Still identifying genome substrings. Consider adjusting input genomes naming. 'Shewanella~sp.~phage~1/4'

[Toscan]

Hello Developers,

‌

thank you for developing this super nice tool!!

I am running into an interesting issue here.

At the step “----------------------------Exporting results files-----------------------------” I get the following error:

“Still identifying genome substrings. Consider adjusting input genomes naming.
'Shewanella~sp.~phage~1/4'“

And then that is it, the execution stops…

Snapshot of my .out file from SLURM job:

Snapshot of my .err file from SLURM job:

‌

I have used this successfully many times with other datasets, but this particular errors only with this dataset.

I checked to see if the problem was runtime or memory exceeded and it was not:

\$ seff 8841463
Job ID: 8841463
Cluster: eve
User/Group: brizolat/umb
State: COMPLETED (exit code 0)
Cores: 1
CPU Utilized: 14:41:22
CPU Efficiency: 90.48% of 16:14:06 core-walltime
Job Wall-clock time: 16:14:06
Memory Utilized: 129.31 GB
Memory Efficiency: 64.65% of 200.00 GB

‌

I also checked the intermediary files here to provide you some more details:

\$ ls -lh vcontact-output
total 5,7G
-rw-rw-r--+ 1 brizolat eve_umbmsb 3,1M 15. Dez 06:43 c1.clusters
-rw-rw-r--+ 1 brizolat eve_umbmsb 89M 15. Dez 06:36 c1.ntw
-rw-rw-r--+ 1 brizolat eve_umbmsb 15M 15. Dez 03:08 merged_df.csv
-rw-rw-r--+ 1 brizolat eve_umbmsb 431M 14. Dez 17:57 merged.dmnd
-rw-rw-r--+ 1 brizolat eve_umbmsb 418M 14. Dez 17:56 merged.faa
-rw-rw-r--+ 1 brizolat eve_umbmsb 2,3G 14. Dez 22:27 merged.self-diamond.tab
-rw-rw-r--+ 1 brizolat eve_umbmsb 1,6G 14. Dez 22:29 merged.self-diamond.tab.abc
-rw-rw-r--+ 1 brizolat eve_umbmsb 431M 14. Dez 23:01 merged.self-diamond.tab.mci
-rw-rw-r--+ 1 brizolat eve_umbmsb 41M 14. Dez 23:20 merged.self-diamond.tab_mcl20.clusters
-rw-rw-r--+ 1 brizolat eve_umbmsb 47M 14. Dez 23:01 merged.self-diamond.tab_mcxload.tab
-rw-rw-r--+ 1 brizolat eve_umbmsb 419K 15. Dez 07:09 modules_mcl_5.0.clusters
-rw-rw-r--+ 1 brizolat eve_umbmsb 259K 15. Dez 07:10 modules_mcl_5.0_modules.pandas
-rw-rw-r--+ 1 brizolat eve_umbmsb 7,9M 15. Dez 07:10 modules_mcl_5.0_pcs.pandas
-rw-rw-r--+ 1 brizolat eve_umbmsb 134M 15. Dez 07:09 modules.ntwk
-rw-rw-r--+ 1 brizolat eve_umbmsb 196K 15. Dez 07:14 sig1.0_mcl2.0_clusters.csv
-rw-rw-r--+ 1 brizolat eve_umbmsb 17M 15. Dez 07:14 sig1.0_mcl2.0_contigs.csv
-rw-rw-r--+ 1 brizolat eve_umbmsb 204K 15. Dez 07:14 sig1.0_mcl2.0_modsig1.0_modmcl5.0_minshared3_link_mod_cluster.csv
-rw-rw-r--+ 1 brizolat eve_umbmsb 158K 15. Dez 07:14 sig1.0_mcl5.0_minshared3_modules.csv
-rw-rw-r--+ 1 brizolat eve_umbmsb 11M 15. Dez 03:08 vConTACT_contigs.csv
-rw-rw-r--+ 1 brizolat eve_umbmsb 8,1M 15. Dez 03:08 vConTACT_pcs.csv
-rw-rw-r--+ 1 brizolat eve_umbmsb 53M 15. Dez 03:08 vConTACT_profiles.csv
-rw-rw-r--+ 1 brizolat eve_umbmsb 123M 15. Dez 03:08 vConTACT_proteins.csv
-rw-rw-r--+ 1 brizolat eve_umbmsb 3,0M 15. Dez 07:56 viral_cluster_overview.csv

‌

Could you please help me out on this one?

Thanks a lot and thank you for developing this amazing tool.

‌

Best,

Rodolfo

[Adhip Mukhopadhyay]

Hello!

Thanks for developing this nice tool.

I am also facing the same issue as mentioned by Rodolfo.

However, I am not sure whether it is an error or not, as the run ends with only the message:

----------------------------Exporting results files-----------------------------

There were 687 genomes (including refs) that were singleton, outlier or overlaps.

Still identifying genome substrings. Consider adjusting input genomes naming.

'nchoe_02_contig_11'

There was no error message or warning even!

Interestingly in the output folder, I am missing the important genome_by_genome_overview.csv file.

The run log is provided below

I am a beginner, so please pardon and guide me.

