details.
This GDB was configured as "x86_64-redhat-linux-gnu".
For bug reporting instructions, please see:
http://www.gnu.org/software/gdb/bugs/...
Reading symbols from /gpfs/gpfs1/home/blarison/programs/maximum-likelihood-relatedness-estimation/lcmlkin...done.
[New LWP 39476]
[New LWP 39477]
[New LWP 36347]
[New LWP 39470]
[New LWP 39471]
[New LWP 39472]
[New LWP 39474]
[New LWP 39473]
[New LWP 39475]
[Thread debugging using libthread_db enabled]
Using host libthread_db library "/lib64/libthread_db.so.1".
Core was generated by `lcmlkin -i out_wild.vcf -o wild.relate -g all -t 8'.
Program terminated with signal 11, Segmentation fault.
#0 isinf (__x=<error reading variable: Cannot access memory at address 0x0>) at /usr/include/c++/4.8.2/cmath:605
605 { return __builtin_isinf(__x); }
Missing separate debuginfos, use: debuginfo-install glibc-2.17-157.el7.x86_64 libgcc-4.8.5-11.el7.x86_64 libstdc++-4.8.5-11.el7.x86_64
(gdb) print return
No symbol "return" in current context.
(gdb) print x
No symbol "x" in current context.
(gdb) list
600 isinf(float __x)
601 { return __builtin_isinf(__x); }
602
603 constexpr bool
604 isinf(double __x)
605 { return __builtin_isinf(__x); }
606
607 constexpr bool
608 isinf(long double __x)
609 { return __builtin_isinf(__x); }
(gdb) print __x
Cannot access memory at address 0x0

###VCF THAT RAN
#HEAD
[blarison@login02 kinship]$ head -n 5 out_quagga.vcf
##Custom variant caller for_lcMLkin
##Bayesian_caller=0,MappingQuality_filter=20,BaseQuality_filter=5,GenotypeQuality_filter=0.1,bamlist=/gpfs/gpfs1/home/blarison/lowcov/kinship/bam.list.quagga,filenameout=/gpfs/gpfs1/home/blarison/lowcov/kinship/out_quagga.vcf,SNPfile=/gpfs/gpfs1/home/blarison/lowcov/kinship/quagga.snp.list
##Time created: 11:13:33 21/09/2020
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT PZ0075 PZ0076 PZ0077 PZ0078 PZ0079 PZ0080 PZ0081 PZ0082 PZ0084 PZ0085 PZ0088 PZ0089 PZ0090 PZ0092 PZ0093 PZ0094 PZ0097 PZ0099 PZ0101 PZ0103 PZ0104 PZ0233 PZ0235 PZ0236 PZ0237 PZ0242 PZ0243 PZ0245 PZ0246 PZ0247 PZ0248 PZ0250 PZ0251 PZ0252 PZ0257 PZ0302 PZ0303 PZ0305 PZ0319 PZ0320 PZ0321 PZ0322 PZ0323 PZ0324 PZ0325 PZ0326 PZ0327 PZ0328 PZ0329 PZ0333 PZ0334 PZ0335 PZ0337 PZ0339 PZ0340 PZ0341 PZ0342 PZ0343 PZ0344 PZ0348 PZ0349 PZ0350 PZ0351 PZ0352 PZ0353 PZ0354 PZ0355 PZ0356 PZ0357 PZ0359 PZ0360 PZ0361 PZ0362 PZ0363 PZ0364 PZ0365 PZ0366 PZ0367 PZ0372 PZ0373 PZ0374 PZ0375 PZ0376 PZ0379 PZ0380 PZ0381 PZ0382 PZ0383 PZ0384 PZ0386 PZ0387 PZ0388 PZ0389 PZ0390 PZ0391
