Error message in q2-metaphlan2 tutorial

Hi Everyone,

I’m going trough the q2-metaphlan2 tutorial, and I’ve been getting the same error message.
This is my first time using this plugin.
I think the plugin was installed correctly. I’m using Windows Subsystem for Linux on Windows 10 (maybe this is important).

See above for debug info.
(qiime2-2018.11) [email protected]:/mnt/d/q2-metaphlan2# qiime info
System versions
Python version: 3.5.5
QIIME 2 release: 2018.11
QIIME 2 version: 2018.11.0
q2cli version: 2018.11.0

Installed plugins
alignment: 2018.11.0
composition: 2018.11.0
cutadapt: 2018.11.0
dada2: 2018.11.0
deblur: 2018.11.0
demux: 2018.11.0
diversity: 2018.11.0
emperor: 2018.11.0
feature-classifier: 2018.11.0
feature-table: 2018.11.0
fragment-insertion: 2018.11.0
gneiss: 2018.11.0
longitudinal: 2018.11.0
metadata: 2018.11.0
phylogeny: 2018.11.0
q2-metaphlan2: 2.7.8
quality-control: 2018.11.0
quality-filter: 2018.11.0
sample-classifier: 2018.11.0
taxa: 2018.11.0
types: 2018.11.0
vsearch: 2018.11.0

Application config directory
/root/.config/q2cli

Getting help
To get help with QIIME 2, visit https://qiime2.org

[email protected]:/mnt/d/q2-metaphlan2# source activate qiime2-2018.11
(qiime2-2018.11) [email protected]:/mnt/d/q2-metaphlan2# qiime q2-metaphlan2 profile-single-fastq --i-raw-data SRS019033.qza --o-biom-table SRS019033_profile.biom --p-nproc 4 --verbose

Running external command line application. This may print messages to stdout and/or stderr.
Command: metaphlan2.py /tmp/qiime2-archive-23g97c78/f295660f-b780-4078-94ef-3df399258456/data --input_type multifastq --biom /tmp/tmp3bchjg0h/mp2_tmp_output.biom --nproc 4

