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Trio-binning genome assembly and juicer error #344

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Larkinhi opened this issue Feb 20, 2024 · 0 comments
Open

Trio-binning genome assembly and juicer error #344

Larkinhi opened this issue Feb 20, 2024 · 0 comments

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@Larkinhi
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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

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