Hi, I can successfully run SweeD on a vcf file, but when I subset the vcf for a set of the samples, I get the following error:
~/bin/sweed/SweeD -name test -input test.vcf -grid 4718 -folded SweeD version 3.3.1 released by Nikolaos Alachiotis and Pavlos Pavlidis in January 2015.
Command:
/home/brian/bin/sweed/SweeD -name test -input test.vcf -grid 4718 -folded
Input file format (0:ms, 1:fasta, 2:macs, 3:vcf, 4:sf): 3
Total number of samples in the VCF: 4
Samples excluded from the analysis: 0
Alignment 1
ERROR: There are more than 6 nucleotides in line 76. Expected 6 (according to the first SNP in line 72).
SweeD: SweeD_Input.c:3742: readLine_VCF: Assertion `j<*SNP_SZ' failed.
Chromosome: chrom_1Aborted (core dumped)
Here are the lines that it is referring to:
71 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT 618 581 580 573
72 chrom_1 528 . A G 1105.31 . . GT:GQ:DP:AD:RO:QR:AO:QA:GL 0/0:0:3:3,0:3:108:0:0:0,-0.90309,-10.0752 1/1:18:2:0,2:0:0:2:72:-6.83672,-0.60206,0 72 .:.:.:.:.:.:.:.:. .:.:.:.:.:.:.:.:.
73 chrom_1 534 . G A 1206.52 . . GT:GQ:DP:AD:RO:QR:AO:QA:GL 0/0:0:3:3,0:3:108:0:0:0,-0.90309,-10.0752 1/1:22:2:0,2:0:0:2:72:-6.83672,-0.60206,0 73 .:.:.:.:.:.:.:.:. .:.:.:.:.:.:.:.:.
74 chrom_1 2453 . CA TG 419.43 . . GT:GQ:DP:AD:RO:QR:AO:QA:GL 0/0:99:58:58,0:58:2038:0:0:0,-17.4597,-183.691 .:.:.:.:.:.:.:.:. 0/0:99:59:59,0:59 74 :2041:0:0:0,-17.7608,-183.958 1/1:0:20:0,18:0:0:18:646:-58.1206,-5.41854,0
75 chrom_1 2497 . AAAGAGAC AGAAGAGAC 1305.07 . . GT:GQ:DP:AD:RO:QR:AO:QA:GL 0/0:99:49:48,0:48:1647:0:0:0,-14.4494,-148.371 .:.:.:.:.:.:.:.:. 0 75 /0:99:55:55,0:55:1890:0:0:0,-16.5566,-170.378 1/1:99:47:0,46:0:0:46:1604:-144.306,-13.8474,0
76 chrom_1 2557 . T C 1835.23 . . GT:GQ:DP:AD:RO:QR:AO:QA:GL 0/0:99:73:73,0:73:2510:0:0:0,-21.9752,-226.149 .:.:.:.:.:.:.:.:. 0/0:99:62:62,0:62 76 :2130:0:0:0,-18.6639,-191.96 1/1:99:61:0,61:0:0:61:2154:-194.127,-18.3628,0
I don't understand what the error is referring to.
Thanks,
Brian