Error with test data

[Former user]

Hi,

thanks for bringing up this great software. I just tried to run with the test data using singularity built from the def file in your repository, and run it with test data, got the following error, any idea?

============================This is vConTACT 0.9.11=============================



----------------------------------Pre-Analysis----------------------------------
INFO:vcontact2: Found ClusterONE: /usr/local/bin/cluster_one-1.0.jar
INFO:vcontact2: Found Diamond: /miniconda3/bin/diamond
INFO:vcontact2: Found MCL: /miniconda3/bin/mcxload
INFO:vcontact2: Identified 15 CPUs
INFO:vcontact2: Using reference database: ProkaryoticViralRefSeq85-Merged
INFO:vcontact2: Using existing directory VirSorted_Outputs.


------------------------------Reference databases-------------------------------
INFO:vcontact2: Identified existing 'merged.faa' in output path: re-using...
INFO:vcontact2: Re-using existing Diamond file...


-------------------------------Protein clustering-------------------------------
INFO:vcontact2: Loading proteins...
INFO:vcontact2: Merging ProkaryoticViralRefSeq85-Merged to user gene-to-genome mapping...
[mclIO] writing <VirSorted_Outputs/merged.self-diamond.tab.mci>
.......................................
[mclIO] wrote native interchange 2396x2396 matrix with 9076 entries to stream <VirSorted_Outputs/merged.self-diamond.tab.mci>
[mclIO] wrote 2396 tab entries to stream <VirSorted_Outputs/merged.self-diamond.tab_mcxload.tab>
[mcxload] tab has 2396 entries
[mclIO] reading <VirSorted_Outputs/merged.self-diamond.tab.mci>
.......................................
[mclIO] read native interchange 2396x2396 matrix with 9076 entries
[mcl] pid 84467
 ite -------------------  chaos  time hom(avg,lo,hi) m-ie m-ex i-ex fmv
  1  ...................   4.19  0.01 0.96/0.36/1.80 1.43 1.42 1.42   2
  2  ...................   6.44  0.01 0.88/0.40/1.86 1.27 1.04 1.49   9
  3  ...................   7.54  0.01 0.87/0.29/2.13 1.24 0.85 1.26   9
  4  ...................   6.00  0.01 0.87/0.40/3.06 1.17 0.81 1.02   5
  5  ...................   4.43  0.00 0.88/0.43/1.50 1.04 0.79 0.80   3
  6  ...................   1.80  0.00 0.89/0.50/1.31 1.02 0.80 0.64   1
  7  ...................   1.13  0.00 0.90/0.53/1.00 1.01 0.82 0.53   0
  8  ...................   1.06  0.00 0.93/0.53/1.00 1.00 0.87 0.46   0
  9  ...................   0.79  0.00 0.96/0.63/1.00 1.00 0.86 0.40   0
 10  ...................   0.92  0.00 0.98/0.66/1.00 1.00 0.88 0.35   0
 11  ...................   0.42  0.00 0.99/0.71/1.00 1.00 0.90 0.31   0
 12  ...................   0.24  0.00 0.99/0.78/1.00 1.00 0.93 0.29   0
 13  ...................   0.25  0.00 1.00/0.76/1.00 1.00 0.96 0.28   0
 14  ...................   0.25  0.00 1.00/0.76/1.00 1.00 0.98 0.27   0
 15  ...................   0.25  0.00 1.00/0.77/1.00 1.00 0.99 0.27   0
 16  ...................   0.18  0.00 1.00/0.82/1.00 1.00 1.00 0.27   0
 17  ...................   0.04  0.00 1.00/0.96/1.00 1.00 1.00 0.27   0
 18  ...................   0.00  0.00 1.00/1.00/1.00 1.00 1.00 0.27   0
 19  ...................   0.00  0.00 1.00/1.00/1.00 1.00 1.00 0.27   0
[mcl] jury pruning marks: <99,99,99>, out of 100
[mcl] jury pruning synopsis: <99.0 or perfect> (cf -scheme, -do log)
[mcl] output is in VirSorted_Outputs/merged.self-diamond.tab_mcl20.clusters
[mcl] 670 clusters found
[mcl] output is in VirSorted_Outputs/merged.self-diamond.tab_mcl20.clusters

