very slow processing
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#1 very slow processing
I've tested MAtCHap_1.0 on two contigs for which I had the VCF and fragment file. I stopped the processes after 48 hours...they were still running.
grep -v '^#' ctg92.vcf | wc
793 7930 353710
wc ctg92.frg
120 7366 56765
grep -v '^#' ctg4.vcf | wc
76307 763070 33890419
wc ctg4.frg
4895 324371 2773751
Have you an example dataset I could use for a test?
may I see the header of the .frg file? How did you obtain the .frg file? Did you use the extractHAIRS from HAPCUT2 tool?
59 05257fe7-7e33-4a86-a0cc-dfef60c485d2_Basecall_1D_template 1 000001 8 100 12 001 16 1 18 110000101 29 1 32 00100 38 01001010110100 53 1001011 61 0 64 00 67 0 69 0011101 80 11 83 0100011 95 00100 101 11 104 1 106 0 109 10100111 118 00010011110 131 0 133 100001 140 000110101110101 156 00001 162 111 167 011 171 00 175 01011100010 187 00 190 0 192 000101 201 1 204 00101001000 217 1000 223 10 226 100000 235 0000 241 00110000000000 258 000100010 268 100010 275 00001100000 287 00 290 101010010 300 0 302 10 305 00 308 0001000 318 1000 323 00010000000000000 341 0001000 350 0000 356 00000 362 000 367 0 378 10000100000 390 0100000 398 01 401 100000100000 --9---E--9--9----9--Q9--9-9------------9-----9-------Q--------,-------E-----Q-----------------,----9--------------------,------9--9---------9---------9--------0-----Q---9/9------E--------E---9-------------------9-+---9-,9-9----+-----------------------------------------9--------9--9-----9-------9--------------------
65 a8b2cb03-05da-4bc5-bfa4-9686224d85e7_Basecall_1D_template 1 010001 8 100 12 001 16 1 18 110000001 29 1 32 0010010100 43 000110100 53 100 57 111 61 0 63 000 67 0 69 0011111 80 11 83 0100011 94 10010001 104 1 106 0 109 10100111100010011 127 10 131 0 133 10000 140 000110 147 01 150 10101 156 000000 163 110 167 011100 175 01011100010000 190 01000101 201 10 206 10100000 217 1000 223 10 226 10000 233 0 235 0000 241 0111 246 1000000 254 0 258 000110010 269 100 273 0 275 000011 283 000 287 00 290 000 294 1000 299 000000100000100000 318 1000 323 000 327 0000000000000 341 00010 347 1 350 00101000000 363 01 367 0100000000 379 000010 386 000 390 0 392 00000 398 01 401 100000 408 000000 --9-----D7--9----9--99--9-9------,-----9--9----------Q-----------------E-----O--------------------,-9-------------------------9---9---------9----99-----9-8,---+9----E---9-9------9-------E---/----------------9---9-99-,--------------------E-9------,-----------------------+-----9-9-----99------9------9-------------------
29 2015a1d9-ca76-4ba5-b8af-ff29a3d780b0_Basecall_1D_template 1 000001 8 100 12 001 16 1 18 110000 25 01 29 1 33 01 37 10100101011010 53 1001011 61 01000 69 0011100 80 11 83 01 86 0 88 11 95 00100011 104 1 106 0 108 11 111 1001 116 110 120 010011110 131 001 135 0001 140 000110101100101 158 00101110 167 011100 176 10111 --9,--9-C9--9----9-Q9-9-------+-----7-9--9--------E--------,---9-E------Q-----------------------------------,-------------9---9-----,
74 54d7532f-af75-405a-ae8b-f2e1eba05be7_Basecall_1D_template 1 111 5 10 8 011 12 11 16 010001 23 1 25 10 29 0 32 110110 39 0110101001011 53 0110 58 00 61 1 67 1 69 11000 75 0 80 00 83 1011100 94 011011100 104 0 108 00101 114 000011101 124 00001 131 11011110 142 10010 148 0 150 010 156 111101000 167 100001 175 101000111 185 1011110111010 204 11010110111 218 1 223 0 235 111 241 11 244 0101110 252 111 258 11101 264 101 268 011101 275 1011001 283 111 287 11 290 0 292 0101 297 01 300 1 302 111 306 11 310 101111 318 0 320 11 323 011 327 11111011011 339 111110110 350 1 352 110111111 364 0 367 1011111111 378 0111 383 011111 390 1 392 11111 398 10 401 0111 407 011011 415 010110110 426 0011111 434 111110 441 111110 448 0 451 0011 457 101 --9--E-19-9------Q---9-6-----,------9--9--8----E-------------9--E------E----------------------9--------------,--,----9---,---------9---9-------9------E9----Q+------,--E9-9----------------,-9----9-99-9-------------,-E-9------------------------9---------9------99-------9-------,-----------------------9--------9--E----------------
ok....frg files look correct....You stopped the process after 48 hours....network files were generated?
