LiftOff error

[GabrieleRigano99]

Hi, thank you for the amazing tool! I am getting an error with the LiftOff process using singularity. singularity run TrEMOLO.simg snakemake --snakefile run.snk --configfile config.yaml could you help me out please? thank you! Snakefile_outsider.log Snakefile_outsider.err.txt LIFT_OFF.err.txt

[M-D75]

Hi,

Do you have the same problem with the test dataset?

If not, could you run the following commands and let me know the results:

singularity exec TrEMOLO.simg liftoff

singularity exec TrEMOLO.simg python

import numpy as np
print(np.__version__)
np.int

Do you encounter any errors when running the above commands ?

Best, M-D

[GabrieleRigano99]

Hi, thanks for the reply! The test works perfectly. singularity exec TrEMOLO.simg liftoff /home/gab/Schenckii/Final_schenckii_project/SVs2/INPUT/SS02_cactus.fa /home/gab/Schenckii/Final_schenckii_project/SVs2/INPUT/SS01_cactus.fa -g ~/Schenckii/Final_schenckii_project/SVs2/OUTSIDER/INSIDER_VR/INOUTSIDER.gff -f list_liftoff liftoff asks for a list of types of features to lift, so i made it and it worked. (repeat_element)

singularity exec TrEMOLO.simg python Python 3.8.10 (default, Nov 22 2023, 10:22:35) [GCC 9.4.0] on linux My version of numpy in conda is 1.21.1 Thanks!

[M-D75]

Hi,

OK, thank you. I believe I have identified the problem. Please wait until Tuesday, I will make an update that you can test.

Best, M-D

[M-D75]

Hi,

Updated on a new branch.

Command to fetch the update:

git clone -b fix_issue_23 https://github.com/DrosophilaGenomeEvolution/TrEMOLO.git

However, you should rebuild the Singularity container with this update.

sudo singularity build TrEMOLO.simg TrEMOLO/Singularity

I have a question though: did you build the previous container yourself, or did you download the one available here?

Best, M-D