<html><head><meta http-equiv="Content-Type" content="text/html; charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">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."<br class=""><div><br class=""></div><div>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.</div><div><br class=""></div><div>—Carson</div><div><br class=""></div><div><br class=""><blockquote type="cite" class=""><div class="">On Dec 9, 2020, at 9:14 AM, Gumbi,Bonginkosi C <<a href="mailto:bonginkosi.gumbi@ufl.edu" class="">bonginkosi.gumbi@ufl.edu</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><meta charset="UTF-8" class=""><div style="font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;" class=""><div style="caret-color: rgb(34, 34, 34); color: rgb(34, 34, 34); font-family: Arial, Helvetica, sans-serif;" class=""><font class=""><span style="font-family: Arial, Helvetica, sans-serif; font-size: 12pt;" class=""></span><span style="font-family: Arial, Helvetica, sans-serif; font-size: 12pt;" class="">Dear maker support team </span></font></div><div style="caret-color: rgb(34, 34, 34); color: rgb(34, 34, 34); font-family: Arial, Helvetica, sans-serif;" class=""><font class=""><span class=""><br class=""></span></font></div><div style="caret-color: rgb(34, 34, 34); color: rgb(34, 34, 34); font-family: Arial, Helvetica, sans-serif;" class=""><font class=""><span style="font-family: Arial, Helvetica, sans-serif; font-size: 12pt;" class="">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. </span></font></div><div style="caret-color: rgb(34, 34, 34); color: rgb(34, 34, 34); font-family: Arial, Helvetica, sans-serif;" class=""><span style="background-color: rgb(255, 255, 255);" class=""><font class=""></font></span></div><div dir="ltr" style="caret-color: rgb(34, 34, 34); color: rgb(34, 34, 34); font-family: Arial, Helvetica, sans-serif;" class=""><span style="" class=""><br class=""></span></div><div dir="ltr" style="caret-color: rgb(34, 34, 34); color: rgb(34, 34, 34); font-family: Arial, Helvetica, sans-serif;" class=""><span style="font-family: Arial, Helvetica, sans-serif; font-size: 12pt;" class="">Slurm script </span><br class=""></div><div dir="ltr" style="caret-color: rgb(34, 34, 34); color: rgb(34, 34, 34); font-family: Arial, Helvetica, sans-serif;" class=""><div style="margin: 0px;" class=""><span style="font-variant-ligatures: no-common-ligatures; background-color: rgb(255, 255, 255);" class=""><font face="monospace" class=""><span style="font-family: Arial, Helvetica, sans-serif; font-size: 12pt;" class="">#!/bin/bash</span></font></span></div><div style="margin: 0px;" class=""><span style="font-variant-ligatures: no-common-ligatures; background-color: rgb(255, 255, 255);" class=""><font face="monospace" class=""><span style="font-family: Arial, Helvetica, sans-serif; font-size: 12pt;" class="">#SBATCH --account=austin</span></font></span></div><div style="margin: 0px;" class=""><font face="monospace" style="background-color: rgb(255, 255, 255);" class=""><span style="font-variant-ligatures: no-common-ligatures; font-family: Arial, Helvetica, sans-serif; font-size: 12pt;" class="">#SBATCH --job-name=</span><span style="font-variant-ligatures: no-common-ligatures; font-family: Arial, Helvetica, sans-serif; font-size: 12pt;" class="">maker</span></font></div><div style="margin: 0px;" class=""><span style="font-variant-ligatures: no-common-ligatures; background-color: rgb(255, 255, 255);" class=""><font face="monospace" class=""><span style="font-family: Arial, Helvetica, sans-serif; font-size: 12pt;" class="">#SBATCH --mail-type=ALL</span></font></span></div><div style="margin: 0px;" class=""><span style="font-variant-ligatures: no-common-ligatures; background-color: rgb(255, 255, 255);" class=""><font face="monospace" class=""><span style="font-family: Arial, Helvetica, sans-serif; font-size: 12pt;" class="">#SBATCH --mail-user=</span><a href="mailto:charlesgumbi@ufl.edu" target="_blank" style="color: rgb(17, 85, 204);" class=""><span style="font-family: Arial, Helvetica, sans-serif; font-size: 12pt;" class="">charlesgumbi@ufl.edu</span><wbr class=""></a></font></span></div><div style="margin: 0px;" class=""><span style="font-variant-ligatures: no-common-ligatures; background-color: rgb(255, 255, 255);" class=""><font