Hi Mike, Great - yes making sure all database references in the pep.xml match the reference in the prot.xml exactly fixes it.
Thanks for your help! Alastair On Tuesday, 22 June 2021 at 17:19:04 UTC+2 [email protected] wrote: > Hi Alastair, > > Yes, you can try this workaround and it should convert: > > > > 1. Open up your ipro.pep.xml file in a text editor > > 2. Find and replace all instances of > “../../../../Databases/EhuxAllproteins_MCC_decoy.fasta” with > “../../Databases/EhuxAllproteins_MCC_decoy.fasta” > > 3. Save the file and then run tpp2mzid on your prot.xml file > > > > I would suggest you make a backup of your ipro.pep.xml file first. Keep > the backup under a different file name; do not change the name of the > ipro.pep.xml file that you are altering. The bug was that you used the same > fasta file from two different locations in your searches, and therefore the > converter assumes that they are two different databases. It then gets > confused later when all the protein entries in each database are identical > (which is the bug I have to fix). Simply pointing all fasta files to the > same location fixes your problem. > > > > Cheers, > > Mike > > > > *From:* 'Alastair Skeffington' via spctools-discuss < > [email protected]> > *Sent:* Tuesday, June 22, 2021 2:05 AM > *To:* spctools-discuss <[email protected]> > *Subject:* Re: [spctools-discuss] tpp2mzid help - 'no peptide evidence > found ...' > > > > Hi Mike, > > > > Thanks for looking into it! I'm not quite sure I understand ... all IDs in > the database (and therefore search space?) are unique - do you mean two > identical databases in the file system were somehow used at different > points? Is there any quick fix I can apply by editing the xml file, if it's > going to take you a while? > > > > Cheers, > > Alastair > > On Monday, 21 June 2021 at 23:07:01 UTC+2 [email protected] > wrote: > > Hi Alastair, > > I can definitely reproduce the error, which is caused by the presence of > two identical fasta databases in your search space. I’ll need some time to > fix the bug and report back to you. > > Cheers, > > Mike > > > > *From:* 'Alastair Skeffington' via spctools-discuss < > [email protected]> > *Sent:* Monday, June 21, 2021 11:29 AM > *To:* spctools-discuss <[email protected]> > *Subject:* Re: [spctools-discuss] tpp2mzid help - 'no peptide evidence > found ...' > > > > Hi Eric, > > > > Very happy to test it! > > Thanks, > > Alastair > > On Monday, 21 June 2021 at 20:04:36 UTC+2 Eric Deutsch wrote: > > I have not yet created a container for 6 but I should. I could try to do > that soon if there is demand to use it/test it. > > > > Thanks, > > Eric > > > > > > *From:* 'Alastair Skeffington' via spctools-discuss < > [email protected]> > *Sent:* Monday, June 21, 2021 8:59 AM > *To:* spctools-discuss <[email protected]> > *Subject:* Re: [spctools-discuss] tpp2mzid help - 'no peptide evidence > found ...' > > > > Hi Mike, > > > > Thanks for getting back to me so quickly. Here's the database: > https://we.tl/t-wZsZ3uSq1r > > > > Is version 6 available as a container? I've never managed to install TPP > properly on a linux machine ... > > > > Alastair > > On Monday, 21 June 2021 at 17:50:24 UTC+2 [email protected] > wrote: > > Hi Alastair, > > There is a much newer version of tpp2mzid in our current release > candidates of TPP version 6. I’m hoping that the error messages have been > resolved in this new version. However, I also need the fasta search > database file to run the conversion with the newer tpp2mzid. Could you also > provide a link to that file and I will finish my tests and let you know the > result? > > Thanks, > > Mike > > > > *From:* 'Alastair Skeffington' via spctools-discuss < > [email protected]> > *Sent:* Monday, June 21, 2021 6:45 AM > *To:* spctools-discuss <[email protected]> > *Subject:* [spctools-discuss] tpp2mzid help - 'no peptide evidence found > ...' > > > > I'm at the end of a multi-year odyssey of a project, and I just need to > submit data to PRIDE. > > > > Unfortunately, when I run tpp2mzid for some prot.xml files, I get an error > such as this: > > > > Warning (A), no peptide evidence found for (mod): EENAFVQKIAE from > Br20418.t2 > > > > This only happens for some prot.xml files, but I'm not sure why. The > pep.xml files from which the prot.xml are derived convert fine. > > > > I've put an example here: