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metagenome-atlas / atlas

ATLAS - Three commands to start analyzing your metagenome data
https://metagenome-atlas.github.io/
BSD 3-Clause "New" or "Revised" License
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DAS-TOOL Step Fails due to missing Dynamic Library libicui18n.so.58 #282

Closed LeeBergstrand closed 4 years ago

LeeBergstrand commented 4 years ago

rule: run_das_tool atlas version: 2.0.6

Error output:

identifying single copy genes using diamond version 0.9.30
evaluating bin-sets
starting bin selection from 30 bins
||||||
bin selection complete: 6 bins above score threshold selected. 
Error in dyn.load(file, DLLpath = DLLpath, ...) : 
  unable to load shared object '/Data/reference_databases/atlas/2.2.x/conda_envs/f53dbdbc/lib/R/library/stringi/libs/stringi.so':
  libicui18n.so.58: cannot open shared object file: No such file or directory
Calls: DER_Plot ... namespaceImport -> loadNamespace -> library.dynam -> dyn.load
Execution halted
Waiting at most 5 seconds for missing files.
MissingOutputException in line 488 of /home/lhbergst/anaconda3/envs/atlas-metagenomics/lib/python3.6/site-packages/atlas/rules/binning.snakefile:
Missing files after 5 seconds:
L2-Joined/binning/DASTool/L2-Joined_DASTool_scores.pdf
This might be due to filesystem latency. If that is the case, consider to increase the wait time with --latency-wait.
Removing output files of failed job run_das_tool since they might be corrupted:
L2-Joined/binning/DASTool/L2-Joined_DASTool_summary.txt, L2-Joined/binning/DASTool/L2-Joined_DASTool_hqBins.pdf, L2-Joined/binning/DASTool/L2-Joined_metabat.eval, L2-Joined/binning/DASTool/L2-Joined_concoct.eval, L2-Joined/binning/DASTool/L2-Joined_maxbin.eval, L2-Joined/binning/DASTool/cluster_attribution.tsv
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Note the path to the log file for debugging.

libicui18n.so.58 appears to be missing.

This may be related

https://stackoverflow.com/questions/51152664/could-not-find-libicui18n-so-58-in-ubuntu-16-04

What I did to solve the problem.

  1. Activated the das_tool conda enviroment atlas generated.
  2. Uninstalled das_tool, pyicu and icu (libicu-dev) conda packages.
  3. Reinstalled the das_tool, pyicu and icu (libicu-dev) conda packages.
  4. Activate original atlas enviroment.
LeeBergstrand commented 4 years ago

Atlas has now completed its run. Looks like the R code was failing to find the ICU lib. So it is likely that it was either the ICU or Das_Tool versions required to be updated.