kalan-lab / lsabgc Goto Github PK

While testing lsaBGC on multiple macs and unix systems tends to work as expected, there are rare instances where R ends up not being properly setup in the conda environment resulting in figures not being produced. The final spreadsheet should still be produced in these cases because R is only used for plotting and visualization.

For GSeeF & lsaBGC-See resulting directories will also contain newick trees + iTol tracks for alternative visualization using the iTol webserver.

Future aims

• Develop a Docker container for the lsaBGC-Easy.py and lsaBGC-Euk-Easy.py worfklows
• Might also try to tinker the yaml file to set more flexible dependency version requirements to allow conda to properly install R in these environments where it is failing.

I installed and attempted to run run tests.sh, but the final plots in the see folder were not pdf files, but rather text files with values.

Hello @raufs,

I am using lsaBGC, and I have encountered a few issues that I need a little help with. The same issues have occurred on my UNIX (Macbook) and Ubuntu (remote machine).

Here are the issues I am facing:

1. I am having trouble downloading annotations through setup_annotation_dbs.py after TIGR04571.1.HMM. I've tried a few times with always the same issue

x hmm_PGAP.HMM/TIGR04571.1.HMM
Error: issues with downloading or seting up annotation database files! Please post to Github issues if unable to figure out!

2. When running lsaBGC-EASY.py I get an error message at step 5. I added a print statement above the error line and it looks like it's not creating Primary_Sample_Annotation_Files.txt. I've had a dig around in lsaBGC-Ready.py and potentially this is an issue arising from the code block from line 453 but it's slightly beyond my abilities

Checking file path: /home/samw/lsaBGC/lsaBGC_for_Kitasatospora/lsaBGC_Ready_Results/Final_Results/Primary_Sample_Annotation_Files.txt
Traceback (most recent call last):
  File "/home/samw/lsaBGC/workflows/lsaBGC-Easy.py", line 722, in runCmdViaSubprocess
    assert (os.path.isfile(cf))
AssertionError
.......
RuntimeError: Had an issue running: lsaBGC-Ready.py -i /Users/sw17073/lsaBGC/lsaBGC_for_Kitasatospora/Primary_Genomes.txt -l /Users/sw17073/lsaBGC/lsaBGC_for_Kitasatospora/BGCs_in_Primary_Genomes.txt -o /Users/sw17073/lsaBGC/lsaBGC_for_Kitasatospora/lsaBGC_Ready_Results/ -c 8 -p GECCO -m GENOME_WIDE -lc -lci 4.0 -lcj 20.0 -lcr 0.7 -a

Please let me know if you need any further information or if there's something I can try on my end to resolve these issues.

Thanks,
Sam

Nice to meet you!
I would like to use this software, but the following error is preventing me from using it. Please let me know the solution.

setup_annotation_dbs.py
Error: Provided directory for downloading annotation files does not exist!
Error: issues with downloading or seting up annotation database files! Please post to Github issues if unable to figure out!