miraligner error

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I have 48 files to align among which 38 files were aligned. Although I did not get the alignment statistics with every file, but .mirna files showed the aligned sequences. I have no idea why I am getting below error with rest 10 fastq files -

Exception in thread "main" java.lang.StringIndexOutOfBoundsException: begin 79, end 82, length 79
at java.base/java.lang.String.checkBoundsBeginEnd(String.java:3107)
at java.base/java.lang.String.substring(String.java:1873)
at miraligner.map.readseq(map.java:285)
at miraligner.Main.main(Main.java:86)

These 10 fastq files are not even that huge (some are smaller than the aligned ones). Also, I noticed other java out of bounds error with aligned sequences too but still they were aligned.
How can I get these 10 files done with alignment without this error? With these files I am getting empty '.mirna' as well as '.nomap' files.

p.s.
I checked same codes after using an empty 'Mirna.str' file and interestingly I got the alignment statistics with these 10 files too, but output.mirna file was blank and .nomap file was blank too.

Start with the stack trace at miraligner/map.java:285 and the call from miraligner/Main.java:86, comparing the failing FASTQ files with files that align successfully. Check how Mirna.str affects processing, then reproduce the error and define completion as producing non-empty, valid .mirna and .nomap outputs with alignment statistics for the affected files.

Written by the indexing model from the issue text.