[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 <bonginkosi.gumbi at 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=charlesgumbi at ufl.edu <mailto: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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