Can't copy GTF file

[GoogleCodeExporter]

Hi,
I am running Fluxsimulator20100526, and getting the following error:
created 36 temporary files, removed 36 files, failed to remove 0 files.
moving [FATAL] couldn't copy: 
/home/khan/readSim/FluxSimulator/HumReadSim/Homo_sapiens.GRCh37.58_sorted.gtf 
(No such file or directory)
java.io.FileNotFoundException: 
/home/khan/readSim/FluxSimulator/HumReadSim/Homo_sapiens.GRCh37.58_sorted.gtf 
(No such file or directory)
at java.io.FileInputStream.open(Native Method)
at java.io.FileInputStream.<init>(FileInputStream.java:106)
at java.io.FileReader.<init>(FileReader.java:55)
at genome.io.B.A(Unknown Source)
at genome.io.B.ö(Unknown Source)
at genome.io.B.B.<init>(Unknown Source)
at genome.sequencing.rnaseq.simulation.C.Ã(Unknown Source)
at genome.sequencing.rnaseq.simulation.C.Ã(Unknown Source)
at genome.sequencing.rnaseq.simulation.C.run(Unknown Source)
at genome.sequencing.rnaseq.simulation.FluxSimulator.F(Unknown Source)
at genome.sequencing.rnaseq.simulation.FluxSimulator.run(Unknown Source)
at genome.sequencing.rnaseq.simulation.FluxSimulator.main(Unknown Source)
Reading reference annotation found 0 transcripts
I have checked the folder permissions, etc…
Appreciate any suggestion/advice.

Thanks.

Original issue reported on code.google.com by gmicha@gmail.com on 7 Jun 2010 at 7:41

[GoogleCodeExporter]

Original comment by gmicha@gmail.com on 7 Jun 2010 at 7:41

• Added labels: Simulator

[GoogleCodeExporter]

Confirmed. The issue is reproduceable for unsorted GTF files located in the 
project directory. Triggers a move with identical from/to files.

Original comment by gmicha@gmail.com on 11 Jun 2010 at 11:58

• Changed state: Accepted

[GoogleCodeExporter]

Added in Profiler.getGFFReader() the line
  if (!refFile.equals(settings.getRefFile())) 

before
  if (!FileHelper.move(refFile, settings.getRefFile(), Constants.progress))

fixed in build 20100611
  http://code.google.com/p/fluxcapacitor/downloads/detail?name=FluxSimulator-20100611.tar.gz&can=2

Original comment by gmicha@gmail.com on 11 Jun 2010 at 12:02

• Changed state: Fixed