1 3934 . T C 100 ALT ALT_AF=0.675324675325 GT:GL:GQ 0/1:2.6475504633e-05,0.249973523093,2.6475504633e-05:40 1/1:4.66268671035e-14,0.124970136122,0.999641646128:9 0/0:0.999920567177,0.499973522392,2.64776078241e-05:3 0/0:0.999841140663,0.249973523093,7.01063716089e-10:6 0/0:0.999761720458,0.124980142846,1.85624901343e-14:9 0/0:0.999761720458,0.124980142846,1.85624901343e-14:9 0/0:0.999841140663,0.249973523093,7.01063716089e-10:6 ./.:-9.0,-9.0,-9.0:0 0/1:2.64368294513e-05,0.0312162559499,7.78897809576e-17:31 0/0:0.999369042656,0.499789680885,0.000210319114827:3 0/1:2.6475504633e-05,0.249973523093,2.6475504633e-05:40 1/1:5.5687470403e-09,0.249881607207,0.999289659951:6 0/0:0.999920567177,0.499973522392,2.64776078241e-05:3 0/0:0.999682306562,0.0624867622476,4.91490334017e-19:12 1/1:4.66268671035e-14,0.124970136122,0.999641646128:9 ./.:-9.0,-9.0,-9.0:0 ./.:-9.0,-9.0,-9.0:0 0/0:0.999289659951,0.249881607207,5.5687470403e-09:6 0/0:0.999721056794,0.249953508585,1.76099243607e-09:6 0/0:0.93656852228,0.0598567072199,9.80652141635e-16:12 0/0:0.999523497693,0.0156200361057,3.44566039988e-28:18 1/1:1.76099243607e-09,0.249953508585,0.999721056794:6 0/0:0.999761720458,0.124980142846,1.85624901343e-14:9 1/1:2.64776078241e-05,0.499973522392,0.999920567177:3 ./.:-9.0,-9.0,-9.0:0 ./.:-9.0,-9.0,-9.0:0 0/1:2.6475504633e-05,0.249973523093,2.6475504633e-05:40 0/0:0.99940154073,0.124950125077,2.9419564249e-13:9 ./.:-9.0,-9.0,-9.0:0 0/1:2.6475504633e-05,0.249973523093,2.6475504633e-05:40 0/0:0.999920567177,0.499973522392,2.64776078241e-05:3 0/0:0.999482843718,0.0312392252078,3.26884047212e-23:15 0/0:0.936419739626,0.0149625919845,6.87499634605e-25:18 1/1:4.66268671035e-14,0.124970136122,0.999641646128:9 0/0:0.999682306562,0.0624867622476,4.91490334017e-19:12 0/0:0.993690426555,0.497896808852,0.00210319114827:3 0/0:0.999920567177,0.499973522392,2.64776078241e-05:3 1/1:2.64776078241e-05,0.499973522392,0.999920567177:3 0/0:0.999800473769,0.499933491256,6.65087438323e-05:3 0/0:0.999920567177,0.499973522392,2.64776078241e-05:3 ./.:-9.0,-9.0,-9.0:0 0/0:0.999920567177,0.499973522392,2.64776078241e-05:3 0/0:0.999600987348,0.24993349568,4.42341300615e-09:6 1/1:7.01063716089e-10,0.249973523093,0.999841140663:6 0/0:0.999841140663,0.249973523093,7.01063716089e-10:6 1/1:6.65087438323e-05,0.499933491256,0.999800473769:3 0/0:0.999920567177,0.499973522392,2.64776078241e-05:3 0/0:0.998004737685,0.499334912562,0.000665087438323:3 0/1:1.85610156633e-14,0.0624867622476,2.64712987519e-05:34 ./.:-9.0,-9.0,-9.0:0 0/0:0.999920567177,0.499973522392,2.64776078241e-05:0/0:0.999682306562,0.0624867622476,4.91490334017e-19:12 0/1:7.00952345572e-10,0.0624867622476,7.00952345572e-10:80 0/0:0.999800473769,0.499933491256,6.65087438323e-05:3 0/1:0.000210269000084,0.0624637857098,1.85507779949e-14:25 0/0:0.999920567177,0.499973522392,2.64776078241e-05:3 0/1:2.64734016089e-05,0.124980142846,7.01008028619e-10:37 0/0:0.999920567177,0.499973522392,2.64776078241e-05:3 0/1:7.00812487192e-10,0.0312392252078,4.66194599903e-14:76 ./.:-9.0,-9.0,-9.0:0 ./.:-9.0,-9.0,-9.0:0 