Novoalign query

[slp]

I am running into problems trying to run novoalign. We ran a 96 bp paired end exome sequencing exp. But the fastq files have reads ranging from 35-96bp (because of adapter trimming).
Each fast file has about 10s of Millions of reads. But when I try to align the reads with the following command
novoalign -d hg38.nix -f read1.fastq read2.fastq -o SAM > Out.sam

only few hundred reads are processed out of the Millions of reads (Please see below). I am not sure whats going wrong here.

Interpreting input files as Illumina FASTQ, Casava Pipeline 1.8 & later.
# Index Build Version: 3.3
# Hash length: 14
# Step size: 2
# Paired Reads: 259
# Proper Pairs: 193 (74.5%)
# Read Sequences: 518
# Unique Alignment: 469 (90.5%)
# Multi Mapped: 36 ( 6.9%)
# No Mapping Found: 7 ( 1.4%)
# QC Failures...
# Read Length: 6 ( 1.2%)
# Elapsed Time: 5.855 (secs.)
# CPU Time: 12.41 (secs.)
# Fragment Length Distribution
# From To Count
# 45 59 11
# 60 74 18
# 75 89 3
# 90 104 33
# 105 119 23
# 120 134 19
# 135 149 17
# 150 164 9
# 165 179 9
# 180 194 7
# 195 209 4
# 210 224 3
# 225 239 4
# 240 254 3
# 255 269 2
# 270 284 1
# 285 299 1
# 300 314 2
# 315 329 0
# 330 344 0
# 345 359 0
# 360 374 0
# 375 389 0
# 390 404 1
# 405 419 1
# Mean 132, Std Dev 62.0
# Done at Mon Nov 9 20:31:31 2015


Any help is much appreciated.