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RepeatModeler:Input has potential formatting error

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: enter image description here

This is the first 5 lines of fasta genome assembly: enter image description here

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!

assembly
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updated by tothepoint tothepoint • written by slin023 • slin023

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.

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written by tothepoint tothepoint

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

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written by slin023 • slin023

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

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written by lieven.sterck lieven.sterck

1 answer

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?

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written by lieven.sterck lieven.sterck

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