lfse: IndexError: list index out of range

[Dieunel]

Dear Lfse users/developpers

 

I am running lfse using koeken , but having  a strange error , here is  my input command and the output error :

koeken.py -i otu_table_no_decimal.biom -o koen_out -m mapping_nodecimal.txt -l 4 --class AverageVertical_distancefromground_in_feet -pc -sp  AverageVertical_distancefromground_in_feet

Koeken v0.2.6: Linear Discriminant Analysis (LEfSe) on a Longitudinal Microbial Dataset.

Written by Thomas W. Battaglia (tb1...@nyu.edu)

 

LEfSe Credits: "Metagenomic biomarker discovery and explanation"

Nicola Segata, Jacques Izard, Levi Waldron, Dirk Gevers, Larisa Miropolsky, Wendy S Garrett, and Curtis Huttenhower

Genome Biology, 12:R60, 2011

 

WARNING:root:Output folder already exists. Warning: Errors may be produced. Please delete or change output folder before running again!.

 

Running QIIME's summarize_taxa.py... 

 

Traceback (most recent call last):

  File "/home/linuxbrew/miniconda3/envs/qiime1/bin/summarize_taxa.py", line 4, in <module>

   __import__('pkg_resources').run_script('qiime==1.9.1', 'summarize_taxa.py')

  File "/home/linuxbrew/miniconda3/envs/qiime1/lib/python2.7/site-packages/pkg_resources/__init__.py", line 658, in run_script

   self.require(requires)[0].run_script(script_name, ns)

  File "/home/linuxbrew/miniconda3/envs/qiime1/lib/python2.7/site-packages/pkg_resources/__init__.py", line 1438, in run_script

   exec(code, namespace, namespace)

  File "/home/linuxbrew/miniconda3/envs/qiime1/lib/python2.7/site-packages/qiime-1.9.1-py2.7.egg-info/scripts/summarize_taxa.py", line 20, in <module>

    from biom.table import Table

  File "/home/linuxbrew/miniconda3/envs/qiime1/lib/python2.7/site-packages/biom/__init__.py", line 51, in <module>

    from .table import Table

  File "/home/linuxbrew/miniconda3/envs/qiime1/lib/python2.7/site-packages/biom/table.py", line 200, in <module>

    from ._filter import _filter

  File "__init__.pxd", line 155, in init biom._filter (biom/_filter.c:6725)

ValueError: numpy.dtype has the wrong size, try recompiling. Expected 88, got 96

Traceback (most recent call last):

  File "/home/linuxbrew/miniconda3/envs/qiime1/bin/koeken.py", line 277, in <module>

   main(args)

  File "/home/linuxbrew/miniconda3/envs/qiime1/bin/koeken.py", line 178, in main

   sumtaxa_df = pd.read_table(sumtaxa_loc[0])

IndexError: list index out of range

 

All the directories created are empty , please could you help me understand where I am wrong ?

 

Cordially

 

[Colin Brislawn]

Good afternoon,

That error, 'numpy.dtype has the wrong size, try recompiling' can show up when you have the wrong version of numpy installed. I think the developer of koeken should be able to help you solve this issue. 

https://github.com/twbattaglia/koeken/issues 

If that does not work, you could try posting this question to the LEfSe forums. 

https://groups.google.com/forum/#!forum/lefse-users 

(This forum is for supporting Qiime 1, so I'm don't know much about LEfSe. I wish I could help more.)

Colin

[Dieunel]

Dear Colin

Thank you for your response and suggestion

Regards

DD