No newick file

[Dabiguina94]

Hi! I'm having problems with the generation of the newick file with FastTree, I wrote the next command:

FastTree -nt -gtr roaryresult/core_gene_alignment.aln > roaryresult/mytree.newick

and I have this answer:

FastTree Version 2.1.11 Double precision (No SSE3) Alignment: roaryresult/core_gene_alignment.aln Nucleotide distances: Jukes-Cantor Joins: balanced Support: SH-like 1000 Search: Normal +NNI +SPR (2 rounds range 10) +ML-NNI opt-each=1 TopHits: 1.00*sqrtN close=default refresh=0.80 ML Model: Generalized Time-Reversible, CAT approximation with 20 rate categories Initial topology in 24.29 secondshits for 1 of 34 seqs
Refining topology: 20 rounds ME-NNIs, 2 rounds ME-SPRs, 10 rounds ML-NNIs Total branch-length 0.067 after 279.50 sec 1 of 32 splits
ML-NNI round 1: LogLk = -4294141.116 NNIs 8 max delta 2413.17 Time 461.72 GTR Frequencies: 0.2964 0.1899 0.2146 0.2992ep 12 of 12
GTR rates(ac ag at cg ct gt) 1.1495 4.9822 0.9215 0.9770 7.1425 1.0000 Switched to using 20 rate categories (CAT approximation)20 of 20
Rate categories were divided by 0.644 so that average rate = 1.0 CAT-based log-likelihoods may not be comparable across runs Use -gamma for approximate but comparable Gamma(20) log-likelihoods ML-NNI round 2: LogLk = -4084497.611 NNIs 1 max delta 0.00 Time 2152.76 Turning off heuristics for final round of ML NNIs (converged) ML-NNI round 3: LogLk = -4084497.534 NNIs 0 max delta 0.00 Time 2481.43 (final) Optimize all lengths: LogLk = -4084497.534 Time 2580.40 Terminado (killed)

but the newick file is empty!

I haven't had this problem before, I hope you can help me, please

Dafne

[ldipotetjob]

Hi @Dabiguina94 we're facing to the same problem, do you have any clue about the solution? best regards, luis D.

[ldipotetjob]

The problem is the RAM or CPUs, so the system kills the process. You can review the documentation to check the RAM needed for an specific number of CPUs .