vinay104
commented
6 years ago Hello,
I am Vinay kumar reddy nannuru again and still have a issue generating tree with my vcf data. I am posting you the log and error "(ve) vinay410@server230:vcfkit > vk phylo tree nj --plot gbs27_maf001_minmax2_mis65_dp3.recode.vcf [W::bcf_hdr_check_sanity] PL should be declared as Number=G [W::vcf_parse] contig '1' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig '2' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig '3' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig '4' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig '5' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig '6' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig '7' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig '8' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig '9' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig '10' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'B73V4_CTG10' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'B73V4_CTG104' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'B73V4_CTG110' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'B73V4_CTG115' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'B73V4_CTG119' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'B73V4_CTG121' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'B73V4_CTG123' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'B73V4_CTG125' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'B73V4_CTG129' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'B73V4_CTG130' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'B73V4_CTG133' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'B73V4_CTG134' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'B73V4_CTG150' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'B73V4_CTG165' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'B73V4_CTG178' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'B73V4_CTG181' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'B73V4_CTG182' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'B73V4_CTG190' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'B73V4_CTG193' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'B73V4_CTG2' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'B73V4_CTG203' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'B73V4_CTG204' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'B73V4_CTG205' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'B73V4_CTG224' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'B73V4_CTG239' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'B73V4_CTG24' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'B73V4_CTG245' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'B73V4_CTG253' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'B73V4_CTG26' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'B73V4_CTG3' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'B73V4_CTG31' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'B73V4_CTG36' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'B73V4_CTG38' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'B73V4_CTG5' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'B73V4_CTG51' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'B73V4_CTG53' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'B73V4_CTG56' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'B73V4_CTG58' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'B73V4_CTG6' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'B73V4_CTG65' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'B73V4_CTG68' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'B73V4_CTG7' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'B73V4_CTG73' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'B73V4_CTG75' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'B73V4_CTG83' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'B73V4_CTG91' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'MT' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig 'PT' is not defined in the header. (Quick workaround: index the file with tabix.)
Generating Fasta
Generating neighborjoining TreeMUSCLE v3.8.31 by Robert C. Edgar
http://www.drive5.com/muscle This software is donated to the public domain. Please cite: Edgar, R.C. Nucleic Acids Res 32(5), 1792-97.
