Usage
[HELLO] I am the Flux Simulator (version 1.2), nice to meet you!

[INIT] I am collecting information on the run.
        initializing profiler  **********
[CAUTION] I overwrite the expression values in file testRun.pro, please confirm:
        (Yes,No,Don't know) y

[WARNING] I will overwrite the library file testRun.lib, please confirm:
        (Yes,No,Don't know) y

[ATTENTION] I am going to delete the sequencing file testRun.bed, please confirm:
        (Yes,No,Don't know) y

[PROFILING] I am assigning the expression profile
        NB_CELLS        50
        NB_MOLECULES    5000000
        EXPRESSION_K    -0.6
        EXPRESSION_X0   5.0E7
        EXPRESSION_X1   9500.0
        PRO_FILE_NAME   /users/rg/msammeth/Simulator/FluxSimulator-v1.2-j1.5/demo/testRun.pro
        profiling       OK 
        Updating .pro file      molecules       4999489.0

[LIBRARY] creating the cDNA libary
        FRAG_LAMBDA     500.0
        FRAG_SIGMA      0.05
        FRAG_THRESHOLD  0.1
        FRAG_B4_RT      false
        RT_MIN  500
        RT_MAX  5500
        RT_PRIMER       POLY-DT
        FILTERING       false
        FILT_MIN        200
        FILT_MAX        250
        PRO_FILE_NAME   /users/rg/msammeth/Simulator/FluxSimulator-v1.2-j1.5/demo/testRun.pro
        TMP_DIR /tmp

        Initializing Fragmentation File **********
        Reverse Transcription **********
        Copying results **********
        Updating .pro file  *

[SEQUENCING] getting the reads
        READ_LENGTH     75
        PRO_FILE_NAME   /users/rg/msammeth/Simulator/FluxSimulator-v1.2-j1.5/demo/testRun.pro
        SEQ_FILE_NAME   /users/rg/msammeth/Simulator/FluxSimulator-v1.2-j1.5/demo/testRun.bed
        sequencing init **********
        sequencing **********
        Moving temporary BED file *
        Updating .pro file  *

[END] I finished, took me 73 sec.

Warning: The Flux Simulator will overwrite the corresponding files .PRO, .LIB and .BED, if already the flag -f is used.

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