Hi David, The new executable works perfectly and seems to give me sensible results through the rest of the pipeline.
Many thanks for your help in getting this working! Another little question has come up - but I'll put this in a new thread in case it's useful for others. Thanks again, Alastair Am Samstag, 13. Oktober 2018 00:44:06 UTC+2 schrieb David Shteynberg: > > Hello Alastair, > > I made the change in the code and recompiled an ubuntu binary for you. > Please try the following executable: > > https://www.dropbox.com/s/9xzz5md2hrf03lb/Mascot2XML?dl=0 > > Let me know if this works for you. > > -David > > On Tue, Oct 2, 2018 at 4:53 AM alastair.skeffington via spctools-discuss < > [email protected] <javascript:>> wrote: > >> Hi David, >> >> I've had a look into the scan information problem. >> >> The following spectrum in the mzML file (generated from thermo a RAW file >> with MSconvert): >> >> <spectrum index="24629" id="controllerType=0 controllerNumber=1 >> scan=24630" defaultArrayLength="85"> >> ... >> <cvParam cvRef="MS" accession="MS:1000796" name="spectrum >> title" value="A1.24630.24630.2 >> >> is equivalent to this in the .dat file: >> >> scans=24629 >> title=controllerType%3d0%20controllerNumber%3d1%20scan%3d24630 >> >> So I think we should be using the scan number from the "title=..." line >> when converting the .dat file. >> >> As I understand it you (reasonably) used the information from the "scans= >> " line from the .dat file. >> >> Would you be able to generate another version that uses the other number? >> >> Thanks for your continuing help, >> Alastair >> >> Am Dienstag, 2. Oktober 2018 11:56:03 UTC+2 schrieb >> [email protected]: >>> >>> Hello David, >>> >>> Thanks for the new version and for spotting the issue with the scan >>> information. >>> >>> I was ill for a while and then away, but will now look into it and see >>> if I can get it working. >>> >>> Many thanks, >>> Alastair >>> >>> Am Freitag, 14. September 2018 20:08:40 UTC+2 schrieb David Shteynberg: >>>> >>>> Hello Alastair, >>>> >>>> I have a version of Mascot2XML for Ubuntu that fixes the crash you >>>> saw. It is available here: >>>> https://www.dropbox.com/s/3ug6vqpuvr0iega/Mascot2XML?dl=0 >>>> >>>> However, there are some issues with the dat file itself that I couldn't >>>> figure out, specifically the scans= information does not match the title= >>>> information for the same spectrum (it is an off by one issue and I am not >>>> sure which one is right) >>>> >>>> e.g. >>>> >>>> ... >>>> >>>> Content-Type: application/x-Mascot; name="query1790" >>>> >>>> scans=38239 >>>> title=controllerType%3d0%20controllerNumber%3d1%20scan%3d38240 >>>> rtinseconds=3636.1 >>>> charge=1+ >>>> mass_min=53.038956 >>>> mass_max=236.991165 >>>> >>>> ... >>>> >>>> >>>> I tried to resolve the names based on your msgf+ results in the pepXML >>>> file you uploaded, but I could not, so I used the scan= info for spectrum >>>> naming purposes in Mascot2XML. >>>> >>>> >>>> This could create an issue if you intend to combine the results of >>>> different search engines with iProphet (since iProphet relies on spectra >>>> to >>>> be named in a consistent way between searched.) >>>> >>>> Can you test the new binary to verify that it gives you a functional >>>> pep.xml result? Can you verify what is the proper scan number information? >>>> >>>> Thanks, >>>> -David >>>> >>>> >>>> On Fri, Sep 14, 2018 at 2:11 AM, alastair.skeffington via >>>> spctools-discuss <[email protected]> wrote: >>>> >>>>> Here it is: https://we.tl/t-SFnvr0PIBS >>>>> >>>>> Thanks! >>>>> >>>>> Am Freitag, 14. September 2018 01:16:32 UTC+2 