Here's what I've done thus far: I have used sequest search to generate OUT files for all my samples. I successfully converted all the out files into appropriate pepxml files. I have all the pepxml fiels all in the same directory. For example, this the location for 1of 360 of my files c:/Inetpub/wwwroot/ISB/data/MyelomaGelLC2010-Sayeef/ 011311_U266_1-run1.pep.xml.
So when I open peptide prophet, I have selected all the pepxml files. And then I accept all the default selectionsa nd perss runxineract! It finishes quickly and says the output file is unreadable? I tried decreasing the number of files to see if that made a difference but still no solution. In other words, after I click run analysis, it says: Command Status [ Show / Hide ] Status as of: Fri Oct 7 17:30:27 2011View results of previous commands. Output Files c:/Inetpub/wwwroot/ISB/data/MyelomaGelLC2010-Sayeef/interact.pep.shtml [ Unreadable! ] Command 1 [Fri Oct 7 17:29:25 2011] [ Show / Hide ] run_in c:/Inetpub/wwwroot/ISB/data/MyelomaGelLC2010-Sayeef; c:\Inetpub \tpp-bin\xinteract -Ninteract.pep.xml -p0.05 -l7 -O c:/Inetpub/ wwwroot/ISB/data/MyelomaGelLC2010-Sayeef/011311_U266_1-run1.pep.xml c:/ Inetpub/wwwroot/ISB/data/MyelomaGelLC2010-Sayeef/011311_U266_10- run1.pep.xml c:/Inetpub/wwwroot/ISB/data/MyelomaGelLC2010-Sayeef/ 011311_U266_11-run1.pep.xml c:/Inetpub/wwwroot/ISB/data/ MyelomaGelLC2010-Sayeef/011311_U266_12-run1.pep.xml c:/Inetpub/wwwroot/ ISB/data/MyelomaGelLC2010-Sayeef/011311_U266_13-run1.pep.xml c:/ Inetpub/wwwroot/ISB/data/MyelomaGelLC2010-Sayeef/011311_U266_14- run1.pep.xml c:/Inetpub/wwwroot/ISB/data/MyelomaGelLC2010-Sayeef/ 011311_U266_15-run1.pep.xml c:/Inetpub/wwwroot/ISB/data/ MyelomaGelLC2010-Sayeef/011311_U266_16-run1.pep.xml c:/Inetpub/wwwroot/ ISB/data/MyelomaGelLC2010-Sayeef/011311_U266_17-run1.pep.xml c:/ Inetpub/wwwroot/ISB/data/MyelomaGelLC2010-Sayeef/011311_U266_18- run1.pep.xml c:/Inetpub/wwwroot/ISB/data/MyelomaGelLC2010-Sayeef/ 011311_U266_19-run1.pep.xml c:/Inetpub/wwwroot/ISB/data/ MyelomaGelLC2010-Sayeef/011311_U266_2-run1.pep.xml c:/Inetpub/wwwroot/ ISB/data/MyelomaGelLC2010-Sayeef/011311_U266_20-run2.pep.xml c:/ Inetpub/wwwroot/ISB/data/MyelomaGelLC2010-Sayeef/011311_U266_3- run1.pep.xml c:/Inetpub/wwwroot/ISB/data/MyelomaGelLC2010-Sayeef/ 011311_U266_4-run1.pep.xml c:/Inetpub/wwwroot/ISB/data/ MyelomaGelLC2010-Sayeef/011311_U266_5-run1.pep.xml c:/Inetpub/wwwroot/ ISB/data/MyelomaGelLC2010-Sayeef/011311_U266_6-run1.pep.xml c:/Inetpub/ wwwroot/ISB/data/MyelomaGelLC2010-Sayeef/011311_U266_7-run1.pep.xml c:/ Inetpub/wwwroot/ISB/data/MyelomaGelLC2010-Sayeef/011311_U266_8- run1.pep.xml c:/Inetpub/wwwroot/ISB/data/MyelomaGelLC2010-Sayeef/ 011311_U266_9-run1.pep.xml c:/Inetpub/wwwroot/ISB/data/ MyelomaGelLC2010-Sayeef/012811_LR6_1-run1.pep.xml c:/Inetpub/wwwroot/ ISB/data/MyelomaGelLC2010-Sayeef/012811_LR6_10-run1.pep.xml