Help message for read_fastx.py
#SampleID Metaphlan2_Analysis
k__Bacteria 100.0
k__Bacteria|p__Firmicutes 70.51555
k__Bacteria|p__Proteobacteria 23.32658
k__Bacteria|p__Actinobacteria 6.15787
k__Bacteria|p__Firmicutes|c__Clostridia 56.39248
k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria 23.32658
k__Bacteria|p__Firmicutes|c__Bacilli 14.12307
k__Bacteria|p__Actinobacteria|c__Actinobacteria 6.15787
k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales 56.39248
k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales 23.32658
k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales 14.12307
k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Actinomycetales 6.15787
k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Clostridiales_Family_XI_Incertae_Sedis 56.39248
k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae 23.32658
k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Staphylococcaceae 14.12307
k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Actinomycetales|f__Propionibacteriaceae 6.15787
k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Clostridiales_Family_XI_Incertae_Sedis|g__Finegoldia 43.64644
k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter 23.32658
k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus 14.12307
k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Clostridiales_Family_XI_Incertae_Sedis|g__Peptoniphilus 12.74604
k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Actinomycetales|f__Propionibacteriaceae|g__Propionibacterium 6.15787
k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Clostridiales_Family_XI_Incertae_Sedis|g__Finegoldia|s__Finegoldia_magna 43.64644
k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter_ureolyticus 23.32658
k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus_epidermidis
14.12307
k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Clostridiales_Family_XI_Incertae_Sedis|g__Peptoniphilus|s__Peptoniphilus_rhinitidis 12.74604
k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Actinomycetales|f__Propionibacteriaceae|g__Propionibacterium|s__Propionibacterium_acnes 6.15787
k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Clostridiales_Family_XI_Incertae_Sedis|g__Finegoldia|s__Finegoldia_magna|t__Finegoldia_magna_unclassified 43.64644
k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter_ureolyticus|t__Campylobacter_ureolyticus_unclassified 23.32658
k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus_epidermidis|t__Staphylococcus_epidermidis_unclassified 14.12307
k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Clostridiales_Family_XI_Incertae_Sedis|g__Peptoniphilus|s__Peptoniphilus_rhinitidis|t__GCF_000246925 12.74604
k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Actinomycetales|f__Propionibacteriaceae|g__Propionibacterium|s__Propionibacterium_acnes|t__Propionibacterium_acnes_unclassified 6.15787
Traceback (most recent call last):
File “/root/miniconda3/envs/qiime2-2018.11/bin/metaphlan2.py”, line 4, in
import(‘pkg_resources’).run_script(‘q2-metaphlan2==2.7.8’, ‘metaphlan2.py’)
File “/root/miniconda3/envs/qiime2-2018.11/lib/python3.5/site-packages/pkg_resources/init.py”, line 661, in run_script
self.require(requires)[0].run_script(script_name, ns)
File “/root/miniconda3/envs/qiime2-2018.11/lib/python3.5/site-packages/pkg_resources/init.py”, line 1441, in run_script
exec(code, namespace, namespace)
File “/root/miniconda3/envs/qiime2-2018.11/lib/python3.5/site-packages/q2_metaphlan2-2.7.8-py3.5.egg-info/scripts/metaphlan2.py”, line 1565, in
metaphlan2()
File “/root/miniconda3/envs/qiime2-2018.11/lib/python3.5/site-packages/q2_metaphlan2-2.7.8-py3.5.egg-info/scripts/metaphlan2.py”, line 1496, in metaphlan2
maybe_generate_biom_file(tree, pars, outpred)
File “/root/miniconda3/envs/qiime2-2018.11/lib/python3.5/site-packages/q2_metaphlan2-2.7.8-py3.5.egg-info/scripts/metaphlan2.py”, line 1344, in maybe_generate_biom_file
input_is_dense = True
File “/root/miniconda3/envs/qiime2-2018.11/lib/python3.5/site-packages/biom/table.py”, line 508, in init
errcheck(self)
File “/root/miniconda3/envs/qiime2-2018.11/lib/python3.5/site-packages/biom/err.py”, line 472, in errcheck
raise ret
biom.exception.TableException: Size of observation metadata differs from matrix size!
Traceback (most recent call last):
File “/root/miniconda3/envs/qiime2-2018.11/lib/python3.5/site-packages/q2cli/commands.py”, line 274, in call
results = action(**arguments)
File “”, line 2, in profile_single_fastq
File “/root/miniconda3/envs/qiime2-2018.11/lib/python3.5/site-packages/qiime2/sdk/action.py”, line 231, in bound_callable
output_types, provenance)
File “/root/miniconda3/envs/qiime2-2018.11/lib/python3.5/site-packages/qiime2/sdk/action.py”, line 362, in callable_executor
output_views = self._callable(**view_args)
File “/root/miniconda3/envs/qiime2-2018.11/lib/python3.5/site-packages/q2_metaphlan2/_metaphlan2.py”, line 33, in profile_single_fastq
metaphlan2_helper(raw_data, nproc, ‘multifastq’, tmp_output_biom)
File “/root/miniconda3/envs/qiime2-2018.11/lib/python3.5/site-packages/q2_metaphlan2/_metaphlan2.py”, line 24, in metaphlan2_helper
sb.run(cmd, check=True)
File “/root/miniconda3/envs/qiime2-2018.11/lib/python3.5/subprocess.py”, line 398, in run
output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command ‘[‘metaphlan2.py’, ‘/tmp/qiime2-archive-23g97c78/f295660f-b780-4078-94ef-3df399258456/data’, ‘–input_type’, ‘multifastq’, ‘–biom’, ‘/tmp/tmp3bchjg0h/mp2_tmp_output.biom’, ‘–nproc’, ‘4’]’ returned non-zero exit status 1

Plugin error from q2-metaphlan2:

Command ‘[‘metaphlan2.py’, ‘/tmp/qiime2-archive-23g97c78/f295660f-b780-4078-94ef-3df399258456/data’, ‘–input_type’, ‘multifastq’, ‘–biom’, ‘/tmp/tmp3bchjg0h/mp2_tmp_output.biom’, ‘–nproc’, ‘4’]’ returned non-zero exit status 1

See above for debug info.
(qiime2-2018.11) [email protected]:/mnt/d/q2-metaphlan2#

Could you help me to understand what I’ve done wrong?

Thanks very much,
FS

Hello FS,

Thanks for posting your full error message and mentioning you are using WSL. In this case, I think I found the main error in the very middle of that error text:

biom.exception.TableException: Size of observation metadata differs from matrix size!

Looks like this user also ran into this error. Does that looks related to you?

We could also see if @gmdouglas has any suggestions about PICRUSt2 running on WSL.

Colin

Hi there,

Sorry I don’t have any experience with WSL unfortunately, @colinbrislawn ! The only thing that comes to mind is to double-check that the expected version of biom-format is installed in the qiime2-2018.11 environment.

Best,

Gavin

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