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/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 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. 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