schrieb David Shteynberg: >>>>>> >>>>>> Can you also link the database? >>>>>> >>>>>> Thanks! >>>>>> >>>>>> On Thu, Sep 13, 2018 at 4:14 PM, David Shteynberg < >>>>>> [email protected]> wrote: >>>>>> >>>>>>> Hello Alastair, >>>>>>> >>>>>>> The link to the mzML file actually links to the pepXML file. Can >>>>>>> you please upload and link the mzML data file? >>>>>>> >>>>>>> Thanks, >>>>>>> -David >>>>>>> >>>>>>> On Thu, Sep 13, 2018 at 4:24 AM, alastair.skeffington via >>>>>>> spctools-discuss <[email protected]> wrote: >>>>>>> >>>>>>>> Hi David, >>>>>>>> >>>>>>>> So now I no longer get the 'cannot open' error, but I get a >>>>>>>> segmentation fault again. Here's what prints to stdout. >>>>>>>> >>>>>>>> Completing 506147 prev_aa and next_aa attributes by parsing through >>>>>>>> the database... >>>>>>>> Replacing 35749 protein id with full ids by parsing through the >>>>>>>> database... >>>>>>>> searching >>>>>>>> ../databases/Ehux_JGIbest_NCMC_nostar.fasta.....5%.....10%.....15%.....20%.....30%.....35%.....40%.....45%.....50%.....60%.....65%.....70%.....75%.....80%.....90%.....95%...done >>>>>>>> Skipping .dta, .out and .tgz generation >>>>>>>> Segmentation fault (core dumped) >>>>>>>> >>>>>>>> >>>>>>>> Here's the mzML file: https://we.tl/t-votxgo5HOI >>>>>>>> >>>>>>>> The .dat file is here: https://we.tl/t-kKGYJ81HbQ >>>>>>>> <https://we.tl/t-kKGYJ81HbQ> >>>>>>>> >>>>>>>> Hopfully we're nearly there! >>>>>>>> >>>>>>>> Thanks, >>>>>>>> Alastair >>>>>>>> >>>>>>>> >>>>>>>> Am Freitag, 7. September 2018 18:36:25 UTC+2 schrieb David >>>>>>>> Shteynberg: >>>>>>>>> >>>>>>>>> Hello Alastair, >>>>>>>>> >>>>>>>>> It appears that Mascot2XML cannot read the mzML file to get >>>>>>>>> spectrum and instrument info. Your dat file should be renamed to >>>>>>>>> have the >>>>>>>>> same basename as you mzML file. For instance, if your mzML file is >>>>>>>>> MYDATA.mzML your dat file should be renamed to MYDATA.dat, then the >>>>>>>>> converter applied. If you can post your mzML data I can test the >>>>>>>>> process >>>>>>>>> to completion on my system. >>>>>>>>> >>>>>>>>> Thanks, >>>>>>>>> -David >>>>>>>>> >>>>>>>>> On Wed, Sep 5, 2018 at 1:53 AM, alastair.skeffington via >>>>>>>>> spctools-discuss <[email protected]> wrote: >>>>>>>>> >>>>>>>>>> Hi David, >>>>>>>>>> >>>>>>>>>> Thanks for the idea. It looks like we're moving in the right >>>>>>>>>> direction... >>>>>>>>>> >>>>>>>>>> When I run this command: >>>>>>>>>> >>>>>>>>>> Mascot2XML A1_JGIbest_mascot.dat >>>>>>>>>> -D../databases/Ehux_JGIbest_NCMC_nostar.fasta -Etrypsin -notgz -nodta >>>>>>>>>> >>>>>>>>>> I get the following on stout and it writes an empty pep.xml file. >>>>>>>>>> What file is it trying to open for reading scan numbers and >>>>>>>>>> instrument info? >>>>>>>>>> >>>>>>>>>> A stored as 71.0371 >>>>>>>>>> B stored as 114.535 >>>>>>>>>> C stored as 160.031 >>>>>>>>>> D stored as 115.027 >>>>>>>>>> E stored as 129.043 >>>>>>>>>> F stored as 147.068 >>>>>>>>>> G stored as 57.0215 >>>>>>>>>> H stored as 137.059 >>>>>>>>>> I stored as 113.084 >>>>>>>>>> J stored as 113.084 >>>>>>>>>> K stored as 128.095 >>>>>>>>>> L stored as 113.084 >>>>>>>>>> M stored as 131.04 >>>>>>>>>> N stored as 114.043 >>>>>>>>>> O stored as 237.148 >>>>>>>>>> P stored as 97.0528 >>>>>>>>>> Q stored as 128.059 >>>>>>>>>> R stored as 156.101 >>>>>>>>>> S stored as 87.032 >>>>>>>>>> T stored as 101.048 >>>>>>>>>> U stored as 150.954 >>>>>>>>>> V stored as 99.0684 >>>>>>>>>> W stored as 186.079 >>>>>>>>>> X stored as 111 >>>>>>>>>> Y stored as 163.063 >>>>>>>>>> Z stored as 128.551 >>>>>>>>>> c stored as 17.0027 >>>>>>>>>> n stored as 