RepeatModeler:Input has potential formatting error

Question

[slin023]

Greeting, I have followed this guide. So far I have configured all the required tools, but when I build database as first step (/home/slin023/RepeatModeler-2.0.1/BuildDatabase -name Phormia /home/slin023/asm.contigs.fasta )this is the error I ran into:

This is the first 5 lines of fasta genome assembly:

Did I do something wrong with the command? Or do I need to do additional steps to fix the format? Any advice or suggestion is welcomed, thank you for your time!

[tothepoint]

I am not sure if this is version issue but I have seen similar error in RepeatModeler-2.0.1 but able to build database using RepeatModeler-2.0 version.

[slin023]

I figured it out. RepeatModeler is looking for path to "makeblastdb", but it's inside the /bin, so you either copy to /rmblast-2.10.0/ or transfer the files from ~/rmblast-2.10.0/bin to ~/rmblast-2.10.0

[lieven.sterck]

you can also (and perhaps even better approach) include the path to the binary files in your $PATH variable.

Answer 1

[lieven.sterck]

long shot, but did you check whether you still have storage space available?

and that the blast binaries (rmblast in this case) are OK installed? and available from where you execute the repeatmodeler tool?