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thlee / SNPhylo

A pipeline to generate a phylogenetic tree from huge SNP data
http://chibba.pgml.uga.edu/snphylo/
GNU General Public License v2.0
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vcf.file is too small to run this script! #39

Open Yichel518 opened 4 years ago

Yichel518 commented 4 years ago

Hello! I also want to consult the following VCF file format for calling single-cell SNPS and I want to built tree, but file has several thousand, I simply use bcftools merge and then I ran SNPhylo error: VCF file (/ home/yxtu/Data/single_cell / 10 xgenomics/OVAR45 / later/merge VCF) is too small to run this script! How to solve this kind of mistake? Thanks a lot! ps: A part of my vcf file:

CHROM | POS | ID | REF | ALT | QUAL | FILTER | INFO | FORMAT | output_OVAR | 2:output_OVAR | 3:output_OVAR | 4:output_OVAR | 5:output_OVAR | 6:output_OVAR | 7:output_OVAR | 8:output_OVAR | 9:output_OVAR | 10:output_OVAR | 11:output_OVAR | 12:output_OVAR | 13:output_OVAR | 14:output_OVAR

-- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- NC_002333.2 | 235 | . | AC | A | 3.42698 | . | INDEL;IDV=3;IMF=0.75;VDB=0.0846253;SGB=-0.511536;MQSB=1;MQ0F=0;AF1=0.542992;AC1=1;MQ=20;FQ=-26.5388;PV4=0.25,0,1,1;DP=4;DP4=1,0,0,3 | GT:PL | ./.:. | ./.:. | ./.:. | ./.:. | ./.:. | ./.:. | ./.:. | ./.:. | ./.:. | ./.:. | ./.:. | ./.:. | ./.:. | ./.:. NC_002333.2 | 339 | . | A | G | 27.5204 | . | VDB=0.02;SGB=-0.453602;MQ0F=0;AF1=1;AC1=2;MQ=20;FQ=-32.989;DP=45;DP4=0,0,17,28 | GT:PL | ./.:. | ./.:. | ./.:. | ./.:. | ./.:. | ./.:. | ./.:. | ./.:. | ./.:. | ./.:. | ./.:. | ./.:. | ./.:. | ./.:. NC_002333.2 | 501 | . | A | C | 6.01528 | . | VDB=0.02;SGB=-0.453602;MQ0F=0;AF1=1;AC1=2;MQ=20;FQ=-32.989;DP=2;DP4=0,0,0,2 | GT:PL | ./.:. | ./.:. | ./.:. | ./.:. | ./.:. | ./.:. | ./.:. | ./.:. | ./.:. | ./.:. | ./.:. | ./.:. | ./.:. | ./.:. NC_002333.2 | 582 | . | C | T | 58.1325 | . | VDB=0.336489;SGB=-0.511536;MQSB=1;MQ0F=0;AF1=1;AC1=2;MQ=20;FQ=-35.9869;DP=36;DP4=0,0,17,19 | GT:PL | ./.:. | ./.:. | ./.:. | ./.:. | ./.:. | ./.:. | ./.:. | ./.:. | ./.:. | ./.:. | ./.:. | ./.:. | ./.:. | ./.:. NC_002333.2 | 635 | . | C | T | 119 | . | VDB=0.06;SGB=-0.453602;MQ0F=0;AF1=1;AC1=2;MQ=20;FQ=-32.989;MQSB=1;DP=49;DP4=0,0,27,20 | GT:PL | ./.:. | ./.:. | ./.:. | ./.:. | ./.:. | ./.:. | ./.:. | ./.:. | ./.:. | ./.:. | ./.:. | ./.:. | ./.:. | ./.:. NC_002333.2 | 825 | . | G | T | 6.01528 | . | VDB=0.02;SGB=-0.453602;MQ0F=0;AF1=1;AC1=2;MQ=20;FQ=-32.989;DP=2;DP4=0,0,0,2 | GT:PL | ./.:. | ./.:. | ./.:. | ./.:. | ./.:. | ./.:. | ./.:. | ./.:. | ./.:. | ./.:. | ./.:. | ./.:. | ./.:. | ./.:. NC_002333.2 | 826 | . | A | C | 6.01528 | . | VDB=0.02;SGB=-0.453602;MQ0F=0;AF1=1;AC1=2;MQ=20;FQ=-32.989;DP=2;DP4=0,0,0,2 | GT:PL | ./.:. | ./.:. | ./.:. | ./.:. | ./.:. | ./.:. | ./.:. | ./.:. | ./.:. | ./.:. | ./.:. | ./.:. | ./.:. | ./.:. NC_002333.2 | 959 | . | A | T | 6.01528 | . | VDB=0.02;SGB=-0.453602;MQ0F=0;AF1=1;AC1=2;MQ=20;FQ=-32.989;DP=2;DP4=0,0,2,0 | GT:PL | ./.:. | ./.:. | ./.:. | ./.:. | ./.:. | ./.:. | ./.:. | ./.:. | ./.:. | ./.:. | ./.:. | ./.:. | ./.:. | ./.:. NC_002333.2 | 1018 | . | C | G | 59.9973 | . | VDB=0.02;SGB=-0.453602;MQ0F=0;AF1=1;AC1=2;MQ=20;FQ=-32.989;RPB=1;MQB=1;BQB=1;PV4=1,0.275646,1,0.342519;DP=1525;DP4=1,0,1496,0 | GT:PL | 1/1:36,6,0 | 1/1:36,6,0 | ./.:. | ./.:. | ./.:. | ./.:. | ./.:. | 1/1:68,15,0 | 1/1:49,9,0 | ./.:. | 1/1:74,18,0 | 1/1:49,9,0 | 1/1:36,6,0 | ./.:. NC_002333.2 | 1019 | . | A | G,C | 59.9973 | . | VDB=0.02;SGB=-0.453602;MQ0F=0;AF1=1;AC1=2;MQ=20;FQ=-32.989;RPB=1;MQB=1;BQB=1;PV4=1,0.275646,1,0.342519;DP=1539;DP4=1,0,1514,0 | GT:PL | 1/1:36,6,0,.,.,. | 1/1:36,6,0,.,.,. | ./.:. | ./.:. | ./.:. | ./.:. | ./.:. | 1/1:60,12,0,.,.,. | 1/1:49,9,0,.,.,. | ./.:. | 1/1:74,18,0,.,.,. | 1/1:49,9,0,.,.,. | 1/1:36,6,0,.,.,. | ./.:. NC_002333.2 | 1020 | . | C | A,G | 55.0056 | . | VDB=0.02;SGB=-0.453602;MQ0F=0;AF1=1;AC1=2;MQ=20;FQ=-32.989;RPB=1;MQB=1;BQB=1;PV4=1,0.333333,1,1;DP=1426;DP4=58,0,1315,0 | GT:PL | 1/1:36,6,0,.,.,. | 1/1:36,6,0,.,.,. | ./.:. | ./.:. | ./.:. | ./.:. | ./.:. | 1/1:60,12,0,.,.,. | 1/1:49,9,0,.,.,. | ./.:. | 1/1:74,18,0,.,.,. | 1/1:49,9,0,.,.,. | 1/1:36,6,0,.,.,. | ./.:. NC_002333.2 | 1767 | . | A | C | 46.0654 | . | VDB=0.0389723;SGB=-0.511536;MQ0F=0;AF1=1;AC1=2;MQ=20;FQ=-35.987;MQSB=1;RPB=1;MQB=1;BQB=1;PV4=1,1,1,0.0591488;DP=220;DP4=1,0,217,1 | GT:PL | ./.:. | ./.:. | ./.:. | ./.:. | ./.:. | ./.:. | ./.:. | ./.:. | ./.:. | ./.:. | ./.:. | ./.:. | ./.:. | ./.:. NC_002333.2 | 2042 | . | A | G | 