Alberto Magi posted a comment on ticket #1

can you share the new vcf file?

Christophe Klopp posted a comment on ticket #1

Header snapshot

Alberto Magi posted a comment on ticket #1

in the header there are no ## and # in all lines. Can you make a snapshot of 'head ctg92.vcf'.

Christophe Klopp posted a comment on ticket #1

fileformat=VCFv4.2 FORMAT=<id=ad,number=r,type=integer,description="allelic and="" for="" alleles="" order="" depths="" listed"="" in="" the="" ref="" alt=""></id=ad,number=r,type=integer,description="allelic> FORMAT=<id=ad,number=r,type=integer,description="number allele"="" of="" observation="" for="" each=""></id=ad,number=r,type=integer,description="number> FORMAT=<id=ao,number=a,type=integer,description="alternate allele="" count"="" observation=""></id=ao,number=a,type=integer,description="alternate>...

Alberto Magi posted a comment on ticket #1

can you show me the header?

Christophe Klopp posted a comment on ticket #1

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.

Alberto Magi posted a comment on ticket #1

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...

Christophe Klopp posted a comment on ticket #1

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

Alberto Magi posted a comment on ticket #1

Ok. Thank You. It could be a problem of convergence. Could You kindly provide me the .frg and .vcf files?

Christophe Klopp posted a comment on ticket #1

Yes, it took 7 minutes to create the files for the large contig ls -ltr ctg4_MAtCHapHairs_dir/Network total 614664 -rw-r--r-- 1 klopp BIOINFO 142336 Dec 4 10:54 ctg4_MAtCHapHairs_NA.txt -rw-r--r-- 1 klopp BIOINFO 210393 Dec 4 10:56 ctg4_MAtCHapHairs_IA.txt -rw-r--r-- 1 klopp BIOINFO 105074307 Dec 4 10:56 ctg4_MAtCHapHairs_JA.txt -rw-r--r-- 1 klopp BIOINFO 523969568 Dec 4 10:56 ctg4_MAtCHapHairs_XA.txt and one minute for the small contig ls -ltr ctg92_MAtCHapHairs_dir/Network total 9032 -rw-r--r--...

Alberto Magi posted a comment on ticket #1

ok....frg files look correct....You stopped the process after 48 hours....network files were generated?

Christophe Klopp posted a comment on ticket #1

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...

Alberto Magi posted a comment on ticket #1

may I see the header of the .frg file? How did you obtain the .frg file? Did you use the extractHAIRS from HAPCUT2 tool?

Christophe Klopp created ticket #1

very slow processing

MAtCHap released /MAtCHap_1.0.tar.gz