https://we.tl/t-Z9qNNjDC0k > > > > I was running TPP via the docker > container: digitalproteomes/tpp:version-5.2.0.1 > > > > Here is the stdout in full: > > Reading: HCLC_EhN.prot.xml > > Reading: /data/HCLC_EhN_ipro.pep.xml > > Unknown xx modification: B = 114.535 42.5515 > > Unknown xx modification: J = 113.084 44.0023 > > Unknown xx modification: O = 237.148 80.0613 > > Unknown xx modification: U = 150.954 6.13277 > > Unknown xx modification: X = 111 46.0864 > > Unknown xx modification: Z = 128.551 28.5358 > > Unknown xx modification: B = 114.535 42.5515 > > Unknown xx modification: J = 113.084 44.0023 > > Unknown xx modification: O = 237.148 80.0613 > > Unknown xx modification: U = 150.954 6.13277 > > Unknown xx modification: X = 111 46.0864 > > Unknown xx modification: Z = 128.551 28.5358 > > Unknown xx modification: B = 114.535 42.5515 > > Unknown xx modification: J = 113.084 44.0023 > > Unknown xx modification: O = 237.148 80.0613 > > Unknown xx modification: U = 150.954 6.13277 > > Unknown xx modification: X = 111 46.0864 > > Unknown xx modification: Z = 128.551 28.5358 > > Unknown xx modification: B = 114.535 42.5515 > > Unknown xx modification: J = 113.084 44.0023 > > Unknown xx modification: O = 237.148 80.0613 > > Unknown xx modification: U = 150.954 6.13277 > > Unknown xx modification: X = 111 46.0864 > > Unknown xx modification: Z = 128.551 28.5358 > > Unknown xx modification: B = 114.535 42.5515 > > Unknown xx modification: J = 113.084 44.0023 > > Unknown xx modification: O = 237.148 80.0613 > > Unknown xx modification: U = 150.954 6.13277 > > Unknown xx modification: X = 111 46.0864 > > Unknown xx modification: Z = 128.551 28.5358 > > Unknown xx modification: B = 114.535 42.5515 > > Unknown xx modification: J = 113.084 44.0023 > > Unknown xx modification: O = 237.148 80.0613 > > Unknown xx modification: U = 150.954 6.13277 > > Unknown xx modification: X = 111 46.0864 > > Unknown xx modification: Z = 128.551 28.5358 > > Unknown xx modification: B = 114.535 42.5515 > > Unknown xx modification: J = 113.084 44.0023 > > Unknown xx modification: O = 237.148 80.0613 > > Unknown xx modification: U = 150.954 6.13277 > > Unknown xx modification: X = 111 46.0864 > > Unknown xx modification: Z = 128.551 28.5358 > > Unknown xx modification: B = 114.535 42.5515 > > Unknown xx modification: J = 113.084 44.0023 > > Unknown xx modification: O = 237.148 80.0613 > > Unknown xx modification: U = 150.954 6.13277 > > Unknown xx modification: X = 111 46.0864 > > Unknown xx modification: Z = 128.551 28.5358 > > 17648 psms read. > > Warning (A), no peptide evidence found for (mod): EENAFVQKIAE from > Br20418.t2 > > > > Help would be very much appreciated! > > Thanks, > > Alastair > > -- > 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 [email protected]. > To view this discussion on the web visit > https://groups.google.com/d/msgid/spctools-discuss/f3791dbe-d3d4-43cf-aeda-65792741656fn%40googlegroups.com > > <https://groups.google.com/d/msgid/spctools-discuss/f3791dbe-d3d4-43cf-aeda-65792741656fn%40googlegroups.com?utm_medium=email&utm_source=footer> > . > > -- > 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 [email protected]. > > To view this discussion on the web visit > https://groups.google.com/d/msgid/spctools-discuss/15675077-97af-476e-b471-d6315c5ec078n%40googlegroups.com > > <https://groups.google.com/d/msgid/spctools-discuss/15675077-97af-476e-b471-d6315c5ec078n%40googlegroups.com?utm_medium=email&utm_source=footer> > . > > -- > 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 [email protected]. > > To view this discussion on the web visit > https://groups.google.com/d/msgid/spctools-discuss/affabbfa-f4da-470d-a9d4-78a8da5b364bn%40googlegroups.com > > <https://groups.google.com/d/msgid/spctools-discuss/affabbfa-f4da-470d-a9d4-78a8da5b364bn%40googlegroups.com?utm_medium=email&utm_source=footer> > . > > -- > 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 [email protected]. > > To view this discussion on the web visit > https://groups.google.com/d/msgid/spctools-discuss/c4a48fae-d42a-4329-9aa6-ba6c64944756n%40googlegroups.com > > <https://groups.google.com/d/msgid/spctools-discuss/c4a48fae-d42a-4329-9aa6-ba6c64944756n%40googlegroups.com?utm_medium=email&utm_source=footer> > . > -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. 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