Details
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Story
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Status: Resolved
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Major
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Resolution: Fixed
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Simulator 1.0 (API 1.01), Simulator 1.1 (API 1.15)
Description
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