1.00782 >>>>>>>>>> variable modification 1, delta mass 15.9949 for Oxidation (M): >>>>>>>>>> residues: M >>>>>>>>>> nterm: 0 >>>>>>>>>> cterm: 0 >>>>>>>>>> protterm: 0 >>>>>>>>>> >>>>>>>>>> Incomplete file name. No file loaded: >>>>>>>>>> warning: cannot open "" for reading scan numbers. >>>>>>>>>> trypsin : cut(KR) nocuts(P) sense(C) >>>>>>>>>> Completing 399999 prev_aa and next_aa attributes by parsing >>>>>>>>>> through the database... >>>>>>>>>> Replacing 33816 protein id with full ids by parsing through the >>>>>>>>>> database... >>>>>>>>>> searching >>>>>>>>>> ../databases/Ehux_JGIbest_NCMC_nostar.fasta.....5%.....10%.....15%.....20%.....30%.....35%.....40%.....45%.....50%.....60%.....65%.....70%.....75%.....80%.....90%.....95%...done >>>>>>>>>> Skipping .dta, .out and .tgz generation >>>>>>>>>> Incomplete file name. No file loaded: >>>>>>>>>> warning: cannot open "" for reading MS instrument info. >>>>>>>>>> Segmentation fault (core dumped) >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> Thanks for your continuing help, >>>>>>>>>> Alastair >>>>>>>>>> >>>>>>>>>> Am Dienstag, 4. September 2018 18:32:30 UTC+2 schrieb David >>>>>>>>>> Shteynberg: >>>>>>>>>>> >>>>>>>>>>> Can you try ypur command using options -notgz and -nodta? >>>>>>>>>>> >>>>>>>>>>> Thanks, >>>>>>>>>>> David >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> On Mon, Sep 3, 2018, 1:21 AM alastair.skeffington via >>>>>>>>>>> spctools-discuss <[email protected]> wrote: >>>>>>>>>>> >>>>>>>>>>>> Hi David, >>>>>>>>>>>> >>>>>>>>>>>> Thanks for the patched version. >>>>>>>>>>>> >>>>>>>>>>>> The segmentation fault is gone, but I still get the following >>>>>>>>>>>> warnings: >>>>>>>>>>>> >>>>>>>>>>>> *Incomplete file name. No file loaded:* >>>>>>>>>>>> * warning: cannot open "" for reading scan numbers.* >>>>>>>>>>>> *error writing file* /home/ >>>>>>>>>>>> mpimp-golm.mpg.de/skeffington/winhome/linux/Pacbio_data1_2017/120718_analysis5/search_stability/converter/A1_JGIbest_mascot.43142.43142.1.dta: >>>>>>>>>>>> >>>>>>>>>>>> *Numeric group ID too large* >>>>>>>>>>>> >>>>>>>>>>>> Are you able to download the data from this link >>>>>>>>>>>> https://we.tl/t-FSq4TWEATd >>>>>>>>>>>> <https://www.google.com/url?q=https%3A%2F%2Fwe.tl%2Ft-FSq4TWEATd&sa=D&sntz=1&usg=AFQjCNF0WLtoevgiHOFZ5LHqDZ_PsW9gvA> >>>>>>>>>>>> or >>>>>>>>>>>> shall I send it to you another way (eg our Max Planck secure >>>>>>>>>>>> transfer >>>>>>>>>>>> server - but this is mediated via email)? >>>>>>>>>>>> >>>>>>>>>>>> Many thanks, >>>>>>>>>>>> Alastair >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> Am Freitag, 31. August 2018 22:28:34 UTC+2 schrieb David >>>>>>>>>>>> Shteynberg: >>>>>>>>>>>>> >>>>>>>>>>>>> Hello Alastair, >>>>>>>>>>>>> >>>>>>>>>>>>> I have a patched version of Mascot2XML for you to try >>>>>>>>>>>>> available here: >>>>>>>>>>>>> https://www.dropbox.com/s/mm719r4hcxn8zv7/Mascot2XML?dl=0 >>>>>>>>>>>>> >>>>>>>>>>>>> Please let me know whether you encounter more errors or not. >>>>>>>>>>>>> >>>>>>>>>>>>> Thanks, >>>>>>>>>>>>> -David >>>>>>>>>>>>> >>>>>>>>>>>>> On Fri, Aug 31, 2018 at 2:54 AM, alastair.skeffington via >>>>>>>>>>>>> spctools-discuss <[email protected]> wrote: >>>>>>>>>>>>> >>>>>>>>>>>>>> Short update - I also get segmentation faults now when I run >>>>>>>>>>>>>> other TPP commants (eg xinteract) on files that previously ran >>>>>>>>>>>>>> without >>>>>>>>>>>>>> errors. Can replacing the Mascot2XML executable really have had >>>>>>>>>>>>>> this effect? >>>>>>>>>>>>>> Alastair >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> Am Freitag, 31. August 2018 11:08:48 UTC+2 schrieb >>>>>>>>>>>>>> [email protected]: >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> Hi David, >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> Thanks for sending the latest version. As you suggested we >>>>>>>>>>>>>>> simply replaced the old file with the new one. It does run, but >>>>>>>>>>>>>>> unfortunately I get a 'segmentation fault (core dumped)' after >>>>>>>>>>>>>>> it's read in >>>>>>>>>>>>>>> the variable modifications. Does it try to access or write to >>>>>>>>>>>>>>> different >>>>>>>>>>>>>>> directories than does the original version? >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> I've put an example .dat file here: >>>>>>>>>>>>>>> https://we.tl/t-FSq4TWEATd <https://we.tl/t-FSq4TWEATd> if >>>>>>>>>>>>>>> you have time to have a look. >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> Thanks for your help! >>>>>>>>>>>>>>> Alastair >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> Am Donnerstag, 30. August 2018 21:44:11 UTC+2 schrieb David >>>>>>>>>>>>>>> Shteynberg: >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> I put Mascot2XML from the latest code version, compiled on >>>>>>>>>>>>>>>> same version of Ubuntu, at the following link: >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> https://www.dropbox.com/s/mm719r4hcxn8zv7/Mascot2XML?dl=0 >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> Let me know if this version works any better for your data. >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> -David >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> On Thu, Aug 30, 2018 at 1:40 AM, alastair.skeffington via >>>>>>>>>>>>>>>> spctools-discuss <[email protected]> wrote: >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> Great, it's Ubuntu 16.04.4 LTS. >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> Thanks, >>>>>>>>>>>>>>>>> Alastair >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> Am Mittwoch, 29. August 2018 23:12:46 UTC+2 schrieb David >>>>>>>>>>>>>>>>> Shteynberg: >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> It should be as easy to integrate as copying the new >>>>>>>>>>>>>>>>>> executable in place of the old one. Which version of linux >>>>>>>>>>>>>>>>>> are you using? >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Thanks, >>>>>>>>>>>>>>>>>> -David >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> On Wed, Aug 29, 2018 at 1:29 PM, alastair.skeffington via >>>>>>>>>>>>>>>>>> spctools-discuss <[email protected]> wrote: >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> Hello David, >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> Many thanks for your prompt reply. >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> The new executable would be fantastic. Will that be easy >>>>>>>>>>>>>>>>>>> to incorporate to an existing Linux build of TPP? >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> Thanks again, >>>>>>>>>>>>>>>>>>> Alastair >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> Am Mittwoch, 29. August 2018 18:11:12 UTC+2 schrieb >>>>>>>>>>>>>>>>>>> David Shteynberg: >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> Hello Alastair, >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> There have been some changes to the Mascot format that >>>>>>>>>>>>>>>>>>>> required Mascot2XML code changes that I implemented a >>>>>>>>>>>>>>>>>>>> couple of month ago. >>>>>>>>>>>>>>>>>>>> I can either send you my new executable or if you can post >>>>>>>>>>>>>>>>>>>> your Mascot >>>>>>>>>>>>>>>>>>>> output file where I can download it I can make sure the >>>>>>>>>>>>>>>>>>>> converter works on >>>>>>>>>>>>>>>>>>>> your