[maker-devel] MAKER caught in loop

[Charles Warden]

Hi,

I am encountering some issues running MAKER on my Mac.

I’ve run MAKER in the past, and I was even able to run MAKER very quickly (I think less than 1 minute) for 1 of my 2 assemblies.

For the successful run, I installed some headers from /Library/Developer/CommandLineTools/Packages/macOS_SDK_headers_for_macOS_10.14.pkg, and MAKER worked (but the files were not visible on my PC).  Actually, on my Mac, I could see from my terminal, but not even through the Mac file browser (after a restart).

I’ve attached a copy of my configuration files, and I am running MAKER with the following command:

/opt/maker/bin/maker -nolock -fix_nucleotides

I upgraded my OS within the past few months, but it seems like there is some issue with the permissions for the files being created.

I testing running MAKER from my Mac’s local hard drive (instead of the network folder).  However, the run time is considerably longer than the assembly that ran to completion (but those .gff file is not visuable through several interfaces, for some reason).

For example, MAKER has been stuck on this step since last Friday (for a 45,013 bp sequence), whereas annotation for a larger sequence completed within minutes:


STATUS: Parsing control files...

WARNING: You have chosen to turn locking off which may create

race conditions if running in parallel.  You have been warned.



STATUS: Processing and indexing input FASTA files...

STATUS: Setting up database for any GFF3 input...

A data structure will be created for you at:

/Users/cwarden/Documents/MAKER/AC270418_270441.maker.output/AC270418_270441_datastore



To access files for individual sequences use the datastore index:

/Users/cwarden/Documents/MAKER/AC270418_270441.maker.output/AC270418_270441_master_datastore_index.log



STATUS: Now running MAKER...

examining contents of the fasta file and run log







--Next Contig--



#---------------------------------------------------------------------

Now starting the contig!!

SeqID: AC270418_270441

Length: 45015

#---------------------------------------------------------------------


Can you please help me troubleshoot this issue?

Thank You,
Charles

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