Alamut annotation issue

Question

[hwandong]

Hi,

We have hit one issue for couple of days already: we always got partial(incomplete) annotation results. Some error information below(detailed log is attached):

alamut-batch version 1.5.2 (standalone no-qsettings fixtk starok) / Qt 5.3.2
******************************************************
| This software program is a genomic variant         |
| interpretation support system that must be used    |
| by human genetics professionals and with           |
| critical judgment.                                 |
| Although Interactive Biosoftware is committed to   |
| ensure a high quality level of this program, it    |
| cannot guarantee the accuracy of information and   |
| predictions it provides.                           |
******************************************************
License valid until ....
Connected to database alamut_db on /mnt/fvg01vol1/bioinfx/annotation/Alamut/Alamut_170920/alamut_db-1.5-2017.09.20.db
Database version 2017.09.20 (2017.09.20)
Connected to a-ht-na.interactive-biosoftware.com
HGMD credentials OK
Total Variant Count: 1578
Program parameters:
   Input file: 123456.vcf
   Annotation file: 1802050251.txt
   Unprocessed variants file: 1802050251_unann.txt
   Genome assembly: GRCh37
   Strand: 1
   Transcript file: preferred_transcripts.txt
   Annotating on all other transcripts: no
   No GeneSplicer predictions
--------------------------------------------
Annotation batch started 2/7/18 4:18 PM
Launching 15 annotation processes
...
Process 26685 FAILED
WARNING: Sub-process 26685finished with exit code 1
...
All sub-processes terminated, some of them WITH ERRORS
Collecting annotations...done
Annotation batch finished 2/7/18 4:18 PM
---------------------------------------------
alamut-batch-standalone-noqsettings-fixtk-starok-1.5.2 returned only 268 annotations but expected at least 1578 annotations for 1712097 1802050251...

Try again, still fail...

[WouterDeCoster]

As far as I know that's commercial software, so you should ask the company for help.

[Kevin Blighe]

It is indeed commercial.

If you have purchased a licence for Alamut and are not using a pirated version, then you should additionally have a support agreement warranty.