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] <javascript:>> 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] <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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