face="monospace" class=""><span style="font-family: Arial, Helvetica, sans-serif; font-size: 12pt;" class="">#SBATCH --mem=30gb</span></font></span></div><div style="margin: 0px;" class=""><span style="font-variant-ligatures: no-common-ligatures; background-color: rgb(255, 255, 255);" class=""><font face="monospace" class=""><span style="font-family: Arial, Helvetica, sans-serif; font-size: 12pt;" class="">#SBATCH --ntasks=1</span></font></span></div><div style="margin: 0px;" class=""><span style="font-variant-ligatures: no-common-ligatures; background-color: rgb(255, 255, 255);" class=""><font face="monospace" class=""><span style="font-family: Arial, Helvetica, sans-serif; font-size: 12pt;" class="">#SBATCH --cpus-per-task2</span></font></span></div><div style="margin: 0px;" class=""><span style="font-variant-ligatures: no-common-ligatures; background-color: rgb(255, 255, 255);" class=""><font face="monospace" class=""><span style="font-family: Arial, Helvetica, sans-serif; font-size: 12pt;" class="">#SBATCH --time=48:00:00</span></font></span></div><div style="margin: 0px;" class=""><font face="monospace" style="background-color: rgb(255, 255, 255);" class=""><span style="font-variant-ligatures: no-common-ligatures; font-family: Arial, Helvetica, sans-serif; font-size: 12pt;" class="">#SBATCH --output=</span><span style="font-variant-ligatures: no-common-ligatures; font-family: Arial, Helvetica, sans-serif; font-size: 12pt;" class="">maker</span><span style="font-variant-ligatures: no-common-ligatures; font-family: Arial, Helvetica, sans-serif; font-size: 12pt;" class="">%j.out</span></font></div><div style="margin: 0px;" class=""><font face="monospace" style="background-color: rgb(255, 255, 255);" class=""><span style="font-variant-ligatures: no-common-ligatures; font-family: Arial, Helvetica, sans-serif; font-size: 12pt;" class="">#SBATCH --error=</span><span style="font-variant-ligatures: no-common-ligatures; font-family: Arial, Helvetica, sans-serif; font-size: 12pt;" class="">maker</span><span style="font-variant-ligatures: no-common-ligatures; font-family: Arial, Helvetica, sans-serif; font-size: 12pt;" class="">%j.err</span></font></div><div style="margin: 0px;" class=""><font face="monospace" style="background-color: rgb(255, 255, 255);" class=""><span style="font-variant-ligatures: no-common-ligatures; font-family: Arial, Helvetica, sans-serif; font-size: 12pt;" class="">date;hostname;</span><span style="font-variant-ligatures: no-common-ligatures; font-family: Arial, Helvetica, sans-serif; font-size: 12pt;" class="">pwd</span></font></div><div style="margin: 0px; min-height: 13px;" class=""><font face="monospace" style="background-color: rgb(255, 255, 255);" class=""><span style="font-variant-ligatures: no-common-ligatures;" class=""></span><br class=""></font></div><div style="margin: 0px;" class=""><span style="font-variant-ligatures: no-common-ligatures; background-color: rgb(255, 255, 255);" class=""><font face="monospace" class=""><span style="font-family: Arial, Helvetica, sans-serif; font-size: 12pt;" class="">#loading modules</span></font></span></div><div style="margin: 0px;" class=""><span style="font-variant-ligatures: no-common-ligatures; background-color: rgb(255, 255, 255);" class=""><font face="monospace" class=""><span style="font-family: Arial, Helvetica, sans-serif; font-size: 12pt;" class="">module purge</span></font></span></div><div style="margin: 0px;" class=""><font face="monospace" style="background-color: rgb(255, 255, 255);" class=""><span style="font-variant-ligatures: no-common-ligatures; font-family: Arial, Helvetica, sans-serif; font-size: 12pt;" class="">module load </span><span style="font-variant-ligatures: no-common-ligatures; font-family: Arial, Helvetica, sans-serif; font-size: 12pt;" class="">maker</span><span style="font-variant-ligatures: no-common-ligatures; font-family: Arial, Helvetica, sans-serif; font-size: 12pt;" class="">/3.01.03</span></font></div><div style="margin: 0px; min-height: 13px;" class=""><span style="font-variant-ligatures: no-common-ligatures;" class=""><font face="monospace" class=""><br class=""></font></span></div><div style="margin: 0px; min-height: 13px;" class=""><span style="font-variant-ligatures: no-common-ligatures;" class=""><font face="monospace" class=""><span