AssertionError: 3 columns passed, passed data had 47 columns

[gabyrech]

Hi! Any idea on what's going on here?
I am getting this error at the end of the execution, when hundo starts to build the report...

        python /home/gabriel/miniconda3/envs/hundo_env/lib/python3.6/site-packages/hundo/scripts/build_report.py --biom OTU.biom --txt OTU.txt             --zip hundo_results.zip --env /home/gabriel/miniconda3/envs/hundo_env/lib/python3.6/site-packages/hundo/environment.yml --params PARAMS.txt             --eeplot 'logs/*_merged_filtered_eestats.txt'             --r1quals 'logs/*_R1_eestats.txt'             --raw 'logs/raw_counts/*_R1.count' --omitted ''             --html summary.html --author 'Gaby'             --version 'hundo, version 1.2.4' --samples SAMPLES.txt
        
ESC[33mJob counts:
        count   jobs
        1       build_report
        1ESC[0m
ESC[33m
        python /home/gabriel/miniconda3/envs/hundo_env/lib/python3.6/site-packages/hundo/scripts/build_report.py --biom OTU.biom --txt OTU.txt             --zip hundo_results.zip --env /home/gabriel/miniconda3/envs/hundo_env/lib/python3.6/site-packages/hundo/environment.yml --params PARAMS.txt             --eeplot 'logs/*_merged_filtered_eestats.txt'             --r1quals 'logs/*_R1_eestats.txt'             --raw 'logs/raw_counts/*_R1.count' --omitted ''             --html summary.html --author 'Gaby'             --version 'hundo, version 1.2.4' --samples SAMPLES.txt
        ESC[0m
Traceback (most recent call last):
  File "/home/gabriel/miniconda3/envs/hundo_env/lib/python3.6/site-packages/hundo/scripts/build_report.py", line 629, in <module>
    args.samples,
  File "/home/gabriel/miniconda3/envs/hundo_env/lib/python3.6/site-packages/hundo/scripts/build_report.py", line 359, in main
    index=["shannon", "simpson", "invsimpson"],
  File "/media/gabriel/BariData/gabriel/others/hundo/enviromen20190307/condaEnviroment/39469222/lib/python3.6/site-packages/relatively/relatively.py", line 342, in calculate_diversity
    t = pd.DataFrame(t.values.tolist(), index=t.index, columns=index)
  File "/media/gabriel/BariData/gabriel/others/hundo/enviromen20190307/condaEnviroment/39469222/lib/python3.6/site-packages/pandas/core/frame.py", line 435, in __init__
    arrays, columns = to_arrays(data, columns, dtype=dtype)
  File "/media/gabriel/BariData/gabriel/others/hundo/enviromen20190307/condaEnviroment/39469222/lib/python3.6/site-packages/pandas/core/internals/construction.py", line 404, in to_arrays
    dtype=dtype)
  File "/media/gabriel/BariData/gabriel/others/hundo/enviromen20190307/condaEnviroment/39469222/lib/python3.6/site-packages/pandas/core/internals/construction.py", line 436, in _list_to_arrays
    coerce_float=coerce_float)
  File "/media/gabriel/BariData/gabriel/others/hundo/enviromen20190307/condaEnviroment/39469222/lib/python3.6/site-packages/pandas/core/internals/construction.py", line 492, in _convert_object_array
    con=len(content)))
AssertionError: 3 columns passed, passed data had 47 columns
ESC[32m[Thu Mar  7 17:42:14 2019]ESC[0m
ESC[31mError in rule build_report:ESC[0m
ESC[31m    jobid: 0ESC[0m
ESC[31m    output: summary.htmlESC[0m
ESC[31m    conda-env: /media/gabriel/BariData/gabriel/others/hundo/enviromen20190307/condaEnviroment/39469222ESC[0m
ESC[31mESC[0m
ESC[31mRuleException:
CalledProcessError in line 972 of /home/gabriel/miniconda3/envs/hundo_env/lib/python3.6/site-packages/hundo/Snakefile:
Command 'source activate /media/gabriel/BariData/gabriel/others/hundo/enviromen20190307/condaEnviroment/39469222; set -euo pipefail;  
        python /home/gabriel/miniconda3/envs/hundo_env/lib/python3.6/site-packages/hundo/scripts/build_report.py --biom OTU.biom --txt OTU.txt             --zip hundo_results.zip --env /home/gabriel/miniconda3/envs/hundo_env/lib/python3.6/site-packages/hundo/environment.yml --params PARAMS.txt             --eeplot 'logs/*_merged_filtered_eestats.txt'             --r1quals 'logs/*_R1_eestats.txt'             --raw 'logs/raw_counts/*_R1.count' --omitted ''             --html summary.html --author 'Gaby'             --version 'hundo, version 1.2.4' --samples SAMPLES.txt ' returned non-zero exit status 1.
  File "/home/gabriel/miniconda3/envs/hundo_env/lib/python3.6/site-packages/hundo/Snakefile", line 972, in __rule_build_report
  File "/home/gabriel/miniconda3/envs/hundo_env/lib/python3.6/concurrent/futures/thread.py", line 56, in runESC[0m
ESC[31mExiting because a job execution failed. Look above for error messageESC[0m
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message

Any help is much appreciated!
Gabriel

[colinbrislawn]

Good morning,

This looks like an issue with the final build_report.py step that builds the HTML summary dashboard. Means means that (hopefully!) all the other steps have completed successfully and you have an annotated .biom table and .tre file.

I'm not super familiar with the relatively.py plotting package, so I'll Joe comment on this one.

[brwnj]

can you try pip install -U hundo to grab 1.2.5 and see if this persists? re-open if the problem is still being seen.