Alexander Banguela Castillo - 2018-03-16

This is my command line to excec ksnp3: ./kSNP3 -in CoryInFile -outdir K_result2 -k 15
My parsimony tree is file is always empty (I runned it two times). Interesting I have this "consensus tree" (?), but never the parsimony tree. I am analyzing genomes of fungi from the same species.
Kspn3 runned for more than 30 h and use 150 Gbytes of my hdisk....
I will appreciate any help with this issue,
This is the las part of the log:

Consensus tree written to file "outtree"
Consensus tree program, version 3.696

Settings for this run:
C Consensus type (MRe, strict, MR, Ml): Majority rule (extended)
O Outgroup root: No, use as outgroup species 1
R Trees to be treated as Rooted: No
T Terminal type (IBM PC, ANSI, none): ANSI
1 Print out the sets of species: Yes
2 Print indications of progress of run: Yes
3 Print out tree: Yes
4 Write out trees onto tree file: Yes

Are these settings correct? (type Y or the letter for one to change)

Consensus tree written to file "outtree"

Output written to file "outfile"

Done.

number nodes 77
number new nodes 77
FastTree Version 2.1.3 SSE3, OpenMP (8 threads)
Alignment: SNPs_all_matrix.fasta
Nucleotide distances: Jukes-Cantor Joins: balanced Support: SH-like 1000
Start at tree from outtree.resolved (no NNI) (no SPR)
ML Model: Generalized Time-Reversible, CAT approximation with 20 rate categories
Pseudocount weight for comparing sequences with little overlap: 1.000
Total branch-length 2.415 after 98.02 secuences
1 rounds ML lengths: LogLk = -64433521.086 Max-change 0.2704 Time 575.30
GTR Frequencies: 0.2494 0.2573 0.2506 0.2427ep 12 of 12
GTR rates(ac ag at cg ct gt) 1.0226 1.8406 1.3403 0.8291 1.8386 1.0000
Switched to using 20 rate categories (CAT approximation)20 of 20
Rate categories were divided by 0.749 so that average rate = 1.0
CAT-based log-likelihoods may not be comparable across runs
2 rounds ML lengths: LogLk = -62615488.142 Max-change 0.1190 Time 5444.11
3 rounds ML lengths: LogLk = -62613799.899 Max-change 0.0325 Time 5945.53
4 rounds ML lengths: LogLk = -62613680.983 Max-change 0.0088 Time 6440.12
5 rounds ML lengths: LogLk = -62613663.177 Max-change 0.0037 Time 6934.68
Segmentation fault (core dumped)
Can't call method "get_leaf_nodes" on an undefined value at find_unresolved_clusters.pl line 16.
Qui Mar 15 20:47:00 -03 2018
Finding nodes
mv: No match.
mv: No match.
mv: No match.
Annotating SNPs.
Qui Mar 15 20:47:00 -03 2018
Traceback (most recent call last):
File "ParAnn.py", line 112, in <module>
IOError: [Errno 2] No such file or directory: 'genbank_from_NCBI.gbk'
Failed to execute script ParAnn
Finished running kSNP
Qui Mar 15 20:47:01 -03 2018
Elapsed time for kSNP in hours: 33.1988888888889