style="font-family: Arial, Helvetica, sans-serif; font-size: 12pt;" class="">#runing maker </span></font></span></div><div style="margin: 0px; min-height: 13px;" class=""><font face="monospace" class=""><span style="font-variant-ligatures: no-common-ligatures; font-family: Arial, Helvetica, sans-serif; font-size: 12pt;" class="">maker</span><span style="font-variant-ligatures: no-common-ligatures; font-family: Arial, Helvetica, sans-serif; font-size: 12pt;" class=""> </span><span style="font-variant-ligatures: no-common-ligatures; font-family: Arial, Helvetica, sans-serif; font-size: 12pt;" class="">-base</span><span style="font-variant-ligatures: no-common-ligatures; font-family: Arial, Helvetica, sans-serif; font-size: 12pt;" class=""> natalensis </span><span style="font-variant-ligatures: no-common-ligatures; font-family: Arial, Helvetica, sans-serif; font-size: 12pt;" class="">-fix_</span><span style="font-variant-ligatures: no-common-ligatures;" class=""><wbr class=""></span><span style="font-variant-ligatures: no-common-ligatures; font-family: Arial, Helvetica, sans-serif; font-size: 12pt;" class="">nucleotides</span><span style="font-variant-ligatures: no-common-ligatures; font-family: Arial, Helvetica, sans-serif; font-size: 12pt;" class=""> </span><span style="font-variant-ligatures: no-common-ligatures; font-family: Arial, Helvetica, sans-serif; font-size: 12pt;" class="">-dsindex</span><span style="font-variant-ligatures: no-common-ligatures; font-family: Arial, Helvetica, sans-serif; font-size: 12pt;" class=""> maker_</span><span style="font-variant-ligatures: no-common-ligatures;" class=""><wbr class=""></span><span style="font-variant-ligatures: no-common-ligatures; font-family: Arial, Helvetica, sans-serif; font-size: 12pt;" class="">bopts.ctl maker_exe.ctl maker_opts.ctl</span><br class=""></font></div><div style="margin: 0px; min-height: 13px;" class=""><font face="monospace" style="background-color: rgb(255, 255, 255);" class=""><span style="font-variant-ligatures: no-common-ligatures;" class=""></span><br class=""></font></div><div style="margin: 0px;" class=""><span style="font-variant-ligatures: no-common-ligatures; background-color: rgb(255, 255, 255);" class=""><font face="monospace" class=""><span style="font-family: Arial, Helvetica, sans-serif; font-size: 12pt;" class="">#making gff3 files</span></font></span></div><div style="margin: 0px;" class=""><font face="monospace" style="background-color: rgb(255, 255, 255);" class=""><span style="font-variant-ligatures: no-common-ligatures; font-family: Arial, Helvetica, sans-serif; font-size: 12pt;" class="">cd</span><span style="font-variant-ligatures: no-common-ligatures; font-family: Arial, Helvetica, sans-serif; font-size: 12pt;" class=""> natalensis.maker.output</span></font></div><div style="margin: 0px;" class=""><font face="monospace" style="background-color: rgb(255, 255, 255);" class=""><span style="font-variant-ligatures: no-common-ligatures; font-family: Arial, Helvetica, sans-serif; font-size: 12pt;" class="">gff3_merge </span><span style="font-variant-ligatures: no-common-ligatures; font-family: Arial, Helvetica, sans-serif; font-size: 12pt;" class="">-d</span><span style="font-variant-ligatures: no-common-ligatures; font-family: Arial, Helvetica, sans-serif; font-size: 12pt;" class=""> natalensis.</span><span style="font-variant-ligatures: no-common-ligatures;" class=""><wbr class=""></span><span style="font-variant-ligatures: no-common-ligatures; font-family: Arial, Helvetica, sans-serif; font-size: 12pt;" class="">maker.output/natalensis_</span><span style="font-variant-ligatures: no-common-ligatures;" class=""><wbr class=""></span><span style="font-variant-ligatures: no-common-ligatures; font-family: Arial, Helvetica, sans-serif; font-size: 12pt;" class="">master_datastore_index.log</span></font></div><div style="margin: 0px;" class=""><font face="monospace" style="background-color: rgb(255, 255, 255);" class=""><span style="font-variant-ligatures: no-common-ligatures; font-family: Arial, Helvetica, sans-serif; font-size: 12pt;" class="">fasta_merge </span><span style="font-variant-ligatures: no-common-ligatures; font-family: Arial, Helvetica, sans-serif; font-size: 12pt;" class="">-d</span><span style="font-variant-ligatures: no-common-ligatures; font-family: Arial, Helvetica, sans-serif; font-size: 12pt;" class=""> natalensis.