tree_dir/tree.nw does not exist

[shuifeng1988]

  I have completed the installation of the Docker-CarineRey/pcoc and downloaded the data files (ali.fa and tree_dir/tree.nw). But  when i run the command, "sudo $CMD_PCOC_DOCKER pcoc_num_tree.py -t /home/shuifeng/Git/pcoc/example/tree_dir/tree.nw -o num_tree.pdf", it shows the tree_dir/tree.nw not exist whether used the relative path or absolute file. 

(base) [shuifeng@localhost PCOC_docker]$ sudo $CMD_PCOC_DOCKER pcoc_num_tree.py -t /home/shuifeng/Git/pcoc/example/tree_dir/tree.nw -o num_tree.pdf
Working directory : /home/shuifeng/Git/pcoc/example
User / docker
Starting with UID : 1000
/home/shuifeng/Git/pcoc/example/tree_dir/tree.nw does not exist
(base) [shuifeng@localhost PCOC_docker]$ sudo $CMD_PCOC_DOCKER pcoc_num_tree.py -t tree_dir/tree.nw -o num_tree.pdf
Working directory : /home/shuifeng/Git/pcoc/example
User / docker
Starting with UID : 1000
tree_dir/tree.nw does not exist
(base) [shuifeng@localhost PCOC_docker]$ ll tree_dir/tree.nw
-rw-rw-r--. 1 shuifeng shuifeng 3180 Jul 18 17:27 tree_dir/tree.nw
(base) [shuifeng@localhost PCOC_docker]$ sudo $CMD_PCOC_DOCKER pcoc_num_tree.py -t ENSG00000001626_CFTR.txt -o num_tree.pdf
Working directory : /home/shuifeng/Git/pcoc/example
User / docker
Starting with UID : 1000
ENSG00000001626_CFTR.txt does not exist

[Wenfei-Xian]

Hi,
I also meet this error ,have you solved this ?

[CarineRey]

Hi,

Thank you for report this error but I can't reproduce it on my computer.
Can you bring more details ? For example, how do you define CMD_PCOC_DOCKER ? Did you change of directory between its definition and its usage ?

[milesroberts-123]

Hello, I ran into this same issue using singularity. Here are the exact commands I ran to generate the error.

#get the PEPC protein alignment for sedges (plant species at C3/C4 transition), and rename this alignment with shorter name
wget  https://raw.githubusercontent.com/CarineRey/pcoc/master/data/det/cyp_coding.aa.coor_mays.fa
mv cyp_coding.aa.coor_mays.fa ali.fa

#get the corresponding tree, rename it and move it to a new folder
mkdir -p tree_dir
wget https://raw.githubusercontent.com/CarineRey/pcoc/master/data/det/cyp_coding.phy_phyml_tree.txt -P tree_dir
mv tree_dir/cyp_coding.phy_phyml_tree.txt tree_dir/tree.nw

# pull software
singularity pull docker://carinerey/pcoc

# print help command, this works as expected 
singularity exec ./pcoc_latest.sif pcoc_num_tree.py -h

# number tree
singularity exec ./pcoc_latest.sif pcoc_num_tree.py -t tree_dir/tree.nw -o num_tree.pdf

The output I get from the last line is simply tree_dir/tree.nw does not exist even though I can see that it clearly does exist. I tried typing in the absolute file path instead of the relative path, but that generated the same error.

Any help you can provide would be greatly appreciated! I hope this repo is still maintained because I saw it was updated in Dec. 2021. It would be a shame if not, because this tool seems really useful!

I generated this error with PCOC v1.1.0