jnpaulson
commented
8 years ago Hi @kathfi,
The other potential issue can be that you have a single or more samples with at most 1 OTU present. I'm happy to take a closer look at the biome file if you send it to jpaulson@jimmy.harvard.edu. Unfortunately, we are not experts on using qiime and your questions might be better suited for here: https://github.com/biocore/qiime/issues.
Dear all,
I wonder if anyone could help me with the following: I would like to normalize an out.biom table using CSS, and I keep getting the following error message:
_Traceback (most recent call last): File "/usr/local/bin/normalize_table.py", line 157, in
main()
File "/usr/local/bin/normalize_table.py", line 140, in main
normalize_CSS(input_path, out_path, output_CSS_statistics)
File "/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 "/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 "/usr/local/lib/python2.7/dist-packages/qiime/util.py", line 1968, in call
(exit_status, command, stdout, stderr))
burrito.util.ApplicationError: Unacceptable application exit status: 1
command: cd "/home/qiime/Desktop/sandlance/alldata/Normalization/"; R --slave --args --source_dir /usr/local/lib/python2.7/dist-packages/qiime/support_files/R -i /tmp/QIIME-normalize-table-temp-table-5uGkcm.biom -o otu_table_silvamod_css.biom -s otu_table_silvamod_css_CSS_statistics.txt < /usr/local/lib/python2.7/dist-packages/qiime/support_files/R/CSS.r
stdout:
stderr: Loading required namespace: biomformat Found more than one class "file" in cache; using the first, from namespace 'BiocGenerics' Found more than one class "file" in cache; using the first, from namespace 'BiocGenerics' Error in cumNormStatFast(obj) : Warning sample with one or zero features Calls: CSS -> cumNormStatFast Execution halted_
I am using an OTU-table that has taxonomy already assigned and samples with <1000 reads excluded, hence I should not have a sample with 1 or 0 features as the message indicates. Am I overlooking something else? Why does this message persist?
Another issue I am experiencing is with DESeq2, maybe you can help me here, too? I am executing these 3 commands to normalize, create a .tab file with taxonomy info and then reassign the taxonomy to the normalized file:
_biom convert -i otu_table_silvamod.biom -o otu_table_silvamod.tab --to-tsv --header-key taxonomy normalize_table.py -i otu_table_silvamod.biom -o otu_table_silvamod_deseq.biom -a DESeq2 -z biom add-metadata -i otu_table_silvamod_deseq.biom -o otu_table_silvamod_deseq_tax.biom --observation-metadata-fp otu_tablesilvamod.tab --observation-header OTUID,taxonomy
These commands work, however taxonomy = 0 in all but 1 case in the file “otu_table_silvamod_deseq_tax.biom”. Why may this be the case? I have created PCoA plots, PCA plots, rarefaction curves etc. with the non-rarefied samples and they look fine.
Any help on these two issues would be greatly appreciated.
Many thanks in advance, Katharina