Error message in q2-metaphlan2 tutorial


(Fernando Studart) #1

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


(Colin Brislawn) #2

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


(Gavin Douglas) #3

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


(Matthew Ryan Dillon) #7

(Matthew Ryan Dillon) #8

(Matthew Ryan Dillon) #9

(Matthew Ryan Dillon) #10