Fail to read header from fasta input

[gustavogregoracci]

Hi,
I'm trying to align (BWA 0.7) a somewhat large fasta file (~17Gb) against a indexed database of similar size. Indexing went ok. But all I'm getting is fail to read header from sam file, then afterwards, it is not possible to convert to bam or work with the sam.
I tried the normal header, similar to the original fastq (with : and +, and a few spaces in some sequences) (1), tried to replace symbols with dashes (: and + turned to _)(2), tried to trim spaces (3), and tried to replace the header altogether for Seq[number]_sample (4). They all fail to read the header from the sam file. Samtools view also failed to read the sam headers. I tried bwa mem and bwasw, and both failed. The input is a single mate fasta file, put together from joined pairs and singlets, so there are minor differences inbetween the headers, which are unique. Any ideas on how to tackle this issue?