I could success to convert 10 concatenate files into groomer files except 4 of them! I was waiting and reloading many times but they can not convert to groomer files.I have still 67% using free space.
Could you please help and direct me to go through this problem.
Thanks
Do you have jobs waiting(grey) or do they fail(red)?
There is no job waiting or and even when I add only one job it is failing so.
By "failing" you mean datasets turning red?
Yes! After error the datasets are turning to red. I am in basic option with Sanger & Illumina 1.8+. The message is "Error Parsing quality String. ASCII quality strings cannot contain spaces". Thanks your time helping me.
Well it seems the quality scores of the datasets in question contain space. Can you please try to correct that on your side and try again?
You can use the following Galaxy tool for that by e.g. adding "c3.strip()" - Python - in the Add expression and after execution you will get dataset with new column as a result of that expression.
Dear Martin! Actually the first file was big and I did again concatenate my FASTQ files and did run again groomer, but still I have same problem with only size of 6-7 GB files. Previously I had 12 files, all were the same procedure and all of them were successful now I am in bowtie steps, but excepts these four files! I was wondering if was wrong it should be affected with all of them not just with 4 files.
I tryed your way but I can not see concatenate files in file to groom function. Only I can see bowtie files! Sorry again