twopaco: error while loading shared libraries: libtbb.so.2: cannot open shared object file: No such file or directory

[Karimi-81]

Hi there,
I used conda to install the sibeliaz:
conda install -c bioconda sibeliaz
However, I tried to run the program, I encountered with following error:
(base) -bash-4.2$ sibeliaz assembly_mini.fasta
Constructing the graph...
twopaco: error while loading shared libraries: libtbb.so.2: cannot open shared object file: No such file or directory
TwoPaco: 0.00 seconds elapsed, 216 KB memory used
Loading the graph...
error: Can't read the input file
SibeliaZ-LCB: 0.05 seconds elapsed, 2048 KB memory used
rm: cannot remove './sibeliaz_out/de_bruijn_graph.dbg': No such file or directory
bash: global_alignment: command not found
Alignment: 0.05 seconds elapsed, 1724 memory used

Is this issue related to installation of required libraries. Do you have any idea to solve the problem.
Thank you

[iminkin]

Hi @Karimi-81 , do you have root privileges on the machine you are using?

[iminkin]

In the meanwhile, I found a similar issue with another project. Could you try a solution described there, i.e. downgrading tbb by running

conda install tbb=2020.2

?

Link to the thread: https://www.biostars.org/p/494922/

[Karimi-81]

Thank you. The suggested solution worked well. Now, program runs smoothly. Best, ======================================== Karim Karimi Ph.D in Animal Breeding & Genetics Postdoctoral Fellowship in Mink Genomics Department of Animal Science and Aquaculture Dalhousie University Tel: (902) 814 4442

…

________________________________ From: Ilia Minkin ***@***.***> Sent: Saturday, May 22, 2021 1:49 PM To: medvedevgroup/SibeliaZ ***@***.***> Cc: Karim Karimi ***@***.***>; Mention ***@***.***> Subject: Re: [medvedevgroup/SibeliaZ] twopaco: error while loading shared libraries: libtbb.so.2: cannot open shared object file: No such file or directory (#28) CAUTION: The Sender of this email is not from within Dalhousie. In the meanwhile, I found a similar issue with another project. Could you try a solution described there? https://www.biostars.org/p/494922/ — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub<#28 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/ATA6XJCAKC2ICQSE2U5F2Y3TO7OA5ANCNFSM45DVN6CQ>.

[Karimi-81]

Sorry to interrupt you again. I got another error:
Constructing the graph...
Threads = 16
Vertex length = 25
Hash functions = 5
Filter size = 68719476736
Capacity = 1
Files:
/scratch/karimi81/sibeliaz/genome1.fasta
/Pacbio_data/NCBI_Prep/assembly_new_IDs.fasta

Round 0, 0:68719476736
Pass Filling Filtering
1 188 335
2 130 22
True junctions count = 51616635
False junctions count = 34209474
Hash table size = 85826109
Candidate marks count = 724970458

Reallocating bifurcations time: 31
True marks count: 688877364
Edges construction time: 137

Distinct junctions = 51616635

Loading the graph...
Analyzing the graph...
[..................................................]
Generating the output...
Blocks found: 2148015
Coverage: 0.23
bash: global_alignment: command not found

is this issue related to aligner? should I install or load aligner separately. I used the last version of software in conda.