0/1:6.56829586028e-10,0.119729340536,0.0210285703672:8 0/1:6.6503460855e-05,0.249953508585,2.64723248468e-05:36 0/0:0.936755429561,0.119729340536,1.47447100205e-11:9 ./.:-9.0,-9.0,-9.0:0 0/1:2.6475504633e-05,0.249973523093,2.6475504633e-05:40 0/0:0.999920567177,0.499973522392,2.64776078241e-05:3 1/1:6.65087438323e-05,0.499933491256,0.999800473769:3 1/1:7.01063716089e-10,0.249973523093,0.999841140663:6 0/0:0.999761720458,0.124980142846,1.85624901343e-14:9 1/1:2.64776078241e-05,0.499973522392,0.999920567177:3 0/1:0.000210285703672,0.124934187337,7.00621374788e-10:28 0/0:0.936904265552,0.478968088517,0.0210319114827:3 0/0:0.936904265552,0.478968088517,0.0210319114827:3 0/0:0.999010914889,0.0624587844524,9.80652141635e-18:12 0/1:1.76085255547e-08,0.124820507296,2.64226790563e-05:37 0/1:2.64691960619e-05,0.0312417266238,4.91451293552e-19:31 1/1:2.64776078241e-05,0.499973522392,0.999920567177:3 ./.:-9.0,-9.0,-9.0:0 ./.:-9.0,-9.0,-9.0:0 1/1:1.17121394821e-13,0.124960130199,0.999521586219:9 0/0:0.999841140663,0.249973523093,7.01063716089e-10:6 0/0:0.999761720458,0.124980142846,1.85624901343e-14:9 1/1:9.80652141635e-18,0.0624587844524,0.999010914889:12 ./.:-9.0,-9.0,-9.0:0 0/0:0.999841140663,0.249973523093,7.01063716089e-10:6 0/0:0.999841140663,0.249973523093,7.01063716089e-10:6 ./.:-9.0,-9.0,-9.0:0 0/0:0.999841140663,0.249973523093,7.01063716089e-10:./.:-9.0,-9.0,-9.0:0 ./.:-9.0,-9.0,-9.0:0 0/0:0.999682306562,0.0624867622476,4.91490334017e-19:12 1/1:5.5687470403e-08,0.248935221309,0.993611494919:6 ./.:-9.0,-9.0,-9.0:0 1/1:1.47447100205e-12,0.124461019446,0.993532569552:9

 #TAIL

[blarison@login02 kinship]$ tail -n 1 out_quagga.vcf
X 128155102 . T C 100 ALT ALT_AF=0.0147058823529 GT:GL:GQ 0/1:2.64723248468e-05,0.249953508585,6.6503460855e-05:36 ./.:-9.0,-9.0,-9.0:0 1/1:3.44566039988e-28,0.0156200361057,0.999523497693:18 1/1:4.42341300615e-08,0.249789725119,0.998738483418:6 ./.:-9.0,-9.0,-9.0:0 1/1:1.85624901343e-14,0.124980142846,0.999761720458:9 1/1:4.66268671035e-14,0.124970136122,0.999641646128:9 1/1:6.65087438323e-05,0.499933491256,0.999800473769:3 ./.:-9.0,-9.0,-9.0:0 ./.:-9.0,-9.0,-9.0:0 1/1:2.64776078241e-05,0.499973522392,0.999920567177:3 0/1:0.0210260447739,0.119719754225,1.64988132496e-09:8 1/1:1.23456790123e-17,0.0624069486998,0.997766933573:12 1/1:2.64776078241e-05,0.499973522392,0.999920567177:3 ./.:-9.0,-9.0,-9.0:0 1/1:2.64776078241e-05,0.499973522392,0.999920567177:3 1/1:1.85624901343e-14,0.124980142846,0.999761720458:9 ./.:-9.0,-9.0,-9.0:0 ./.:-9.0,-9.0,-9.0:0 1/1:2.64776078241e-05,0.499973522392,0.999920567177:3 1/1:2.64776078241e-05,0.499973522392,0.999920567177:3 1/1:2.64776078241e-05,0.499973522392,0.999920567177:3 1/1:6.65087438323e-05,0.499933491256,0.999800473769:3 1/1:2.64776078241e-05,0.499973522392,0.999920567177:3 