I try to run http://qiime.org/scripts/normalize_table.html on my data. The script requires R with Biocondcuctor.
The environment is Ubuntu 14.04 LTS, R 3.3.3 (/usr/bin/R) and QIIME 1.9.
The script has halted at several points, in which R couldnt find specific libraries, e.g. optparse, (installed from repository), biom (installed from local file, as it is not available for 3.3.3), and biomformat (installed via bioclite).
Now, it breaks again giving this output:
normalize_table.py -i otu_table.biom -a CSS -o CSS_normalized_otu_table.biom Traceback (most recent call last): File "/opt/qiime-1.9.0/usr/local/bin/normalize_table.py", line 142, in <module> main() File "/opt/qiime-1.9.0/usr/local/bin/normalize_table.py", line 125, in main normalize_CSS(input_path, out_path, output_CSS_statistics) File "/opt/qiime-1.9.0/usr/local/lib/python2.7/dist-packages/qiime/normalize_table.py", line 38, in normalize_CSS run_CSS(temp_fh.name, out_path, output_CSS_statistics=output_CSS_statistics) File "/opt/qiime-1.9.0/usr/local/lib/python2.7/dist-packages/qiime/normalize_table.py", line 76, in run_CSS app_result = rsl(command_args=command_args, script_name='CSS.r') File "/opt/qiime-1.9.0/usr/local/lib/python2.7/dist-packages/qiime/util.py", line 1946, in __call__ (exit_status, command, stdout, stderr)) burrito.util.ApplicationError: Unacceptable application exit status: 1 command: cd "/media/4tb/trichter/ScaleMic/Analysis_2017/OTU_picker/results/"; R --slave --args --source_dir /opt/qiime-1.9.0/usr/local/lib/python2.7/dist-packages/qiime/support_files/R -i /tmp/QIIME-normalize-table-temp-table-y1HnW4.biom -o CSS_normalized_otu_table.biom < /opt/qiime-1.9.0/usr/local/lib/python2.7/dist-packages/qiime/support_files/R/CSS.r stdout: stderr: Loading required namespace: biomformat Error in if (!object$type %in% biomtypevals) { : argument is of length zero Calls: CSS ... initialize -> validObject -> anyStrings -> validityMethod In addition: Warning message: 'load_biom' is deprecated. Use 'load_biom' instead. See help("Deprecated") and help("metagenomeSeq-deprecated"). Execution halted
This all tells me, that i probably have a faulty setup of R, bioconductor, and QIIME. But i dont know how to fix this problem without guidance.
Here are my library paths of R. Note, that R-Studio (1.xxx, latest version) gives me a User Library, and a System Library (which doesnt happen with windows). R is not included in path, as per .bashrc, but can be run from shell.
[1] "/media/4tb/trichter/R/x86_64-pc-linux-gnu-library/3.3" [2] "/usr/local/lib/R/site-library" [3] "/usr/lib/R/site-library" [4] "/usr/lib/R/library"
here is a session.info
> sessionInfo() R version 3.3.3 (2017-03-06) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 14.04 LTS locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 [4] LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C [10] LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] BiocInstaller_1.24.0 loaded via a namespace (and not attached): [1] tools_3.3.3