50.0313 | . | VDB=0.02;SGB=-0.453602;MQ0F=0;AF1=1;AC1=2;MQ=20;FQ=-32.989;RPB=1;MQB=1;BQB=1;PV4=1,0,1,1;DP=357;DP4=4,0,350,0 | GT:PL | ./.:. | ./.:. | ./.:. | ./.:. | ./.:. | ./.:. | ./.:. | ./.:. | ./.:. | ./.:. | ./.:. | ./.:. | ./.:. | ./.:. NC_002333.2 | 2285 | . | G | A | 88.0318 | . | VDB=0.377852;SGB=-0.616816;MQ0F=0;AF1=1;AC1=2;MQ=20;FQ=-44.9861;MQSB=1;RPB=1;MQB=1;BQB=1;PV4=1,1,1,0.297664;DP=3426;DP4=1,0,3334,38 | GT:PL | 1/1:74,18,0 | 1/1:60,12,0 | ./.:. | 1/1:36,6,0 | 1/1:60,12,0 | 1/1:60,12,0 | ./.:. | 1/1:56,9,0 | 1/1:60,12,0 | 1/1:60,12,0 | 1/1:49,9,0 | ./.:. | 1/1:68,15,0 | ./.:. NC_002333.2 | 2421 | . | C | T | 76.0316 | . | VDB=0.26;SGB=-0.453602;MQ0F=0;AF1=1;AC1=2;MQ=20;FQ=-32.989;MQSB=1;DP=1590;DP4=0,0,1507,41 | GT:PL | 1/1:36,6,0 | ./.:. | ./.:. | ./.:. | 1/1:69,12,0 | 1/1:49,9,0 | ./.:. | ./.:. | 1/1:49,9,0 | 1/1:36,6,0 | 1/1:60,12,0 | 1/1:36,6,0 | 1/1:49,9,0 | 1/1:36,6,0 NC_002333.2 | 3080 | . | A | G,T,C | 45.1325 | . | VDB=0.142856;SGB=-0.511536;MQ0F=0;AF1=1;AC1=2;MQ=20;FQ=-35.987;MQSB=1;RPB=1;MQB=1;BQB=0.666667;PV4=1,0.209877,1,0.301823;DP=1444;DP4=74,2,1252,19 | GT:PL | 1/1:49,9,0,.,.,.,.,.,.,. | 2/2:43,31,28,17,0,11,.,.,.,. | ./.:. | ./.:. | ./.:. | ./.:. | ./.:. | 2/2:71,51,45,31,0,19,.,.,.,. | ./.:. | ./.:. | 2/2:87,53,41,53,0,41,.,.,.,. | ./.:. | ./.:. | ./.:. NC_002333.2 | 3250 | . | A | G | 88.0318 | . | VDB=0.144271;SGB=-0.662043;MQ0F=0;AF1=1;AC1=2;MQ=20;FQ=-53.9861;RPB=1;MQB=1;BQB=1;PV4=1,1,1,0.457034;MQSB=1;DP=3201;DP4=119,0,2904,25 | GT:PL | 1/1:86,27,0 | 1/1:60,12,0 | 1/1:36,6,0 | ./.:. | 1/1:79,21,0 | 1/1:49,9,0 | 0/1:47,0,5 | 1/1:36,6,0 | ./.:. | 1/1:49,9,0 | 1/1:108,48,0 | 1/1:49,9,0 | 1/1:49,9,0 | 0/1:69,0,2 NC_002333.2 | 3314 | . | C | G | 12.272 | . | VDB=8.63276e-06;SGB=-0.662043;RPB=0.153334;MQB=1;BQB=0.000552776;MQ0F=0;AF1=0.499984;AC1=1;MQ=20;FQ=15.1231;PV4=1,5.1488e-11,1,1;DP=22;DP4=13,0,9,0 | GT:PL | ./.:. | ./.:. | ./.:. | ./.:. | ./.:. | ./.:. | ./.:. | ./.:. | ./.:. | ./.:. | ./.:. | ./.:. | ./.:. | ./.:. NC_002333.2 | 3938 | . | A | G | 52.2632 | . | VDB=0.0221621;SGB=-0.511536;MQ0F=0;AF1=1;AC1=2;MQ=20;FQ=-35.987;MQSB=1;DP=50;DP4=0,0,35,13 | GT:PL | ./.:. | 1/1:49,9,0 | ./.:. | ./.:. | ./.:. | ./.:. | ./.:. | ./.:. | ./.:. | ./.:. | ./.:. | ./.:. | ./.:. | ./.:. NC_002333.2 | 