V-Phaser-2 Error: can't open file /V4528_assembly.0.499.region

[michael.pa...@gmail.com]

Note, I do not have root access on my machine. Latest version of V-Phaser2 from broad's site.

$ bin/variant_caller -i TestData/4528.454.indelRealigned.bam

--------------------------------------------------------
Program runs with the following Parameter setting:

    input BAM file    =    TestData/4528.454.indelRealigned.bam
    output Directory    =   
    errModel        =    pileup + phase
    alpha        =    0.05
    ignoreBases     =    0
    (var_matepair, var_cycle, var_dt, var_qt)    =    1,1,1,20
    pSample        =    30%
    windowSz    =    500
    delta    =    2

--------------------------------------------------------


    1 bam file(s) found:
        TestData/4528.454.indelRealigned.bam


Parse bam header: get refSeq info & sanity check

    V4528_assembly len =10621

    1 ref sequence(s) found:
        Name: V4528_assembly
            BamfileID = 0    RefID = 0


    1 platform(s) found: 454   


Get maxQ, minQ, maxReadLen, avgFragSz, stdFragSz from bam files ...

    Total Reads = 26771
    # Mapped Reads = 26755
    # Reads used for checking Q scores = 26755
    minQ = 33    maxQ=73        maxRL = 540
    (avgfragSz, std) = 0    0
[WARNING]: Apparently the BAM file is not set properly such that the Fragment length cannot be measured IF this is Illumina paired alignment file


Generate qual -> quantile map ...


Set up paired read map arrays ...

    # total mapped reads: 26755
    # mapped mate-pairs = 13377
    recalculated frag size and std0, 0

Prepare aln columns file...

 Ref: V4528_assembly , len = 10621


        create file: /V4528_assembly.0.499.region
[EXIT]: create_output_file: can't open file /V4528_assembly.0.499.region