Yes, it took 7 minutes to create the files for the large contig
and one minute for the small contig
Ok. Thank You. It could be a problem of convergence. Could You kindly provide me the .frg and .vcf files?
You can download the files from
http://genoweb.toulouse.inra.fr/~klopp/matchap_tests/ctg4.frg
http://genoweb.toulouse.inra.fr/~klopp/matchap_tests/ctg4.vcf
http://genoweb.toulouse.inra.fr/~klopp/matchap_tests/ctg92.frg
http://genoweb.toulouse.inra.fr/~klopp/matchap_tests/ctg92.vcf
The VCF files are not properly formatted. They do not have mandatory header lines.
alberto@neo:~/HaplotypeAssembly/DataKlopp> head ctg4.vcf
ctg4 31 . T C 1011.1 . AB=0.483871;ABP=3.22044;AC=1;AF=0.5;AN=2;AO=45;CIGAR=1X;DP=93;DPB=93;DPRA=0;EPP=3.05855;EPPR=3.73412;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=232.814;PAIRED=0.733333;PAIREDR=0.770833;PAO=0;PQA=0;PQR=0;PRO=0;QA=1619;QR=1677;RO=48;RPL=1;RPP=92.2337;RPPR=75.3927;RPR=44;RUN=1;SAF=23;SAP=3.05855;SAR=22;SRF=28;SRP=5.9056;SRR=20;TYPE=snp GT:DP:AD:RO:QR:AO:QA:GL 0/1:93:48,45:48:1677:45:1619:-117.971,0,-123.184
ctg4 46 . A G 1252.9 . AB=0.525773;ABP=3.56996;AC=1;AF=0.5;AN=2;AO=51;CIGAR=1X;DP=97;DPB=97;DPRA=0;EPP=3.05288;EPPR=3.76559;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=242.466;PAIRED=0.764706;PAIREDR=0.76087;PAO=0;PQA=0;PQR=0;PRO=0;QA=1851;QR=1618;RO=46;RPL=7;RPP=61.2994;RPPR=51.3492;RPR=44;RUN=1;SAF=25;SAP=3.05288;SAR=26;SRF=26;SRP=4.70971;SRR=20;TYPE=snp GT:DP:AD:RO:QR:AO:QA:GL 0/1:97:46,51:46:1618:51:1851:-137.644,0,-116.673
ctg4 69 . TCG ACC 1104.35 . AB=0.510417;ABP=3.10078;AC=1;AF=0.5;AN=2;AO=49;CIGAR=1X1M1X;DP=96;DPB=96.6667;DPRA=0;EPP=5.18177;EPPR=6.75262;GTI=0;LEN=3;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=254.286;PAIRED=0.836735;PAIREDR=0.808511;PAO=1;PQA=34;PQR=0;PRO=0;QA=1633;QR=1647;RO=47;RPL=9;RPP=45.5977;RPPR=27.4509;RPR=40;RUN=1;SAF=24;SAP=3.05462;SAR=25;SRF=24;SRP=3.0565;SRR=23;TYPE=complex GT:DP:AD:RO:QR:AO:QA:GL 0/1:96:47,49:47:1647:49:1633:-121.081,0,-119.298
ctg4 76 . A C 1240.6 . AB=0.526316;ABP=3.58174;AC=1;AF=0.5;AN=2;AO=50;CIGAR=1X;DP=95;DPB=95;DPRA=0;EPP=4.57376;EPPR=8.84915;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=256.007;PAIRED=0.84;PAIREDR=0.8;PAO=0;PQA=0;PQR=0;PRO=0;QA=1790;QR=1638;RO=45;RPL=13;RPP=28.0257;RPPR=16.956;RPR=37;RUN=1;SAF=25;SAP=3.0103;SAR=25;SRF=22;SRP=3.05855;SRR=23;TYPE=snp GT:DP:AD:RO:QR:AO:QA:GL 0/1:95:45,50:45:1638:50:1790:-132.76,0,-119.087
ctg4 115 . A T 1074.76 . AB=0.473684;ABP=3.58174;AC=1;AF=0.5;AN=2;AO=45;CIGAR=1X;DP=95;DPB=95;DPRA=0;EPP=3.44459;EPPR=3.70517;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=247.472;PAIRED=0.888889;PAIREDR=0.86;PAO=0;PQA=0;PQR=0;PRO=0;QA=1576;QR=1805;RO=50;RPL=22;RPP=3.05855;RPPR=3.18402;RPR=23;RUN=1;SAF=21;SAP=3.44459;SAR=24;SRF=23;SRP=3.70517;SRR=27;TYPE=snp GT:DP:AD:RO:QR:AO:QA:GL 0/1:95:50,45:50:1805:45:1576:-113.491,0,-134.112
ctg4 163 . G A 1206.11 . AB=0.539326;ABP=4.20583;AC=1;AF=0.5;AN=2;AO=48;CIGAR=1X;DP=89;DPB=89;DPRA=0;EPP=14.5915;EPPR=3.06326;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=234.813;PAIRED=0.9375;PAIREDR=0.902439;PAO=0;PQA=0;PQR=0;PRO=0;QA=1715;QR=1502;RO=41;RPL=25;RPP=3.19126;RPPR=9.41879;RPR=23;RUN=1;SAF=25;SAP=3.19126;SAR=23;SRF=18;SRP=4.33437;SRR=23;TYPE=snp GT:DP:AD:RO:QR:AO:QA:GL 0/1:89:41,48:41:1502:48:1715:-127.817,0,-108.659
