can not run the sortmerna #448
Description
I recently run (computecanada) the sortmerna to filter my rRNA sequence from metatranscprtomic data with paired -end fastq file, previously I used the following command and it works well:
INPUT_DIR=/home/guokang/scratch/24metatranscriptome_hostremoval
DB_PATH=/home/guokang/scratch/rna-seq/sortmerna_databases_v4
OUTPUT_DIR=/home/guokang/scratch/rna-seq
sortmerna --ref $DB_PATH/smr_v4.3_default_db.fasta --reads $INPUT_DIR/602D_remove_R1.fastq --reads $INPUT_DIR/602D_remove_R2.fastq --paired_in --fastx --other $OUTPUT_DIR/602D.non_rRNA --threads 8
However, when I add some parameters to run again, it always told me "[process:1434] ESC[0;31mERRORESC[0m: the value provided without a flag/option. Note that e.g. '-ref' or '-reads' have to be used with Each file. See 'sortmerna -h'.
This is the new code for running and the error happened. My sortmerna version is 4.3.7 and I have double checked the --ref is okay for me from the github, could you help me to check out what is something wrong with my code? thank you!
sortmerna --ref $DB_PATH/smr_v4.3_default_db.fasta --reads $INPUT_DIR/602D_remove_R1.fastq --reads $INPUT_DIR/1.602D_remove_R2.fastq --paired_in --fastx --other $OUTPUT_DIR/602D.non_rRNA --threads 8 -e 1e-7 -num_alignments 1