Multithreading on Linux does not work

[lfaller]

Hi all,

I installed a fresh copy of sortmerna today by following the instructions on the github README page. Unfortunately, the multithreading option does not seem to work.

$ /home/lina/sortmerna/build/Release/src/sortmerna/sortmerna --ref /home/lina/sortmerna/rRNA_databases/silva-bac-16s-id90.fasta,/home/lina/sortmerna/index/silva-bac-16s-db:/home/lina/sortmerna/rRNA_databases/silva-bac-23s-id98.fasta,/home/lina/sortmerna/index/silva-bac-23s-db:/home/lina/sortmerna/rRNA_databases/silva-arc-16s-id95.fasta,/home/lina/sortmerna/index/silva-arc-16s-db:/home/lina/sortmerna/rRNA_databases/silva-arc-23s-id98.fasta,/home/lina/sortmerna/index/silva-arc-23s-db:/home/lina/sortmerna/rRNA_databases/silva-euk-18s-id95.fasta,/home/lina/sortmerna/index/silva-euk-18s-db:/home/lina/sortmerna/rRNA_databases/silva-euk-28s-id98.fasta,/home/lina/sortmerna/index/silva-euk-28s:/home/lina/sortmerna/rRNA_databases/rfam-5s-database-id98.fasta,/home/lina/sortmerna/index/rfam-5s-db:/home/lina/sortmerna/rRNA_databases/rfam-5.8s-database-id98.fasta,/home/lina/sortmerna/index/rfam-5.8s-db --reads 3718208_merged.fastq --num_alignments 1 --fastx --aligned Sample_3718208/sortmerna_out/3718208_rrna_reads --other Sample_3718208/sortmerna_out/3718208_rrna_free_reads --paired_in -a 39 --log -v --blast 1

Information about software version:

$ /home/lina/sortmerna/build/Release/src/sortmerna/sortmerna

  Program:     SortMeRNA version 2.1b, 03/03/2016
  Copyright:    2012-17 Bonsai Bioinformatics Research Group:
                LIFL, University Lille 1, CNRS UMR 8022, INRIA Nord-Europe
                2014-17 Knight Lab:
                Department of Pediatrics, UCSD, La Jolla
  Disclaimer:   SortMeRNA comes with ABSOLUTELY NO WARRANTY; without even the
                implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
                See the GNU Lesser General Public License for more details.
  Contributors: Jenya Kopylova   jenya.kopylov@gmail.com
                Laurent Noé      laurent.noe@lifl.fr
                Pierre Pericard  pierre.pericard@lifl.fr
                Daniel McDonald  wasade@gmail.com
                Mikaël Salson    mikael.salson@lifl.fr
                Hélène Touzet    helene.touzet@lifl.fr
                Rob Knight       robknight@ucsd.edu

  For help or more information on usage, type `./sortmerna -h'

$ gcc --version
gcc (Ubuntu 5.4.0-6ubuntu1~16.04.4) 5.4.0 20160609
Copyright (C) 2015 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

I have definitely gotten the -a option to work in the past. Is there another trick to enabling multithreading?

Thanks a bunch!

[ekopylova]

Hello,

Did you install SortMeRNA from the Linux binary distribution? If so, I've updated the binary (sortmerna-2.1b-linux.tar.gz) and the new one has been working for many users so far. You can find it here : https://github.com/biocore/sortmerna/releases/tag/2.1b

Otherwise, if you installed from source, could you open a new thread on the forum and I can continue to help there?

Thanks! Jenya

[lfaller]

Thank you! The new version you linked to above works for me! I had compiled the tool from source as suggested on the main page of the github repo using gcc version 5.4.0:

mkdir -p $SMR_HOME/build/Release
pushd $SMR_HOME/build/Release
cmake -G "Unix Makefiles" -DCMAKE_BUILD_TYPE=Release ../..
make

Maybe this did not enable multithreading.

Thank you for the help!