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
•
written
by
joaopedrocoelho18 •
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
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.
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Try to install libiconv package by typing
conda install -c conda-forge libiconvThe 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:
Hi, Did you get the solution for your error? If yes, please can you share with me? I got the same error.
Thanks