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amnh / PCG

𝙋𝙝𝙮𝙡𝙤𝙜𝙚𝙣𝙚𝙩𝙞𝙘 𝘾𝙤𝙢𝙥𝙤𝙣𝙚𝙣𝙩 𝙂𝙧𝙖𝙥𝙝 ⸺ Haskell program and libraries for general phylogenetic graph search
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Dynamic character re-rooting error #159

Open Boarders opened 5 years ago

Boarders commented 5 years ago

When running pcg-test-flu-net with the following script:

read("flu_small_hxnx_hsa_seg1_PB2.fasta")
read("flu_small_hxnx_hsa_seg2_PB1.fasta")       
read("flu_small_hxnx_hsa_seg3_PA.fasta")
read("flu_small_hxnx_hsa_seg4_HA.fasta")
read("flu_small_hxnx_hsa_seg5_NP.fasta")
read("flu_small_hxnx_hsa_seg6_NA.fasta")
read("flu_small_hxnx_hsa_seg7_MP.fasta")
read("flu_small_hxnx_hsa_seg8_NS.fasta")
read("flu_small_poy_edges.tre")
build(1,network)
report(data,("output.data",overwrite))

it begins by adding a number of network edges but then gives the error:

pcg: Could not find one or more of the contexts:
...
CallStack (from HasCallStack):
  error, called at pcg-data-structures/src/Bio/Graph/PhylogeneticDAG/DynamicCharacterRerooting.hs:187:40 in pcg-core-0.2.0-7FaigluLazHH41lWpzuBkf-pcg-data-structures:Bio.Graph.PhylogeneticDAG.DynamicCharacterRerooting

It is not immediately clear where the source of the error is.