No results after Site-Specific Posterior Analysis

[e44z]

Hi there!

I would like to kindly ask for help with Grand-conv, in particular, why I don't get any results from the third part of the analysis while requesting site-specific data for branch-pairs of interest. Although I don't get any error message after running commands, the html file siteSpecific-index.html is showing no data within the graphs. The commands and input data I used are below.

Thank you very much for any help!
With best wishes,
Eliska

/gc-estimate --in=gene103968507.phy --seqtype=aa --tree=sp_treeshrink_good.raxml.bestTree_rooted.nwk --gencode=1 --dir=output --free-bl=0
./gc-discover --dir=output --nthreads=4
./gc-discover --dir=output --nthreads=4 --branch-pairs="(53,56)" --visualize=1

input tree:
((((((((((((Kaempferia-fissa_S642:0.004803000000000002,Kaempferia-fissa_S644:0.007051000000000002):0.0053500000000000075,Kaempferia-fissa_S652:0.015299999999999994):0.001556999999999989,Kaempferia-fissa_S648:0.014803999999999984):9.840000000000126E-4,(Kaempferia-fissa_S654:0.010279999999999997,Kaempferia-fallax_S631:0.014946000000000001):0.003268000000000007):0.0061279999999999946,Kaempferia-rupicola_S653:0.017140000000000002):0.0057900000000000035,(Kaempferia-filifolia_S641:0.019402000000000003,Kaempferia-filifolia_S649:0.016770000000000007):0.004060999999999995):0.005218,((Kaempferia-attapeuensis_S643:0.023314,Kaempferia-leucantha_S646:0.021727999999999997):0.003506000000000009,Kaempferia-nemoralis_S651:0.025971999999999995):0.00488799999999999):0.014848,Kaempferia-gigantiphylla_S645:0.03275499999999999):0.009982000000000005,(((Kaempferia-rotunda_S639:0.020332000000000003,Kaempferia-rotunda_S636:0.020289):0.006033000000000011,(Kaempferia-noctiflora_S632:0.02175500000000001,Kaempferia-xiengkhouangensis_S634:0.018406000000000006):0.0024969999999999992):0.0025029999999999913,Kaempferia-xiengkhouangensis_S633:0.023141999999999996):0.013162999999999994):0.004488999999999993,(((((Kaempferia-tomentosa_S638:0.015964000000000006,Kaempferia-lilacina_S635:0.017723000000000003):0.0020860000000000045,Kaempferia-galanga_S637:0.017587999999999993):0.0011789999999999995,Kaempferia-subintegra_S647:0.026232999999999992):0.002939999999999998,Kaempferia-dasygyna_S650:0.017033000000000006):0.003719999999999987,Kaempferia-sawanensis_S640:0.02040199999999999):0.022626000000000007):0.019528000000000004,(((((((((Curcuma-aeruginosa_S607:0.017586000000000004,Curcuma-montana_S629:0.015477000000000005):0.004527000000000003,Curcuma-roscoeana_S630:0.025663000000000005):0.0019460000000000033,((Curcuma-caulina_S609:0.018932000000000004,Curcuma-pseudomontana_S610:0.018982000000000013):0.0023249999999999937,Curcuma-scaposa_S611:0.022286999999999987):0.005963999999999997):0.006772,Curcuma-vamana_S622:0.028757999999999992):0.0017630000000000007,(((Curcuma-alismatifolia_S615:0.018096,Curcuma-sparganifolia_S617:0.021030999999999994):0.005356,Curcuma-parviflora_S616:0.022836999999999996):0.006651000000000004,Curcuma-roscoeana_S621:0.028563000000000005):0.0037559999999999955):0.005976999999999996,(((Curcuma-bicolor_S612:0.015473,Curcuma-glans_S614:0.013663999999999996):0.0042210000000000025,Curcuma-ecomata_S613:0.01661):0.008771000000000001,((Curcuma-singularis_S618:0.017321000000000003,Curcuma-pierreana_S628:0.019099000000000005):0.002824999999999994,Curcuma-vitelina_S619:0.022397):0.009614999999999999):0.005185999999999996):0.007817000000000005,Curcuma-angustifolia_S608:0.03911400000000001):0.009311,(Camptandra-ovata_S624:0.016479999999999995,Camptandra-latifolia_S623:0.01743):0.030655):0.004597000000000004,Pyrgophyllum-yunnanense_S627:0.041392):0.004258999999999999):0.016414,(Globba-variabilis_S626:0.04067799999999999,Globba-leucantha_S625:0.03737099999999999):0.01641400000000001);

input phylip:

