4.4 Poly-dT Priming and Nebulization

[INFO] I am collecting information on the run.
[INFO] Checking GTF file
*[WARN] Unsorted in line 27 - chr/strand Chr1 + already read.
********* OK (371481:13948:59)
[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/TAIR9_GFF3_genes_sorted.gtf
[GTF FILE] You might want to update your parameters file
[PROFILING] I am assigning the expression profile
********** OK (371481:13948:59)
        Reading reference annotation **[WARN] merging exon (-21073927,-21073974) with exon (-21073898,-21073924) in transcript AT1G56280.1 because intervening intron has 4 or less nt.
********[WARN] skipped chromosome ChrM
 OK (00:00:03)
        found 38564 transcripts
[PROFILING] Parameters
        NB_MOLECULES    5000000
        EXPRESSION_K    -0.6
        EXPRESSION_X0   5.0E7
        EXPRESSION_X1   9500.0
        PRO_FILE_NAME   /Users/micha/Desktop/t9_nebulization.pro
        profiling ********** OK (00:00:00)
        Updating .pro file  ********** OK (00:00:00)
        molecules       4999389
[LIBRARY] creating the cDNA libary
        Initializing Fragmentation File ********** OK (00:00:06)
        4999389 mol initialized
[LIBRARY] Reverse Transcription
[LIBRARY] Configuration
                Mode: PDT
                PWM: No
                RT MIN: 400
                RT MAX: 2600
        Processing Fragments ********** OK (00:00:17)
                4999389 mol: in 4999389, new 0, out 4999389
                avg Len 1148.562, maxLen 2600
[LIBRARY] Nebulization
[LIBRARY] Configuration
                Lambda: 600.0
                M: 5.0
                Max Length: 2600.0
                Recursions: 5
        Processing Fragments ********** OK (00:00:32)
                8804186 mol: in 4999389, new 3804797, out 8804186
                avg Len 652.202, maxLen 2427
                start amplification
[LIBRARY] PCR disabled, skipping amplification
        Copied results to /Users/micha/Desktop/t9_nebulization.lib
        Updating .pro file  ********** OK (00:00:00)
[SEQUENCING] getting the reads
        Initializing Fragment Index
        Indexing ********** OK (00:00:10)
        8804186 lines indexed (8804186 fragments, 18951 entries)
        sequencing ***[WARN] merging exon (-21073927,-21073974) with exon (-21073898,-21073924) in transcript AT1G56280.1 because intervening intron has 4 or less nt.
*******[WARN] skipped chromosome ChrM
 OK (00:10:22)
found 38564 transcripts
[PROFILING] Parameters
        NB_MOLECULES    5000000
        EXPRESSION_K    -0.6
        EXPRESSION_X0   5.0E7
        EXPRESSION_X1   9500.0
        PRO_FILE_NAME   /Users/micha/Desktop/t9_nebulization.pro
        profiling ********** OK (00:00:00)
        Updating .pro file  ********** OK (00:00:00)
        molecules       4999389
[LIBRARY] creating the cDNA libary
        Initializing Fragmentation File ********** OK (00:00:06)
        4999389 mol initialized
[LIBRARY] Reverse Transcription
[LIBRARY] Configuration
                Mode: PDT
                PWM: No
                RT MIN: 400
                RT MAX: 2600
        Processing Fragments ********** OK (00:00:17)
                4999389 mol: in 4999389, new 0, out 4999389
                avg Len 1148.562, maxLen 2600
[LIBRARY] Nebulization
[LIBRARY] Configuration
                Lambda: 600.0
                M: 5.0
                Max Length: 2600.0
                Recursions: 5
        Processing Fragments ********** OK (00:00:32)
                8804186 mol: in 4999389, new 3804797, out 8804186
                avg Len 652.202, maxLen 2427
                start amplification
[LIBRARY] PCR disabled, skipping amplification
        Copied results to /Users/micha/Desktop/t9_nebulization.lib
        Updating .pro file  ********** OK (00:00:00)
[SEQUENCING] getting the reads
        Initializing Fragment Index
        Indexing ********** OK (00:00:10)
        8804186 lines indexed (8804186 fragments, 18951 entries)
        sequencing ***[WARN] merging exon (-21073927,-21073974) with exon (-21073898,-21073924) in transcript AT1G56280.1 because intervening intron has 4 or less nt.
*******[WARN] skipped chromosome ChrM
 OK (00:10:22)
        8804186 fragments found (8804186 without PCR duplicates)
        3995704 reads sequenced
        1251847 reads fall in poly-A tail
        3770 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 695 sec.