This is my first time trying out a fastq -> VCF pipeline, so I don't have the experience to be able to determine if things are working as I'm chugging through each step (from trimming, to alignment, to variant calling).
I just tried to create an index using hg19.fa on my MacBook Air which has 4 gigs of RAM. I ran
bwa index hg19.fa
and after 695 iterations (and 3063 seconds) the program stops with:
[bwa_index] Update BWT... [fwrite] No space left on device.
I have about 2 gigs left on my hard drive, for what it's worth. But right now I'm just wondering what exactly was left to be done, since I got to the point where it says
Finished constructing BWT
Can I use the files (4 of them) that were created to align my paired-end fastq's? (From my understanding, there are supposed to be a lot more.) Also, if I clear some memory on my computer, can I resume this process (assuming that it in fact is not finished) from where it left off, using these 4 files? This is what was created so far:
hg19.fa.amb hg19.fa.ann hg19.fa.bwt hg19.fa.pac