What is the end flag of mapper.pl

[yy549159265]

Log to parse_mappings.pl

current dir:    /home/yuanshuai20/DP/Transcribe/srna/mirdeep_output
mapper command: ../mirdeep2-master/src/mapper.pl ../exon.intron.filter/all.fa -v -u -c -l 17 -r 10 -n -q -p ../gene_index/MG8 -t all_aligned.arf

timestamp:  28_11_2022_t_19_57_35

discarding short reads
fastaparse.pl ../exon.intron.filter/all.fa -a 17 > dir_mapper_seq_all.fa_6075277583_28_11_2022_t_19_57_35/reads_no_short.fa 2>dir_mapper_seq_all.fa_6075277583_28_11_2022_t_19_57_35/reads_too_short
mapping reads to genome index
bowtie -p 1 -f -n 1 -e 80 -l 18 -a -m 10 --best --strata  ../gene_index/MG8  --al dir_mapper_seq_all.fa_6075277583_28_11_2022_t_19_57_35/all.fa_mapped --un dir_mapper_seq_all.fa_6075277583_28_11_2022_t_19_57_35/all.fa_not_mapped  dir_mapper_seq_all.fa_6075277583_28_11_2022_t_19_57_35/reads_no_short.fa dir_mapper_seq_all.fa_6075277583_28_11_2022_t_19_57_35/mappings.bwt 2>bowtie.log

convert_bowtie_output.pl dir_mapper_seq_all.fa_6075277583_28_11_2022_t_19_57_35/mappings.bwt > dir_mapper_seq_all.fa_6075277583_28_11_2022_t_19_57_35/mappings.arf
trimming unmapped nts in the 3' ends
parse_mappings.pl dir_mapper_seq_all.fa_6075277583_28_11_2022_t_19_57_35/mappings.arf -j > dir_mapper_seq_all.fa_6075277583_28_11_2022_t_19_57_35/mappings_trim.arf

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Terminal output

(base) [yuanshuai20@ZH404 mirdeep_output]$ ../mirdeep2-master/src/mapper.pl ../exon.intron.filter/all.fa -v -u -c -l 17 -r 10 -n -q -p ../gene_index/MG8 -t all_aligned.arf

discarding short reads
mapping reads to genome index
trimming unmapped nts in the 3' ends
Log file for this run is in mapper_logs and called mapper.log_10723

[yy549159265]

My arf file has content，but the terminal does not output

Mapping statistics

#desc   total   mapped  unmapped    %mapped %unmapped

[Drmirdeep]

Is there any specific issue ?