files. Let me know what you prefer. >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> Cheers, >>>>>>>>>>>>>>>>>>>> -David >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> On Wed, Aug 29, 2018 at 5:34 AM, alastair.skeffington >>>>>>>>>>>>>>>>>>>> via spctools-discuss <[email protected]> >>>>>>>>>>>>>>>>>>>> wrote: >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> Update: >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> Running MascotXML on windows produces the same set or >>>>>>>>>>>>>>>>>>>>> errors, but not the last "error writing file errors". >>>>>>>>>>>>>>>>>>>>> Unlike running the >>>>>>>>>>>>>>>>>>>>> program on linux, on windows it does produce a pepxml >>>>>>>>>>>>>>>>>>>>> output. The question >>>>>>>>>>>>>>>>>>>>> is is this output reliable, given all the 'could not find >>>>>>>>>>>>>>>>>>>>> scan number' >>>>>>>>>>>>>>>>>>>>> warnings? >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> Alastair >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> Am Mittwoch, 29. August 2018 11:49:20 UTC+2 schrieb >>>>>>>>>>>>>>>>>>>>> [email protected]: >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> Hello, >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> I'm trying to incorporate Mascot search results into >>>>>>>>>>>>>>>>>>>>>> a TPP analysis, but am having great trouble doing so. >>>>>>>>>>>>>>>>>>>>>> I'm working with TPP >>>>>>>>>>>>>>>>>>>>>> (installed a couple of months ago) on the linux command >>>>>>>>>>>>>>>>>>>>>> line but running >>>>>>>>>>>>>>>>>>>>>> Mascot (2.5) on a windows server. >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> When I run the .dat output from Mascot through >>>>>>>>>>>>>>>>>>>>>> Mascot2XML I get various errors: >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> First the program reads the amino acid masses and >>>>>>>>>>>>>>>>>>>>>> modifications then I get this: >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> *Incomplete file name. No file loaded:* >>>>>>>>>>>>>>>>>>>>>> * warning: cannot open "" for reading scan numbers.* >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> then lots of errors of this type: >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> *Warning: could not find scan numbers of spectrum >>>>>>>>>>>>>>>>>>>>>> A1.5108.5108.2(intensity=4388884.9462)* >>>>>>>>>>>>>>>>>>>>>> *Set to 0000* >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> And finally this: >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> *error writing file >>>>>>>>>>>>>>>>>>>>>> /home/mpimp-golm.mpg.de/skeffington/winhome/linux/Pacbio_data1_2017/120718_analysis5/search_stability/converter/Wed_Aug_29_10-57-47_2018.spectrum30.00000.00000.2.dta >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> <http://mpimp-golm.mpg.de/skeffington/winhome/linux/Pacbio_data1_2017/120718_analysis5/search_stability/converter/Wed_Aug_29_10-57-47_2018.spectrum30.00000.00000.2.dta>: >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> Numeric group ID too large* >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> I've tried two methods of generating the mgf input to >>>>>>>>>>>>>>>>>>>>>> Mascot: first peak picking with progenesis and export as >>>>>>>>>>>>>>>>>>>>>> mgf, and secondy >>>>>>>>>>>>>>>>>>>>>> converting the RAW file to mzML with MSconvert and then >>>>>>>>>>>>>>>>>>>>>> convering this to a >>>>>>>>>>>>>>>>>>>>>> mgf with MzXML2Search. Both times the .dat file exported >>>>>>>>>>>>>>>>>>>>>> from Mascot gives >>>>>>>>>>>>>>>>>>>>>> the above errors. The .dat file definitely has unix text >>>>>>>>>>>>>>>>>>>>>> encoding. >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> Looking