MAKER caught in loop

classic Classic list List threaded Threaded
1 message Options
Reply | Threaded
Open this post in threaded view

MAKER caught in loop

Charles Warden



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:



To access files for individual sequences use the datastore index:



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,



This message and any attachments are intended solely for the individual or entity to which they are addressed. This communication may contain information that is privileged, confidential, or exempt from disclosure under applicable law (e.g., personal health information, research data, financial information). Because this e-mail has been sent without encryption, individuals other than the intended recipient may be able to view the information, forward it to others or tamper with the information without the knowledge or consent of the sender. If you are not the intended recipient, or the employee or person responsible for delivering the message to the intended recipient, any dissemination, distribution or copying of the communication is strictly prohibited. If you received the communication in error, please notify the sender immediately by replying to this message and deleting the message and any accompanying files from your system. If, due to the security risks, you do not wish to receive further communications via e-mail, please reply to this message and inform the sender that you do not wish to receive further e-mail from the sender. (LCP301)

maker-devel mailing list
[hidden email]

maker_bopts.ctl (682 bytes) Download Attachment
maker_exe.ctl (486 bytes) Download Attachment
maker_opts.ctl (1K) Download Attachment