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medvedevgroup / SibeliaZ

A fast whole-genome aligner based on de Bruijn graphs
http://medvedevgroup.com/
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twopaco: error while loading shared libraries: libtbb.so.2: cannot open shared object file: No such file or directory #28

Open Karimi-81 opened 3 years ago

Karimi-81 commented 3 years ago

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 commented 3 years ago

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

iminkin commented 3 years ago

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 commented 3 years ago

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 GitHubhttps://github.com/medvedevgroup/SibeliaZ/issues/28#issuecomment-846434439, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ATA6XJCAKC2ICQSE2U5F2Y3TO7OA5ANCNFSM45DVN6CQ.

Karimi-81 commented 3 years ago

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.