1/1:2.64776078241e-05,0.499973522392,0.999920567177:3 1/1:1.30134883135e-23,0.0312417266238,0.999602898973:15 ./.:-9.0,-9.0,-9.0:0 1/1:1.85624901343e-14,0.124980142846,0.999761720458:9 1/1:8.21095602868e-23,0.031236723992,0.999362802882:15 ./.:-9.0,-9.0,-9.0:0 1/1:2.64776078241e-05,0.499973522392,0.999920567177:1/1:1.85624901343e-14,0.124980142846,0.999761720458:9 1/1:3.90404649404e-18,0.0624637857098,0.999130913458:12 1/1:2.64776078241e-05,0.499973522392,0.999920567177:3 1/1:1.85624901343e-14,0.124980142846,0.999761720458:9 ./.:-9.0,-9.0,-9.0:0 ./.:-9.0,-9.0,-9.0:0 1/1:7.01063716089e-10,0.249973523093,0.999841140663:6 ./.:-9.0,-9.0,-9.0:0 1/1:4.66268671035e-13,0.124820507296,0.997846195314:9 1/1:7.01063716089e-10,0.249973523093,0.999841140663:6 1/1:2.64776078241e-05,0.499973522392,0.999920567177:3 1/1:4.91490334017e-19,0.0624867622476,0.999682306562:12 1/1:2.64776078241e-05,0.499973522392,0.999920567177:3 ./.:-9.0,-9.0,-9.0:0 1/1:3.10109435989e-18,0.062476756454,0.999442191397:12 1/1:2.64776078241e-05,0.499973522392,0.999920567177:3 ./.:-9.0,-9.0,-9.0:0 ./.:-9.0,-9.0,-9.0:0 ./.:-9.0,-9.0,-9.0:0 1/1:1.76099243607e-08,0.249654235087,0.997925463351:6 1/1:2.64776078241e-05,0.499973522392,0.999920567177:3 1/1:2.64776078241e-05,0.499973522392,0.999920567177:3 1/1:2.64776078241e-05,0.499973522392,0.999920567177:3 ./.:-9.0,-9.0,-9.0:0 1/1:2.64776078241e-05,0.499973522392,0.999920567177:3 ./.:-9.0,-9.0,-9.0:01/1:7.01063716089e-10,0.249973523093,0.999841140663:6 1/1:3.26884047212e-23,0.0312392252078,0.999482843718:15 1/1:2.64776078241e-05,0.499973522392,0.999920567177:3 ./.:-9.0,-9.0,-9.0:0 1/1:3.7037037037e-13,0.124924184292,0.999090275451:9 ./.:-9.0,-9.0,-9.0:0 1/1:2.64776078241e-05,0.499973522392,0.999920567177:3 1/1:7.01063716089e-10,0.249973523093,0.999841140663:6 1/1:2.64776078241e-05,0.499973522392,0.999920567177:3 1/1:1.76099243607e-09,0.249953508585,0.999721056794:6 1/1:4.42341300615e-08,0.249789725119,0.998738483418:6 1/1:7.01063716089e-10,0.249973523093,0.999841140663:6 1/1:2.64776078241e-05,0.499973522392,0.999920567177:3 1/1:2.64776078241e-05,0.499973522392,0.999920567177:3 1/1:2.64776078241e-05,0.499973522392,0.999920567177:3 1/1:1.76099243607e-09,0.249953508585,0.999721056794:6 1/1:2.64776078241e-05,0.499973522392,0.999920567177:3 ./.:-9.0,-9.0,-9.0:0 1/1:2.64776078241e-05,0.499973522392,0.999920567177:3 1/1:2.64776078241e-05,0.499973522392,0.999920567177:3 1/1:7.01063716089e-10,0.249973523093,0.999841140663:6 ./.:-9.0,-9.0,-9.0:0 ./.:-9.0,-9.0,-9.0:0 1/1:7.01063716089e-10,0.249973523093,0.999841140663:6 1/1:1.47447100205e-13,0.124934187337,0.999210283552:9 1/1:2.64776078241e-05,0.499973522392,0.999920567177:3 ./.:-9.0,-9.0,-9.0:0 1/1:0.000665087438323,0.499334912562,0.998004737685:3 