NONMEM Users Network Archive

Hosted by Cognigen

Re: FDATA file missing

From: Mahmoud Tareq Abdelwahab <mah.tareq87>
Date: Tue, 26 Nov 2019 19:21:58 +0200

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 <sfcook

> 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: sfcook
> Phone: (570) 362-2981
> ------------------------------
> *From:* owner-nmusers
> behalf of Mark Tepeck <mark.tepeck
> *Sent:* Tuesday, November 26, 2019 11:13 AM
> *To:* nmusers
> *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: Abdmah009

Received on Tue Nov 26 2019 - 12:21:58 EST

The NONMEM Users Network is maintained by ICON plc. Requests to subscribe to the network should be sent to: nmusers-request@iconplc.com.

Once subscribed, you may contribute to the discussion by emailing: nmusers@globomaxnm.com.