Question: bfast index is so hard
0
gravatar for laihui126cn
5.2 years ago by
laihui126cn40
Australia
laihui126cn40 wrote:

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!

index bfast • 1.8k views
ADD COMMENTlink modified 5.2 years ago • written 5.2 years ago by laihui126cn40

Well it's failing with a MALLOC error, so I would imagine it's running out of RAM.  How much RAM do you have in the machine?

ADD REPLYlink written 5.2 years ago by george.ry1.1k

However, my machine has at least 300G RAM, maybe it's not the RAM problem.

ADD REPLYlink written 5.2 years ago by laihui126cn40

Hello laihui126cn!

It appears that your post has been cross-posted to another site: http://seqanswers.com/forums/showthread.php?t=46573

This is typically not recommended as it runs the risk of annoying people in both communities.

ADD REPLYlink written 5.2 years ago by Pierre Lindenbaum124k

Pierre: have you scripted some kind of cross-post detection system or are you just very present online?

ADD REPLYlink written 5.2 years ago by Matt Shirley9.2k
1

I've got a RSS feed for SE.

ADD REPLYlink written 5.2 years ago by Pierre Lindenbaum124k

Glad I'm not the only person who takes this approach ;)

 

ADD REPLYlink written 5.2 years ago by Daniel Swan13k

I am so sorry for disturbing you in both communities. I was so impatient for my trying about bfast index and nothing got. Sorry again, I promise this will never happen from me.

ADD REPLYlink written 5.2 years ago by laihui126cn40
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