Naibin
commented
1 year ago the next steps will fix this error 1 unzip everything in the "example_data" folder. sometimes it is difficult to unzip bgz files on Linux . simply download it at https://bx.bio.jhu.edu/data/panagram/example_data.zip on Windows, decompress the package , and upload the whole folder to the root of panagram on Linux server.
2 in the example_data directory , run "panagram index conf.toml"
3 ls anchor/ ecoli.100.bgz ecoli.100.gzi ecoli.1.bgz ecoli.1.gzi ecoli_K12.100.bgz ecoli_K12.100.gzi ecoli_K12.1.bgz ecoli_K12.1.gzi klebsiella.100.bgz klebsiella.100.gzi klebsiella.1.bgz klebsiella.1.gzi salmonella.100.bgz salmonella.100.gzi salmonella.1.bgz salmonella.1.gzi shigella.100.bgz shigella.100.gzi shigella.1.bgz shigella.1.gzi You will find a list of genomes. ecoli, klebsiella,salmonella,shigella is the genome parameter. and there is no "kakabo" ! 4 vim /site-packages/panagram/view.py file change kakapo to 'ecoli' also you can change it to "lebsiella","salmonella","shigella" [dsfsdfsdf example_data]$ panagram view . Dash is running on http://127.0.0.1:8050/
- Serving Flask app 'panagram'
- Debug mode: on it is ok now.
next step for me is to let the service public , and running other than localhost.
I have successfully git and installed panagram. then I downloaded example data , panagram index conf.toml ------------------------this step is ok
[fsdfdsf example_data]$ panagram view . Traceback (most recent call last): File "/home/naibin/.local/bin/panagram", line 8, in
sys.exit(main())
File "/home/naibin/.local/lib/python3.9/site-packages/panagram/main.py", line 122, in main
args.main.run()
File "/home/naibin/.local/lib/python3.9/site-packages/panagram/main.py", line 107, in run
return self.cmd.run()
File "/home/naibin/.local/lib/python3.9/site-packages/panagram/main.py", line 60, in run
view(self)
File "/home/naibin/.local/lib/python3.9/site-packages/panagram/view.py", line 1081, in view
for i in range(1, num_chrs[anchor_name]+1):
KeyError: 'kakapo'
I found a Kakapo-related error, and I installed Kakapo.
[affdsfsfdt example_data]$ kakapo Kakapo version: 0.9.4 Python version: 3.9.13 Operating system: Fedora 34 System info: 40 physical and 80 logical cores, 472.26 GB RAM (x86_64)
Configuration file was not provided. Nothing to do.
usage: kakapo --cfg project_configuration_file --ss search_strategies_file
optional arguments: --cfg path Path to a kakapo project configuration file. --ss path Path to a kakapo search strategies file. --ncpu count Number of CPUs to use. --stop-after-filter Stop kakapo after Kraken2/Bowtie2 filtering step. --force-deps Force the use of kakapo-installed dependencies, even if they are already available on the system. --install-deps Install kakapo dependencies and quit. --dnld-kraken-dbs Download Kraken2 databases and quit. --clean-data-dir Remove cached NCBI taxonomy data and all software dependencies downloaded by kakapo. -v, --version Print kakapo version. -h, --help Print kakapo help information.
kakapo in just an example of a genome.