MakeBlastDB requires

[moorembioinfo]

Hi!

Panseq cuts out for me citing:

2014/04/03 12:32:00 INFO | SegmentMaker.pm:155> Segmenting /pub19/matthew/Panseq/Panseq-master/BasenucmerTempFile2ThuApr31230132014493417855614_pan_final_novelRegions_final_novelRegions into 500bp segments 2014/04/03 12:32:01 FATAL | MakeBlastDB.pm:57> Modules::Alignment::MakeBlastDB requires

2014/04/03 12:32:01 FATAL | MakeBlastDB.pm:57>

2014/04/03 12:32:01 FATAL | MakeBlastDB.pm:57> 'dbtype'

2014/04/03 12:32:01 FATAL | MakeBlastDB.pm:57>

2014/04/03 12:32:01 FATAL | MakeBlastDB.pm:57> 'out'

2014/04/03 12:32:01 FATAL | MakeBlastDB.pm:57>

2014/04/03 12:32:01 FATAL | MakeBlastDB.pm:57> 'title'

2014/04/03 12:32:01 FATAL | MakeBlastDB.pm:57>

2014/04/03 12:32:01 FATAL | MakeBlastDB.pm:57> 'in'

2014/04/03 12:32:01 FATAL | MakeBlastDB.pm:57>

2014/04/03 12:32:01 FATAL | MakeBlastDB.pm:57> 'logfile'

I've checked the scripts and can't discern any issue and the blast directory is correct and makeblastdb is working.

Many many thanks for any help with this advance!!

Best regards,

Matt Moore.

[chadlaing]

Hi Matt,

The information needed for the check that is failing should be provided in the config file used to launch Panseq. This file should be tab-delimited. The two required options for the MakeBlastDB.pm module to function correctly are the 'baseDirectory' and 'blastDirectory'. Make sure these are both specified, and end the directory with a '/'.

eg: baseDirectory /home/matt/output/ blastDirectory /usr/bin/

Let me know if this helps or not.

Chad

[moorembioinfo]

Thanks for such a quick reply!

The base directory didn't end in '/', which I should have noticed from the prefixes, thanks for the fix, it has no problems with that module now!

Matt

[chadlaing]

No problem Matt. I will code a fix to the directory must-end-in-slash issue, it is easy enough and could save some user headache.