[INFO] I am collecting information on the run.
initializing profiler **********
[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. |