phylogenetic tree about vcf-kit

[vinay104]

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 Tree

MUSCLE 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
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)
TypeError: an integer is required
(ve) vinay410@server230:vcfkit >
"
I do not see any output file produced or maybe i donno where it is saved.
Please help me out of this issue. Badly struggling with the error more than five days now.

Thanks,
Vinay Kumar Reddy Nannuru.

[danielecook]

Addressed previously.