Align to refrence

[sowmiyakathir]

Hi, I have cloned this repository to have a try.I have checked the path,Version of the software installed etc.,Still I don't know why this error occurs.

code: if [ -z $RAW_READS_R2 ] #if RAW_READS_R2 variable not set in parameters file, then align single-end reads to reference genome then parallel --max-procs $NUM_CORES --keep-order --link "bwa mem $REF_GENOME {} | samtools sort -o Intermediate_files/2.bam_alignments/{/.}.sorted_bam; samtools index Intermediate_files/2.bam_alignments/{/.}.sorted_bam" ::: ls Intermediate_files/1.Demultiplexed_reads/*.R1.fastq.gz

elif [ -n $RAW_READS_R2 ] #if RAW_READS_R2 variable set in parameters file, then align paired-end reads to reference genome then parallel --max-procs $NUM_CORES --keep-order --link "bwa mem $REF_GENOME {1} {2} | samtools sort -o Intermediate_files/2.bam_alignments/{1/.}.sorted_bam; samtools index Intermediate_files/2.bam_alignments/{1/.}.sorted_bam" ::: ls Intermediate_files/1.Demultiplexed_reads/*.R1.fastq.gz ::: ls Intermediate_files/1.Demultiplexed_reads/*.R2.fastq.gz fi parallel: Error: Parsing of --jobs/-j/--max-procs/-P failed.

Thank you in advance, Mia