3939 | . | T | C | 17.0581 | . | VDB=0.0221621;SGB=-0.511536;MQ0F=0;AF1=1;AC1=2;MQ=20;FQ=-35.987;DP=3;DP4=0,0,3,0 | GT:PL | ./.:. | ./.:. | ./.:. | ./.:. | ./.:. | ./.:. | ./.:. | ./.:. | ./.:. | ./.:. | ./.:. | ./.:. | ./.:. | ./.:. NC_002333.2 | 3962 | . | T | C | 52.2632 | . | VDB=0.0221621;SGB=-0.511536;MQ0F=0;AF1=1;AC1=2;MQ=20;FQ=-35.987;MQSB=1;DP=67;DP4=0,0,53,13 | GT:PL | ./.:. | 1/1:49,9,0 | ./.:. | ./.:. | ./.:. | ./.:. | ./.:. | ./.:. | ./.:. | ./.:. | ./.:. | ./.:. | ./.:. | ./.:. NC_002333.2 | 3987 | . | T | C | 6.01528 | . | VDB=0.02;SGB=-0.453602;MQ0F=0;AF1=1;AC1=2;MQ=20;FQ=-32.989;DP=2;DP4=0,0,2,0 | GT:PL | ./.:. | ./.:. | ./.:. | ./.:. | ./.:. | ./.:. | ./.:. | ./.:. | ./.:. | ./.:. | ./.:. | ./.:. | ./.:. | ./.:. NC_002333.2 | 4005 | . | G | T | 17.0581 | . | VDB=0.0221621;SGB=-0.511536;MQ0F=0;AF1=1;AC1=2;MQ=20;FQ=-35.987;DP=3;DP4=0,0,3,0 | GT:PL | ./.:. | ./.:. | ./.:. | ./.:. | ./.:. | ./.:. | ./.:. | ./.:. | ./.:. | ./.:. | ./.:. | ./.:. | ./.:. | ./.:. NC_002333.2 | 4099 | . | T | C | 6.01528 | . | VDB=0.02;SGB=-0.453602;MQ0F=0;AF1=1;AC1=2;MQ=20;FQ=-32.989;DP=2;DP4=0,0,0,2 | GT:PL | ./.:. | ./.:. | ./.:. | ./.:. | ./.:. | ./.:. | ./.:. | ./.:. | ./.:. | ./.:. | ./.:. | ./.:. | ./.:. | ./.:. NC_002333.2 | 4225 | . | T | G | 11.3383 | . | VDB=0.0058656;SGB=-0.556411;RPB=0.62023;MQB=0.992367;BQB=0.992367;MQ0F=0;AF1=0.5;AC1=1;MQ=20;FQ=11.3361;PV4=1,1,1,1;DP=8;DP4=4,0,4,0 | GT:PL | ./.:. | ./.:. | ./.:. | ./.:. | ./.:. | ./.:. | ./.:. | ./.:. | ./.:. | ./.:. | ./.:. | ./.:. | ./.:. | ./.:. NC_002333.2 | 4289 | . | T | TT | 9.89959 | . | INDEL;IDV=3;IMF=1;VDB=0.0221621;SGB=-0.511536;MQ0F=0;AF1=1;AC1=2;MQ=20;FQ=-43.5253;DP=3;DP4=0,0,3,0 | GT:PL | ./.:. | ./.:. | ./.:. | ./.:. | ./.:. | ./.:. | ./.:. | ./.:. | ./.:. | ./.:. | ./.:. | ./.:. | ./.:. | ./.:. NC_002333.2 | 4322 | . | A | G | 73.9972 | . | VDB=0.00794932;SGB=-0.616816;MQ0F=0;AF1=1;AC1=2;MQ=20;FQ=-44.9861;MQSB=1;DP=228;DP4=0,0,208,9 | GT:PL | 1/1:74,18,0 | ./.:. | ./.:. | ./.:. | ./.:. | ./.:. | ./.:. | ./.:. | ./.:. | ./.:. | 1/1:36,6,0 | ./.:. | ./.:. | ./.:.

starskyzheng commented 3 years ago

CHROM must be numeric

Xiong-tong commented 1 month ago

Have you solved your problem? Does CHROM have to be changed to something similar to 1, 2, 3, or chr1