No multithread for bowtie2-build about irap HOT 12 CLOSED

Hi,

In general you may define the number of threads in the configuration file (max_threads
parameter) - https://github.com/nunofonseca/irap/wiki/8-Configuration-file

However, currently this parameter it is not passed to the bowtie2-build program.

It seems that bowtie2-build program (version 2.2.6) does not support multi-threading. Is there a parameter to enable multi-threading in bowtie2-build?

Cheers

from irap.

Hey,

I tried hisat2 as mapper, and there is the same problem. The -p option is not passed to hisat2-build.

Best regars

from irap.

Yes, for hisat2-build the -p option was not being enabled - it is now fixed in the devel branch.

Thanks.

from irap.

Hey,

I found the parameter for bowtie2-build:

--threads <int> By default bowtie2-build is using only one thread. Increasing the number of threads will speed up the index building considerably in most cases.

Is it enough if I change
bowtie2_index_params=$(bowtie2_index_options)
to
bowtie2_index_params=--threads $(max_threads) $(bowtie2_index_options)
to enable the option for bowtie2-build?

Edit: this option was added in bowtie2 version 2.2.7... Is it possible to upgrade to a newer verison in iRAP?

from irap.

Hi,
yes to both questions. I'll try to include bowtie2 2.2.7 (or later) version in the next release of iRAP.
Cheers.

from irap.

Hey,
sounds good! Do you have a plan when to release next version of iRAP?
Cheers,

from irap.

It should happen in February.
Cheers.

from irap.

Hi,
I just pushed a (minor) new release of iRAP that includes bowtie 2.2.9 and multi-thread support for bowtie2-build. Please let me know if it works for you to close this issue.
Thanks.

from irap.

Hey,
Thanks for the fast response!

I updated as in the Wiki described, but:

1. `./scripts/irap_install.sh -a -s .` from Wiki did not work -> `./scripts/irap_install.sh -s . -a` did work.
   

2. Then I got an error
   Makefile:490: recipe for target 'yapi.o' failed make: *** [yapi.o] Error 1

I try do a full reinstall and report to you.
The log file: 2301171046.txt

Edit: Full reinstall worked, data is analysed atm.

from irap.

Hi,
Thanks for the report. The full update (./scripts/irap_install.sh -s . -a) should be working now (devel branch).
You may quickly update the core iRAP code and bowtie2 by running
./scripts/irap_install.sh -s . -u
./scripts/irap_install.sh -s . -x bowtie2

Cheers.

from irap.

Everything works fine for me atm. Data is analysed without error and I did not see problems regarding multithreading so far. Thank you for the help!
Cheers

from irap.

Great! Thanks for reporting the issues!
Cheers.

from irap.