Hi Achille, > - the fneighbor app fails everytime with errors like this : > Error: Distances file found 0 rows, expected 15
This problem looks like have been fixed in CVS version of EMBOSS, as i get reasonable output when i run CVS version of fneighbor with your input file. This suggests current patches don't include the fixes I thought they have. It is my fault that i didn't double check it before returning you. > I don't understand the "Standard error stream" explanation! about datafile > and the "-auto" param. "-auto" is an emboss parameter which means EMBOSS should try runing an application without asking further questions but using the inputs/parameters available on the command line. We will consider removing it from Soaplab job reports. "Standard error stream" is a term used by Soaplab meaning "error output of the job", it looks like we can improve its wording. > Instead If I use, for exsample, a 48 sequences alignment input I have a > java heap space error (is it my computer fault?). This is most probably related to memory used by your Taverna Java process. I tested your 48 sequence alignment with all 3 workflows attached, i didn't get any memory errors but i use a quite generous -Xmx setting in my runme.sh file. You may try increasing the default -Xmx setting in your taverna runme.sh file. Alternatively, as far as i know memory used grows each time i run a new workflow in taverna, you may try closing existing workflow run tabs before running a new workflow. > -the timeout limit for the jobs is 60 minutes!? , it is a restriction of > EBI that is impossible to avoid I suppose! this was a good enough timeout limit previously, i think we can increase it, let me discuss this with relevant people, if i execute the same fproml job outside LSF it takes about 80 minutes which suggests a 2 hour limit should allow your fproml jobs completed. > for example a fproml job with 48 seq align is more than 60 minutes long I > think because after 1 hour it returns a completed job message with empty > output. This is a bug in Soaplab (introduced by me), it should report the status terminated, rather than completed successfully. Regards, Mahmut ------------------------------------------------------------------------------ The NEW KODAK i700 Series Scanners deliver under ANY circumstances! Your production scanning environment may not be a perfect world - but thanks to Kodak, there's a perfect scanner to get the job done! With the NEW KODAK i700 Series Scanner you'll get full speed at 300 dpi even with all image processing features enabled. http://p.sf.net/sfu/kodak-com _______________________________________________ taverna-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/taverna-users Documentation: http://www.mygrid.org.uk/usermanual1.7/ FAQ: http://www.mygrid.org.uk/wiki/Mygrid/TavernaFaq Biological Services: http://www.mygrid.org.uk/wiki/Mygrid/BiologicalWebServices
