Hi, Finally got around to fixing the indexing and it works great. One thing that thew me off was the that the line endings had to be in the correct format (Unix default LF instead of Windows default CR LF) otherwise the indexing was incorrect.
Thanks for the help! Connor On Tuesday, August 8, 2017 at 10:12:15 AM UTC-5, Connor Hoffmann wrote: > > Hi Mike, > > Thank you for the quick reply. This does indeed seem to be the problem so > I will have to recalculate the offset.... I'll report back when completed > in case others have a similar problem. > > Thanks! > Connor > > On Monday, August 7, 2017 at 6:09:29 PM UTC-5, Michael Hoopmann wrote: >> >> Hi Connor, >> >> In the example file you provided, I see that your >> <indexListOffset>761801</indexListOffset> points to the middle of the >> intensity array of scan 100 and not to the start of the indexList. >> >> >> >> Your actual indexListOffset looks to be 769983. The error message is >> because the indexListOffset needs to be set to the correct position. >> >> >> >> Similarly, all your scan indexes listed in the <offset> tags point to the >> wrong places. You can’t see that yet because the TPP stopped reading the >> file when it gave you the first error message. >> >> >> >> I am not sure what openMS does when a bad index is found; perhaps it just >> recomputes it on the fly at your expense without notifying you. This is >> probably undesired behavior if your goal is to reduce overhead. I will see >> if I can get the TPP to output more verbose error messages in the future, >> to perhaps notify you of the specific problem with the index. >> >> >> >> Cheers, >> >> Mike >> >> >> >> *From:* spctools...@googlegroups.com [mailto:spctools...@googlegroups.com] >> *On Behalf Of *Connor Hoffmann >> *Sent:* Monday, August 07, 2017 3:26 PM >> *To:* spctools-discuss >> *Subject:* [spctools-discuss] TPP Search Software not working with >> generated mzML files >> >> >> >> Hi all, >> >> >> >> My group is working on software capable of generating mzML files that can >> be searched/viewed with TPP and other software. >> >> >> >> The mzML files we generate are openable and viewable in programs like >> seeMS. MS/MS searches can also be conducted on our generated files in >> programs like Mascot (through their server) and MSGF+. >> >> >> >> The issue is that when I try to run out mzML file in a comet search(or >> any other search part of the TPP pipeline) this error is thrown: >> >> >> >> >> test.mzml(1) : error 2: Syntax error parsing XML. >> >> >> >> I understand that this is probably an error with how the mzML files are >> getting formatted. Does anyone have any advice as to why our files can be >> searched in other software that's not part of the TPP? Do searches like >> Comet have more strict formatting standards? >> >> >> >> Also our generated mzML files pass xml and mzML validation put out by >> openMS. >> >> >> >> I know a workaround is to convert the mzML into a TPP comatible mzML >> using MsConvert, however if at possible I would like if our generated files >> were compatible with TPP searches without the added overhead of converting >> them. >> >> >> >> I have attached an example of one of our generated mzML files should you >> like yo view it. >> >> >> >> Thank you! >> >> >> >> Connor Hoffmann >> >> -- >> You received this message because you are subscribed to the Google Groups >> "spctools-discuss" group. >> To unsubscribe from this group and stop receiving emails from it, send an >> email to spctools-discu...@googlegroups.com. >> To post to this group, send email to spctools...@googlegroups.com. >> Visit this group at https://groups.google.com/group/spctools-discuss. >> For more options, visit https://groups.google.com/d/optout. >> > -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To unsubscribe from this group and stop receiving emails from it, send an email to spctools-discuss+unsubscr...@googlegroups.com. To post to this group, send email to spctools-discuss@googlegroups.com. Visit this group at https://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout.
