Can't find FastTreeMP

[alexximalayaunlv]

Hi, I installed Fasttree and set several aliases in modulefiles. But when I run the code below, there is an error.
graftM create --output /tmp/my.gpkg --sequences 61_otus.fasta --taxonomy 61_otu_taxonomy.txt

                         GraftM 0.11.1

02/12/2019 09:08:53 PM ERROR: The following programs appear to be missing, and need to be updated or installed before GraftM can continue:
"02/12/2019 09:08:53 PM ERROR: FastTreeMP/FastTree http://www.microbesonline.org/fasttree/"

However, when I type command below, it seems fasttree is correctly installed (I also use the software to build a tree). It's really odd that graftm can't find the software.

"FastTreeMP -h
Unknown or incorrect use of option -h
FastTree protein_alignment > tree
FastTree < protein_alignment > tree
FastTree -out tree protein_alignment
FastTree -nt nucleotide_alignment > tree
FastTree -nt -gtr < nucleotide_alignment > tree
FastTree < nucleotide_alignment > tree..."

I need your help.. Thanks!!!

[wwood]

Hi, what version of FastTree are you running?

…

On Feb 13 2019, at 1:13 pm, alexximalayaunlv ***@***.***> wrote: Hi, I install Fasttree and set several aliases in modulefiles. But when I run the code below, there is an error. graftM create --output /tmp/my.gpkg --sequences 61_otus.fasta --taxonomy 61_otu_taxonomy.txt GraftM 0.11.1 02/12/2019 09:08:53 PM ERROR: The following programs appear to be missing, and need to be updated or installed before GraftM can continue: "02/12/2019 09:08:53 PM ERROR: FastTreeMP/FastTree http://www.microbesonline.org/fasttree/" However, when I type below, it seems fasttree is correctly installed (I also use the software to build a tree). It seems odd to me why graftm can't find the software. "FastTreeMP -h Unknown or incorrect use of option -h FastTree protein_alignment > tree FastTree < protein_alignment > tree FastTree -out tree protein_alignment FastTree -nt nucleotide_alignment > tree FastTree -nt -gtr < nucleotide_alignment > tree FastTree < nucleotide_alignment > tree..." I need your help.. Thanks!!! — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub (#258), or mute the thread (https://github.com/notifications/unsubscribe-auth/AAA79NfVctoBW8vWIZn-vNwQCrkuaYIyks5vM58AgaJpZM4a4oBw).

[alexximalayaunlv]

I used FastTreeMP 2.1.9. Does that matter?

[wwood]

It does seem to matter, apparently. Running FastTree -h with 2.1.9 fails, where on 2.1.10 it works.

GraftM would work with 2.1.9, except that the check procedure to make sure FastTree is present is causing problems.

Let me know if that doesn't work.
THanks, ben

[alexximalayaunlv]

Interesting! version 2.1.10 works! Thanks for your help!