ctg4 216 . AGG GGA 889.532 . AB=0.452381;ABP=4.66476;AC=1;AF=0.5;AN=2;AO=38;CIGAR=1X1M1X;DP=84;DPB=84;DPRA=0;EPP=3.23888;EPPR=3.76559;GTI=0;LEN=3;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=204.822;PAIRED=0.947368;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=1337;QR=1605;RO=46;RPL=23;RPP=6.66752;RPPR=3.76559;RPR=15;RUN=1;SAF=17;SAP=3.9246;SAR=21;SRF=24;SRP=3.19912;SRR=22;TYPE=complex GT:DP:AD:RO:QR:AO:QA:GL 0/1:84:46,38:46:1605:38:1337:-95.3211,0,-119.425
ctg4 222 . CAGTG TGGTA 1037.63 . AB=0.525641;ABP=3.45573;AC=1;AF=0.5;AN=2;AO=41;CIGAR=2X2M1X;DP=78;DPB=79.8;DPRA=0;EPP=3.48696;EPPR=3.25157;GTI=0;LEN=5;MEANALT=2;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=228.035;PAIRED=1;PAIREDR=0.972222;PAO=0;PQA=0;PQR=101;PRO=4;QA=1487;QR=1333;RO=36;RPL=22;RPP=3.48696;RPPR=3.9754;RPR=19;RUN=1;SAF=20;SAP=3.06326;SAR=21;SRF=17;SRP=3.25157;SRR=19;TYPE=complex GT:DP:AD:RO:QR:AO:QA:GL 0/1:78:36,41:36:1333:41:1487:-109.695,0,-104.925
ctg4 232 . G A 901.013 . AB=0.45679;ABP=4.32391;AC=1;AF=0.5;AN=2;AO=37;CIGAR=1X;DP=81;DPB=81;DPRA=0;EPP=3.5385;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=207.466;PAIRED=0.972973;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=1335;QR=1535;RO=44;RPL=20;RPP=3.5385;RPPR=3.20771;RPR=17;RUN=1;SAF=18;SAP=3.06899;SAR=19;SRF=21;SRP=3.20771;SRR=23;TYPE=snp GT:DP:AD:RO:QR:AO:QA:GL 0/1:81:44,37:44:1535:37:1335:-96.0488,0,-114.024
ctg4 240 . GAT CTC 636.824 . AB=0.405405;ABP=8.76177;AC=1;AF=0.5;AN=2;AO=30;CIGAR=3X;DP=74;DPB=74.6667;DPRA=0;EPP=7.64277;EPPR=5.48477;GTI=0;LEN=3;MEANALT=2;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=146.634;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=36;PRO=1;QA=1026;QR=1541;RO=43;RPL=14;RPP=3.29983;RPPR=3.46479;RPR=16;RUN=1;SAF=13;SAP=4.16842;SAR=17;SRF=18;SRP=5.48477;SRR=25;TYPE=mnp GT:DP:AD:RO:QR:AO:QA:GL 0/1:74:43,30:43:1541:30:1026:-70.3264,0,-119.897
I've added the header to the vcf file and get the same behavior.
The R script runs now for 3 days on the small contig and is not finished.
can you show me the header?
fileformat=VCFv4.2
FORMAT=<id=ad,number=r,type=integer,description="allelic depths="" for="" the="" ref="" and="" alt="" alleles="" in="" order="" listed"=""></id=ad,number=r,type=integer,description="allelic>
FORMAT=<id=ad,number=r,type=integer,description="number of="" observation="" for="" each="" allele"=""></id=ad,number=r,type=integer,description="number>
FORMAT=<id=ao,number=a,type=integer,description="alternate allele="" observation="" count"=""></id=ao,number=a,type=integer,description="alternate>
FORMAT=<id=dp,number=1,type=integer,description="approximate read="" depth="" (reads="" with="" mq="255" or="" bad="" mates="" are="" filtered)"=""></id=dp,number=1,type=integer,description="approximate>
FORMAT=<id=dp,number=1,type=integer,description="read depth"=""></id=dp,number=1,type=integer,description="read>
FORMAT=<id=ft,number=.,type=string,description="genotype-level filter"=""></id=ft,number=.,type=string,description="genotype-level>
