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geronimp / graftM

GraftM - Rapid community profiles from metagenomes
http://geronimp.github.io/graftM/
GNU General Public License v3.0
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Can't find FastTreeMP #258

Closed alexximalayaunlv closed 5 years ago

alexximalayaunlv commented 5 years ago

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 commented 5 years ago

Hi, what version of FastTree are you running?

On Feb 13 2019, at 1:13 pm, alexximalayaunlv notifications@github.com 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 (https://github.com/geronimp/graftM/issues/258), or mute the thread (https://github.com/notifications/unsubscribe-auth/AAA79NfVctoBW8vWIZn-vNwQCrkuaYIyks5vM58AgaJpZM4a4oBw).

alexximalayaunlv commented 5 years ago

I used FastTreeMP 2.1.9. Does that matter?

wwood commented 5 years ago

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 commented 5 years ago

Interesting! version 2.1.10 works! Thanks for your help!