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Parameter
NB_MOLECULES | 5,000,000 |
TSS_MEAN | 25 |
POLYA_SCALE | 300 |
POLYA_SHAPE | 2 |
FRAG_SUBSTRATE | RNA |
FRAG_METHOD | UR |
FRAG_UR_ETA | 170 |
FRAG_UR_D0 | 1 |
RTRANSCRIPTION | YES |
RT_PRIMER | RH |
RT_LOSSLESS | YES |
RT_MIN | 500 |
RT_MAX | 5,500 |
PCR_DISTRIBUTION | default |
FILTERING | YES |
SIZE_SAMPLING | MH |
READ_NUMBER | 15,000,000 |
READ_LENGTH | 75 |
PAIRED_END | YES |
[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.