#Starting miRDeep2
/home/shared/mirdeep2/bin/miRDeep2.pl /home/shared/8TB_HDD_01/sam/data/P_evermanni/sRNAseq/mirtrace.config.output/qc_passed_reads.all.collapsed/no_spaces-sRNA-POR-79-S1-TP2.flexbar_trim.20230621-cat.fasta /home/shared/8TB_HDD_01/sam/data/P_evermanni/genomes/Porites_evermanni_v1.fa no_spaces-sRNA-POR-79-S1-TP2.flexbar_trim.20230621-cat.fasta.arf none none none

miRDeep2 started at 18:33:32


mkdir mirdeep_runs/run_09_08_2023_t_18_33_32

readline() on closed filehandle IN at /home/shared/mirdeep2/bin/miRDeep2.pl line 363.
Use of uninitialized value in pattern match (m//) at /home/shared/mirdeep2/bin/miRDeep2.pl line 363.
Error: Mapping file no_spaces-sRNA-POR-79-S1-TP2.flexbar_trim.20230621-cat.fasta.arf is not in arf format

Each line of the mapping file must consist of the following fields
readID_wo_whitespaces  length  start  end read_sequence genomicID_wo_whitspaces length  start   end     genomic_sequence  strand  #mismatches editstring
The editstring is optional and must not be contained
The readID must end with _xNumber and is not allowed to contain whitespaces.
The genomeID is not allowed to contain whitespaces.