Error when building SQLite DB molloylab2019  2019-03-18
 

Hi,
so I just encountered a problem while trying to generate the SQLite DB for one of our datasets. I included the immediate window output. It looks like the tool expects more lines in the skyline output than there are. I tried running AvG with the demo set and another of our datasets and it worked just fine. I processed the data the same as always so I don't know what is causing this error. It would be great if you could have a look at it.
System info:
Windows 10, 64-Bit
i9-7960X @ 2.80Ghz
64 GB RAM
AvG version: 0.0.1.0
Skyline version: 4.2.0

If you need any additional info or the data itself please let me know.
Cheers,
Pascal

 
 
S.Vaca responded:  2019-04-03

Hi Pascal,

Sorry I didn't set the email alerts for the message board correctly and missed this post. Thanks for reporting this bug.
From the error message, it seems that the problem comes from the function that reads the CSV file and converts it to the SQLite database. To avoid having to read a large CSV file into memory this function reads only a chunk of it. By default, the chunk size is 20,000 lines. It seems that the problem comes from the last chunk where the function tries to skip more lines than there are in the CSV file. This should not happen. Could you share with me the CSV file that you were trying to convert into an SQLite DB?
You can export it from:
Export--> Report --> and select the template called "AvantGardeDIA_Export".

Best,
Sebastian
svaca@broadinstitute.org