Hello!

I have been trying to run AlignGraph to extend the scaffolds of my de novo assembly, but the only output I get is the help message. There are no error messages to give me any clue of what I am doing wrong. I have 3 Illumina libraries and a reference gnome. My command is:

./AlignGraph --read1 Shotgun_1.fq --read2 Shotgun_2.fq --contig ABYSS60.fa --genome reference.fna --distanceLow 875 --distanceHigh 1125 --insertLow 294 --insertHigh 1000 --extendedContig Superscaffolds.fa --remainingContig Contigs_remaining.fa

When I remove "--insertLow" and "--insertHigh" from the command, the program runs for about 1 hour and show me the help message again.

I really would appreciate some help here. Thank you