Wrong reference genome indicated in the juicer.log

[Audald]

Hi there,

I am running Juicer as follows (as reported by the aligned/header file):

Experiment description: Juicer version 1.6; BWA 0.7.17-r1188; 20 threads; openjdk version "11.0.19" 2023-04-18; /opt/scripts/juicer.sh -d /path/to/folder -D /opt/ -p /path/to/folder/ref/clean.chrom.sizes -y /path/to/folder/ref/sites.txt -z /path/to/folder/ref/genome.fasta -t 20

However, the juicer.log indicates that I am aligning my reads against the hg19 genome.

(-: Looking for fastq files...fastq files exist
(-: Aligning files matching /path/to/folder/fastq/*_R*.fastq* to genome hg19 with site file /path/to/folder/ref/sites.txt
(-: Created /path/to/folder/splits and /path/to/folder/aligned.

I suspect this is a bug/error (confirmed by the Arima Technical Support Team) because when I try to force the mapping to hg19 (instead of my -z genome.fasta) with -g hg19:

Reference sequence /opt//references/homo_sapiens_assembly19.fasta does not exist (as expected)

Just raising this bug in case you want to correct the way the log files are being reported. Best!

[lscnsdad]

hi，How to solve this problem？

[Audald]

I don't think there is a fix yet. It seems to be a reporting problem but hopefully does not impact the results.

[PhyloJuice]

use -g your_genome can help you.

[Audald]

use -g your_genome can help you.

-z seems to be the correct flag when the reference genome file is provided. As far as I understand -g is adequate for widely used reference genomes (hg19 or mm10).

[PhyloJuice]

yeah, it is not impact the results. -g only alter the name of your genome in the log file but only -z can provide reference genome