RepeatClassifier error "No database indicated or it is an empty file."

[kdarragh1994]

I ran RepeatModeler and got consensi.fa and families.stk files. There was an error in the installation which prevented the final classification step so I wanted to re-run RepeatClassifier on the output files to classify them for RepeatMasker use.

I ran RepeatClassifer using singularity like this: singularity exec /N/slate/kdarrag/programs/dfam-tetools-latest.sif RepeatClassifier -consensi consensi.fa -stockholm families.stk

The only error message was "No database indicated or it is an empty file." However neither consensi.fa nor families.stk are empty.

Thank you for your help. Kathy

[asgray]

It seems to be working for me. I built the sandbox image tetools and was able to run RepeatClassifier successfully.

singularity exec tetools RepeatClassifier -consensi ../../scratch/test_data/example.fa -stockholm ../../scratch/test_data/fam-small.stk 
perl: warning: Setting locale failed.
perl: warning: Please check that your locale settings:
        LANGUAGE = (unset),
        LC_ALL = (unset),
        LC_CTYPE = "en_US.UTF-8",
        LANG = "C"
    are supported and installed on your system.
perl: warning: Falling back to the standard locale ("C").
RepeatClassifier Version 2.0.5
======================================
  - Looking for Simple and Low Complexity sequences..
  - Looking for similarity to known repeat proteins..
  - Looking for similarity to known repeat consensi..

Are you able to include the complete output message?

A few things to try:

• Singularity automatically binds in your current working directory, so relative file paths could work ex:./consensi.fa if its located where you're running the command
• If that doesn't work, can you confirm your working directory is visible from inside the container? Running these commands should show you the contents of your working directory, but there may be permission issues. singularity shell /N/.../dfam-tetools-latest.sif ls -al

[kdarragh1994]

The error message states "No database indicated or it is an empty file." and then shows the options for running Repeatclassifier. I tried with ./consensi.fa and it didn't work. I think you are right that it is an issue with the directories because I do not see my working directory when I follow the second step. What can I do to resolve this?

[asgray]

Singularity binds your working directory into the container by default (as described here), so it's likely that your admins (I assume you have admins) have disabled that feature for their own reasons. You might be able to make the binding by hand with singularity exec -B $PWD /.../container.sif <args>, but if that doesn't work you'll need to work with whoever is in charge of your system.

[kdarragh1994]

That worked, thank you!