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medvedevgroup / SibeliaZ

A fast whole-genome aligner based on de Bruijn graphs
http://medvedevgroup.com/
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Genome size #5

Closed RenzoTale88 closed 5 years ago

RenzoTale88 commented 5 years ago

Hi, I need to align multiple mammalian-sized genomes (4 genomes of 2.7Gb each, 11Gb in one fasta). My question is regarding the limitation in chromosomes length (4294967296 bp). Is it to be intended as the sums of all chromosomes into the fasta file? Or is it intended as the max length per single chromosome?

Thank you in advance Andrea

iminkin commented 5 years ago

Hi,

It is the max length per single chromosome; there is no hard limit on the total size of the input.

RenzoTale88 commented 5 years ago

Thank you very much for the quick reply. One more question: do you have an estimated amount of memory and time per genome (with the genome size above described)?

iminkin commented 5 years ago

I would aim for at least 4-5 hours and maybe 100-150 GB of RAM. But it depends a lot on how close the genomes are.

RenzoTale88 commented 5 years ago

Hi, sorry again, I've compiled the software using the fix present in https://github.com/medvedevgroup/TwoPaCo/issues/13. After that, I've tried to run the software on two bacterial genomes to check whether the program is working or not. At the beninning, the program start running without problems, but then suddenly stop at the filling/filering with the following error:

.../sibeliaZ/bin/twopaco: symbol lookup error: .../sibeliaZ/bin/twopaco: undefined symbol: _ZN3tbb8internal24concurrent_queue_base_v818internal_push_moveEPKv

Is it a known issue? Thank you again

iminkin commented 5 years ago

It could be that TBB is not properly installed on your system. What Linux distro are you using? If it is Debian-based, the easiest way to install it is sudo apt-get install libtbb-dev or ask your system administrator to do that if you don't have the root rights.

RenzoTale88 commented 5 years ago

I'm working on a cluster environment and I've no admin rights, so I was trying to install it in a local folder, create all the variables and install SibeliaZ afterwards. Using the latest version of TBB it's not working. However, using the version tbb44_20151115 and using the bug above mentioned, allowed the proper installation of the software.

Thank you for your quick reply.

Andrea

iminkin commented 5 years ago

Andrea,

Did you manage to make it work? Just in case, you can try to ask your sysadmin to install TBB using a package manager, it is a very widely available library.

RenzoTale88 commented 5 years ago

Yes, it is working. I have to test it on larger genomes, but the software is running. Thank you again for your support!

Andrea

iminkin commented 5 years ago

No problem, let me know if you encounter any problems.