CMD: bowtie2 --threads 2 --local --no-unal -x trinity_out_dir/Trinity.fasta -q -k 10 -1 /gscratch/srlab/sam/data/P_trituberculatus/RNAseq/SRR10757128.sra_1.fastq -2 --right stat: Bad file descriptor Warning: Could not open read file "--right" for reading; skipping... Error: No input read files were valid (ERR): bowtie2-align exited with value 1 Error, cmd: bowtie2 --threads 2 --local --no-unal -x trinity_out_dir/Trinity.fasta -q -k 10 -1 /gscratch/srlab/sam/data/P_trituberculatus/RNAseq/SRR10757128.sra_1.fastq -2 --right died with ret (256) at /gscratch/srlab/programs/trinityrnaseq-v2.9.0/util/misc/../../PerlLib/Process_cmd.pm line 19. Process_cmd::process_cmd('bowtie2 --threads 2 --local --no-unal -x trinity_out_dir/Trin...') called at /gscratch/srlab/programs/trinityrnaseq-v2.9.0/util/misc/run_bowtie2.pl line 84 [main_samview] fail to read the header from "-". samtools sort: failed to read header from "-"