Re: [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

[Carson Holt]

The problem is the bioperl or even perl installation —> “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."

You may have a custom install of perl without BerkleyDB setup, or need to update BioPerl.  If you installed MAKER with MiniConda, then it tried to setup a custom perl and BioPerl that is broken. You probably need to reinstall MAKER. Using the system perl may be the easiest.

—Carson

On Dec 9, 2020, at 9:14 AM, Gumbi,Bonginkosi C <bonginko...@ufl.edu> wrote:

​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=charle...@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