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.