47 50
Kaempferia-attapeuensis_S643 MGGGGAERWC VVTGGRGFAA RHLVEMLLRT DDWCVRVADL APSISLEAHE EAGVLGRALR
Curcuma-bicolor_S612 MGGGGAERWC VVTGARGFAA RHLVEMLLRT DDWCVRVADL APSISLEAHE EVGVLGRALR
Globba-variabilis_S626 MGGGGAERWC VVTGGRGFAA RHLVEMLLRT DDWCVRVADL APSISLEAHE EAGVLGRALR
Kaempferia-rotunda_S636 MGGGGAERWS VVTGGRGFAA RHLVEMLLRT DDWCVRVADL APSISLEAHE EAGVLGRALR
Kaempferia-xiengkhouangensis_S MGGGGAERWS VVTGGRGFAA RHLVEMLLRT DDWCVRVADL APSISLEAHE EAGVLGRALR
Curcuma-singularis_S618 MGGGGAERWC VVTGGRGFAA RHLVEMLLRT DDWCVRVADL APSISLEAHE EAGVLGRALR
Kaempferia-fissa_S642 MGGGGAERWC VVTGGRGFAA RHLVEMLLRT DDWCVRVADL APSISLEAHE EAGVLGRALR
Kaempferia-rotunda_S639 MGGGGAERWS VVTGGRGFAA RHLVEMLLRT DDWCVRVADL APSISLEAHE EAGVLGRALR
Kaempferia-sawanensis_S640 MGGGGAERWC VVTGGRGFAA RHLVEMLLRT DDWCVRVADL APSISLEAHE EAGVLGRALR
Curcuma-caulina_S609 MGGGGAERWC VVTGGRGFAG RHLVEMLLRT DDWCVRVADL APSISLEAHE EAGVLGRALR
Kaempferia-tomentosa_S638 MGGGGAERWC VVTGGRGFAA RHLVEMLLRT DDWCVRVADL APSISLEAHE EAGVLGRALR
Globba-leucantha_S625 MGGGGAERWC VVTGGRGFAA RHLVEMLLRT DDWCVRVADL APSISLEAHE EAGVLGRALR
Kaempferia-gigantiphylla_S645 MGGGGAERWC VVTGGRGFAA RHLVEMLLRT DDWCVRVADL APSISLEAHE EAGVLGRALR
Curcuma-sparganifolia_S617 MGGGGAERWC VVTGGRGFAA RHLVEMLLRT DDWCVRVADL APSISLEAHE EAGVLGRALR
Kaempferia-noctiflora_S632 -GGGGAERWS VVTGGRGFAA RHLVEMLLRT DDWCVRVADL APSISLEAHE EAGVLGRALR
Kaempferia-nemoralis_S651 MGGGGAERWC VVTGGRGFAA RHLVEMLLRT DDWCVRVADL APSISLEAHE EAGVLGRALR
Kaempferia-xiengkhouangensis_S MGGGGAERWC VVTGGRGFAA RHLVEMLLRT DDWCVRVADL APSISLEAHE EAGVLGRALR
Kaempferia-rupicola_S653 MGGGGAERWC VVTGGRGFAA RHLVEMLLRT DDWCVRVADL APSISLEAHE EAGVLGRALR
Curcuma-angustifolia_S608 MGGGGAERWC VVTGGRGFAA RHLVEMLLRS DDWCVRVADL APSISLEAHE EAGVLGRALR
Curcuma-glans_S614 MGGGGAERWC VVTGGRGFAA RHLVEMLLRT DDWCVRVADL APSISLEAHE EVGVLGRALR
Curcuma-parviflora_S616 MGGGGAERWC VVTGGRGFAA RHLVEMLLRT DDWCVRVADL APSISLEAYE EAGVLGRALR
Pyrgophyllum-yunnanense_S627 MGGGGAERWC VVTGGRGFAA RHLVEMLLRT DDWCVRVADL SPSISLEAHE EAGVLGRALR
Kaempferia-dasygyna_S650 MGGGGAERWC VVTGGRGFAA RHLVEMLLRT DDWCVRVADL APSISLEAHE EAGVLGRALR
