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

Question

[joaopedrocoelho18]

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

[Andrzej Zielezinski]

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

[joaopedrocoelho18]

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.

[khemlalnirmalkar]

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

Thanks

Answer 1

[Rks]

Did you try using option --use-ftp

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

[Juan MONROY-NIETO]

This will solve the issue but you need to modify one of the commands in the download script. check this GitHub comment to learn how