CheckM/gtdb-tk tables?

[bcpd]

Hi - It would be awesome if nanophase allowed for an option to keep the outputs of checkm (run with -tab_table) and gtdb -- i.e. the gtdbtk.*summary.tsv files. Both are useful for downstream applications. It also looks like the final genome.summary table doesn't display species-level information or other useful pieces of information such as ANI, etc.

[Hydro3639]

Thanks for your suggestion. I have revised the nanophase meta script so that checkm and gtdbtk results were kept in the final output (_path_tooutput/03-Polishing/checkm-result and _path_tooutput/03-Polishing/gtdbtk-result). The new features will be included in the next conda release (together with other new upgrades, e.g., checkm1 -> checkm2), but, currently, I would suggest to replace nanophase.meta script with the new one following the instruction below:

1) conda activate nanophase ## activate nanophase env
2) wget https://raw.githubusercontent.com/Hydro3639/NanoPhase/main/bin/nanophase.meta -O $(which nanophase.meta) && chmod +x $(which nanophase.meta)

If you want to generate the above-mentioned results, please remove the folder of path_to_output/03-Polishing/Final-bins and the file of path_to_output/03-Polishing/nanophase.ont.genome.summary or path_to_output/03-Polishing/nanophase.hybrid.genome.summary; then re-run the same command. Please let me know if you need more help.

[bcpd]

Great - thank you.

[bcpd]

Thanks again for the updates. I did run into the following issue (it was not happening with v. 0.2.2): fastANI: error while loading shared libraries: libopenblas.so.0: cannot open shared object file

This is a fairly generic error with not straightforward solution. Have you seen this?

[Hydro3639]

Sorry to hear you have such an error.

Exactly, I have seen this once on one of our servers before. I am not sure if you can try installing libopenblas-base using command: sudo apt-get install libopenblas-base (require sudo). You can simply check by "fastANI -h" to see if you still have this error.

If it cannot solve your issue or you do not have sudo permission, you may uninstall fastANI and re-install it manually. (Sorry for all these manually things)

## remove fastANI
rm -rf $(which fastANI)
## download fastANI binary file
wget https://github.com/ParBLiSS/FastANI/releases/download/v1.33/fastANI-Linux64-v1.33.zip
## unzip
unzip -d $(dirname $(which nanophase)) fastANI-Linux64-v1.33.zip
## check
fastANI -h

Please let me know if it works.

[bcpd]

Installing the library (within the environment) worked; thank you! (The checkm-result folder does not have the checkm_results.tsv file, however; is it stored somewhere else?)

[Hydro3639]

Good to hear you have fixed this error.

If you want to have the full result of checkm, it is quite easy to re-generate it using the following command as you have checkm-result folder

checkm qa checkm-result/lineage.ms checkm-result/

It should be finished in 1-2 mins. I have revised the nanophase meta script, and you can update it as described above, then you don't need to re-run this qa command manually in the next time. And the checkm_results.tsv file should be in checkm-result folder.

[bcpd]

Excelent - thank you.