#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-73-S1-TP2.flexbar_trim.20230621-cat.fasta /home/shared/8TB_HDD_01/sam/data/P_evermanni/genomes/Porites_evermanni_v1.fa 20230809-peve-miRNA-mirdeep2-no_spaces-sRNA-POR-73-S1-TP2.flexbar_trim.20230621-cat.fasta.arf none none none

miRDeep2 started at 14:34:56


mkdir mirdeep_runs/run_09_08_2023_t_14_34_56

#testing input files
sanity_check_reads_ready_file.pl /home/shared/8TB_HDD_01/sam/data/P_evermanni/sRNAseq/mirtrace.config.output/qc_passed_reads.all.collapsed/no_spaces-sRNA-POR-73-S1-TP2.flexbar_trim.20230621-cat.fasta

started: 14:35:07
Error: problem with /home/shared/8TB_HDD_01/sam/data/P_evermanni/sRNAseq/mirtrace.config.output/qc_passed_reads.all.collapsed/no_spaces-sRNA-POR-73-S1-TP2.flexbar_trim.20230621-cat.fasta
Error in line 2.880.372: The sequence

CCTGTCTTTATTGAGTCTCA

occures at least twice in sample seq in your reads file.

At first it occured at line 282.546

Please make sure that your reads file only contains unique sequences within each sample.