Please cite:
    Stijn van Dongen, Graph Clustering by Flow Simulation.  PhD thesis,
    University of Utrecht, May 2000.
       (  http://www.library.uu.nl/digiarchief/dip/diss/1895620/full.pdf
       or  http://micans.org/mcl/lit/svdthesis.pdf.gz)
OR
    Stijn van Dongen, A cluster algorithm for graphs. Technical
    Report INS-R0010, National Research Institute for Mathematics
    and Computer Science in the Netherlands, Amsterdam, May 2000.
       (  http://www.cwi.nl/ftp/CWIreports/INS/INS-R0010.ps.Z
       or  http://micans.org/mcl/lit/INS-R0010.ps.Z)

INFO:vcontact2: Loading the clusters (this may take some time...)
INFO:vcontact2: Saving intermediate files...


----------------------------------Loading data----------------------------------
INFO:vcontact2: Read 2340 entries (dropped 2765 singletons) from VirSorted_Outputs/vConTACT_profiles.csv


--------------------------------Adding Taxonomy---------------------------------


------------------------Calculating Similarity Networks-------------------------


------------------------Contig Clustering & Affiliation-------------------------
INFO:vcontact2:         entries  reference_entries  classified_entries  reference_classes  ...  precision  recall  specificity  fmeasure
order      2879               1821                   0                  2  ...        0.0     0.0          1.0       NaN
genus      2879                942                   0                266  ...        0.0     0.0          1.0       NaN
family     2879               1960                   0                 22  ...        0.0     0.0          1.0       NaN

[3 rows x 10 columns]
ERROR:vcontact2: Error in viral clusters
ERROR:vcontact2: cannot set a frame with no defined columns
Traceback (most recent call last):
  File "/miniconda3/bin/vcontact", line 622, in main
    vc = vcontact.cluster_refinements.ViralClusters(gc.contigs, profiles_fp, optimize=options.optimize)
  File "/miniconda3/lib/python3.7/site-packages/vcontact/cluster_refinements.py", line 106, in __init__
    evaluations = vcontact.evaluations.Evaluations(adj_contigs, levels=['genus'],  focus='rev_pos_cluster')
  File "/miniconda3/lib/python3.7/site-packages/vcontact/evaluations.py", line 42, in __init__
    clustering_wise_ppv, clustering_wise_sensitivity, accuracy = self.performance_metrics(contingency_tbl)
  File "/miniconda3/lib/python3.7/site-packages/vcontact/evaluations.py", line 59, in performance_metrics
    ppv_tbl = self.calc_ppv(contingency_table)
  File "/miniconda3/lib/python3.7/site-packages/vcontact/evaluations.py", line 111, in calc_ppv
    counts.loc['sum'] = counts.sum(axis=0)  # adds a new ROW with sum of column
  File "/miniconda3/lib/python3.7/site-packages/pandas/core/indexing.py", line 205, in __setitem__
    self._setitem_with_indexer(indexer, value)
  File "/miniconda3/lib/python3.7/site-packages/pandas/core/indexing.py", line 406, in _setitem_with_indexer
    return self._setitem_with_indexer_missing(indexer, value)
  File "/miniconda3/lib/python3.7/site-packages/pandas/core/indexing.py", line 635, in _setitem_with_indexer_missing
    raise ValueError("cannot set a frame with no defined columns")
ValueError: cannot set a frame with no defined columns


--------------------------------Protein modules---------------------------------


---------------------------Link modules and clusters----------------------------


----------------------------Exporting results files-----------------------------
ERROR:vcontact2: Error in exporting the final summary data: 'NoneType' object has no attribute 'contigs'

Thanks in advance!

Best, Shengwei

[Shengwei Hou]

Just a quick update. It worked with my own data, no idea.

Cheers,

Shengwei

[Ben Bolduc]

Hi Shengwei,

Thanks for reporting this. This is a known bug with the resume functionality. Setting a fresh run, with either the original inputs or using legacy inputs (pcs, profiles, contigs) usually “fixes” this problem.

Cheers,

Ben

[Ben Bolduc]

Known bug, minor priority (as it's usually easily fixed by re-running). Future major versions may include a fix.