Which command ro run MAKER pipeline for gene annotation ?

Question

[Sony]

Hello everyone,

I am newbie using MAKER pipeline for genome annotation. I followed this tutorial to do the annotation for my assembled sequence. I generated 4 necessary files with maker -CTL, including: maker_bopts.ctl maker_evm.ctl maker_exe.ctl round1_maker_opts.ctl . I already set up parameter in the .ctl file (configuration file). But I don't know how to write command to run MAKER. I install MAKER 3.01.03 via conda.

In the tutorial, the author described like this: "construct the MAKER command in a Bash script so it is easy to run and keep track of.

cat round1_run_maker.sh
mpiexec -n 12 maker -base Bcon_rnd1 round1_maker_opts.ctl maker_bopts.ctl maker_exe.ctl

Then we run MAKER.

bash ./round1_run_maker.sh 2>&1 | tee round1_run_maker.log"

But I don't understand what is "Bcon_rnd1" in this command. Does anyone can help me How can I run MAKER? Thank you everyone for any suggestions.

Answer 1

[Philipp Bayer]

Bcon_rnd1 is the -base parameter for the MAKER run - in this case it's 'just' the base name for output filenames. So everything will start with Bcon_rnd1 in the filename. In this case it probably means 'Boa constrictor round 1'.

[Sony]

Thank you, DR. Philipp for your response.

I run this script for MAKER:

#!/bin/bash

mpiexec -n 12 maker -base Oi_ERR3890951_round1 round1_maker_opts.ctl maker_bopts.ctl maker_exe.ctl

The command I run for this script:

bash ./Oi_ERR3890951_IRGSP_round1.sh 2>&1 | tee Oi_ERR3890951_round1_run_maker.log

But I got this error:

Ignoring PCI device with non-16bit domain.
Pass --enable-32bits-pci-domain to configure to support such devices
(warning: it would break the library ABI, don't enable unless really needed).
Ignoring PCI device with non-16bit domain.
Pass --enable-32bits-pci-domain to configure to support such devices
(warning: it would break the library ABI, don't enable unless really needed).
Ignoring PCI device with non-16bit domain.
Pass --enable-32bits-pci-domain to configure to support such devices
(warning: it would break the library ABI, don't enable unless really needed).
Ignoring PCI device with non-16bit domain.
Pass --enable-32bits-pci-domain to configure to support such devices
(warning: it would break the library ABI, don't enable unless really needed).
Ignoring PCI device with non-16bit domain.
Pass --enable-32bits-pci-domain to configure to support such devices
(warning: it would break the library ABI, don't enable unless really needed).
STATUS: Parsing control files...
ERROR: Could not determine if DFam is installed
--> rank=NA, hostname=hpz6

===================================================================================
=   BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
=   PID 3414350 RUNNING AT hpz6
=   EXIT CODE: 9
=   CLEANING UP REMAINING PROCESSES
=   YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
===================================================================================
YOUR APPLICATION TERMINATED WITH THE EXIT STRING: Killed (signal 9)
This typically refers to a problem with your application.
Please see the FAQ page for debugging suggestions

Do I need to install DFam ? I thought that DFam already inside MAKER pipeline (https://anaconda.org/bioconda/maker)

[Philipp Bayer]

Some instructions for that error here: https://github.com/bioconda/bioconda-recipes/issues/26529

[GenoMax]

Sony : When responding to existing posts/comments in threads please use ADD REPLY/ADD COMMENT to keep the threads logically organized. SUBMIT ANSWER is for new answers to the original question.