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. 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