stat: Bad file descriptor

[YuanChihLee]

I tried to align test data with GRCm39 indexed genome download from the Bowtie2 website, and write a job script:

#!/bin/bash
#SBATCH -A MST112171                  # Account name/project number
#SBATCH -J SRR6512731.alignment # Job name
#SBATCH -p ct56                              # Partition name
#SBATCH -n 24                                 # Number of MPI tasks (i.e. processes)
#SBATCH -c 1                                   # Number of cores per MPI task
#SBATCH -N 1                                  # Maximum number of nodes to be allocated
#SBATCH --ntasks-per-node=56     # Maximu number of tasks on each node
#SBATCH --mem=8192                   # memory request=8G
#SBATCH -o %j.out                          # Path to the standard output file
#SBATCH -e %j.err                           # Path to the standard error ouput file

ml biology/bowtie2/2.4.2
ml biology/Samtools/1.15.1
ml compiler/gcc/10.4.0
cd /home/j120885731/pepatac/genome_folder/alignment
reads1=trimmed.paired.SRR6512731.R1.fastq.gz
reads2=trimmed.paired.SRR6512731.R2.fastq.gz
bowtie2 --very-sensitive -X 2000 -k 1 -D 20 -R 3 -N 1 -L 20 -i S,1,0.50 -p 4 \
-x /home/j120885731/pepatac/genome_folder/index/GRCm39 GRCm39 -1 $reads1 -2 $reads2 | samtools view -bS - > -S SRR6512731.fastq.gz.ba

But I got the error, this is the error log:

stat: Bad file descriptor
Warning: Could not open read file "GRCm39" for reading; skipping...
Error: No input read files were valid
(ERR): bowtie2-align exited with value 1
[main_samview] fail to read the header from "-".

I'm not sure how to fix this error, please give me some suggestion, thanks!