1/1:2.64776078241e-05,0.499973522392,0.999920567177:3 ./.:-9.0,-9.0,-9.0:0 1/1:2.9419564249e-08,0.119079733561,0.92913522443:9 1/1:7.01063716089e-10,0.249973523093,0.999841140663:6 1/1:5.5687470403e-08,0.248935221309,0.993611494919:6 ./.:-9.0,-9.0,-9.0:0 1/1:0.000210319114827,0.499789680885,0.999369042656:3 ./.:-9.0,-9.0,-9.0:0 1/1:7.01063716089e-10,0.249973523093,0.999841140663:6 1/1:3.7037037037e-10,0.11957641177,0.934960623316:9

###VCT THAT PRODUCED SEGFAULT
#HEAD
[blarison@login02 kinship]$ head -n 5 out_wild.vcf
##Custom variant caller for_lcMLkin
##Bayesian_caller=0,MappingQuality_filter=20,BaseQuality_filter=5,GenotypeQuality_filter=0.1,bamlist=/gpfs/gpfs1/home/blarison/lowcov/kinship/bam.list.wild,filenameout=/gpfs/gpfs1/home/blarison/lowcov/kinship/out_wild.vcf,SNPfile=/gpfs/gpfs1/home/blarison/lowcov/kinship/wild.snp.list
##Time created: 20:38:27 01/10/2020
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT F117 F119 F16 F22 F24 F30 F36 HKO_003 HKO_005 HKO_006 KR04_000 KR06_129 KR06_130 KR06_131 KR06_132 KR07_01 KR07_368 KR07_369 KR09_944 KR09_957 KR09_958 KR11_330 KR11_331 KR11_872 KR12_315 M4 M5 M77 PZ0030 PZ0124 PZ0128 PZ0129 PZ0130 PZ0131 PZ0132 PZ0133 PZ0133 PZ0134 PZ0135 PZ0136 PZ0137 PZ0138 PZ0138 PZ0141 PZ0142 PZ0145 PZ0147 PZ0150 PZ0152 PZ0155 PZ0156 PZ0166 PZ0173 PZ0179 PZ0185 PZ0190 PZ0410 PZ0411 PZ0412 PZ0413 PZ0414 PZ0415 PZ0416 PZ0417 PZ0418 PZ0419 PZ0420 PZ0421 PZ0422 PZ0423 PZ0424 PZ0424 PZ0425 PZ0425 PZ0426 PZ0427 PZ0428 PZ0429 PZ0430 PZ0431 PZ0432 PZ0433 PZ0434 PZ0435 PZ0436 PZ0437 PZ0438 PZ0439
1 3934 . T C 100 ALT ALT_AF=0.79012345679 GT:GL:GQ 0/0:0.999841140663,0.249973523093,7.01063716089e-10:6 0/1:2.6475504633e-05,0.249973523093,2.6475504633e-05:40 0/0:0.999800473769,0.499933491256,6.65087438323e-05:3 0/1:6.6503460855e-05,0.249953508585,2.64723248468e-05:36 0/0:0.93656852228,0.0598567072199,9.80652141635e-16:12 0/0:0.999721056794,0.249953508585,1.76099243607e-09:6 1/1:0.000210319114827,0.499789680885,0.999369042656:3 0/1:2.64660170334e-05,0.0312392252078,1.23446983602e-18:31 0/0:0.999841140663,0.249973523093,7.01063716089e-10:6 0/0:0.999841140663,0.249973523093,7.01063716089e-10:6 0/0:0.999761720458,0.124980142846,1.85624901343e-14:9 0/0:0.999210283552,0.124934187337,1.47447100205e-13:9 0/0:0.999920567177,0.499973522392,2.64776078241e-05:3 0/0:0.999920567177,0.499973522392,2.64776078241e-05:3 0/0:0.999920567177,0.499973522392,2.64776078241e-05:3 0/0:0.999841140663,0.249973523093,7.01063716089e-10:6 0/0:0.997925463351,0.249654235087,1.76099243607e-08:6 0/0:0.999289659951,0.249881607207,5.5687470403e-09:6 0/0:0.999920567177,0.499973522392,2.64776078241e-05:3 0/0:0.999920567177,0.499973522392,2.64776078241e-05:3 0/0:0.999841140663,0.249973523093,7.01063716089e-10:6 0/0:0.999841140663,0.249973523093,7.01063716089e-10:6 