Trio-binning genome assembly and juicer error

[Larkinhi]

Hi,

I have been working on trio-binning of hybrid genome using PacBio long read sequencing. Step 1: I YAK paternal and maternal genome and assembled de novo genome ~400 Mb using HIFIASM "pat.mat.asm.fas". Step 2: Following BWA MEM I mapped HIC data to the "pat.mat.asm.fas" assembly. Step 3: SAMTOLS to converted SAM to BAM. Step 4: JUICER

python generate_site_positions.py DpnII H1 pat.mat.asm.fas > H1_DpnII.txt

awk 'BEGIN{OFS="\t"}{print $1, $NF}' H1_DpnII.txt > genome_ID_sizes

sh ~/script/juicer.sh -t 32 -g H1 -d ~/Juicer -s DpnII -p genome_ID_sizes -y H1_DpnII.txt -z pat.mat.asm.fas HiC1.fastq.gz HiC2.fastq.gz -q batch -l batch

Error

Using H1_DpnII.txt as site file (-: Looking for fastq files...fastq files exist (-: Aligning files matching ~/H1/Juicer/fastq/_R.fastq* in queue batch to genome H1 with no fragment delimited maps. --- Using already created files in ~/H1/Juicer/splits

(-: Starting job to launch other jobs once splitting is complete (-: Finished adding all jobs... Now is a good time to get that cup of coffee... Last job id 1762416

debug - folder head-1762353.err - /var/spool/slurmd/job1762353/slurm_script: line 10: spack: command not found head-1762353.out

aligned folder is empty

Any suggestion/comment. I appreciate your help in helping me out.

Thank you LK