c:/Inetpub/ wwwroot/ISB/data/MyelomaGelLC2010-Sayeef/012811_LR6_11-run1.pep.xml c:/ Inetpub/wwwroot/ISB/data/MyelomaGelLC2010-Sayeef/012811_LR6_12- run1.pep.xml c:/Inetpub/wwwroot/ISB/data/MyelomaGelLC2010-Sayeef/ 012811_LR6_13-run1.pep.xml c:/Inetpub/wwwroot/ISB/data/ MyelomaGelLC2010-Sayeef/012811_LR6_14-run1.pep.xml c:/Inetpub/wwwroot/ ISB/data/MyelomaGelLC2010-Sayeef/012811_LR6_15-run1.pep.xml c:/Inetpub/ wwwroot/ISB/data/MyelomaGelLC2010-Sayeef/012811_LR6_16-run1.pep.xml c:/ Inetpub/wwwroot/ISB/data/MyelomaGelLC2010-Sayeef/012811_LR6_17- run1.pep.xml c:/Inetpub/wwwroot/ISB/data/MyelomaGelLC2010-Sayeef/ 012811_LR6_18-run1.pep.xml c:/Inetpub/wwwroot/ISB/data/ MyelomaGelLC2010-Sayeef/012811_LR6_19-run1.pep.xml c:/Inetpub/wwwroot/ ISB/data/MyelomaGelLC2010-Sayeef/012811_LR6_2-run1.pep.xml c:/Inetpub/ wwwroot/ISB/data/MyelomaGelLC2010-Sayeef/012811_LR6_20-run1- ReRun.pep.xml c:/Inetpub/wwwroot/ISB/data/MyelomaGelLC2010-Sayeef/ 012811_LR6_3-run1.pep.xml c:/Inetpub/wwwroot/ISB/data/MyelomaGelLC2010- Sayeef/012811_LR6_4-run1.pep.xml c:/Inetpub/wwwroot/ISB/data/ MyelomaGelLC2010-Sayeef/012811_LR6_5-run1.pep.xml c:/Inetpub/wwwroot/ ISB/data/MyelomaGelLC2010-Sayeef/012811_LR6_6-run1.pep.xml c:/Inetpub/ wwwroot/ISB/data/MyelomaGelLC2010-Sayeef/012811_LR6_7-run1.pep.xml c:/ Inetpub/wwwroot/ISB/data/MyelomaGelLC2010-Sayeef/012811_LR6_8- run1.pep.xml c:/Inetpub/wwwroot/ISB/data/MyelomaGelLC2010-Sayeef/ 012811_LR6_9-run1.pep.xml c:/Inetpub/wwwroot/ISB/data/MyelomaGelLC2010- Sayeef/102210_8226_1-run1.pep.xml c:/Inetpub/wwwroot/ISB/data/ MyelomaGelLC2010-Sayeef/102210_8226_10-run1.pep.xml c:/Inetpub/wwwroot/ ISB/data/MyelomaGelLC2010-Sayeef/102210_8226_11-run1.pep.xml c:/ Inetpub/wwwroot/ISB/data/MyelomaGelLC2010-Sayeef/102210_8226_12- run1.pep.xml c:/Inetpub/wwwroot/ISB/data/MyelomaGelLC2010-Sayeef/ 102210_8226_13-run1.pep.xml c:/Inetpub/wwwroot/ISB/data/ MyelomaGelLC2010-Sayeef/102210_8226_14-run1.pep.xml c:/Inetpub/wwwroot/ ISB/data/MyelomaGelLC2010-Sayeef/102210_8226_15-run1.pep.xml c:/ Inetpub/wwwroot/ISB/data/MyelomaGelLC2010-Sayeef/102210_8226_16- run1.pep.xml c:/Inetpub/wwwroot/ISB/data/MyelomaGelLC2010-Sayeef/ 102210_8226_17-run1.pep.xml c:/Inetpub/wwwroot/ISB/data/ MyelomaGelLC2010-Sayeef/102210_8226_18-run1.pep.xml c:/Inetpub/wwwroot/ ISB/data/MyelomaGelLC2010-Sayeef/102210_8226_19-run1.pep.xml c:/ Inetpub/wwwroot/ISB/data/MyelomaGelLC2010-Sayeef/102210_8226_2- run1.pep.xml c:/Inetpub/wwwroot/ISB/data/MyelomaGelLC2010-Sayeef/ 102210_8226_20-run1.pep.xml c:/Inetpub/wwwroot/ISB/data/ MyelomaGelLC2010-Sayeef/102210_8226_3-run1.pep.xml c:/Inetpub/wwwroot/ ISB/data/MyelomaGelLC2010-Sayeef/102210_8226_4-run1.pep.xml c:/Inetpub/ wwwroot/ISB/data/MyelomaGelLC2010-Sayeef/102210_8226_5-run1.pep.xml c:/ Inetpub/wwwroot/ISB/data/MyelomaGelLC2010-Sayeef/102210_8226_6- run1.pep.xml c:/Inetpub/wwwroot/ISB/data/MyelomaGelLC2010-Sayeef/ 