Hi Patrick,
I have SUMmOn installed on two different machines. When I run summon -c <conditionfile> <inputfile> on them none of them shows a menu of choices(according to your quickstart guide). They immediately starts calculating charges, peaks, average charges etc. so ultimately I am end up with no XML file. Additionally on one of the machine it ends with following output and keeps going creating hundreds of png images and (kind of hang).
*******************Creating png images
Warning: empty x range [531.326:531.326], adjusting to [526.013:536.639]
Warning: empty x range [531.326:531.326], adjusting to [526.013:536.639]
I would appreciate you would let me know how to overcome these issues.
Thank You,
poly_guy
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Hi Patrick,
I understood from code that by default it takes option 5 and calls prepareSumoXML() function, from there it creats png files but I end up with NO XML file. Now I think I dont have proper input files as I am just a programmer guy, if you have a proper combination of sample mzXML file, condition file and subDB.fasta file then I can test better. if you could provide me those samples.
still dont know why I am getting those "Warning : empty x range ..." stuff in one machine.
my email is : poly_guy@indiatimes.com
Thank You,
poly_guy
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Hi poly_guy,
if you would like to use the interactive menu, please make sure that your condition file has the following line <nonInteractive value="0"/>.
The "Warning: empty x range [531.326:531.326], adjusting to [526.013:536.639]" is a message from gnuplot, which is used for the generation of the spectra, you can simply ignore it.
The real problem is however that you don't get an XML file at the end of the analysis! Does the program crash? Does it give you any specific error message? Did you wait untill the end of the creation of the .png files (I know this can take quite a bit of time)? One thing you can try is to re-compile SUMmOn after uncomenting "#define DOPNGS" from the "macros" file. This will create a version of SUMmOn that does not generate the .pngs. Please let me know if you have an XML file at the end of the analysis if you do this.
Cheers,
Patrick
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Hi Patrick,
I did all your step, program doesnt give any errors, it doesnt crash, even after recompiled it doesnt generate xml file. I think I would be doing fresh install on new machine and will check again. Will let you know about output.
Thanks,
Poly guy
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
Hi Patrick,
I have SUMmOn installed on two different machines. When I run summon -c <conditionfile> <inputfile> on them none of them shows a menu of choices(according to your quickstart guide). They immediately starts calculating charges, peaks, average charges etc. so ultimately I am end up with no XML file. Additionally on one of the machine it ends with following output and keeps going creating hundreds of png images and (kind of hang).
*******************Creating png images
Warning: empty x range [531.326:531.326], adjusting to [526.013:536.639]
Warning: empty x range [531.326:531.326], adjusting to [526.013:536.639]
I would appreciate you would let me know how to overcome these issues.
Thank You,
poly_guy
Hi Patrick,
I understood from code that by default it takes option 5 and calls prepareSumoXML() function, from there it creats png files but I end up with NO XML file. Now I think I dont have proper input files as I am just a programmer guy, if you have a proper combination of sample mzXML file, condition file and subDB.fasta file then I can test better. if you could provide me those samples.
still dont know why I am getting those "Warning : empty x range ..." stuff in one machine.
my email is : poly_guy@indiatimes.com
Thank You,
poly_guy
Hi poly_guy,
if you would like to use the interactive menu, please make sure that your condition file has the following line <nonInteractive value="0"/>.
The "Warning: empty x range [531.326:531.326], adjusting to [526.013:536.639]" is a message from gnuplot, which is used for the generation of the spectra, you can simply ignore it.
The real problem is however that you don't get an XML file at the end of the analysis! Does the program crash? Does it give you any specific error message? Did you wait untill the end of the creation of the .png files (I know this can take quite a bit of time)? One thing you can try is to re-compile SUMmOn after uncomenting "#define DOPNGS" from the "macros" file. This will create a version of SUMmOn that does not generate the .pngs. Please let me know if you have an XML file at the end of the analysis if you do this.
Cheers,
Patrick
Hi Patrick,
I did all your step, program doesnt give any errors, it doesnt crash, even after recompiled it doesnt generate xml file. I think I would be doing fresh install on new machine and will check again. Will let you know about output.
Thanks,
Poly guy