difficulties with pplacer in CheckM.

[itiago]

I cannot use CheckM since it cannot "find" pplacer...

I have downloaded pplacer-Linux-v1.1.alpha17.zip, unziped and runned : "python setup.py install" then set path:

sudo nano /etc/bash.bashrc export PATH=$PATH:/home/igor/CheckM/pplacer-Linux-v1.1.alpha17/pplacer export PATH=$PATH:/home/igor/CheckM/pplacer-Linux-v1.1.alpha17/guppy export PATH=$PATH:/home/igor/CheckM/pplacer-Linux-v1.1.alpha17/rppr

sudo nano /home/igor/.bashrc export PATH=$PATH:/home/igor/CheckM/pplacer-Linux-v1.1.alpha17/pplacer export PATH=$PATH:/home/igor/CheckM/pplacer-Linux-v1.1.alpha17/guppy export PATH=$PATH:/home/igor/CheckM/pplacer-Linux-v1.1.alpha17/rppr

sudo nano /etc/profile

export PATH=$PATH:/home/igor/CheckM/pplacer-Linux-v1.1.alpha17/pplacer export PATH=$PATH:/home/igor/CheckM/pplacer-Linux-v1.1.alpha17/pplacer/scripts export PATH=$PATH:/home/igor/CheckM/pplacer-Linux-v1.1.alpha17/guppy export PATH=$PATH:/home/igor/CheckM/pplacer-Linux-v1.1.alpha17/rppr

THEN runned CheckM:

"igor@ubuntu:~/metaBAT/bin/AC3_ANVIo_metaBat_bining/CheckM_results$ checkm lineage_wf -x fa /home/igor/metaBAT/bin/AC3_ANVIo_metaBat_bining /home/igor/metaBAT/bin/AC3_ANVIo_metaBat_bining/CheckM_results/

[CheckM - tree] Placing bins in reference genome tree.

Identifying marker genes in 45 bins with 1 threads: Finished processing 45 of 45 (100.00%) bins. Saving HMM info to file.

Calculating genome statistics for 45 bins with 1 threads: Finished processing 45 of 45 (100.00%) bins.

Extracting marker genes to align. Parsing HMM hits to marker genes: Finished parsing hits for 45 of 45 (100.00%) bins. Extracting 43 HMMs with 1 threads: Finished extracting 43 of 43 (100.00%) HMMs. Aligning 43 marker genes with 1 threads: Finished aligning 43 of 43 (100.00%) marker genes.

[Error] Make sure pplacer is on your system path.

Controlled exit resulting from an unrecoverable error or warning. "

Could you please help? Thank you

[donovan-h-parks]

You need to put pplacer on your system path. You can find detailed information on how to do this at: http://www.troubleshooters.com/linux/prepostpath.htm

[itiago]

Hi but I did: I added:

this: export PATH=$PATH:/home/igor/CheckM/pplacer-Linux-v1.1.alpha17/pplacer export PATH=$PATH:/home/igor/CheckM/pplacer-Linux-v1.1.alpha17/guppy export PATH=$PATH:/home/igor/CheckM/pplacer-Linux-v1.1.alpha17/rppr

to the three files: bash.bashrc, .bashrc, profile by editing them using:

sudo nano /etc/bash.bashrc sudo nano /home/igor/.bashrc sudo nano /etc/profile

isn't this the correct way to do it? Thanks

[donovan-h-parks]

Hello. You need to log in and out of your terminal for the .bashrc script to be re-executed. Once pplacer is correctly on your path, you will be able to type pplacer -h to bring up its help menu.

[itiago]

Hi, if I do that, nothing happens, If I go to pplacer folder the same, but if I write ./pplacer -h it gives me the menu. I don't think i was able to install pplacer. I've runned the "python setup.py install" command on the pplacer/scripts folder, but still..... Could you please advise me on how to install pplacer properly? Thanks

[donovan-h-parks]

I think the problem is that your system path should only point to the directory containing pplacer and not the executable file itself. Try adding the following to your .bashrc file: export PATH=$PATH:/home/igor/CheckM/pplacer-Linux-v1.1.alpha17/

Remember that you need reload your .bashrc file before this will take effect. Easiest way to do this is to simply log off your system and log back in.

[itiago]

THANK YOU! CheckM was able to fetch pplacer! waiting for results ;)

Appreciated your help! Best

[donovan-h-parks]

Excellent. Glad it is working!