bfast index is so hard
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9.8 years ago
laihui126cn ▴ 40

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 • 2.9k views
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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?

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

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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.

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

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I've got a RSS feed for SE.

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

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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.

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