RE: MUMmer path issue

[Malabady]

Hi,

I running finisherSc.py using the following command:

``
python $P2F/finisherSC.py -par 16 -l True ../finisherSC /home/msa/software/MUMmer3.23/
'''

The run keeps on throwing the following errors and eventually creates many core dump files. I am running it on a node with 900Gb and 16 processors.

ERROR: The following critical files could not be used
ERROR: The following critical files could not be used
ERROR: The following critical files could not be used
ERROR: The following critical files could not be used
ERROR: The following critical files could not be used
ERROR: The following critical files could not be used
ERROR: The following critical files could not be used
ERROR: The following critical files could not be used
ERROR: The following critical files could not be used
ERROR: The following critical files could not be used
ERROR: The following critical files could not be used
ERROR: The following critical files could not be used
ERROR: The following critical files could not be used
ERROR: The following critical files could not be used
ERROR: The following critical files could not be used
ERROR: The following critical files could not be used
/Users/kakitlam/Downloads/MUMmer3.23/aux_bin/postnuc
/Users/kakitlam/Downloads/MUMmer3.23/aux_bin/postnuc
/Users/kakitlam/Downloads/MUMmer3.23/aux_bin/postnuc
/Users/kakitlam/Downloads/MUMmer3.23/aux_bin/postnuc
/Users/kakitlam/Downloads/MUMmer3.23/aux_bin/postnuc
/Users/kakitlam/Downloads/MUMmer3.23/aux_bin/postnuc
/Users/kakitlam/Downloads/MUMmer3.23/aux_bin/postnuc
/Users/kakitlam/Downloads/MUMmer3.23/aux_bin/postnuc
/Users/kakitlam/Downloads/MUMmer3.23/aux_bin/postnuc
/Users/kakitlam/Downloads/MUMmer3.23/aux_bin/postnuc
/Users/kakitlam/Downloads/MUMmer3.23/aux_bin/postnuc
/Users/kakitlam/Downloads/MUMmer3.23/aux_bin/postnuc
/Users/kakitlam/Downloads/MUMmer3.23/aux_bin/postnuc
/Users/kakitlam/Downloads/MUMmer3.23/aux_bin/postnuc
/Users/kakitlam/Downloads/MUMmer3.23/aux_bin/prenuc
/Users/kakitlam/Downloads/MUMmer3.23/aux_bin/postnuc
/Users/kakitlam/Downloads/MUMmer3.23/aux_bin/postnuc
/Users/kakitlam/Downloads/MUMmer3.23/aux_bin/prenuc
/Users/kakitlam/Downloads/MUMmer3.23/aux_bin/prenuc
/Users/kakitlam/Downloads/MUMmer3.23/aux_bin/prenuc
/Users/kakitlam/Downloads/MUMmer3.23/aux_bin/prenuc
/Users/kakitlam/Downloads/MUMmer3.23/aux_bin/prenuc
/Users/kakitlam/Downloads/MUMmer3.23/aux_bin/prenuc
/Users/kakitlam/Downloads/MUMmer3.23/aux_bin/prenuc
/Users/kakitlam/Downloads/MUMmer3.23/aux_bin/prenuc
/Users/kakitlam/Downloads/MUMmer3.23/aux_bin/prenuc
/Users/kakitlam/Downloads/MUMmer3.23/aux_bin/prenuc
/Users/kakitlam/Downloads/MUMmer3.23/aux_bin/prenuc
/Users/kakitlam/Downloads/MUMmer3.23/aux_bin/prenuc
/Users/kakitlam/Downloads/MUMmer3.23/aux_bin/prenuc

Here is the nucmer.error file.

20220321|081252| 25126| ERROR: The following critical files could not be used
20220321|081252| 25126| /Users/kakitlam/Downloads/MUMmer3.23/aux_bin/postnuc
20220321|081252| 25126| /Users/kakitlam/Downloads/MUMmer3.23/aux_bin/prenuc
20220321|081252| 25126| /Users/kakitlam/Downloads/MUMmer3.23/mgaps
20220321|081252| 25126| /Users/kakitlam/Downloads/MUMmer3.23/mummer
20220321|081252| 25126| Check your paths and file permissions and try again
nucmer.error (END)

Any suggestions?

Thanks,

[kakitone]

I recommend git clone FinisherSC from source and use absolute paths.

You may find this thread useful. #19 (comment)

[Malabady]

Hey,

That's what I did. when I git clone it, it comes with a MUMmer3.23 folder. Do you suggest that I install MUMmer separately?

Thanks

[kakitone]

Yes