</span><span style="font-variant-ligatures: no-common-ligatures;" class=""><wbr class=""></span><span style="font-variant-ligatures: no-common-ligatures; font-family: Arial, Helvetica, sans-serif; font-size: 12pt;" class="">maker.output/natalensis_</span><span style="font-variant-ligatures: no-common-ligatures;" class=""><wbr class=""></span><span style="font-variant-ligatures: no-common-ligatures; font-family: Arial, Helvetica, sans-serif; font-size: 12pt;" class="">master_datastore_index.log. </span></font></div><div style="margin: 0px; color: rgb(33, 255, 6);" class=""><span style="font-variant-ligatures: no-common-ligatures; background-color: rgb(238, 238, 238);" class=""><font face="arial, sans-serif" class=""><br class=""></font></span></div><div style="margin: 0px;" class=""><span style="font-variant-ligatures: no-common-ligatures; background-color: rgb(238, 238, 238);" class=""><font face="arial, sans-serif" class=""><br class=""></font></span></div><div style="margin: 0px;" class=""><span style="font-family: Arial, Helvetica, sans-serif; background-color: rgb(238, 238, 238); font-size: 12pt;" class="">Error file</span><br class=""></div><div style="margin: 0px;" class=""><span style="font-family: Arial, Helvetica, sans-serif; font-size: 12pt;" class="">Possible precedence issue with control flow operator at /apps/maker/3.01.03/lib/site_</span><span style="font-family: monospace; font-size: 11px;" class=""><wbr class=""></span><span style="font-family: Arial, Helvetica, sans-serif; font-size: 12pt;" class="">perl/5.26.2/Bio/DB/</span><span style="font-family: monospace; font-size: 11px;" class=""><wbr class=""></span><span style="font-family: Arial, Helvetica, sans-serif; font-size: 12pt;" class="">IndexedBase.pm line 805.</span><br class=""></div><div style="margin: 0px; font-size: 11px;" class=""><span style="font-variant-ligatures: no-common-ligatures; background-color: rgb(255, 255, 255);" class=""><font face="monospace" class=""><span style="font-family: Arial, Helvetica, sans-serif; font-size: 12pt;" class="">STATUS: Parsing control files...</span></font></span></div><div style="margin: 0px; font-size: 11px;" class=""><span style="font-variant-ligatures: no-common-ligatures; background-color: rgb(255, 255, 255);" class=""><font face="monospace" class=""><span style="font-family: Arial, Helvetica, sans-serif; font-size: 12pt;" class="">STATUS: Processing and indexing input FASTA files...</span></font></span></div><div style="margin: 0px; font-size: 11px;" class=""><span style="font-variant-ligatures: no-common-ligatures; background-color: rgb(255, 255, 255);" class=""><font face="monospace" class=""><span style="font-family: Arial, Helvetica, sans-serif; font-size: 12pt;" class="">STATUS: Setting up database for any GFF3 input...</span></font></span></div><div style="margin: 0px; font-size: 11px;" class=""><span style="font-variant-ligatures: no-common-ligatures; background-color: rgb(255, 255, 255);" class=""><font face="monospace" class=""><span style="font-family: Arial, Helvetica, sans-serif; font-size: 12pt;" class="">A data structure will be created for you at:</span></font></span></div><div style="margin: 0px; font-size: 11px;" class=""><span style="font-variant-ligatures: no-common-ligatures; background-color: rgb(255, 255, 255);" class=""><font face="monospace" class=""><span style="font-family: Arial, Helvetica, sans-serif; font-size: 12pt;" class="">/blue/austin/bonginkosi.gumbi/</span><wbr class=""><span style="font-family: Arial, Helvetica, sans-serif; font-size: 12pt;" class="">mastomys/genome/wtdg/</span><wbr class=""><span style="font-family: Arial, Helvetica, sans-serif; font-size: 12pt;" class="">annotation/maker/natalensis.