[wgs-assembler-users] BOGART error due to large data

[Yeo Z. X. <zhe...@ya...>]

Dear wgs-assembler admins,

I am new to runCA. The IT supports from my institute had installed CA8.0 a few months ago. 

I managed to generate an assembly using my Illumina Miseq data with both the BOG and BOGART Unitiggers. However, only BOGART failed to complete when I included a bigger Hiseq dataset on top of the Miseq dataset (see attached unittiger.err: "terminate called after throwing an instance of 'std::bad_alloc'"). Since BOGART is the recommended Unitigger for Illumina data, we hope to apply it to generate our assembly using all the data we have. 

For your information, the BOGART is working when I used a subset of the Miseq + Hiseq dataset for assembly by setting the frgMinLen=100 and ovlMinLen=50, suggesting the error is likely due to the size of input data. Our Hiseq data is ~80M of paired-reads (~160M read fragments in total) with most of them are 100bp read after merTrim trimming ( ~50GB of data). The Miseq data is ~10 times smaller than the Hiseq data.

Thank you for your supports.

Best regards,
Zhen Xuan YEO
------------------------------------------------------------
Senior Bioinformatics Specialist @ Yale-NUS College
Centre for BioImaging Sciences
Department of Biological Sciences
Blk S1A, 14 Science Drive 4
Lee Wee Kheng Building
117557 Singapore
(O) +65 65162723
(F) +65 67767882
Email: zhe...@ya...