FORMAT=<id=gl,number=g,type=float,description="genotype likelihood,="" log10-scaled="" likelihoods="" of="" the="" data="" given="" called="" genotype="" for="" each="" possible="" generated="" from="" reference="" and="" alternate="" alleles="" sample="" ploidy"=""></id=gl,number=g,type=float,description="genotype>
FORMAT=<id=gq,number=1,type=integer,description="genotype quality"=""></id=gq,number=1,type=integer,description="genotype>
FORMAT=<id=gt,number=1,type=string,description="genotype"></id=gt,number=1,type=string,description="genotype">
FORMAT=<id=min_dp,number=1,type=integer,description="minimum depth="" in="" gvcf="" output="" block."=""></id=min_dp,number=1,type=integer,description="minimum>
FORMAT=<id=ne,number=1,type=float,description="the confidence="" (phred-scaled)="" that="" the="" snv="" is="" not="" a="" mismatch="" (single="" snv)="" error."=""></id=ne,number=1,type=float,description="the>
FORMAT=<id=pl,number=g,type=integer,description="normalized, phred-scaled="" likelihoods="" for="" genotypes="" as="" defined="" in="" the="" vcf="" specification"=""></id=pl,number=g,type=integer,description="normalized,>
FORMAT=<id=pr,number=1,type=integer,description="1 if="" hapcut2="" pruned="" this="" variant="" when="" using="" --discrete_pruning,="" 0="" otherwise"=""></id=pr,number=1,type=integer,description="1>
FORMAT=<id=ps,number=1,type=integer,description="phase set="" for="" the="" genotype="" (position="" of="" first="" variant)"=""></id=ps,number=1,type=integer,description="phase>
FORMAT=<id=qa,number=a,type=integer,description="sum of="" quality="" the="" alternate="" observations"=""></id=qa,number=a,type=integer,description="sum>
FORMAT=<id=qr,number=1,type=integer,description="sum of="" quality="" the="" reference="" observations"=""></id=qr,number=1,type=integer,description="sum>
FORMAT=<id=ro,number=1,type=integer,description="reference allele="" observation="" count"=""></id=ro,number=1,type=integer,description="reference>
FORMAT=<id=se,number=1,type=float,description="the confidence="" (phred-scaled)="" that="" there="" is="" not="" a="" switch="" error="" occurring="" immediately="" before="" the="" snv"=""></id=se,number=1,type=float,description="the>
INFO=<id=ab,number=a,type=float,description="allele balance="" at="" heterozygous="" sites:="" a="" number="" between="" 0="" and="" 1="" representing="" the="" ratio="" of="" reads="" showing="" reference="" allele="" to="" all="" reads,="" considering="" only="" from="" individuals="" called="" as="" heterozygous"=""></id=ab,number=a,type=float,description="allele>
INFO=<id=abp,number=a,type=float,description="allele balance="" probability="" at="" heterozygous="" sites:="" phred-scaled="" upper-bounds="" estimate="" of="" the="" observing="" deviation="" between="" abr="" and="" aba="" given="" e(abr="" aba)="" ~="" 0.5,="" derived="" using="" hoeffding's="" inequality"=""></id=abp,number=a,type=float,description="allele>
INFO=<id=ac,number=a,type=integer,description="total number="" of="" alternate="" alleles="" in="" called="" genotypes"=""></id=ac,number=a,type=integer,description="total>
INFO=<id=af,number=a,type=float,description="estimated allele="" frequency="" in="" the="" range="" (0,1]"=""></id=af,number=a,type=float,description="estimated>
