Commit ad28fa5d authored by Marie CARIOU's avatar Marie CARIOU
Browse files

quality check

parent 8a4f0cb4
#!/bin/bash
# Les lignes commançant par #SBATCH sont interprétées par SLURM.
# Elles permettent demander les ressources nécessaires au job.
# Nombre de Noeuds
#SBATCH --nodes=1
# Nombre de processeur par noeud
#SBATCH --ntasks-per-node=1
# Nom du job
#SBATCH --job-name=QC_crino
# Quantité de RAM par noeud
#SBATCH --mem=10Go
# Quel type de machine demander (type_1 ou type_2)
#SBATCH --partition=type_1
# Chargement des modules
module load userspace/tr17.10
module load biology
module load java-JRE-OpenJDK/11.0.8
module load fastQC
DATA="/mnt/beegfs/mcariou/CRINO_Data/X204SC22064920-Z01-F001/01.RawData/"
OUT="/mnt/beegfs/mcariou/2022_Eleaume/out_FastQC/"
/trinity/home/mcariou/2022_eleaume/2022_eleaume/src/1_data_QC.sh \
$DATA/A609/ \
$OUT
/trinity/home/mcariou/2022_eleaume/2022_eleaume/src/1_data_QC.sh \
$DATA/A610/ \
$OUT
/trinity/home/mcariou/2022_eleaume/2022_eleaume/src/1_data_QC.sh \
$DATA/A621/ \
$OUT
/trinity/home/mcariou/2022_eleaume/2022_eleaume/src/1_data_QC.sh \
$DATA/A658/ \
$OUT
echo "end"
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Analysis complete for A609_EKDN220020643-1A_HTMCVDSX3_L1_1.fq.gz
Started analysis of A609_EKDN220020643-1A_HTMCVDSX3_L1_2.fq.gz
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Started analysis of A609_EKDN220020643-1A_HTMCWDSX3_L1_1.fq.gz
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Failed to process file A609_EKDN220020643-1A_HTMCWDSX3_L1_1.fq.gz
uk.ac.babraham.FastQC.Sequence.SequenceFormatException: ID line didn't start with '@'
at uk.ac.babraham.FastQC.Sequence.FastQFile.readNext(FastQFile.java:158)
at uk.ac.babraham.FastQC.Sequence.FastQFile.next(FastQFile.java:125)
at uk.ac.babraham.FastQC.Analysis.AnalysisRunner.run(AnalysisRunner.java:77)
at java.base/java.lang.Thread.run(Unknown Source)
Started analysis of A609_EKDN220020643-1A_HTMCWDSX3_L1_2.fq.gz
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#!/bin/bash
DATA=$1
OUT=$2
mkdir -p $OUT
fastqc $DATA/*.fq.gz -o $OUT
echo "end"
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