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 < spctools-discuss@googlegroups.com> 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 > alastair.s...@googlemail.com: >> >> 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 <spctools...@googlegroups.com> 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 <spctools...@googlegroups.com> 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 <spctools...@googlegroups.com> 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 >>>>>>>> alastair.s...@googlemail.com: >>>>>>>>> >>>>>>>>> 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/curre >>>>>>>>> nt/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|Emihu >>>>>>>>> 1|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+005,365.1805 >>>>>>>>> 40:7.352e+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+004,502.667 >>>>>>>>> 720:7425,120.080620:1.568e+005,200.183460:1.14e+005,311.1700 >>>>>>>>> 10:4.379e+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+004,157.129 >>>>>>>>> 850:4876,157.133100:3.958e+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+0 >>>>>>>>> 04,301.187160:8614,306.159450:8586,312.191350:1.242e+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 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