INFO=<id=an,number=1,type=integer,description="total number="" of="" alleles="" in="" called="" genotypes"=""></id=an,number=1,type=integer,description="total>
INFO=<id=ao,number=a,type=integer,description="count of="" full="" observations="" this="" alternate="" haplotype."=""></id=ao,number=a,type=integer,description="count>
INFO=<id=cigar,number=a,type=string,description="the extended="" cigar="" representation="" of="" each="" alternate="" allele,="" with="" the="" exception="" that="" '=" is replaced by " m'="" to="" ease="" vcf="" parsing.="" note="" indel="" alleles="" do="" not="" have="" first="" matched="" base="" (which="" is="" provided="" by="" default,="" per="" spec)="" referred="" cigar."=""></id=cigar,number=a,type=string,description="the>
INFO=<id=dp,number=1,type=integer,description="total read="" depth="" at="" the="" locus"=""></id=dp,number=1,type=integer,description="total>
INFO=<id=dpb,number=1,type=float,description="total read="" depth="" per="" bp="" at="" the="" locus;="" bases="" in="" reads="" overlapping="" haplotype"=""></id=dpb,number=1,type=float,description="total>
INFO=<id=dpra,number=a,type=float,description="alternate allele="" depth="" ratio.="" ratio="" between="" in="" samples="" with="" each="" called="" alternate="" and="" those="" without."=""></id=dpra,number=a,type=float,description="alternate>
INFO=<id=end,number=1,type=integer,description="last position="" (inclusive)="" in="" gvcf="" output="" record."=""></id=end,number=1,type=integer,description="last>
INFO=<id=epp,number=a,type=float,description="end placement="" probability:="" phred-scaled="" upper-bounds="" estimate="" of="" the="" probability="" observing="" deviation="" between="" el="" and="" er="" given="" e(el="" er)="" ~="" 0.5,="" derived="" using="" hoeffding's="" inequality"=""></id=epp,number=a,type=float,description="end>
INFO=<id=eppr,number=1,type=float,description="end placement="" probability="" for="" reference="" observations:="" phred-scaled="" upper-bounds="" estimate="" of="" the="" observing="" deviation="" between="" el="" and="" er="" given="" e(el="" er)="" ~="" 0.5,="" derived="" using="" hoeffding's="" inequality"=""></id=eppr,number=1,type=float,description="end>
INFO=<id=gti,number=1,type=integer,description="number of="" genotyping="" iterations="" required="" to="" reach="" convergence="" or="" bailout."=""></id=gti,number=1,type=integer,description="number>
INFO=<id=len,number=a,type=integer,description="allele length"=""></id=len,number=a,type=integer,description="allele>
INFO=<id=meanalt,number=a,type=float,description="mean number="" of="" unique="" non-reference="" allele="" observations="" per="" sample="" with="" the="" corresponding="" alternate="" alleles."=""></id=meanalt,number=a,type=float,description="mean>
INFO=<id=min_dp,number=1,type=integer,description="minimum depth="" in="" gvcf="" output="" block."=""></id=min_dp,number=1,type=integer,description="minimum>
INFO=<id=mqm,number=a,type=float,description="mean mapping="" quality="" of="" observed="" alternate="" alleles"=""></id=mqm,number=a,type=float,description="mean>
INFO=<id=mqmr,number=1,type=float,description="mean mapping="" quality="" of="" observed="" reference="" alleles"=""></id=mqmr,number=1,type=float,description="mean>
