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]> 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 >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> .... >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> -- >>>>>>>>>>>>>>>>>>>> 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 post to this group, send email to >>>>>>>>>>>>>>>>>>>> [email protected]. >>>>>>>>>>>>>>>>>>>> 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 >>>>>>>>>>>>>>>>>> [email protected]. >>>>>>>>>>>>>>>>>> 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>>>>>>>>>>> >>>>>>>>>> -- >>>>>>>>> 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 post to this group, send email to [email protected]. >>>>>>>>> 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 [email protected]. >>>>>>> To post to this group, send email to [email protected]. >>>>>>> Visit this group at https://groups.google.com/group/spctools-discuss >>>>>>> . >>>>>>> For more options, visit https://groups.google.com/d/optout. >>>>>>> >>>>>> >>>>>> 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