4.3 Poly-dT Priming and DNAse Digestion

[INFO] I am collecting information on the run.
    initializing profiler  **********
[CAUTION] I overwrite the expression values in file sacCer3_enzyme.pro, please confirm:
    (Yes,No,Don't know) y
[INFO] Checking GTF file
*[WARN] Unsorted in line 5 - cannot perform gene clustering: chrI + YAL069W @ 335 after YAL012W @ 130799
********* OK (00:00:02)
[GTF FILE] The GTF reference file given is not sorted, but we found a sorted version.
[GTF FILE] The Simulator will use /Users/micha/Desktop/sacCer3_SGDGenes_fromUCSC120515_sorted.gtf
[GTF FILE] You might want to update your parameters file
[PROFILING] I am assigning the expression profile
********** OK (00:00:02)
    Reading reference annotation *[WARN] merging exon (31229,35248) with exon (29935,31227) in transcript YBL100W-B because intervening intron has 4 or less nt.
[WARN] merging exon (222636,226598) with exon (221330,222634) in transcript YBL005W-B because intervening intron has 4 or less nt.
*********[WARN] merging exon (-854953,-856257) with exon (-850989,-854951) in transcript YPR158C-D because intervening intron has 4 or less nt.
 OK (00:00:01)
    found 6664 transcripts
[PROFILING] Parameters
    NB_MOLECULES    5000000
    EXPRESSION_K    -0.6
    EXPRESSION_X0    5.0E7
    EXPRESSION_X1    9500.0
    PRO_FILE_NAME    /Users/micha/Desktop/sacCer3_enzyme.pro
    profiling ********** OK (00:00:00)
    Updating .pro file  ********** OK (00:00:00)
    molecules    4999971
[LIBRARY] creating the cDNA libary
    Initializing Fragmentation File ********** OK (00:00:04)
    4999971 mol initialized
[LIBRARY] Reverse Transcription
[LIBRARY] Configuration
        Mode: PDT
        PWM: No
        RT MIN: 500
        RT MAX: 2500
    Processing Fragments ********** OK (00:00:15)
        4999971 mol: in 4999971, new 0, out 4999971
        avg Len 969.7831, maxLen 2500
    preparing transcript sequences *[WARN] merging exon (31229,35248) with exon (29935,31227) in transcript YBL100W-B because intervening intron has 4 or less nt.
*********[WARN] merging exon (-854953,-856257) with exon (-850989,-854951) in transcript YPR158C-D because intervening intron has 4 or less nt.
 OK (00:00:02)
[LIBRARY] Enzymatic Digestion
[LIBRARY] Configuration
Left Flank : 100
Right Flank : 300
Motif: DNAseI.pwm
    Processing Fragments ********** OK (00:02:38)
        60604099 mol: in 4999971, new 55604128, out 60604099
        avg Len 80.00923, maxLen 2500
        initializing Selected Size distribution
[LIBRARY] Segregating cDNA (MCMC Filter)
    Processing Fragments ********** OK (00:01:47)
        60604099 mol: in 60604099, new 0, out 25719279
        avg Len 47.310493, maxLen 276
        start amplification
[INFO] Loading default PCR distribution
[LIBRARY] Amplification
[LIBRARY] Configuration
        Rounds: 15 
        Mean: 0.5 
        Standard Deviation: 0.1 
    Processing Fragments ********** OK (00:01:05)
    Amplification done.
    In: 25719279 Out: 693695450
        25719279 mol: in 25719279, new 0, out 693695450
        avg Len 47.319595, maxLen 266
    Copied results to /Users/micha/Desktop/sacCer3_enzyme.lib
    Updating .pro file  ********** OK (00:00:00)
[SEQUENCING] getting the reads
    Initializing Fragment Index
    Indexing ********** OK (00:00:14)
    13804020 lines indexed (693695450 fragments, 6534 entries)
    sequencing *[WARN] merging exon (31229,35248) with exon (29935,31227) in transcript YBL100W-B because intervening intron has 4 or less nt.
*********[WARN] merging exon (-854953,-856257) with exon (-850989,-854951) in transcript YPR158C-D because intervening intron has 4 or less nt.
 OK (00:14:03)
    693695450 fragments found (13804020 without PCR duplicates)
    998612 reads sequenced
    226528 reads fall in poly-A tail
    407504 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 1305 sec.