#10 FastaToCA error

[Matthew Kellom]

The FastqToCA script does not seem to be working correctly, or I am not using it correctly. When entering the following command:

fastqToCA -insertsize 300 200 -libraryname GreenCheese -technology illumina-long -type illumina -reads GreenCheese2010_S1_L001_R1_001.fastq,GreenCheese2010_S1_L001_R2_001.fastq > GreenCheese.frg

it creates the attached file

What am I doing wrong?

[Brian Walenz]

You want -mates (mated reads) instead of -reads (single ended reads).

[Matthew Kellom]

I tried -mates as well:

and it gives me the exact same output, attached (new file, but is the same, or very similar)

[Brian Walenz]

The reads aren't copied into the .frg - it just contains link to the original fastq files. When gatekeeper reads this file, it opens the linked reads and loads from there.

What's the specific problem you're seeing?

[Matthew Kellom]

Ah I was unaware of that, I thought there was a format conversion that was going to happen. Thank you very much