Missing genome_by_genome_overview.csv in output directory

Hi,

I’m trying to run 355 phage sequences through vContact2, however although the run appears to complete without any errors I do not get the genome_by_genome_overview.csv. Below is the command I’ve been using:

vcontact -t 30 --raw-proteins all_prophage_proteins.faa --rel-mode "Diamond" --proteins-fp gene_to_genome.csv --db "ProkaryoticViralRefSeq97-Merged" --pcs-mode MCL --vcs-mode ClusterONE --c1-bin /home/Documents/Programs/MAVERICLab-vcontact2-6d6fe8cf260a/bin/cluster_one-1.0.jar --output-dir vContact_output_97 &> vContact_97.log

and this is the output I get after running the vContact command above:

============================This is vConTACT2 0.9.13============================



----------------------------------Pre-Analysis----------------------------------


------------------------------Reference databases-------------------------------


-------------------------------Protein clustering-------------------------------


----------------------------------Loading data----------------------------------


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


------------------------Calculating Similarity Networks-------------------------
Loaded graph with 2901 nodes and 127532 edges
[====================] 100% Growing clusters from seeds...
[====================] 100% Finding highly overlapping clusters...
[====================] 100% Merging highly overlapping clusters...
Detected 351 complexes
.................................................. 1M
.................................................. 2M
..................
[mcl] new tab created
[mcl] pid 13812
 ite -------------------  chaos  time hom(avg,lo,hi) m-ie m-ex i-ex fmv
  1  ................... 126.06  1.99 0.96/0.01/12.04 5.63 1.85 1.85  71
  2  ...................  82.16  4.03 0.72/0.01/4.91 10.17 0.11 0.21  90
  3  ...................   8.43  0.30 0.90/0.07/10.78 1.73 0.22 0.05  14
  4  ...................   1.79  0.03 0.98/0.37/14.44 1.02 0.58 0.03   1
  5  ...................   1.04  0.02 0.99/0.50/8.41 1.00 0.88 0.02   0
  6  ...................   0.31  0.02 1.00/0.58/1.30 1.00 0.96 0.02   0
  7  ...................   0.23  0.02 1.00/0.77/1.00 1.00 0.99 0.02   0
  8  ...................   0.23  0.02 1.00/0.78/1.00 1.00 1.00 0.02   0
  9  ...................   0.00  0.02 1.00/1.00/1.00 1.00 1.00 0.02   0
 10  ...................   0.00  0.02 1.00/1.00/1.00 1.00 1.00 0.02   0
[mcl] cut <1> instances of overlap
[mcl] jury pruning marks: <97,99,99>, out of 100
[mcl] jury pruning synopsis: <97.8 or superb> (cf -scheme, -do log)
[mcl] output is in vContact_output_97/modules_mcl_5.0.clusters
[mcl] 765 clusters found
[mcl] output is in vContact_output_97/modules_mcl_5.0.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)

'Pseudomonas~virus~D3'


------------------------Contig Clustering & Affiliation-------------------------


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


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


----------------------------Exporting results files-----------------------------
There were 564 genomes (including refs) that were singleton, outlier or overlaps.

I think I get all the other files produced in the output directory except that final file. These are the files I get:

$ ls vContact_output_97/
c1.clusters    merged.self-diamond.tab                 modules_mcl_5.0.clusters        sig1.0_mcl2.0_contigs.csv                                          vConTACT_profiles.csv
c1.ntw         merged.self-diamond.tab.abc             modules_mcl_5.0_modules.pandas  sig1.0_mcl2.0_modsig1.0_modmcl5.0_minshared3_link_mod_cluster.csv  vConTACT_proteins.csv
merged_df.csv  merged.self-diamond.tab.mci             modules_mcl_5.0_pcs.pandas      sig1.0_mcl5.0_minshared3_modules.csv                               viral_cluster_overview.csv
merged.dmnd    merged.self-diamond.tab_mcl20.clusters  modules.ntwk                    vConTACT_contigs.csv
merged.faa     merged.self-diamond.tab_mcxload.tab     sig1.0_mcl2.0_clusters.csv      vConTACT_pcs.csv

My phage are present in these files (e.g. the c1.clusters, c1.ntw, and viral_cluster_overview.csv) and have been assigned clusters, so all looks fine as far as I can tell. There just isn’t a genome_by_genome_overview.csv.

Thanks in advance for any help you can give and also thanks for making this tool… minus this little issue I love it!

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