Kaempferia-filifolia_S641 MGGGGAERWC VVTGGRGFAA RHLVEMLLRT DDWCVRVADL APSISLEAHE EAGVLGRALR
Camptandra-ovata_S624 MGGGGAERWC VVTGGRGFAA RHLVEMLLRT DDWCVRVADL APSISLEAHE EAGVLGRALR
Curcuma-vitelina_S619 MGGGGAERWC VVTGGRGFAA RHLVEMLLRT DDWCVRVADL APSISLEAHE EAGVLGRALR
Curcuma-roscoeana_S630 MGGGGAERWC VVTGGRGFAA RHLVEMHLFP VFW------- ---------- ----------
Kaempferia-fissa_S648 MGGGGAERWC VVTGGRGFAA RHLVEMLLRT DDWCVRVADL APSISLEAHE EAGVLGRALR
Curcuma-alismatifolia_S615 MGGGGAERWC VVTGGRGFAA RHLVEMLLRT NDWCVRVADL APSISLEAHE EAGVLGRALR
Kaempferia-fissa_S644 MGGGGAERWC VVTGGRGFAA RHLVEMLLRT DDWCVRVADL APSISLEAHE EAGVLGRALR
Kaempferia-fissa_S654 MGGGGAERWC VVTGGRGFAA RHLVEMLLRT DDWCVRVADL APSISLEAHE EAGVLGRALR
Kaempferia-lilacina_S635 MGGGGAERWC VVTGGRGFAA RHLVEMLLRT DDWCVRVADL APSISLEAHE EAGVLGRALR
Kaempferia-filifolia_S649 MGGGGAERWC VVTGGRGFAA RHLVEMLLRT DDLCVRVADL APSISLEAHE EAGVLGRALR
Curcuma-vamana_S622 MGGGGAERWC VVTGGRGFAA RHLVEMLLRT DDWCVRVADL APSISLEAHE EAGVLGRALR
Camptandra-latifolia_S623 MGGGGAERWC VVTGGRGFAA RHLVELLLRT DDWCVRVADL APSISLEAHE EAGVLGRALR
Curcuma-ecomata_S613 MGGGGAERWC VVTGGRGFAA RHLVEMLLRT DDWYVRVADL APSISLEAHE EVGVLGRALR
Kaempferia-subintegra_S647 MGGGGAERWC VVTGGRGFAA RHLVEMLLRT DDWCVRVADL APSISLEVHE EAGVLGRALR
Curcuma-pierreana_S628 MGGGGAERWC VVTGGRGFAA RHLVEMLLRT DDWCVRVADL APSISLEAHE EAGVLGRALR
Kaempferia-leucantha_S646 MGGGGAERWC VVTGGRGFAA RHLVEMLLRT DDWCVRVADL APSISLEAHE EAGVLGRALR
Curcuma-pseudomontana_S610 MGGGGAERWC VVTGGRGFAA RHLVEMLLRT DDWCVRVADL APSISLEAHE EAGVLGRALR
Curcuma-aeruginosa_S607 -GGGGAERWC VVTGGRGFAA RHLVEMLLRT DDWCVRVADL APSISLEAHE EAGVLGRALR
Curcuma-montana_S629 MGGGGAERWC VVTGGRGFAA RHLVEMLLRT DDWCVRVADL APSISLEAHE EAGVLGRALR
Kaempferia-fallax_S631 MGGGGAERWC VVTGGRGFAA RHLVEMLLRT DDWCVRVADL APSISLEAHE EAGVLGRALR
Curcuma-scaposa_S611 MGGGGAERWC VVTGGRGFAA RHLVEMLLRT DDWCVRVADL APSISLEAHE EAGVLGRALR
Kaempferia-fissa_S652 MGGGGAERWC VVTGGRGFAA RHLVEMLLRT DDWCVRVADL APSISLEAHE EAGVLGRALR
Kaempferia-galanga_S637 MGGGGAERWC VVTGGRGFAA RHLVEMLLRT DDWCVRVADL APSISLEAHE EAGVLGRALR
Curcuma-roscoeana_S621 -GGGGAERWC VVTGGRGFAA RHLVEMLLRT DDWCVRVADL APSISLEAHE EAGVLGRALR