#1 miRDP2- script_err file showing the error

[MP]

This is the script_err file generated when I run the miRDP2 software on fasta file. Did anyone face the same issue with this software? I removed the sequences that contain 'N' in it, still this error is popping up.
Thanks

## reads processed: 11120169
## reads with at least one reported alignment: 40701 (0.37%)
## reads that failed to align: 11079468 (99.63%)
# Reported 40701 alignments
## reads processed: 11120169
## reads with at least one reported alignment: 0 (0.00%)
## reads that failed to align: 11120169 (100.00%)
# No alignments
## reads processed: 0
## reads with at least one reported alignment: 0 (0.00%)
## reads that failed to align: 0 (0.00%)
# No alignments
## reads processed: 0
## reads with at least one reported alignment: 0 (0.00%)
## reads that failed to align: 0 (0.00%)
No alignments
Warning: Empty input file
Error: No unambiguous stretches of characters in the input.  Aborting...
Command: bowtie-build --wrapper basic-0 -f /users/mpate131/Broccoli_data/file_data/processedFiles//N_removed/N_removed_precursors.fa /users/mpate131/Broccoli_data/file_data/processedFiles//N_removed/index/N_removed_precursors 
Could not locate a Bowtie index corresponding to basename "/users/mpate131/Broccoli_data/file_data/processedFiles//N_removed/index/N_removed_precursors"
Command: /apps/pkg/mirdp2/1.1.4/rhel7_u5/gnu/bin/bowtie-align-s --wrapper basic-0 -a -v 0 -f /users/mpate131/Broccoli_data/file_data/processedFiles//N_removed/index/N_removed_precursors /users/mpate131/Broccoli_data/file_data/processedFiles//N_removed/N_removed_filtered.fa