Running Pregap4

When the Run button or Run command (File menu) is used, pregap4 starts processing the files using the selected modules and their configurations. If the configuration is invalid an error message will be produced. For example the following may be written to the error window, and the configure modules panel will be selected with the problematic module automatically highlighted.

Fri 10 Jul 10:04:25 1998 Run: Module sequence_vector_clip needs configuring

Assuming that the configuration is correct, the processing will start and output will be sent to the output window as progress is made. The progress within each module is shown by a series of fullstops (.) for each correctly processed sequence, and an exclamation mark (!) for each failed sequence.

The text output window above shows the early processing stages of 20 sequences. When finished pregap4 will produce a report containing information from each module and the final list of passed and failed sequences. For example:

- Report Production -
Passed files:
    xb54a3.s1.exp (xb54a3.s1SCF.gz) : type EXP
    xb54b12.r1L.exp (xb54b12.r1LSCF.gz) : type EXP
    xb54b12.r1.exp (xb54b12.r1SCF.gz) : type EXP
    xb54b12.s1.exp (xb54b12.s1SCF.gz) : type EXP
    xb54c3.s1.exp (xb54c3.s1SCF.gz) : type EXP

Failed files:
    xb54g5.s1.exp (xb54g5.s1SCF.gz) 'screen_vector_clip:  sequence too short'

- Report from 'Augment Experiment Files' -
xb54a3.s1.exp : added fields SF CF SC SP TN ST PR SI CH.
xb54b12.r1L.exp : added fields SF CF SC SP TN ST PR SI CH.
xb54b12.r1.exp : added fields SF CF SC SP TN ST PR SI CH.
xb54b12.s1.exp : added fields SF CF SC SP TN ST PR SI CH.
xb54g5.s1.exp : added fields SF CF SC SP TN ST PR SI CH.
xb54c3.s1.exp : added fields SF CF SC SP TN ST PR SI CH.

- Report from 'Tag Repeats' -
xb54a3.s1.exp : no repeat found.
xb54b12.r1L.exp : no repeat found.
xb54b12.r1.exp : no repeat found.
xb54b12.s1.exp : no repeat found.
xb54c3.s1.exp : no repeat found.

                       ***   Processing finished   ***

The list of passed and failed files are written to prefix.passed and prefix.failed, where prefix is the output filename prefix specified in the "Files to Process" panel. The reports are written to prefix.report. The passed and failed files contain the most recent filenames associated with each sequence. So if a sequence fails early on it could be listed as something like xb54a3.s1SCF.gz and if it fails later it will be listed like xb54a3.s1.exp. This is because it is the final filename which is important for later processing, such as for assembly into gap4.

A prefix.log file is also created containing a list of passed files, failed files, and the filename history for each file (the intermediates will still exist). The format of the passed section is "filename (file_type) PASSED". The format of the failed section is "filename (file_type) ERROR: error message". The format of the file history lines is a series of "filename (file_type)" segments separated by "<-", with the original filename listed to the right. Filenames containing Tcl meta-characters may be `escaped' using curly braces or back slashes. (The Tcl subst command may be used to generate the original name.) An example of a log file follows. This was produced with the command line "pregap4 "Sample 671" WT5.exp zf89a2.s1.scf xb56e5.s1.scf".

[passed files]
ha59a6.s1.exp (EXP) PASSED
WT5.exp (EXP) PASSED
xb56e5.s1.exp (EXP) PASSED

[failed files]
zf89a2.s1.exp (UNK) ERROR: screen_vector_clip:  sequence too short

[passed file history]
ha59a6.s1.exp (EXP) <- ha59a6.s1.scf (SCF) <- {Sample 671} (ABI)
WT5.exp (EXP)
xb56e5.s1.exp (EXP) <- xb56e5.s1.scf

[failed file history]
zf89a2.s1.exp (UNK) <- zf89a2.s1.scf

Some modules may also keep their own separate records, such as an assembly log. Where this is the case, it will be explained in the help specific to that module.

After running pregap4 it is time to either assemble the data (if this was not done using pregap4) or to edit it. If the data has already been assembled with Pregap4 then you will need to start up gap4 and use `Open Database'. Otherwise one of the gap4 assembly functions should be used, with the filename_prefix.passed file. For more information on this see the Gap4 manual.