[maker-devel] Possible precedence issue with control flow operator at /apps/maker/3.01.03/lib/site_perl/5.26.2/Bio/DB/IndexedBase.pm line 805

[Charles Gumbi]

Dear maker support team
I need your help to troubleshoot this error. I don't know what I'm doing
wrong, this is my first time annotating a genome. I have gone
through almost three  maker tutorials online but it's like the annotation
doesn't generate the datastore folder and I don't know why because I have
provided all the input files.  I am running this analysis on the cluster
platform. Below I have pasted the slurm script and the error message.
Any suggestions and help would be highly appropriated.

Slurm script

#!/bin/bash

#SBATCH --account=austin

#SBATCH --job-name=maker

#SBATCH --mail-type=ALL

#SBATCH --mail-user=charlesgumbi at ufl.edu

#SBATCH --mem=30gb

#SBATCH --ntasks=1

#SBATCH --cpus-per-task2

#SBATCH --time=48:00:00

#SBATCH --output=maker%j.out

#SBATCH --error=maker%j.err

date;hostname;pwd


#loading modules

module purge

module load maker/3.01.03


#runing maker

maker -base natalensis -fix_nucleotides -dsindex maker_bopts.ctl
maker_exe.ctl maker_opts.ctl


#making gff3 files

cd natalensis.maker.output

gff3_merge -d natalensis.maker.output/natalensis_master_datastore_index.log

fasta_merge -d natalensis.maker.output/natalensis_master_datastore_index.log.




Error file

Possible precedence issue with control flow operator at
/apps/maker/3.01.03/lib/site_perl/5.26.2/Bio/DB/IndexedBase.pm line 805.

STATUS: Parsing control files...

STATUS: Processing and indexing input FASTA files...

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

A data structure will be created for you at:

/blue/austin/bonginkosi.gumbi/mastomys/genome/wtdg/annotation/maker/natalensis.maker.output/natalensis_datastore


To access files for individual sequences use the datastore index:

/blue/austin/bonginkosi.gumbi/mastomys/genome/wtdg/annotation/maker/natalensis.maker.output/natalensis_master_datastore_index.log


ERROR: The file
'natalensis.maker.output/natalensis_master_datastore_index.log' does not
exist

ERROR: The file
'natalensis.maker.output/natalensis_master_datastore_index.log' does not
exist

maker61784163.err (END)


Humble regards

charles
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