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Issue on running : (awk: fatal: can't open source file and Failure during chimera handling) #4

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Hai1983 opened this issue Dec 31, 2021 · 0 comments

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@Hai1983
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Hai1983 commented Dec 31, 2021

Hi everyone.

I try to used Juicer for my work. After download Juicer image .
I running:

(_#!/bin/bash
#SBATCH --time=10:00:00 # hh:mm:ss
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=16
#SBATCH --mem-per-cpu=4000 # megabytes

singularity run -B /scratch/ulg/bbasv/daomhai/DockerJuicer /scratch/users/d/a/daomhai/DockerJuicer/juicer_latest.sif -D /DockerJuicer -z /scratch/ulg/bbasv/daomhai/DockerJuicer/references/pilon1.fasta -p /scratch/ulg/bbasv/daomhai/DockerJuicer/chrom_sizes/pilon1.chrom.sizes -y /scratch/ulg/bbasv/daomhai/DockerJuicer/restriction_sites/pilon1.fasta_MboI.txt -t 16 -g draft_
)
But it get a issue after 5 hour running ;

(-: Looking for fastq files...fastq files exist
(-: Aligning files matching /scratch/ulg/bbasv/daomhai/DockerJuicer/fastq/_R.fastq*
to genome draft with site file /scratch/ulg/bbasv/daomhai/DockerJuicer/restriction_sites/pilon1.fasta_MboI.txt
(-: Created /scratch/ulg/bbasv/daomhai/DockerJuicer/splits and /scratch/ulg/bbasv/daomhai/DockerJuicer/aligned.
/opt/scripts/juicer.sh: line 347: /DockerJuicer/scripts/common/countligations.sh: No such file or directory
Running command bwa mem -SP5M -t 16 /scratch/ulg/bbasv/daomhai/DockerJuicer/references/pilon1.fasta /scratch/ulg/bbasv/daomhai/DockerJuicer/splits/hic_R1.fastq.gz /scratch/ulg/bbasv/daomhai/DockerJuicer/splits/hic_R2.fastq.gz > /scratch/ulg/bbasv/daomhai/DockerJuicer/splits/hic.fastq.gz.sam
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 1080046 sequences (160000267 bp)...
……….
………..
…….
(-: Align of /scratch/ulg/bbasv/daomhai/DockerJuicer/splits/hic.fastq.gz.sam done successfully
awk: fatal: can't open source file `/DockerJuicer/scripts/common/chimeric_blacklist.awk' for reading (No such file or directory)
***! Failure during chimera handling of /scratch/ulg/bbasv/daomhai/DockerJuicer/splits/hic.fastq.gz

In aligned directory have only (header file)
In splited directory ;
-rw-r--r-- 1 daomhai daomhai 0 Dec 31 13:33 hic.fastq.gz_collisions
-rw-r--r-- 1 daomhai daomhai 0 Dec 31 13:33 hic.fastq.gz_collisions.sam
-rw-r--r-- 1 daomhai daomhai 0 Dec 31 13:33 hic.fastq.gz_collisions_low_mapq.sam
-rw-r--r-- 1 daomhai daomhai 0 Dec 31 13:33 hic.fastq.gz_mapq0.sam
-rw-r--r-- 1 daomhai daomhai 0 Dec 31 13:33 hic.fastq.gz_unmapped.sam
-rw-r--r-- 1 daomhai daomhai 369066137534 Dec 31 13:33 hic.fastq.gz.sam

In HIC_tmp directory is emty.
Please help me to figure out what I am doing wrong ??

Thanks in advance
Sincerely
Hai

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