INFO=<id=ns,number=1,type=integer,description="number of="" samples="" with="" data"=""></id=ns,number=1,type=integer,description="number>
INFO=<id=numalt,number=1,type=integer,description="number of="" unique="" non-reference="" alleles="" in="" called="" genotypes="" at="" this="" position."=""></id=numalt,number=1,type=integer,description="number>
INFO=<id=odds,number=1,type=float,description="the log="" odds="" ratio="" of="" the="" best="" genotype="" combination="" to="" second-best."=""></id=odds,number=1,type=float,description="the>
INFO=<id=paired,number=a,type=float,description="proportion of="" observed="" alternate="" alleles="" which="" are="" supported="" by="" properly="" paired="" read="" fragments"=""></id=paired,number=a,type=float,description="proportion>
INFO=<id=pairedr,number=1,type=float,description="proportion of="" observed="" reference="" alleles="" which="" are="" supported="" by="" properly="" paired="" read="" fragments"=""></id=pairedr,number=1,type=float,description="proportion>
INFO=<id=pao,number=a,type=float,description="alternate allele="" observations,="" with="" partial="" observations="" recorded="" fractionally"=""></id=pao,number=a,type=float,description="alternate>
INFO=<id=pqa,number=a,type=float,description="alternate allele="" quality="" sum="" in="" phred="" for="" partial="" observations"=""></id=pqa,number=a,type=float,description="alternate>
INFO=<id=pqr,number=1,type=float,description="reference allele="" quality="" sum="" in="" phred="" for="" partial="" observations"=""></id=pqr,number=1,type=float,description="reference>
INFO=<id=pro,number=1,type=float,description="reference allele="" observation="" count,="" with="" partial="" observations="" recorded="" fractionally"=""></id=pro,number=1,type=float,description="reference>
INFO=<id=qa,number=a,type=integer,description="alternate allele="" quality="" sum="" in="" phred"=""></id=qa,number=a,type=integer,description="alternate>
INFO=<id=qr,number=1,type=integer,description="reference allele="" quality="" sum="" in="" phred"=""></id=qr,number=1,type=integer,description="reference>
INFO=<id=ro,number=1,type=integer,description="count of="" full="" observations="" the="" reference="" haplotype."=""></id=ro,number=1,type=integer,description="count>
INFO=<id=rpl,number=a,type=float,description="reads placed="" left:="" number="" of="" reads="" supporting="" the="" alternate="" balanced="" to="" left="" (5')="" allele"=""></id=rpl,number=a,type=float,description="reads>
INFO=<id=rpp,number=a,type=float,description="read placement="" probability:="" phred-scaled="" upper-bounds="" estimate="" of="" the="" probability="" observing="" deviation="" between="" rpl="" and="" rpr="" given="" e(rpl="" rpr)="" ~="" 0.5,="" derived="" using="" hoeffding's="" inequality"=""></id=rpp,number=a,type=float,description="read>
INFO=<id=rppr,number=1,type=float,description="read placement="" probability="" for="" reference="" observations:="" phred-scaled="" upper-bounds="" estimate="" of="" the="" observing="" deviation="" between="" rpl="" and="" rpr="" given="" e(rpl="" rpr)="" ~="" 0.5,="" derived="" using="" hoeffding's="" inequality"=""></id=rppr,number=1,type=float,description="read>
