Comments (9)
Hi,
It is the max length per single chromosome; there is no hard limit on the total size of the input.
from sibeliaz.
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)?
from sibeliaz.
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.
from sibeliaz.
Hi,
sorry again, I've compiled the software using the fix present in medvedevgroup/TwoPaCo#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
from sibeliaz.
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.
from sibeliaz.
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
from sibeliaz.
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.
from sibeliaz.
Yes, it is working. I have to test it on larger genomes, but the software is running. Thank you again for your support!
Andrea
from sibeliaz.
No problem, let me know if you encounter any problems.
from sibeliaz.
Related Issues (20)
- Large genome files HOT 4
- bash: line 11, 12 and 13: No such file or directory HOT 9
- free -w erro
- How would it deal with phased genomes?
- SibeliaZ/spoa/vendor/bioparser/include/bioparser/parser.hpp:124:19: error: 'gzFile_s' was not declared in this scope
- Installation issues HOT 2
- please include ##sequence-region pragmas in blocks_coords output HOT 4
- more detailed description for output HOT 1
- Conda installation doesn't include maf_to_gfa1.py HOT 2
- support gzip'd input fasta HOT 1
- is it suitable for the very big genome? HOT 2
- Apply the tool to virus HOT 4
- Q on coverage, multi-genome alignment, and maf2synteny HOT 4
- (support oneTBB) fatal error: tbb/mutex.h: No such file or directory HOT 3
- Question about block_coords.gff output
- Unexpected output HOT 1
- PackagesNotFoundError: The following packages are not available from current channels: - sibeliaz HOT 4
- sibeliaZ outputs HOT 2
- # running issue
- Getting alignments after running with "-n"
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