102210_8226_7-run1.pep.xml c:/Inetpub/wwwroot/ISB/data/ MyelomaGelLC2010-Sayeef/102210_8226_8-run1.pep.xml c:/Inetpub/wwwroot/ ISB/data/MyelomaGelLC2010-Sayeef/102210_8226_9-run1.pep.xml c:/Inetpub/ wwwroot/ISB/data/MyelomaGelLC2010-Sayeef/110110_LR5_1-run1.pep.xml c:/ Inetpub/wwwroot/ISB/data/MyelomaGelLC2010-Sayeef/110110_LR5_10- run1.pep.xml c:/Inetpub/wwwroot/ISB/data/MyelomaGelLC2010-Sayeef/ 110110_LR5_11-run1.pep.xml c:/Inetpub/wwwroot/ISB/data/ MyelomaGelLC2010-Sayeef/110110_LR5_12-run1.pep.xml c:/Inetpub/wwwroot/ ISB/data/MyelomaGelLC2010-Sayeef/110110_LR5_13-run1.pep.xml c:/Inetpub/ wwwroot/ISB/data/MyelomaGelLC2010-Sayeef/110110_LR5_14-run1.pep.xml c:/ Inetpub/wwwroot/ISB/data/MyelomaGelLC2010-Sayeef/110110_LR5_15- run1.pep.xml c:/Inetpub/wwwroot/ISB/data/MyelomaGelLC2010-Sayeef/ 110110_LR5_16-run1.pep.xml c:/Inetpub/wwwroot/ISB/data/ MyelomaGelLC2010-Sayeef/110110_LR5_17-run1.pep.xml c:/Inetpub/wwwroot/ ISB/data/MyelomaGelLC2010-Sayeef/110110_LR5_18-run1.pep.xml c:/Inetpub/ wwwroot/ISB/data/MyelomaGelLC2010-Sayeef/110110_LR5_19-run1.pep.xml c:/ Inetpub/wwwroot/ISB/data/MyelomaGelLC2010-Sayeef/110110_LR5_2- run1.pep.xml c:/Inetpub/wwwroot/ISB/data/MyelomaGelLC2010-Sayeef/ 110110_LR5_20-run1.pep.xml c:/Inetpub/wwwroot/ISB/data/ MyelomaGelLC2010-Sayeef/110110_LR5_3-run1.pep.xml c:/Inetpub/wwwroot/ ISB/data/MyelomaGelLC2010-Sayeef/110110_LR5_4-run1.pep.xml c:/Inetpub/ wwwroot/ISB/data/MyelomaGelLC2010-Sayeef/110110_LR5_5-run1.pep.xml c:/ Inetpub/wwwroot/ISB/data/MyelomaGelLC2010-Sayeef/110110_LR5_6- run1.pep.xml c:/Inetpub/wwwroot/ISB/data/MyelomaGelLC2010-Sayeef/ 110110_LR5_7-run1.pep.xml c:/Inetpub/wwwroot/ISB/data/MyelomaGelLC2010- Sayeef/110110_LR5_8-run1.pep.xml c:/Inetpub/wwwroot/ISB/data/ MyelomaGelLC2010-Sayeef/110110_LR5_9-run1.pep.xml c:/Inetpub/wwwroot/ ISB/data/MyelomaGelLC2010-Sayeef/111310_Dox6_1-run1.pep.xml c:/Inetpub/ wwwroot/ISB/data/MyelomaGelLC2010-Sayeef/111310_Dox6_10-run1.pep.xml c:/Inetpub/wwwroot/ISB/data/MyelomaGelLC2010-Sayeef/111310_Dox6_11- run1.pep.xml c:/Inetpub/wwwroot/ISB/data/MyelomaGelLC2010-Sayeef/ 111310_Dox6_12-run1.pep.xml c:/Inetpub/wwwroot/ISB/data/ MyelomaGelLC2010-Sayeef/111310_Dox6_13-run1.pep.xml c:/Inetpub/wwwroot/ ISB/data/MyelomaGelLC2010-Sayeef/111310_Dox6_14-run1.pep.xml c:/ Inetpub/wwwroot/ISB/data/MyelomaGelLC2010-Sayeef/111310_Dox6_15- run1.pep.xml c:/Inetpub/wwwroot/ISB/data/MyelomaGelLC2010-Sayeef/ 111310_Dox6_16-run1.pep.xml c:/Inetpub/wwwroot/ISB/data/ MyelomaGelLC2010-Sayeef/111310_Dox6_17-run1.pep.xml c:/Inetpub/wwwroot/ ISB/data/MyelomaGelLC2010-Sayeef/111310_Dox6_18-run1.pep.xml c:/ Inetpub/wwwroot/ISB/data/MyelomaGelLC2010-Sayeef/111310_Dox6_19- run1.pep.xml c:/Inetpub/wwwroot/ISB/data/MyelomaGelLC2010-Sayeef/ 111310_Dox6_2-run1.pep.xml c:/Inetpub/wwwroot/ISB/data/ MyelomaGelLC2010-Sayeef/111310_Dox6_20-run1.pep.xml c:/Inetpub/wwwroot/ ISB/data/MyelomaGelLC2010-Sayeef/111310_Dox6_3-run1.pep.xml c:/Inetpub/ wwwroot/ISB/data/MyelomaGelLC2010-Sayeef/111310_Dox6_4-run1.pep.xml c:/ Inetpub/wwwroot/ISB/data/MyelomaGelLC2010-Sayeef/111310_Dox6_5- run1.pep.xml c:/Inetpub/wwwroot/ISB/data/MyelomaGelLC2010-Sayeef/ 111310_Dox6_6-run1.pep.xml c:/Inetpub/wwwroot/ISB/data/ MyelomaGelLC2010-Sayeef/111310_Dox6_7-run1.pep.xml c:/Inetpub/wwwroot/ ISB/data/MyelomaGelLC2010-Sayeef/111310_Dox6_8-run1.pep.xml c:/Inetpub/ wwwroot/ISB/data/MyelomaGelLC2010-Sayeef/111310_Dox6_9-run1.pep.xml c:/ Inetpub/wwwroot/ISB/data/MyelomaGelLC2010-Sayeef/112910_Dox40_1- run1.pep.xml c:/Inetpub/wwwroot/ISB/data/MyelomaGelLC2010-Sayeef/ 112910_Dox40_10-run1.pep.xml c:/Inetpub/wwwroot/ISB/data/ MyelomaGelLC2010-Sayeef/112910_Dox40_11-run1-ReRun.pep.xml c:/Inetpub/ wwwroot/ISB/data/MyelomaGelLC2010-Sayeef/112910_Dox40_12-run1.pep.xml c:/Inetpub/wwwroot/ISB/data/MyelomaGelLC2010-Sayeef/112910_Dox40_13- run1.pep.xml c:/Inetpub/wwwroot/ISB/data/MyelomaGelLC2010-Sayeef/ 112910_Dox40_14-run1.pep.xml c:/Inetpub/wwwroot/ISB/data/ MyelomaGelLC2010-Sayeef/112910_Dox40_15-run1.pep.xml c:/Inetpub/ wwwroot/ISB/data/MyelomaGelLC2010-Sayeef/112910_Dox40_16-run1.pep.xml c:/Inetpub/wwwroot/ISB/data/MyelomaGelLC2010-Sayeef/112910_Dox40_17- run1.pep.xml c:/Inetpub/wwwroot/ISB/data/MyelomaGelLC2010-Sayeef/ 112910_Dox40_18-run1-ReRun.pep.xml c:/Inetpub/wwwroot/ISB/data/ MyelomaGelLC2010-Sayeef/112910_Dox40_19-run1-ReRun.pep.xml c:/Inetpub/ wwwroot/ISB/data/MyelomaGelLC2010-Sayeef/112910_Dox40_2-run1- ReRun.pep.xml c:/Inetpub/wwwroot/ISB/data/MyelomaGelLC2010-Sayeef/ 112910_Dox40_20-run1-ReRun.pep.xml c:/Inetpub/wwwroot/ISB/data/ MyelomaGelLC2010-Sayeef/112910_Dox40_3-run1.pep.xml c:/Inetpub/wwwroot/ ISB/data/MyelomaGelLC2010-Sayeef/112910_Dox40_4-run1.pep.xml c:/ Inetpub/wwwroot/ISB/data/MyelomaGelLC2010-Sayeef/112910_Dox40_5- run1.pep.xml c:/Inetpub/wwwroot/ISB/data/MyelomaGelLC2010-Sayeef/ 112910_Dox40_6-run1.pep.xml c:/Inetpub/wwwroot/ISB/data/ MyelomaGelLC2010-Sayeef/112910_Dox40_7-run1-ReRun.pep.xml c:/Inetpub/ wwwroot/ISB/data/MyelomaGelLC2010-Sayeef/112910_Dox40_8-run1- ReRun.pep.xml c:/Inetpub/wwwroot/ISB/data/MyelomaGelLC2010-Sayeef/ 112910_Dox40_9-run1.pep.xml -------------------------------------------------------------------------------- Command FAILED Please let me know what I am doing wrong. Is there a size/quantity restriction? Do mzxml files need to exist in this directory as well? Because I did not use that step since I made pepxml files from out files that I got using seqeust search (bioworks. ) thanks for any help, Sayeef Mirza Moffitt Cancer Center Proteomics -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To post to this group, send email to [email protected]. To unsubscribe from this group, send email to [email protected]. For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en.
