Hi I am new to isomiR analysis and I tried using miraligner with fastq sequences produced from small RNA seq. I have couple of issues-

1. When I run my script- java -jar miraligner.jar -sub 1 -trim 3 -add 3 -s hsa -i /Users/pg2597/Downloads/pilot_fastq/xyz.fastq -db DB -o /Users/pg2597/Desktop/output I get this while process- 'Format is not tabular,guessing fasta '
   I checked the format of fastq files still it's taking it as a fasta plus what does it mean by Format is not tabular.

2. As result I get-

species found Go to mapping... Mismatches: 1 Trimming: 3 Addition: 3 Species: hsa Tue May 29 20:07:44 EDT 2018

Reading reads Number of reads to be mapped: 1086336 Searching in precursors Tue May 29 20:07:48 EDT 2018 Num reads annotated: 0

As can be seen that reads are not annotated. I get a blank output file only with header info not single sequence annotation. Can someone explain this?

I need to find isomiRs in my data.