</span><wbr class=""><span style="font-family: Arial, Helvetica, sans-serif; font-size: 12pt;" class="">maker.output/natalensis_</span><wbr class=""><span style="font-family: Arial, Helvetica, sans-serif; font-size: 12pt;" class="">datastore</span></font></span></div><div style="margin: 0px; font-size: 11px; min-height: 13px;" class=""><span style="background-color: rgb(255, 255, 255);" class=""><font face="monospace" class=""><span style="font-variant-ligatures: no-common-ligatures;" class=""></span><br class=""></font></span></div><div style="margin: 0px; font-size: 11px;" class=""><span style="font-variant-ligatures: no-common-ligatures; background-color: rgb(255, 255, 255);" class=""><font face="monospace" class=""><span style="font-family: Arial, Helvetica, sans-serif; font-size: 12pt;" class="">To access files for individual sequences use the datastore index:</span></font></span></div><div style="margin: 0px; font-size: 11px;" class=""><span style="font-variant-ligatures: no-common-ligatures; background-color: rgb(255, 255, 255);" class=""><font face="monospace" class=""><span style="font-family: Arial, Helvetica, sans-serif; font-size: 12pt;" class="">/blue/austin/bonginkosi.gumbi/</span><wbr class=""><span style="font-family: Arial, Helvetica, sans-serif; font-size: 12pt;" class="">mastomys/genome/wtdg/</span><wbr class=""><span style="font-family: Arial, Helvetica, sans-serif; font-size: 12pt;" class="">annotation/maker/natalensis.</span><wbr class=""><span style="font-family: Arial, Helvetica, sans-serif; font-size: 12pt;" class="">maker.output/natalensis_</span><wbr class=""><span style="font-family: Arial, Helvetica, sans-serif; font-size: 12pt;" class="">master_datastore_index.log</span></font></span></div><div style="margin: 0px; font-size: 11px; min-height: 13px;" class=""><span style="background-color: rgb(255, 255, 255);" class=""><font face="monospace" class=""><span style="font-variant-ligatures: no-common-ligatures;" class=""></span><br class=""></font></span></div><div style="margin: 0px; font-size: 11px;" class=""><span style="font-variant-ligatures: no-common-ligatures; background-color: rgb(255, 255, 255);" class=""><font face="monospace" class=""><span style="font-family: Arial, Helvetica, sans-serif; font-size: 12pt;" class="">ERROR: The file 'natalensis.maker.output/</span><wbr class=""><span style="font-family: Arial, Helvetica, sans-serif; font-size: 12pt;" class="">natalensis_master_datastore_</span><wbr class=""><span style="font-family: Arial, Helvetica, sans-serif; font-size: 12pt;" class="">index.log' does not exist</span></font></span></div><div style="margin: 0px; font-size: 11px;" class=""><span style="font-variant-ligatures: no-common-ligatures; background-color: rgb(255, 255, 255);" class=""><font face="monospace" class=""><span style="font-family: Arial, Helvetica, sans-serif; font-size: 12pt;" class="">ERROR: The file 'natalensis.maker.output/</span><wbr class=""><span style="font-family: Arial, Helvetica, sans-serif; font-size: 12pt;" class="">natalensis_master_datastore_</span><wbr class=""><span style="font-family: Arial, Helvetica, sans-serif; font-size: 12pt;" class="">index.log' does not exist</span></font></span></div><p style="margin: 0px;" class=""><span style="font-variant-ligatures: no-common-ligatures; background-color: rgb(255, 255, 255);" class=""><font face="monospace" class=""></font></span></p><div style="margin: 0px; font-size: 11px;" class=""><span style="font-variant-ligatures: no-common-ligatures; background-color: rgb(255, 255, 255);" class=""><font face="monospace" class=""><span style="font-family: Arial, Helvetica, sans-serif; font-size: 12pt;" class="">maker61784163.err (END)</span></font></span></div><div class=""><span style="font-variant-ligatures: no-common-ligatures; background-color: rgb(255, 255, 255);" class=""><font class=""><br class=""></font></span></div><div style="margin: 0px;" class=""><span style="font-variant-ligatures: no-common-ligatures; background-color: rgb(255, 255, 255);" class=""><font face="arial, sans-serif" class=""><br class=""></font></span></div><div style="margin: 0px;" class=""><span style="font-variant-ligatures: no-common-ligatures; background-color: rgb(255, 255, 255);" class=""><font face="arial, sans-serif" class=""><span style="font-family: Arial, Helvetica, sans-serif; font-size: 12pt;" class="">Humble regards </span></font></span></div><font color="#888888" class=""><div style="margin: 0px;" class=""><span style="font-variant-ligatures: no-common-ligatures; background-color: rgb(255, 255, 255);" class=""><font face="arial, sans-serif" class=""><span style="font-family: Arial, Helvetica, sans-serif; font-size: 12pt;" class="">charles </span></font></span></div></font></div></div></div></blockquote></div><br class=""></body></html>