OMA standalone error during database conversion step: Matches between X/X have been computed for different versions of X.

Question

[Silvia Prieto]

I keep getting the error: 'Matches between CHICK/CHICK have been computed for different version of CHICK’ in the log file when I compute the database conversion step in OMA standalone ( oma_part1 at: https://lab.dessimoz.org/blog/media/2020/04/omastandalone_cheat_sheet.pdf). There is only one CHICK.fa file in the DB folder and everything looks right to me.

[Silvia Prieto]

The error generated because I copied and pasted the OMA standalone folder from a previous run, deleted all the visible files (DB folder files, logs, Cache and Output) and then included the new proteomes of interest in the DB folder. As well as these, there are other files, which are generated when running OMA, that are not so obvious but must be also deleted in this case. These are the build/ folder inside the hog_bottom_up/ folder and the hidden folder .venv/. To solve this, I ran the following commands from the main OMA standalone folder: rm -rf .venv/ and rm -rf hog_bottom_up/build/.

Answer 1

[Adrian Altenhoff]

Hi Silvia,

yes, if you don't install OMA Standalone but simply run it from an extracted tarball, you must be careful whenever you copy the folder and recycle it for a new analysis. OMA Standalone relies on some python modules which are stored in a hidden directory (.venv). This directory contains absolute path variables, so if you remove the orgininal analysis folder, things may break brutally.

Note that if you install OMA Standalone with the install.sh script, you can generate a new parameter file with oma -p in the current directory. This might be easier than copy and removing an existing tarball back and forth.

Best Adrian