at some previous posts issues with this step >>>>>>>>>>>>>>>>>>>>>> weren't enough for me to solve it (something to do with >>>>>>>>>>>>>>>>>>>>>> scan numbers and >>>>>>>>>>>>>>>>>>>>>> title fields...) >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> An example file can be downloaded from here: >>>>>>>>>>>>>>>>>>>>>> https://we.tl/t-reBlJEnXAc but I've copy pasted >>>>>>>>>>>>>>>>>>>>>> examples of the format of the different sections of the >>>>>>>>>>>>>>>>>>>>>> file below in case >>>>>>>>>>>>>>>>>>>>>> that's easier. >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> Any help would be very much appreciated! >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> Thanks, >>>>>>>>>>>>>>>>>>>>>> Alastair >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> sequences=39303 >>>>>>>>>>>>>>>>>>>>>> sequences_after_tax=39303 >>>>>>>>>>>>>>>>>>>>>> residues=13344484 >>>>>>>>>>>>>>>>>>>>>> distribution=39254,0,1,1,15,8,14,2,4,1,2,1 >>>>>>>>>>>>>>>>>>>>>> decoy_type=1 >>>>>>>>>>>>>>>>>>>>>> distribution_decoy=39274,0,0,1,8,5,7,3,2,1,2 >>>>>>>>>>>>>>>>>>>>>> exec_time=337 >>>>>>>>>>>>>>>>>>>>>> date=1535490575 >>>>>>>>>>>>>>>>>>>>>> time=23:09:35 >>>>>>>>>>>>>>>>>>>>>> queries=80990 >>>>>>>>>>>>>>>>>>>>>> min_peaks_for_homology=6 >>>>>>>>>>>>>>>>>>>>>> max_hits=50 >>>>>>>>>>>>>>>>>>>>>> version=2.5.1 >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> fastafile=D:/inetpub/mascot/sequence/Ehux_JGIbest_NCMC/current/Ehux_JGIbest_NCMC_110817.fasta >>>>>>>>>>>>>>>>>>>>>> release=Ehux_JGIbest_NCMC_110817.fasta >>>>>>>>>>>>>>>>>>>>>> taskid=153549023801 >>>>>>>>>>>>>>>>>>>>>> --gc0p4Jq0M2Yt08jU534c0p >>>>>>>>>>>>>>>>>>>>>> Content-Type: application/x-Mascot; name="summary" >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> qmass1=398.226814 >>>>>>>>>>>>>>>>>>>>>> qexp1=200.120683,2+ >>>>>>>>>>>>>>>>>>>>>> qmatch1=0 >>>>>>>>>>>>>>>>>>>>>> qplughole1=0.000000 >>>>>>>>>>>>>>>>>>>>>> qmass2=398.226814 >>>>>>>>>>>>>>>>>>>>>> qexp2=200.120683,2+ >>>>>>>>>>>>>>>>>>>>>> qmatch2=0 >>>>>>>>>>>>>>>>>>>>>> qplughole2=0.000000 >>>>>>>>>>>>>>>>>>>>>> qmass3=398.226860 >>>>>>>>>>>>>>>>>>>>>> qexp3=200.120706,2+ >>>>>>>>>>>>>>>>>>>>>> qmatch3=0 >>>>>>>>>>>>>>>>>>>>>> qplughole3=0.000000 >>>>>>>>>>>>>>>>>>>>>> qmass4=399.221954 >>>>>>>>>>>>>>>>>>>>>> qexp4=200.618253,2+ >>>>>>>>>>>>>>>>>>>>>> qmatch4=0 >>>>>>>>>>>>>>>>>>>>>> qplughole4=0.000000 >>>>>>>>>>>>>>>>>>>>>> qmass5=399.222074 >>>>>>>>>>>>>>>>>>>>>> qexp5=200.618313,2+ >>>>>>>>>>>>>>>>>>>>>> qmatch5=0 >>>>>>>>>>>>>>>>>>>>>> qplughole5=0.000000 >>>>>>>>>>>>>>>>>>>>>> qmass6=399.222328 >>>>>>>>>>>>>>>>>>>>>> qexp6=200.618440,2+ >>>>>>>>>>>>>>>>>>>>>> qmatch6=0 >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> ... >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> q20941_p4=2,1060.617508,-0.002194,3,ARMARVTIK,26,00010000000,4.49,0001002000000000000,0,0;"jgi|Emihu1|229675|gm1.15700096":0:180:188:1 >>>>>>>>>>>>>>>>>>>>>> q20941_p4_terms=R,H >>>>>>>>>>>>>>>>>>>>>> q20941_p4_primary_nl=00020000000 >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> q20941_p5=1,1060.606277,0.009037,4,LNVMLTRAK,42,00001000000,3.59,0000002000000000000,0,0;"jgi|Emihu1|44663|gw1.52.19.1":0:149:157:1 >>>>>>>>>>>>>>>>>>>>>> q20941_p5_terms=R,R >>>>>>>>>>>>>>>>>>>>>> q20941_p5_primary_nl=00001000000 >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> .... >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> q63508_p1_terms=K,- >>>>>>>>>>>>>>>>>>>>>> q63508_p1_primary_nl=000100000000000000000 >>>>>>>>>>>>>>>>>>>>>> q63509_p1=-1 >>>>>>>>>>>>>>>>>>>>>> q63510_p1=-1 >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> q63511_p1=0,1992.930984,0.017676,9,ETEGMDEVTLGTEANLLR,60,00000100000000000000,7.65,2000002010000000000,0,0;"jgi|Emihu1|463299|estExtDG_fgeneshEH_pg.C_230161":0:45:62:1 >>>>>>>>>>>>>>>>>>>>>> q63511_p1_terms=K,M\ >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> ... >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> title=A1%2e48180%2e48180%2e2%20%28intensity%3d1550626%2e6695%29 >>>>>>>>>>>>>>>>>>>>>> scans=48180 >>>>>>>>>>>>>>>>>>>>>> rtinseconds=4637.902 >>>>>>>>>>>>>>>>>>>>>> index=39202 >>>>>>>>>>>>>>>>>>>>>> charge=2+ >>>>>>>>>>>>>>>>>>>>>> mass_min=66.398610 >>>>>>>>>>>>>>>>>>>>>> mass_max=770.192020 >>>>>>>>>>>>>>>>>>>>>> int_min=3319 >>>>>>>>>>>>>>>>>>>>>> int_max=3.549e+006 >>>>>>>>>>>>>>>>>>>>>> num_vals=141 >>>>>>>>>>>>>>>>>>>>>> num_used1=-1 >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> Ions1=86.096660:3.549e+006,199.179960:1.199e+006,357.248570:4.584e+005,444.280060:2.021e+005,487.322240:1.532e+005,600.369630:3.986e+005,713.455020:3.884e+004,770.192020:7872,147.112400:4.108e+005,197.127910:2.67e+005,317.216950:1.678e+005,430.301210:8.45e+004,529.345640:1.558e+004,588.369870:1.166e+005,714.459470:9704,72.081130:2.477e+005,215.138400:2.403e+005,358.251280:1.064e+005,426.269350:7.395e+004,550.296200:1.485e+004,601.372070:1.069e+005,673.825260:7357,129.101970:2.476e+005,227.174790:2.282e+005,365.180540:7.352e+004,445.283690:5.422e+004,543.350650:1.115e+004,602.376530:2.686e+004,688.241390:7128,70.065490:2.41e+005,175.118500:1.172e+005,298.174900:4.843e+004,454.265870:1.403e+004,469.551240:7739,74.060400:1.876e+005,260.196080:1.153e+005,308.159150:4.422e+004,452.285550:1.292e+004,502.667720:7425,120.080620:1.568e+005,200.183460:1.14e+005,311.170010:4.379e+004,442.264250:1.148e+004,130.086000:1.566e+005,211.143750:1.035e+005,284.196290:4.02e+004,396.259830:1.11e+004,136.075380:1.516e+005,183.148790:1.027e+005,329.180820:3.99e+004,383.191410:9470,87.100010:1.442e+005,171.112180:9.939e+004,337.186160:3.741e+004,427.275510:8092,66.398610:7476,69.070260:2.981e+004,71.068760:7072,71.847320:6862,73.084510:1.178e+004,84.044650:1.004e+005,84.081050:1.141e+005,87.093630:9692,93.159360:6454,95.283780:7634,100.701740:8448,101.071040:2.914e+004,101.107370:1.525e+004,102.055060:6.669e+004,110.071190:3.968e+004,113.070880:5.693e+004,115.086430:7442,121.083990:1.449e+004,124.039130:1.091e+004,128.682070:6426,129.065540:3.012e+004,131.081120:1.371e+004,131.089710:8456,141.065400:5.452e+004,141.101940:1.45e+004,143.117430:7.816e+004,148.115490:1.053e+004,155.081120:1.101e+004,157.096530:4.699e+004,157.129850:4876,157.133100:3.958e+004,158.092270:9042,159.076220:4.93e+004,159.090820:7016,166.963810:7044,169.096510:1.182e+004,170.116810:6923,171.148670:4.607e+004,177.101940:1.231e+004,184.152160:7317,185.091710:6.211e+004,185.123340:3319,185.127880:3.533e+004,185.164430:1.273e+004,187.071200:9269,189.122920:8.606e+004,199.107360:7783,201.549090:3.6e+004,202.117870:1.31e+004,209.127430:8030,212.102580:7999,213.158710:8006,225.122740:5.26e+004,226.118640:9989,228.133470:4.721e+004,229.154480:1.473e+004,233.091510:1.15e+004,239.174640:9244,240.133970:1.139e+004,242.186170:4.089e+004,243.134110:8297,244.128800:3.847e+004,244.165070:5.539e+004,245.185180:3.016e+004,251.102390:8286,254.149260:1.123e+004,255.143660:6924,270.180480:2.275e+004,273.119570:7401,278.148990:8556,280.164400:3.296e+004,301.187160:8614,306.159450:8586,312.191350:1.242e+004,313.222900:2.622e+004,315.201870:1.506e+004,323.171140:1.431e+004,326.170290:2.886e+004,339.202150:9492,339.238100:3.735e+004,341.181240:2.631e+004,345.224520:9916,391.875700:7250,403.229950:7642,410.580260:7000,438.265170:7058 >>>>>>>>>>>>>>>>>>>>>> --gc0p4Jq0M2Yt08jU534c0p >>>>>>>>>>>>>>>>>>>>>> Content-Type: application/x-Mascot; name="query10199" >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> title=A1%2e70680%2e70680%2e2%20%28intensity%3d375254%2e7564%29 >>>>>>>>>>>>>>>>>>>>>> scans=70680 >>>>>>>>>>>>>>>>>>>>>> rtinseconds=6914.338 >>>>>>>>>>>>>>>>>>>>>> index=7468 >>>>>>>>>>>>>>>>>>>>>> charge=2+ >>>>>>>>>>>>>>>>>>>>>> mass_min=63.842020 >>>>>>>>>>>>>>>>>>>>>> mass_max=644.440980 >>>>>>>>>>>>>>>>>>>>>> int_min=1827 >>>>>>>>>>>>>>>>>>>>>> int_max=4.968e+005 >>>>>>>>>>>>>>>>>>>>>> num_vals=105 >>>>>>>>>>>>>>>>>>>>>> num_used1=-1 >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> Ions1=86.096690:4.968e+005,185.128020:1.034e+005,288.202120:3.243e+004,401.286380:6.386e+004,529.344060:9.373e+004,642.428220:8.514e+004,157.133160:2.682e+005,175.118550:9.25e+004,355.232360:1.979e+004,402.289310:1.288e+004,512.317380:2.341e+004,643.430240:3.278e+004,70.065510:4.716e+004,242.149150:5.654e+004,271.175420:1.637e+004,384.259920:8715,530.346620:1.705e+004,644.440980:2124,120.080800:3.751e+004,235.106700:2.773e+004,268.165340:9687,408.559200:2663,511.335450:1.032e+004,72.081180:3.3e+004,199.179870:2.649e+004,303.947940:6403,366.178410:2520,513.322940:1.02e+004,131.117550:2.633e+004,197.648350:1.781e+004,272.176420:3824,563.330140:8138,158.136580:2.275e+004,227.174800:1.427e+004,303.931000:2849,531.352230:5067,87.100110:1.905e+004,197.636980:1.292e+004,356.237340:2786,494.307340:4680,87.044280:1.535e+004,170.059630:1.177e+004,298.211940:2697,527.353580:2742,158.092240:1.53e+004,214.154650:9927,265.176760:2483,492.291170:2626,63.842020:2005,66.224640:1899,69.070110:2143,73.266720:2197,82.290240:1866,83.052990:2068,84.044690:1.026e+004,84.081000:8933,84.667250:2618,87.093480:2158,92.023680:2293,101.070970:1.013e+004,102.054810:3958,103.413090:2339,110.071080:2344,112.086830:8846,113.070780:2407,115.086500:7391,116.070680:3806,129.102020:1.159e+004,130.064680:2253,130.085600:3336,132.080470:3841,136.075440:3968,143.117680:5118,147.112550:1.107e+004,156.112780:3412,159.091320:1.044e+004,160.095310:2344,171.112260:2262,175.086440:3021,176.122380:5062,183.148970:2888,185.165280:2258,186.131880:8686,197.127960:3542,197.640200:1827,217.097080:3722,224.138460:3149,225.123030:9809,236.110140:3376,243.152860:4158,249.098460:2229,253.189440:2157,255.148860:2580,256.170380:4852,260.195710:4951,261.368990:2484,263.102390:4062,279.784480:2370,294.600830:2052,332.843440:1898,337.220180:2177,340.478580:1972,355.045900:2028,475.631710:2415,491.980320:2140 >>>>>>>>>>>>>>>>>>>>>> --gc0p4Jq0M2Yt08jU534c0p >>>>>>>>>>>>>>>>>>>>>> Content-Type: application/x-Mascot; name="query10200" >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> .... >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> query72071=2915761 >>>>>>>>>>>>>>>>>>>>>> query72072=2915776 >>>>>>>>>>>>>>>>>>>>>> query72073=2915791 >>>>>>>>>>>>>>>>>>>>>> query72074=2915806 >>>>>>>>>>>>>>>>>>>>>> query72075=2915821 >>>>>>>>>>>>>>>>>>>>>> query72076=2915836 >>>>>>>>>>>>>>>>>>>>>> query72077=2915851 >>>>>>>>>>>>>>>>>>>>>> query72078=2915866 >>>>>>>>>>>>>>>>>>>>>> query72079=2915881 >>>>>>>>>>>>>>>>>>>>>> query72080=2915896 >>>>>>>>>>>>>>>>>>>>>> query72081=2915911 >>>>>>>>>>>>>>>>>>>>>> query72082=2915926 >>>>>>>>>>>>>>>>>>>>>> query72083=2915941 >>>>>>>>>>>>>>>>>>>>>> query72084=2915956 >>>>>>>>>>>>>>>>>>>>>> query72085=2915971 >>>>>>>>>>>>>>>>>>>>>> query72086=2915986 >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> .... >>>>>>>>>>>>>>>>>>>>>> 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