00:00:00 15 MB(-1%) 105 sequences 00:00:01 16 MB(-1%) Iter 0 100.00% Build dist matrix 00:00:01 16 MB(-1%) Iter 0 100.00% Build guide tree 00:00:01 16 MB(-1%) Tree created ( ( ( ( ( ( ( ( ( AM49a:0.187979 , AM38a:0.159693 ):0.00553387 , AM6b:0.176561 ):0.00116366 , AM13a:0.17585 ):0.00273378 , ( ( ( ( ( ( ( ( ( ( ( ( ( ( ( ( ( ( C528c:0.471274 , AM52b:0.485101 ):0.00659975 , ( ( ( ( ( ( ( ( ( ( ( ( ( ( ( ( ( ( ( ( ( ( ( ( ( ( ( ( ( ( ( AM23a:-0.0116615 , AM16b:0.0167747 ):0.0183308 , AM34a:-0.0100982 ):0.0263889 , AM29a:-0.0130451 ):0.0394053 , AM46a:-0.0197372 ):0.335347 , AM31a:-0.279672 ):1.18824 , AM1a:-1.06837 ):0.803972 , AM47b:-0.670525 ):0.441153 , AM48a:-0.309034 ):0.342516 , AM30a:-0.19034 ):0.250336 , AM41a:-0.0859761 ):0.257968 , AM14b:-0.057822 ):0.243121 , AM52a:-0.0219334 ):0.333289 , AM27a:-0.016302 ):0.206704 , AM46b:0.0881668 ):0.120868 , AM25a:0.204514 ):0.089553 , AM32a:0.212512 ):0.0546162 , AM40a:0.245382 ):0.0932238 , AM31b:0.258776 ):0.0554422 , AM33a:0.278082 ):0.17365 , AM48b:0.247526 ):0.112841 , AM44a:0.339195 ):0.0622863 , AM19b:0.372233 ):0.0463884 , AM36a:0.380669 ):0.062137 , AM9b:0.399071 ):0.0617064 , AM13b:0.410671 ):0.0297242 , AM25b:0.450368 ):0.0505373 , AM45a:0.411202 ):0.0577637 , AM51a:0.434494 ):0.0284554 , AM36b:0.435848 ):0.0168408 , AM28b:0.433558 ):0.0143916 , AM26a:0.470629 ):0.015223 ):0.0286023 , AM33b:0.419617 ):0.0404805 , AM30b:0.410076 ):0.0277157 , AM38b:0.400782 ):0.0309643 , AM34b:0.402084 ):0.0203433 , ( AM37b:0.367989 , AM24a:0.454455 ):0.0401244 ):0.0133595 , AM43a:0.399624 ):0.0222803 , AM51b:0.394737 ):0.0103836 , AM5a:0.379325 ):0.00995031 , AM8a:0.367876 ):0.00220096 , AM39b:0.362992 ):0.0168341 , AM55b:0.312213 ):0.0123698 , AM17b:0.322585 ):0.00564981 , AM10b:0.304826 ):0.0073635 , AM32b:0.281778 ):0.00429825 , AM40b:0.257335 ):0.00435181 , AM22b:0.21088 ):0.00874936 ):0.000855483 , ( ( ( ( AM26b:0.191803 , AM29b:0.237797 ):0.0027248 , ( AM3b:0.181577 , AM12:0.189989 ):0.00670221 ):0.00092756 , ( ( AM8b:0.150637 , AM7b:0.209721 ):0.00179566 , AM22a:0.195821 ):0.00295857 ):0.000620216 , ( AM3a:0.149922 , AM14a:0.207705 ):0.00207277 ):0.00121925 ):0.000745689 , ( ( ( AM4b:0.158594 , AM24b:0.190394 ):0.000881782 , ( ( ( ( ( C715b:0.147183 , C715c:0.156906 ):0.0141587 , AM6a:0.175232 ):0.000907451 , ( ( ( ( ( ( C277a:0.13877 , C277b:0.160231 ):0.0197682 , AM53b:0.230188 ):0.00373678 , AM47a:0.185533 ):0.00271322 , ( ( ( AM21a:0.174194 , AM23b:0.270275 ):0.00534377 , ( ( AM54a:0.382371 , AM54b:0.194456 ):0.0223709 , AM2a:0.173131 ):0.0147601 ):0.00342044 , C528a:0.233895 ):0.00644647 ):0.00247861 , ( AM42b:0.201891 , AM55a:0.289881 ):0.00431278 ):0.00302779 , ( ( ( AM11a:0.156016 , AM18b:0.105774 ):0.015624 , AM18a:0.27824 ):0.0154843 , AM11b:0.161052 ):0.0346689 ):0.0022883 ):0.00137175 , ( AM50a:0.160556 , AM21b:0.168665 ):0.00351713 ):0.000460714 , AM56:0.166829 ):0.00587782 ):0.000605017 , ( AM20b:0.204447 , AM7a:0.165186 ):0.00447728 ):0.00123765 ):0.000686805 , ( ( ( AM20a:0.150286 , AM9a:0.143778 ):0.00320077 , AM5b:0.146179 ):0.00109606 , ( AM1b:0.138512 , AM15a:0.16528 ):0.00437597 ):0.00161358 ):0.00026332 , ( ( ( ( AM43b:0.155492 , AM16a:0.146641 ):0.00223732 , AM4a:0.14823 ):0.00155636 , AM10a:0.168842 ):0.000647778 , ( ( AM41b:0.164578 , AM44b:0.210089 ):0.00620662 , AM19a:0.172529 ):0.00198072 ):0.00123185 ):0.000620506 , ( ( AM17a:0.136038 , AM15b:0.147893 ):0.00623766 , AM50b:0.145592 ):0.000620506 ) ;
Traceback (most recent call last):
File "/storage2/active/nvinay/mthesis/ve/lib/python2.7/site-packages/vcfkit/phylo.py", line 101, in
Thanks, Vinay Kumar Reddy Nannuru.
danielecook
Hello,
I am vinay kumar reddy and i am working with vcfkit for phylogenetic tree for my snp data. I could succeed in getting fasta format and distances between the samples but when i used command "vk phylo tree nj |upgma --plot myvcffile", i did get the tree diagram as it is shown in the document i read. It shows an error like this and i dont know wat it is, can you please help me in succeeding with a tree diagram. The error is "Traceback (most recent call last): File "/storage2/active/nvinay/mthesis/ve/lib/python2.7/site-packages/vcfkit/phylo.py", line 101, in
main()
File "/storage2/active/nvinay/mthesis/ve/lib/python2.7/site-packages/vcfkit/phylo.py", line 91, in main
template = open(prefix + "/tree.html",'r').read(tree)
IOError: [Errno 2] No such file or directory: '/storage2/active/nvinay/mthesis/ve/lib/python2.7/site-packages/vcfkit/static/tree.html".
I also tried to do it with the newick.format but i dont know where i can see an outfile. If at all i want to work with R, i need some output file, how can i get it.
Thanks, Vinay Kumar Reddy Nannuru.