Question: FastTree running problem
gravatar for horsedog
2.1 years ago by
horsedog50 wrote:

Hi all, I'm using FastTree Version 2.1.10 SSE3 to do the phylogenetic analysis. But here I ran into a problem, it keeps giving me the error :

Amino acid distances: BLOSUM45 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: Jones-Taylor-Thorton, CAT approximation with 20 rate categories Ignored unknown character X (seen 3 times) Segmentation fault: 11

My file is big amino acids file, with more than 1000 sequence , 500 bps. I tried to put in

FastTree -out tree amino_rename.fasta;

FastTree amino_rename.fasta > tree;

FastTree -wag amino_rename.fasta > tree;

no one works, does anybody have idea?

software error • 1.3k views
ADD COMMENTlink modified 2.1 years ago by h.mon28k • written 2.1 years ago by horsedog50
gravatar for h.mon
2.1 years ago by
h.mon28k wrote:

X is code for an unknown aminoacid at that position, and apparently FastTree doesn't like X. Remove the sequences which have X and try again.

ADD COMMENTlink written 2.1 years ago by h.mon28k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2015 users visited in the last hour