Getting taxit to work for build_marker mode

Tried installing taxtastic today to get taxit to work for build_marker mode. Still having problems.

Followed all the instructions here: https://github.com/fhcrc/taxtastic/blob/master/INSTALL.rst

And after that I can get taxit to give me the help info when i run taxit -h

Buuuut, now when I try to run PhyloSift Build Marker mode, I’m getting this error message:

Uncaught exception: Failure(“‘U’ not a known base in 000000000!”)
Fatal error: exception Failure(“‘U’ not a known base in 000000000!”)
Unable to read from /Users/hollybik/share/phylosift/markers/xeno_18S_SSUalign.eukarya/xeno_18S_SSUalign.eukarya.tmpread.jplace at /Users/hollybik/Desktop/PhyloSift/phylosift_devel_20120824/bin/../lib/Phylosift/Utilities.pm line 92
Phylosift::Utilities::ps_open(‘/Users/hollybik/share/phylosift/markers/xeno_18S_SSUalign.euk…’) called at /Users/hollybik/Desktop/PhyloSift/phylosift_devel_20120824/bin/../lib/Phylosift/MarkerBuild.pm line 383
Phylosift::MarkerBuild::jplace_mangler(‘in’, ‘/Users/hollybik/share/phylosift/markers/xeno_18S_SSUalign.euk…’, ‘out’, ‘/Users/hollybik/share/phylosift/markers/xeno_18S_SSUalign.euk…’) called at /Users/hollybik/Desktop/PhyloSift/phylosift_devel_20120824/bin/../lib/Phylosift/MarkerBuild.pm line 139
Phylosift::MarkerBuild::build_marker(‘self’, ‘Phylosift::Phylosift=HASH(0x7f8c14003ea0)’, ‘alignment’, ‘/Users/hollybik/Desktop/PhyloSift/xeno_18S_search/xeno_18S_SS…’, ‘cutoff’, 0.01, ‘force’, 1, ‘mapping’, …) called at /Users/hollybik/Desktop/PhyloSift/phylosift_devel_20120824/bin/../lib/Phylosift/Phylosift.pm line 263
Phylosift::Phylosift::run(‘Phylosift::Phylosift=HASH(0x7f8c14003ea0)’, ‘force’, 1, ‘custom’, ”, ‘cont’, 0) called at bin/phylosift line 196

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