Query related to output of mirdeep2.pl script of mirdeep2

[99ARITRA]

I recently ran the mirdeep2.pl script for identifying novel miRNA sequences in plants. I got the following message in the log file that was generated after the script finished running:

parsing input file finished checking Rfam for hits to precursors Build bowtie index of Rfam entries

Mapping mature, star and loop sequences against index Setting the index via positional argument will be deprecated in a future release. Please use -x option instead. reads processed: 6347 reads with at least one alignment: 8 (0.13%) reads that failed to align: 6339 (99.87%) Reported 17 alignments

This message is usually displayed after running Bowtie and usually a SAM file and an aligned and/or unaligned fasta file is generated as an output and mirdeep2.pl uses bowtie . But here none of these files generated.

Does the mirdeep2.pl script not generate these files ?

[Drmirdeep]

Did you try to run the tutorial ? intermediate files are usually put into the tmp folder

[99ARITRA]

Yes I did run the tutorial files of C. elegans (reported 0 alignments) and checked the tmp folder in mirdeep_runs. It contained files related to precursors ,precursors_for_randfold, an .mrd, and some .arf files.

I also checked the files in the tmp folder of my own experimental run (which reported 17 alignments) . They are the same files. However, I could not find files related to bowtie.

Also I did find another folder called mirna_results_21_06_2023_t_01_52_23 which contained the .fa and .bed files of novel mature, loops and star mirnas which were created in the final step of mirdeep2.pl. I am not clear if these files are the results of bowtie.

Also for your information this is the command line I used to run mirdeep2.pl: miRDeep2.pl collapsed_reads.fa chickpea_genome_mod.fa novel_prediction_mirna.arf none none none 2>report.log

[Drmirdeep]

maybe plant related. However, If the tutorial produces 0 alignments then your installation maybe faulty