Re: FDATA file missing

On Tue, Nov 26, 2019 at 9:22 AM Mahmoud Tareq Abdelwahab < [email protected]> wrote: > Hello Mark, > > in addition to Sarah's suggestions, you could run NONMEM via psn using > option clean=0 which will stop psn from cleaning the temp files generated > by NONMEM. > > for the data issues, it refers to the actual data that's read into NONMEM > i.e after excluding all ignore statements and dropped columns, a workaround > is to filter out the dataset in the same way it's being filtered in the > NMtran control stream or kill the run before it crashes and you should have > the FDATA file in the NM folder. > > Mahmoud > > On Tue, Nov 26, 2019 at 7:10 PM Cook, Sarah <[email protected]> wrote: > >> Hi Mark, >> >> >> I'm guessing that you are probably running NONMEM via PsN. The default >> behavior of PsN is to suppress some output files, including the FDATA file. >> To request that the FDATA file be retained, you can include the option >> -extra_output=fdata on your PsN execute command line. >> >> >> I don't think there is any way to include the column headings (since they >> are ignored and not actually read into NONMEM), but having the FDATA file >> should help you troubleshoot your problem. As far as I know, the warnings >> relate to the location in the FDATA file, again, because the ignored rows >> are not actually being read in. >> >> >> Best of luck, >> >> Sarah >> >> >> >> Sarah F. Cook, PhD >> Adjunct Assistant Professor >> University at Buffalo >> Department of Pharmaceutical Sciences >> E-mail: [email protected] >> Phone: (570) 362-2981 >> ------------------------------ >> *From:* [email protected] <[email protected]> on >> behalf of Mark Tepeck <[email protected]> >> *Sent:* Tuesday, November 26, 2019 11:13 AM >> *To:* [email protected] >> *Subject:* [NMusers] FDATA file missing >> >> >> During my troubleshooting of a failed NONMEM run, I want to confirm the >> correct exclusion of some records (e.g., IGNORE CMT=2) for the input file. >> However, I could not find the FDATA file in the run directory. Is there any >> way to force NONMEM to generate a FDATA? I am also wondering about the >> possible causes of missing FDATA. >> >> Even the FDATA file is available, is it possible to include the column >> heads (e.g., ID, DV) on the top of the numbers? So, I can confirm which >> column is excluded or retained. >> >> In addition, I am not sure whether the dataset related warnings (e.g., >> DATA WARING 1, RECORD 100, DATA ITEM 11, THE DV IS NULL BUT MDV IS 0) is >> refereeing to the FDATA file or the raw input CSV file. In other words, the >> problematic record 100 represents the row 100 in the FDATA file or the CSV >> file? >> >> Thank you, >> >> Mark >> > > > -- > > > > > > > > > > > *Mahmoud Tareq AbdelwahabPhD StudentPharmacometrics Research GroupDivision > of Clinical PharmacologyDepartment of MedicineUniversity of Cape TownK45 > Old Main BuildingGroote Schuur HospitalObservatory, Cape Town 7925, South > Africa.* > > > *Tel: +27 21 650 4861Email: [email protected] <[email protected]>* > >