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] <javascript:>> 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]. >>>>>>> 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. >>>>> >>>> >>>> -- >> 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] <javascript:>. >> To post to this group, send email to [email protected] >> <javascript:>. >> 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. 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