IndexOutOfBoundsException: fromIndex = -1

[charles-gumbi]

Hello
I git cloned this pipeline to analyses whole genome EM-seq data from rockfish. I was able to get it to work in our cluster using your testing data. But when I run on of rockfish dataset get the following error and the run fails.

"Jun-18 15:34:53.618 [Actor Thread 21] ERROR nextflow.extension.OperatorImpl - @unknown java.lang.IndexOutOfBoundsException: fromIndex = -1."

Can you share some light on what going wrong and if there are any parameters i need to be changing in the .nf and .sh scripts. I have already customized some of the .config files to get them to work our cluster platform. But I'm not sure how to fix the about error.
Herewith attached a log file from the run.

Any assistance would be highly appreciated.
Charles

nextflow.log

[bwlang]

The -1 error is coming from nextflow and i've seen it before when the data is not what's expected.
Maybe we can add more checking...

Looking at the log file... I wonder about this glob:
"ABLG_47592_EMseq_S1_L001*1.fastq.gz"

if you run ls "ABLG_47592_EMseq_S1_L001*1.fastq.gz" does it show your files as you expect?

[charles-gumbi]

Yes, it does show up. And when I less ABLG_47592_EMseq_S1_L001_R1.fastq.gz, it does look similar to the testing data: emseq_testg_R1. fastq.gz. Is it how I call in the main.nf script (params.input_glob ) (see attached as main.txt file ). However, that line is also similar to the main.nf line on this git page.

main.txt

[bwlang]

@charles-gumbi Are you stills seeing problems with the current implementation?