Problem in Phylotyping step

[mherold1]

Hello,

I tried to install amphora2 today. Unfortunately during running the Phylotyping.pl script I get the following errors:

Phylotyping.pl -Method ml:

Can't call method "get_dup" on an undefined value at /opt/apps/resif/devel/v1.0-20150402/core/software/bio/BioPerl/1.6.1-ictce-5.3.0-Perl-5.16.3/lib/perl5/site_perl/5.16.3/Bio/DB/Taxonomy/flatfile.pm line 310, line 1.

In Phylotyping.pl this is probably from:
traverse($root, \%ref_taxon);(~L160)

and in sub traverse(... :
for ($node->each_Descendent) (~L205)

Phylotyping.pl -Method mp:

Cannot open RAxML_equallyParsimoniousPlacements.rplS at /home/users/mherold/TOOLS/AMPHORA2-master/Scripts/Phylotyping.pl line 108.

When I try to run the following system call from the shell, substituting the variables:
system ("$raxml -f y -t $AMPHORA_home/Marker/$marker.tre -s $marker.aln -m PROTGAMMAWAG -n $marker -p 132 1>/dev/null 2>/dev/null")

ERROR: Expecting ':' in tree; found: character ')'
08747-NC_011750:0.0)):1.4E-4,REF-YP_0023
RAxML may be expecting to read a tree that contains branch lengths
raxmlHPC: treeIO.c:1425: treeReadLen: Assertion `0' failed.
Aborted

Do you know what I could do to fix this? I thought this might be related to RAxML. I have tried versions 7.4.2 and 8.1.20, obtaining 7.3.0 was not possible anymore.
Any feedback would be appreciated.

Cheers,

Malte

[carlos88morais]

Same issue here.
$ Phylotyping
Can't call method "get_dup" on an undefined value at /usr/share/perl5/Bio/DB/Taxonomy/flatfile.pm line 336, <GEN0> line 1.
Using Bioperl 1.6.924