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  • Novoalign query

    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.

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