Have you tried the bwtsw method in the bwa mem data manager?

Regarding the 2bit file, even if you make it, are you sure the downstream tool(s) will handle the missing chromosomes/contigs?

Maybe you should use the primary assembly instead (at least for the 2bit file).

Devon

On 10/03/2016 03:50 PM, Nikolaos Tur wrote:
Hi,

I try to build indexes for ch38 (GRCh38.84 Toplevel) using data managers for BWA-MEM and TwoBit.
Both failed.

Error building index:
Error in faToTwoBit, index overflow at CHR_HSCHR4_5_CTG12. The 2bit format does not support indexes larger than 4Gb,
please split up into smaller files.

[bwa_index] Update BWT... [bwt_bwtupdate_core] Failed to allocate 46629609168 bytes at bwtindex.c line 135: Cannot allocate memory
Error building index.

So, how to split genome for TwoBit and how much RAM is needed for BWA indexes? These errors are from runs on machine with 45GB RAM.

Thanx,
Nikolaos


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-- 
Devon Ryan, PhD
Bioinformatician / Data manager
Bioinformatics Core Facility
Max Planck Institute for Immunobiology and Epigenetics
Email: dpryan79@gmail.com