RC454 samToQlx.pl giving empty qlx

[Guinevere Queenie Lee]

Please help.

I'm using macOS Sierra.

Question 1.  

These lines successfully generated a qlx file but the file was empty.

cd /Users/Guin/Desktop/RC454

perl samToQlx.pl 01_AI_D0_V3_Maligned.mkb.sam AH_J0_V3_fna_CONSEQ.fasta 01_AI_D0_V3

Both input files are attached here.

Question 2.

Mosaik aligned the files and save into bam, samtools converted bam into sam.... my question is, why is samToQlx.pl asking for a reference fasta again?

perl samToQlx.pl <saminput.sam> <reference.fasta> <qlxoutput.qlx>

Any one any clue?

Thanks a lot in advance!!!

Guin