Question: kraken and kraken2: Downloading taxonomy tree data...rsync: error while loading shared libraries: libiconv.so.2: cannot open shared object file: No such file or directory
0
gravatar for joaopedrocoelho18
5 weeks ago by
joaopedrocoelho180 wrote:

I'm trying to run kraken v.1.1.1 to perform an analysis of metagenomic data, but when I try to give the

kraken-build -standard --threads 20 --db MY_KRAKEN_DATABASE

command, the following error appears:

Downloading taxonomy tree data ... rsync: error while loading shared libraries: libiconv.so.2: cannot open shared object file: No such file or directory

The program was installed with conda, I tried to install kraken2 to check if it was the program version, but the same error occurred. I'm new to bioinformatics and programming, if anyone can help me solve this problem, it would help a lot.

Complete error:

Downloaded taxonomy tree data

Uncompressing taxonomy data... done.

Untarring taxonomy tree data... done.

Step 1/3: performing rsync dry run...

Rsync dry run complete, removing any non-existent files from manifest.

Step 2/3: Performing rsync file transfer of requested files

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

rsync_from_ncbi.pl: rsync error, exited with code 127

kraken • 166 views
ADD COMMENTlink modified 5 days ago by Rks20 • written 5 weeks ago by joaopedrocoelho180
1

Try to install libiconv package by typing conda install -c conda-forge libiconv

ADD REPLYlink written 5 weeks ago by a.zielezinski9.1k

The moment you sent this message, I installed libsconv with conda and it worked, he downloaded this part, however, now another error has appeared, related to ncbi:

Downloading taxonomy tree data... done.

Untarring taxonomy tree data... done

Step 1/2: Performing rsync file transfer of requested files

Rsync file transfer complete.

Step 2/2: Assigning taxonomic IDs to sequences

Processed 360 projects (553 sequences, 924.99 Mbp)... done

All files processed, cleaning up extra sequence files... done, library complete.

Masking low-complexity regions of downloaded library... done.

rsync: failed to connect to ftp.ncbi.nlm.nih.gov (130.14.250.7): Connection refused (111)

rsync: failed to connect to ftp.ncbi.nlm.nih.gov (2607:f220:41e:250::7): Network is unreachable (101)

rsync error: error in socket IO (code 10) at clientserver.c(127) [Receiver=3.1.3]

Error downloading assembly summary file for bacteria, exiting.

ADD REPLYlink written 5 weeks ago by joaopedrocoelho180

Hi, Did you get the solution for your error? If yes, please can you share with me? I got the same error.

Thanks

ADD REPLYlink written 4 weeks ago by khemlalnirmalkar0
0
gravatar for Rks
5 days ago by
Rks20
European Union
Rks20 wrote:

Did you try using option --use-ftp

kraken-build -standard --threads 20 --db MY_KRAKEN_DATABASE --use-ftp ?

ADD COMMENTlink written 5 days ago by Rks20
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1063 users visited in the last hour