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I am trying to run a program called TEBreak, which detects genetic elements within a genome. However, I keep running into this warning message whenever I run it:

Warning: could not lastdb -4G /tmp/tebreak.concat.fa.b745d57e-0363-4bab-9a48-2aebf31ffd25.fa /tmp/tebreak.concat.fa.b745d57e-0363-4bab-9a48-2aebf31ffd25.fa

Warning: no lastdb index for /tmp/tebreak.concat.fa.b745d57e-0363-4bab-9a48-2aebf31ffd25.fa

What does this mean exactly, and is it a problem with the temp files, or lastdb?

The link to the python script for the program is here: https://github.com/adamewing/tebreak/blob/master/tebreak/tebreak.py

I searched the script for the error messages:

enter image description here

I did contact the author of the program, who suggested this:

The lastdb problem might be due to a missing prerequisite, sorry there are several of those... try running 'lastdb' by itself to see if it's on the system.

I have checked and lastdb is installed, but I can't find the version info - would this make a difference?

Could anyone shed some light on this error, and what I could do to correct it.

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The errors occurs because python's os.path.exists(path) function returns False.

According to documentation there could 2 reasons:

os.path.exists(path)

Return True if path refers to an existing path or an open file descriptor. Returns False for broken symbolic links. On some platforms, this function may return False if permission is not granted to execute os.stat() on the requested file, even if the path physically exists.


1) check if your *.db and *.tis files have consistent symbolic links

2) check read/execute permissions on the above files

  • Thank you. How would I go about checking the *.db and *.tis files? – Roxane Dunbar Oct 25 '17 at 14:34
  • if you know the exact filenames - start with searching/locating them, for ex. find / -type f \( -name "*.db" -o -name "*.tis" \). If the needed files are found, check parmissions with stat <found_filename_path> – RomanPerekhrest Oct 25 '17 at 14:39

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