4.1 RNA Hydrolysis Protocol (M.musculus)

[INFO] Checking GTF file
********** OK (00:00:04)
[PROFILING] I am assigning the expression profile
********** OK (00:00:05)
    Reading reference annotation ********** OK (00:00:07)
    found 28045 transcripts

[PROFILING] Parameters
    NB_MOLECULES    5000000
    EXPRESSION_K    -0.6
    EXPRESSION_X0    5.0E7
    EXPRESSION_X1    9500.0
    PRO_FILE_NAME    /Users/micha/Desktop/mm9_hydrolysis.pro

    profiling ********** OK (00:00:00)
    Updating .pro file  ********** OK (00:00:00)
    molecules    4999457

[LIBRARY] creating the cDNA libary
    Initializing Fragmentation File ********** OK (00:00:05)
    4999457 mol initialized
[LIBRARY] Fragmentation UR
[LIBRARY] Configuration
        D0: 1.0
        Delta:  Not specified, depends on sequence length
        Eta: 170.0

    Processing Fragments ********** OK (00:02:34)
        93363234 mol: in 4999457, new 88363777, out 93363234
        avg Len 154.08191, maxLen 513
    preparing transcript sequences ********** OK (00:01:21)
[LIBRARY] Reverse Transcription
[LIBRARY] Configuration
        Mode: RH
        PWM: No
        RT MIN: 500
        RT MAX: 5500

    Processing Fragments ********** OK (00:05:32)
        93363234 mol: in 93363234, new 0, out 93347200
        avg Len 145.28108, maxLen 506
        initializing Selected Size distribution
[LIBRARY] Segregating cDNA (MCMC Filter)
    Processing Fragments ********** OK (00:03:14)
        93347200 mol: in 93347200, new 0, out 49712978
        avg Len 153.1023, maxLen 299
        start amplification
[INFO] Loading default PCR distribution
[LIBRARY] Amplification
[LIBRARY] Configuration
        Rounds: 15 
        Mean: 0.5 
        Standard Deviation: 0.1 


    Processing Fragments ********** OK (00:03:13)
    Amplification done.
    In: 49712978 Out: 1340698400


        49712978 mol: in 49712978, new 0, out 1340698400
        avg Len 153.10666, maxLen 299
    Copied results to /Users/micha/Desktop/mm9_hydrolysis.lib
    Updating .pro file  ********** OK (00:00:00)

[SEQUENCING] getting the reads
    Initializing Fragment Index
    Indexing ********** OK (00:00:30)
    26681880 lines indexed (1340698400 fragments, 18750 entries)
    sequencing ********** OK (00:35:05)

    1340698400 fragments found (26681880 without PCR duplicates)
    29993750 reads sequenced
    2314644 reads fall in poly-A tail
    2538184 truncated reads

    Moving temporary BED file

    Updating .pro file  ********** OK (00:00:00)
    Updating .pro file  ********** OK (00:00:00)
    Updating .pro file  ********** OK (00:00:00)
    Updating .pro file  ********** OK (00:00:00)

[END] I finished, took me 3252 sec.