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我在尝试运行我的 RNA-seq 单读数据代码时不断收到此错误。这是在使用 STAR 索引基因组和对齐读数之后完成的。

#!/bin/bash
#SBATCH --partition=defq                          # the requested queue
#SBATCH --nodes=1                                 # number of nodes to use
#SBATCH --tasks-per-node=1                        # Number of tasks
#SBATCH --cpus-per-task=10                         # Number of cpu cores  
#SBATCH --mem=10gb                                 # in megabytes, unless unit explicitly stated
#SBATCH --error=%J.err                            # redirect stderr to this file
#SBATCH --output=%J.out                           # redirect stdout to this file


#load some modules
module load picard-2.25.7-gcc-8.4.1-5k5usfb
module load samtools/1.13
module load bedtools2-2.30.0-gcc-8.4.1-mgzzvez

## Useful shortcuts
export workingdir=/mnt/clusters/sponsa/Stage2
export refdir=/mnt/clusters/sponsa/REFS


list=("WT-D7b_S7_merge_R1"
"WT-D7a_S1_merge_R1"
"WT-D10b_S8_merge_R1"
"WT-D10a_S2_merge_R1"
"Tbx2-C3-D7b_S11_merge_R1"
"Tbx2-C3-D7a_S5_merge_R1"
"Tbx2-C3-D10b_S12_merge_R1"
"Tbx2-C3-D10a_S6_merge_R1"
"Tbx2-B10-D7b_S9_merge_R1"
"Tbx2-B10-D7a_S3_merge_R1"
"Tbx2-B10-D10b_S10_merge_R1"
"Tbx2-B10-D10a_S4_merge_R1")

for i in ${list[@]}
do
samtools sort -@ 10 -o $workingdir/star/${i}.sorted.bam $workingdir/star/${i}-unsort.Aligned.out.bam 
samtools index $workingdir/star/${i}-unsort.Aligned.out.bam

picard MarkDuplicates I=$workingdir/star/${i}.sorted.bam O=$workingdir/markdup/${i}.markdup.bam M=$workingdir/markdup/${i}.metrics.markdup.txt REMOVE_DUPLICATES=false VALIDATION_STRINGENCY=SILENT

picard MarkDuplicates I=$workingdir/star/${i}.sorted.bam O=$workingdir/markdup/${i}.rmdup.bam M=$workingdir/markdup/${i}.metrics.rmdup.txt REMOVE_DUPLICATES=true VALIDATION_STRINGENCY=SILENT

done

提前谢谢你的帮助

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