Bfast

[Lv Ray]

Can you help me?
I have read the paper about BFAST, but I am sure I can't index well. My data is about large genome (~2.7Gbp), and the source is mate-pair SOLID reads(length:50bp). I have created a reference genome in nt and another in cs. Now, I run command: bfast index -f hg19.fa -A 1 -m 111111111111111111 -w 18 -n 8
another one: bfast index -f hg19.fa -A 1 -m 1111110011111110011111 -w 18 -n 8
I got the under warnings from both them:
Sorting by thread...
^M^H100.000 percent complete^Mthread 100.000 percent complete^MWaiting for other threads to complete...^MMerging sorts from threads...
Out of 3 required merges, currently on:
0^M1^M2^M3
Merge complete.
Sorted.
************************************************************
^MIn function "RGIndexCreateHash": Fatal Error[MallocMemory]. Variable/Value: index->starts.
Message: Could not allocate memory.
***** Exiting due to errors *****
************************************************************
Can anyone give me some suggestions about bfast index? I feel so hard to get it clean in my main. THank you!

[WhatsOEver]

Message: Could not allocate memory.

Looks like you don't have or you don't provide enough memory for the program.

[Lv Ray]

Looks like you don't have or you don't provide enough memory for the program.

But I have about 300G RAM.

[lindenb]

cross posted on biostars: https://www.biostars.org/p/112402/

[Lv Ray]

cross posted on biostars: https://www.biostars.org/p/112402/

I am so sorry for my hasty, but I will be mad for bfast index. Sorry for the cross posts.

[colindaven]

I would strongly recommend NovoalignCS for Solid data. I know it's commercial, but it's quite cheap and they do have a trial available. Otherwise algorithms for Solid data are fairly limited - and yes, we did test them all...

[Lv Ray]

I would strongly recommend NovoalignCS for Solid data. I know it's commercial, but it's quite cheap and they do have a trial available. Otherwise algorithms for Solid data are fairly limited - and yes, we did test them all...

Thank you. I will use the bfast after my groping it for several days.Maybe I will use NovoalignCS as your said while the bfast is hard to align more reads on ref.
Thank you again.