Error: Reference sequence requires more than 240 blocks.

[cjose]

Hello,

I am running alignment on my data, using CASAVA 1.8, and I am getting this message:

td::exception::what: Reference sequence requires more than 240 blocks. If you are using multiple short reference files, you may get around this issue by concatenating them into a single large one. Otherwise, please reduce the length of your reference sequence.

So, I concatenated all my chr*.fa files into one hg19.fa file. After running the alignment again, the same error happens.

Has anyone seen this before? Tips, suggestions and solutions are welcome. Thanks in advance.

[cjose]

Forgot to add that I changed to config.txt in the Aligned folder so it would point to the new folder with the newly concatenated file.