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  1. Barna Package
  2. BARNA-219

Error while generating reads from a one-transcript gene

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      Hallo

      You must forgive if this issue has been posted on the wrong place. I am new to the simulator and am trying to generate reads from a toy gene, whose only special feature is that it contains only one transcript. The corresponding GTF file contains only one line, namely the following:

      michro FluxSimTest exon 501 1500 . + . transcript_id "mitx";
      gene_id "migene";

      My parameter file looks like this:

      REF_FILE_NAME /toyDirectory/toy.gtf
      GEN_DIR /toyDirectory

      READ_NUMBER 100
      READ_LENGTH 35
      PAIRED_END NO
      FASTA TRUE

      Whenever I run the simulator with these configuration, the following error appears:

      flux -t simulator -p firstToy.par
      [INFO] I am the Flux Toolbox (v1.0-RC5 build 569), nice to meet you!

      [INFO] No mode selected, executing the full pipeline (-x -l -s)
      [INFO] I am collecting information on the run.

      [INFO] Checking GTF file
      OK (374150:24633:46)
      [PROFILING] I am assigning the expression profile
      OK (374150:24633:46)
      Reading reference annotation OK (00:00:00)
      found 1 transcripts

      [PROFILING] Parameters
      NB_MOLECULES 5000000
      EXPRESSION_K -0.6
      EXPRESSION_X0 5.0E7
      EXPRESSION_X1 9500.0
      PRO_FILE_NAME /fs1.data/quant/singleParalog/firstToy/firstToy.pro

      profiling FAILED
      [ERROR] Error while profiling :n must be positive

      %%%%%

      What am I doing wron?

      Thanks in advance,

      Tonatiuh

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            thasso Thasso Griebel
            tonatiuh Tonatiuh Pena Centeno
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