Error q2-metaphlan2:biom.exception.TableException: Cannot delimit self if I don’t have data…


(H) #1

I am working with qiime2-2018.11 environment in conda (Anaconda v4.6.2). My server is CentOS v6.8. I recently installed q2-metaphlan2 using the instructions found here. I even ran the ‘Testing installation’ part successfully. Now imported data and created an artifact file using:

qiime tools import \
--type 'SampleData[PairedEndSequencesWithQuality]' \
--input-path manifest \
--output-path paired-end-demux.qza \
--input-format PairedEndFastqManifestPhred33

After this I just summarized the data using:

qiime demux summarize \
--i-data paired-end-demux.qza \
--o-visualization demux.qzv

All’s good until this point. Now I’m trying to get a biom table from the imported data using q2-metaphlan2 using:

qiime q2-metaphlan2 profile-paired-fastq \
--i-raw-data paired-end-demux.qza \
--o-biom-table paired-end-demux-profile \
--p-nproc 6 \

…and convert the table to a tsv file using:

biom convert \
--input-fp paired-end-demux-biom-table-exported/feature-table.biom \
--output-fp feature-table.tsv \

On this step I get the following error:

Traceback (most recent call last):
File “/root/anaconda3/envs/qiime2-2018.11/bin/biom”, line 11, in
File “/root/anaconda3/envs/qiime2-2018.11/lib/python3.5/site-packages/click/”, line 764, in call
return self.main(*args, **kwargs)
File “/root/anaconda3/envs/qiime2-2018.11/lib/python3.5/site-packages/click/”, line 717, in main
rv = self.invoke(ctx)
File “/root/anaconda3/envs/qiime2-2018.11/lib/python3.5/site-packages/click/”, line 1137, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File “/root/anaconda3/envs/qiime2-2018.11/lib/python3.5/site-packages/click/”, line 956, in invoke
return ctx.invoke(self.callback, **ctx.params)
File “/root/anaconda3/envs/qiime2-2018.11/lib/python3.5/site-packages/click/”, line 555, in invoke
return callback(*args, **kwargs)
File “/root/anaconda3/envs/qiime2-2018.11/lib/python3.5/site-packages/biom/cli/”, line 129, in convert
table_type, process_obs_metadata, tsv_metadata_formatter)
File “/root/anaconda3/envs/qiime2-2018.11/lib/python3.5/site-packages/biom/cli/”, line 185, in _convert
File “/root/anaconda3/envs/qiime2-2018.11/lib/python3.5/site-packages/biom/”, line 4844, in to_tsv
File “/root/anaconda3/envs/qiime2-2018.11/lib/python3.5/site-packages/biom/”, line 1581, in delimited_self
raise TableException(“Cannot delimit self if I don’t have data…”)
biom.exception.TableException: Cannot delimit self if I don’t have data…
/root/anaconda3/envs/qiime2-2018.11/lib/python3.5/site-packages/numpy/core/ RuntimeWarning: Degrees of freedom <= 0 for slice
/root/anaconda3/envs/qiime2-2018.11/lib/python3.5/site-packages/numpy/core/ RuntimeWarning: invalid value encountered in true_divide
arrmean, rcount, out=arrmean, casting=‘unsafe’, subok=False)
/root/anaconda3/envs/qiime2-2018.11/lib/python3.5/site-packages/numpy/core/ RuntimeWarning: invalid value encountered in double_scalars
ret = ret.dtype.type(ret / rcount)
Num samples: 0
Num observations: 0
Total count: 0
Table density (fraction of non-zero values): 0.000

My first thought was there is no data in the artifact file (paired-end-demux.qza) but the .qzv shows data as expected.

I have searched this forum and googled this error (in bold) to no success. Any ideas would be greatly appreciated.