Can't find genome_by_genome_overview.csv output

[Former user]

Hi,

I cant find the genome_by_genome_overview.csv in my output directory. These are all output files of my analysis. Which one is corresponding to the genome_by_genome_overview.csv?

c1.clusters c1.ntw merged_df.csv merged.faa merged.self-diamond.tab.abc merged.self-diamond.tab.mci merged.self-diamond.tab_mcl20.clusters merged.self-diamond.tab_mcxload.tab modules_mcl_5.0.clusters modules_mcl_5.0_modules.pandas modules_mcl_5.0_pcs.pandas modules.ntwk node_table_summary.csv profiles.pkle proteins_df.csv ref_proteins_df.csv sig1.0_mcl2.0_clusters.csv sig1.0_mcl2.0_contigs.csv sig1.0_mcl2.0_modsig1.0_modmcl5.0_minshared3_link_mod_cluster.csv sig1.0_mcl5.0_minshared3_modules.csv summary_df.csv vConTACT_contigs.csv vConTACT.h5 vConTACT_pcs.csv vConTACT_profiles.csv vConTACT_proteins.csv

Best, Yuya

[Guillermo Rangel Piñeros]

Hi,

I’m experiencing the same issue as Yuya. The genome_by_genome_overview.csv file is not generated when I run vcontact on my data.

Thanks,

Guillermo.

[Stephen Nayfach]

Same issue here

[Ben Bolduc]

Hi Yuya,

Thank you for sending a bug report. Could you upload (or copy-and-paste, here) the full output from the tool? There’s usually some sort of indicator that something’s off during processing. I can see you have the node_table_summary file. The genome_by_genome is just re-parsing that file, so, when something happens, it’s usually in the last few lines of the output. Also, what version of the tool are you using? There was a bugfix in the ~0.9.6 version that caught a few of these errors, but it doesn’t look like I caught them all.

Cheers,

Ben

[Yuya Kiguchi]

Hi Ben,

Thank you for your reply. I used vConTACT 0.9.1b and analyzed test_data.

I upload full output files.

https://figshare.com/articles/vContact2_output/10026923

Best,

Yuya

[Ben Bolduc]

Ahh. I see what’s wrong here. Older versions of vConTACT2 used “node_table_summary.csv” instead of “genome_by_genome_overview.csv.” This was updated to more appropriately reflect the contents of the output file. In the files you provided (thank you for that), I found the node_table_summary, along with the clusters each of your input contigs were associated. However, this is a very old version of vConTACT2 and thus does not have singleton, outlier and overlapping contig information. You will need to update your version in order to get these classifications. Anything prior to 0.9.6 will probably be too out-of-date.

I’m going to close this issue, but if you have the same issue with a more current version (> 0.9.6), please re-open!

[Ben Bolduc]

Closing issue as error was due to mis-named file. Please update to a more recent version of the code in order to incorporate updates that reflect fixes.

Re-open if problem persists in more recent version.

Thanks!

[Lu Jingli]

Hi,

The version of my vConTACT2 is 0.9.13, but I can’t find the genome_by_genome_overview.csv in my output directory. I have all output files except to the genome_by_genome_overview.csv.

Best,

Lu Jingli

[Julia Brown]

I am also using vConTACT2 version 0.9.13 and am having the same issue.

[Chuen Lee]

Hi and thank you for creating this tool.

I am also facing this same problem using vConTACT2 version 0.9.11. I have noticed that if at the end of exporting, I get an additional line of text, that also means I do not have the genome_by_genome_overview file. Is that the same for everyone else?

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Appreciate any help from anyone. Thank you in advance.

----------------------------Exporting results files-----------------------------
'Bacillus~virus~G'

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[Julia Brown]

I am seeing this message toward the end of the log file:

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vcontact2: Error in exporting the final summary data: first argument must be string or compiled pattern

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And the final lines in the log read:

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----------------------------Exporting results files-----------------------------
There were 531 genomes (including refs) that were singleton, outlier or overlaps.
Examine:  final summary data: first argument must be string or compiled pattern

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