Closed itiago closed 7 years ago
Have donwloaded 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
This is a CheckM question.
matsen
commented
7 years ago matsen
commented
7 years ago
Have donwloaded 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