No ancestry ancestry_edge_list.txt file output #8
Description
Hello,
Thank you for working on this tool! I was able to run it successfully on some of my own Smart-Seq2 data, but the final output contained only the Amatrix, Umatrix, and clone_tree_edge_list.txt outputs, not the ancestry_edge_list.txt. Does this indicate that a portion of the pipeline failed? The only warnings I received were:
/Users/jayzussman/Dissertation/Bioinformatics/mtDNA_variant_calling/merlin/MERLIN/src/merlin.py:57: RuntimeWarning: invalid value encountered in divide vaf1 = mut1_vars / mut1_tot /Users/jayzussman/Dissertation/Bioinformatics/mtDNA_variant_calling/merlin/MERLIN/src/merlin.py:58: RuntimeWarning: invalid value encountered in divide vaf2 = mut2_vars / mut2_tot
and the output message was:
`Cutting planes:
Learned: 3
Gomory: 1
Cover: 6
Implied bound: 14
MIR: 18
Flow cover: 32
Zero half: 2
RLT: 2
BQP: 1
Explored 26 nodes (9688 simplex iterations) in 14.05 seconds (21.34 work units)
Thread count was 1 (of 14 available processors)
Solution count 10: 3.25431 3.25431 3.25431 ... 3.99279
Optimal solution found (tolerance 1.00e-04)
Best objective 3.254308778022e+00, best bound 3.254067194610e+00, gap 0.0074%`
Should I be concerned about this behavior, or is there another explanation for the lack of the ancestry_edge_list.txt file?