INFO=<id=rpr,number=a,type=float,description="reads placed="" right:="" number="" of="" reads="" supporting="" the="" alternate="" balanced="" to="" right="" (3')="" allele"=""></id=rpr,number=a,type=float,description="reads>
INFO=<id=run,number=a,type=integer,description="run length:="" the="" number="" of="" consecutive="" repeats="" alternate="" allele="" in="" reference="" genome"=""></id=run,number=a,type=integer,description="run>
INFO=<id=saf,number=a,type=integer,description="number of="" alternate="" observations="" on="" the="" forward="" strand"=""></id=saf,number=a,type=integer,description="number>
INFO=<id=sap,number=a,type=float,description="strand balance="" probability="" for="" the="" alternate="" allele:="" phred-scaled="" upper-bounds="" estimate="" of="" observing="" deviation="" between="" saf="" and="" sar="" given="" e(saf="" sar)="" ~="" 0.5,="" derived="" using="" hoeffding's="" inequality"=""></id=sap,number=a,type=float,description="strand>
INFO=<id=sar,number=a,type=integer,description="number of="" alternate="" observations="" on="" the="" reverse="" strand"=""></id=sar,number=a,type=integer,description="number>
INFO=<id=srf,number=1,type=integer,description="number of="" reference="" observations="" on="" the="" forward="" strand"=""></id=srf,number=1,type=integer,description="number>
INFO=<id=srp,number=1,type=float,description="strand balance="" probability="" for="" the="" reference="" allele:="" phred-scaled="" upper-bounds="" estimate="" of="" observing="" deviation="" between="" srf="" and="" srr="" given="" e(srf="" srr)="" ~="" 0.5,="" derived="" using="" hoeffding's="" inequality"=""></id=srp,number=1,type=float,description="strand>
INFO=<id=srr,number=1,type=integer,description="number of="" reference="" observations="" on="" the="" reverse="" strand"=""></id=srr,number=1,type=integer,description="number>
INFO=<id=type,number=a,type=string,description="the type="" of="" allele,="" either="" snp,="" mnp,="" ins,="" del,="" or="" complex."=""></id=type,number=a,type=string,description="the>
commandline="/usr/local/bioinfo/src/FreeBayes/freebayes-1.1.0/freebayes/bin/freebayes --fasta-reference SEQGANO2_select.ctg.lay.racon.freebayes.fa --targets 0.bed SEQGANO2_select.ctg.lay.racon.freebayes.NJ3-1.sort.bam"
contig=<id=ctg1,length=887559></id=ctg1,length=887559>
contig=<id=ctg2,length=1566982></id=ctg2,length=1566982>
contig=<id=ctg3,length=1849764></id=ctg3,length=1849764>
contig=<id=ctg4,length=2598157></id=ctg4,length=2598157>
contig=<id=ctg5,length=1397053></id=ctg5,length=1397053>
contig=<id=ctg6,length=709438></id=ctg6,length=709438>
contig=<id=ctg7,length=638274></id=ctg7,length=638274>
....
contig=<id=ctg873,length=7094></id=ctg873,length=7094>
contig=<id=ctg875,length=13465></id=ctg875,length=13465>
contig=<id=ctg876,length=9942></id=ctg876,length=9942>
fileDate=20190521
phasing=none
reference=SEQGANO2_select.ctg.lay.racon.freebayes.fa
source=freeBayes v1.1.0-1-gf15e66e-dirty
CHROM POS ID REF ALT QUAL FILTER INFO FORMAT unknown
in the header there are no ## and # in all lines. Can you make a snapshot of 'head ctg92.vcf'.
Header snapshot
can you share the new vcf file?