HMMER3

[davidmadariaga]

Hi. Hope you are doing great!., could you help me please? what does this means? where should i install HMMER3? sorry for being this dumb, i really doesnt know about this kind of things. I just installed it from source, using mamba, following the instructions on github. I'd be really thankful if you answer me, whenever you can. Cheers from Chile, South America.

[samhorsfield96]

Hi David,

I just need a few bits of information to help with debugging:

• What command did you run using ggCaller?
• What is the output when you run hmmscan -h?
• What is the output when you run mamba list? If this is too large, you can save this to a file using mamba list > mamba_list.txt and send the file across.

[davidmadariaga]

Hi, thanks for answering, you are very kind!

I first wrote this command on a server: nohup ggcaller --refs input.txt --threads 50 &. The nohup.out file contains this: (base) [mdavid@soroban IMSAR217cc11]$ cat nohup.out Building coloured compacted DBG... Generating graph stop codon index... Mapping contigs to graph... Need HMMER3 to be installed and available in PATH
Downloading databases...

Building coloured compacted DBG... Generating graph stop codon index... Mapping contigs to graph... Need HMMER3 to be installed and available in PATH

then i installed ggcaller on my laptop, and then i run it using ggcaller --refs input.txt --threads 5. It ended up giving me the same message "Need HMMER3 to be installed and available in PATH ".

This is what appears when i write hmmscan -h:

And this when i write mamba list: mambalist.txt

Thanks again, in advance.

Cheers

[samhorsfield96]

Hi David, thanks for sending all of this information through. This was very helpful, I was able to identify the issue (it was due to an update to HMMER3), this is now fixed in commit 1d85587. Please update to the latest commit and rerun python setup.py install