0/1:7.00370304406e-10,0.0156130423977,9.80496355886e-18:73 0/0:0.993611494919,0.248935221309,5.5687470403e-08:6 0/0:0.999920567177,0.499973522392,2.64776078241e-05:3 0/0:0.999920567177,0.499973522392,2.64776078241e-05:3 0/0:0.999920567177,0.499973522392,2.64776078241e-05:3 1/1:2.64776078241e-05,0.499973522392,0.999920567177:3 ./.:-9.0,-9.0,-9.0:0 0/0:0.999841140663,0.249973523093,7.01063716089e-10:6 0/0:0.999369042656,0.499789680885,0.000210319114827:3 0/0:0.999761720458,0.124980142846,1.85624901343e-14:9 0/0:0.999721056794,0.249953508585,1.76099243607e-09:0/0:0.999761720458,0.124980142846,1.85624901343e-14:9 0/0:0.999761720458,0.124980142846,1.85624901343e-14:9 0/0:0.999841140663,0.249973523093,7.01063716089e-10:6 ./.:-9.0,-9.0,-9.0:0 0/0:0.999920567177,0.499973522392,2.64776078241e-05:3 0/0:0.999761720458,0.124980142846,1.85624901343e-14:9 0/0:0.999761720458,0.124980142846,1.85624901343e-14:9 0/0:0.999130913458,0.0624637857098,3.90404649404e-18:12 0/0:0.999841140663,0.249973523093,7.01063716089e-10:6 0/0:0.999521586219,0.124960130199,1.17121394821e-13:9 0/0:0.999641646128,0.124970136122,4.66268671035e-14:0/0:0.999920567177,0.499973522392,2.64776078241e-05:3 0/0:0.999920567177,0.499973522392,2.64776078241e-05:3 0/0:0.999920567177,0.499973522392,2.64776078241e-05:3 0/0:0.999761720458,0.124980142846,1.85624901343e-14:9 0/0:0.999562241769,0.0624817591505,1.23456790123e-18:12 ./.:-9.0,-9.0,-9.0:0 ./.:-9.0,-9.0,-9.0:0 0/0:0.999442191397,0.062476756454,3.10109435989e-18:12 0/1:6.6503460855e-05,0.249953508585,2.64723248468e-05:36 0/0:0.999562241769,0.0624817591505,1.23456790123e-18:12 0/1:2.6475504633e-05,0.249973523093,2.6475504633e-05:40 1/1:2.64776078241e-05,0.499973522392,0.999920567177:3 ./.:-9.0,-9.0,-9.0:0 0/0:0.999562241769,0.0624817591505,1.23456790123e-18:12 0/0:0.999841140663,0.249973523093,7.01063716089e-10:6 0/0:0.999841140663,0.249973523093,7.01063716089e-10:6 0/0:0.999761720458,0.124980142846,1.85624901343e-14:9 0/1:7.01008028619e-10,0.124980142846,2.64734016089e-05:37 0/1:2.6475504633e-05,0.249973523093,2.6475504633e-05:40 0/0:0.999841140663,0.249973523093,7.01063716089e-10:6 0/0:0.999800473769,0.499933491256,6.65087438323e-05:3 0/1:1.75719960231e-09,0.0311993237421,4.66138608557e-13:72 0/0:0.999721056794,0.249953508585,1.76099243607e-09:6 1/1:2.64776078241e-05,0.499973522392,0.999920567177:3 0/0:0.999641646128,0.124970136122,4.66268671035e-14:9 0/0:0.999841140663,0.249973523093,7.01063716089e-10:6 1/1:1.17121394821e-12,0.124810513354,0.997726351044:9 1/1:1.23456790123e-18,0.0624817591505,0.999562241769:12 ./.:-9.0,-9.0,-9.0:0 1/1:7.01063716089e-10,0.249973523093,0.999841140663:6 0/0:0.999682306562,0.0624867622476,4.91490334017e-19:12 1/1:2.64776078241e-05,0.499973522392,0.999920567177:3 ./.:-9.0,-9.0,-9.0:0 0/0:0.999920567177,0.499973522392,2.64776078241e-05:3 0/0:0.999721056794,0.249953508585,1.76099243607e-09:6 0/1:0.000664796290823,0.0311993237421,1.23210461443e-18:17 0/0:0.0210302408586,0.0105153988666,5.5687470403e-07:3 0/1:7.01008028619e-10,0.124980142846,2.64734016089e-05:37 1/1:2.64776078241e-05,0.499973522392,0.999920567177:3 1/1:7.01063716089e-10,0.249973523093,0.999841140663:6 0/0:0.999920567177,0.499973522392,2.64776078241e-05:3 0/1:7.01008028619e-10,0.124980142846,2.64734016089e-05:37 0/1:2.64702220753e-05,0.124970136122,1.76085255547e-09:37 0/1:7.00952345572e-10,0.0624867622476,7.00952345572e-10:80
[blarison@login02 kinship]$

#TAIL
[blarison@login02 kinship]$ tail -n 1 out_wild.vcf
X 127858233 . G A 100 ALT ALT_AF=0.151162790698 GT:GL:GQ 1/1:4.98222903843e-55,0.000121376621853,0.99148131524:39 1/1:1.76099243607e-09,0.249953508585,0.999721056794:6 1/1:4.42341300615e-05,0.238476682815,0.930992799278:6 1/1:3.90404649404e-17,0.0622272142927,0.993453650455:12 1/1:6.65087438323e-05,0.499933491256,0.999800473769:1/1:6.06778190144e-37,0.00390428282886,0.999244687404:24 1/1:1.76099243607e-08,0.249654235087,0.997925463351:6 1/1:1.52415790276e-35,0.00389929593798,0.997330152886:24 ./.:-9.0,-9.0,-9.0:01/1:6.65087438323e-05,0.499933491256,0.999800473769:3 1/1:1.91880111537e-35,0.00388837714484,0.993138036749:24 1/1:5.5687470403e-09,0.249881607207,0.999289659951:6 1/1:1.3988060131e-08,0.249861600059,0.999169642317:6 1/1:6.06778190144e-37,0.00390428282886,0.999244687404:24 1/1:1.63830111339e-19,0.0311480158264,0.995107358549:15 1/1:4.66268671035e-13,0.124820507296,0.997846195314:9 1/1:6.06778190144e-27,0.00356236127788,0.869649745816:24 1/1:3.26884047212e-23,0.0312392252078,0.999482843718:15 1/1:2.17406473589e-24,0.0149582878602,0.93601565839:18 1/1:2.73698534289e-27,0.0156142925796,0.998972192183:18 1/1:4.91490334017e-19,0.0624867622476,0.999682306562:12 1/1:3.7037037037e-12,0.124451054286,0.993413243362:9 1/1:1.76099243607e-08,0.249654235087,0.997925463351:6 1/1:6.52219420766e-18,0.0297938905661,0.930257578951:15 1/1:4.81981048646e-36,0.00390284721435,0.998693535677:24 1/1:1.76099243607e-09,0.249953508585,0.999721056794:6 1/1:7.78959684543e-16,0.0623610627572,0.996666563831:12 1/1:9.30328307967e-11,0.111771767153,0.841275947067:9 1/1:1.30134883135e-16,0.00125869938435,0.0196930950082:12 1/1:2.4632868086e-14,0.0598174857702,0.935648018218:12 0/0:0.999920567177,0.499973522392,2.64776078241e-05:3 0/0:0.999920567177,0.499973522392,2.64776078241e-05:3 0/0:0.0196608852579,0.000628663539624,5.4610037113e-21:15 0/0:0.936642922472,0.119719754225,3.7037037037e-11:9 0/0:0.999761720458,0.124980142846,1.85624901343e-14:9 0/0:0.936606617214,0.0299291650714,1.03369811996e-20:15 0/0:0.999482843718,0.0312392252078,3.26884047212e-23:15 