owl/Athaliana/20180807_wqmaker_run_oly_02

This directory contains the contents needed for and produced by the program WQ-MAKER for Olympia oyster genome annotation.

WQ-MAKER was run on Jetstream, using a total of 22 instances of MAKER 2.31.9 with CCTools v3.1.

See this notebook entry for details on how WQ-MAKER run was prepared:

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FILES:

- log_file.txt: Log file generated by WQ-MAKER. Run stats/performance can be viewed by using the shell command: tail -25 log_file.txt

- maker_bopts.ctl: Maker BLAST options file. Created automatically by Maker running "maker -CTL" command (required to initialize Maker run).

- maker_exe.ctl: Maker executables options file. Tells Maker where various programs are located on system. Created automatically by Maker running "maker -CTL" command (required to initialize Maker run).

- maker_opts.ctl: Maker options file. Customized by user to identify project-specific file locations (e.g. genome FastA files, proteome FastA files, etc.). File template is created automatically by Maker running "maker -CTL" command (required to initialize Maker run). For WQ-MAKER, paths to files must be RELATIVE. Absolute paths cannot be used.

- maker_setup.sh: Script written to generate maker_opts.ctl file and fill populate with file locations.

- master.dbg: WQ-MAKER debug file for MASTER node. Probably only useful for WQ-MAKER developer(s).

- Olurida_v081.all.gff: The GFF3 file containing annotations of all scaffolds.

- task_outputs.txt: Progress report produced by Maker during run.

- test_out_stats.txt: Performance stats of WQ-MAKER WORKER nodes. Probably only useful for WQ-MAKER developer(s).