0/0:0.999721056794,0.249953508585,1.76099243607e-09:6 0/0:0.93645603764,0.0598519147022,2.4632868086e-15:12 0/0:0.997647098823,0.0624019519931,3.10109435989e-17:12 0/0:0.999051549668,0.0312302389633,1.03369811996e-22:15 0/0:0.993690426555,0.497896808852,0.00210319114827:3 0/0:0.936755429561,0.119729340536,1.47447100205e-11:9 1/1:1.76099243607e-08,0.249654235087,0.997925463351:6 1/1:1.76099243607e-09,0.249953508585,0.999721056794:6 1/1:5.5687470403e-09,0.249881607207,0.999289659951:6 1/1:2.64776078241e-05,0.499973522392,0.999920567177:3 1/1:1.3988060131e-07,0.248915289935,0.993492159249:6 1/1:1.85624901343e-14,0.124980142846,0.999761720458:9 1/1:2.64776078241e-05,0.499973522392,0.999920567177:3 1/1:3.7037037037e-11,0.119719754225,0.936642922472:9 1/1:1.47447100205e-13,0.124934187337,0.999210283552:9 1/1:1.9566582623e-14,0.0622814097637,0.994756968951:12 1/1:1.76099243607e-08,0.249654235087,0.997925463351:6 1/1:7.01063716089e-10,0.249973523093,0.999841140663:6 1/1:1.23456790123e-18,0.0624817591505,0.999562241769:12 ./.:-9.0,-9.0,-9.0:0 1/1:1.76099243607e-09,0.249953508585,0.999721056794:6 1/1:2.9419564249e-13,0.124950125077,0.99940154073:9 1/1:1.76099243607e-09,0.249953508585,0.999721056794:6 1/1:2.64776078241e-05,0.499973522392,0.999920567177:3 1/1:1.85624901343e-14,0.124980142846,0.999761720458:9 1/1:1.76099243607e-09,0.249953508585,0.999721056794:6 1/1:2.64776078241e-05,0.499973522392,0.999920567177:1/1:9.80652141635e-18,0.0624587844524,0.999010914889:12 1/1:1.82033457043e-31,0.00780610780283,0.998772871026:21 1/1:7.01063716089e-10,0.249973523093,0.999841140663:6 1/1:3.7037037037e-12,0.124774610486,0.997295814951:9 1/1:4.66268671035e-13,0.124820507296,0.997846195314:9 1/1:3.26884047212e-23,0.0312392252078,0.999482843718:15 1/1:9.80652141635e-15,0.0597850397876,0.934886356754:12 1/1:9.61678622893e-34,0.00389400361255,0.995299733789:24 1/1:3.10109435989e-18,0.062476756454,0.999442191397:12 1/1:2.64776078241e-05,0.499973522392,0.999920567177:3 1/1:4.57247370828e-31,0.00780548279501,0.998652915459:21 1/1:1.47447100205e-11,0.119729340536,0.936755429561:9 1/1:1.47447100205e-13,0.124934187337,0.999210283552:9 1/1:3.10109435989e-18,0.062476756454,0.999442191397:12 1/1:8.21095602868e-20,0.029918160043,0.936090014663:15 1/1:4.66268671035e-14,0.124970136122,0.999641646128:9 1/1:7.01063716089e-10,0.249973523093,0.999841140663:6 1/1:4.57247370828e-31,0.00780548279501,0.998652915459:21 1/1:0.000210319114827,0.499789680885,0.999369042656:3 1/1:5.5687470403e-09,0.249881607207,0.999289659951:6 1/1:1.47447100205e-13,0.124934187337,0.999210283552:9 1/1:1.72692100383e-23,0.000656181415264,0.0209807587801:15 1/1:2.64776078241e-05,0.499973522392,0.999920567177:3 1/1:6.87499634605e-26,0.015594348642,0.99705817976:18