Best

Adhip

‌

(vcontact2) virology@virology:~$ vcontact --raw-proteins ./Documents/Adhip/prodigal_outputs/prodigal_nchoe_02.faa --rel-mode Diamond --proteins-fp ./Documents/Adhip/vcontact2/vc2_g2g_nc_02.csv --db ProkaryoticViralRefSeq94-Merged --pcs-mode MCL --vcs-mode ClusterONE --c1-bin /home/virology/miniconda3/pkgs/clusterone-1.0-hdfd78af_0/lib/cluster_one-v1.0.jar --output-dir ./Documents/Adhip/vcontact2/vc2_nchoe_02/ -t 12

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



----------------------------------Pre-Analysis----------------------------------
INFO:vcontact2: Found Diamond: /home/virology/miniconda3/envs/vcontact2/bin/diamond
INFO:vcontact2: Found MCL: /home/virology/miniconda3/envs/vcontact2/bin/mcxload
INFO:vcontact2: Identified 12 CPUs
INFO:vcontact2: Using reference database: ProkaryoticViralRefSeq94-Merged
INFO:vcontact2: Using existing directory ./Documents/Adhip/vcontact2/vc2_nchoe_02/.


------------------------------Reference databases-------------------------------
INFO:vcontact2: Merging ProkaryoticViralRefSeq94-Merged to user sequences...
INFO:vcontact2: Creating Diamond database and running Diamond...
diamond v2.0.14.152 (C) Max Planck Society for the Advancement of Science
Documentation, support and updates available at http://www.diamondsearch.org
Please cite: http://dx.doi.org/10.1038/s41592-021-01101-x Nature Methods (2021)

#CPU threads: 12
Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1)
Database input file: ./Documents/Adhip/vcontact2/vc2_nchoe_02/merged.faa
Opening the database file...  [0s]
Loading sequences...  [0.222s]
Masking sequences...  [0.309s]
Writing sequences...  [0.041s]
Hashing sequences...  [0.017s]
Loading sequences...  [0s]
Writing trailer...  [0.002s]
Closing the input file...  [0s]
Closing the database file...  [0.002s]

Database sequences  270595
  Database letters  55506732
    Database hash  c401340008b9bf4b11c40fc71c68b6a8
        Total time  0.596000s
diamond v2.0.14.152 (C) Max Planck Society for the Advancement of Science
Documentation, support and updates available at http://www.diamondsearch.org
Please cite: http://dx.doi.org/10.1038/s41592-021-01101-x Nature Methods (2021)

#CPU threads: 12
Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1)
Temporary directory: ./Documents/Adhip/vcontact2/vc2_nchoe_02
#Target sequences to report alignments for: 25
Opening the database...  [0.044s]
Database: ./Documents/Adhip/vcontact2/vc2_nchoe_02/merged.dmnd (type: Diamond database, sequences: 270595, letters: 55506732)
Block size = 2000000000
Opening the input file...  [0.023s]
Opening the output file...  [0s]
Loading query sequences...  [0.207s]
Masking queries...  [0.314s]
Algorithm: Double-indexed
Building query histograms...  [0.993s]
Allocating buffers...  [0s]
Loading reference sequences...  [0.093s]
Masking reference...  [0.324s]
Initializing temporary storage...  [0s]
Building reference histograms...  [1.358s]
Allocating buffers...  [0s]
Processing query block 1, reference block 1/1, shape 1/16, index chunk 1/4.
Building reference seed array...  [0.084s]
Building query seed array...  [0.09s]
Computing hash join...  [0.067s]
Masking low complexity seeds...  [0.025s]
Searching alignments...  [3.74s]
Processing query block 1, reference block 1/1, shape 1/16, index chunk 2/4.
Building reference seed array...  [0.097s]
Building query seed array...  [0.102s]
Computing hash join...  [0.066s]
Masking low complexity seeds...  [0.025s]
Searching alignments...  [2.736s]
Processing query block 1, reference block 1/1, shape 1/16, index chunk 3/4.
Building reference seed array...  [0.1s]
Building query seed array...  [0.103s]
Computing hash join...  [0.066s]
Masking low complexity seeds...  [0.025s]
Searching alignments...  [2.525s]
Processing query block 1, reference block 1/1, shape 1/16, index chunk 4/4.
Building reference seed array...  [0.081s]
Building query seed array...  [0.083s]
Computing hash join...  [0.066s]
Masking low complexity seeds...  [0.025s]
Searching alignments...  [2.43s]
Processing query block 1, reference block 1/1, shape 2/16, index chunk 1/4.
Building reference seed array...  [0.082s]
Building query seed array...  [0.085s]
Computing hash join...  [0.064s]
Masking low complexity seeds...  [0.024s]
Searching alignments...  [2.737s]
Processing query block 1, reference block 1/1, shape 2/16, index chunk 2/4.
Building reference seed array...  [0.099s]
Building query seed array...  [0.101s]
Computing hash join...  [0.065s]
Masking low complexity seeds...  [0.024s]
Searching alignments...  [2.538s]
Processing query block 1, reference block 1/1, shape 2/16, index chunk 3/4.
Building reference seed array...  [0.1s]
Building query seed array...  [0.105s]
Computing hash join...  [0.065s]
Masking low complexity seeds...  [0.024s]
Searching alignments...  [2.425s]
Processing query block 1, reference block 1/1, shape 2/16, index chunk 4/4.
Building reference seed array...  [0.081s]
Building query seed array...  [0.084s]
Computing hash join...  [0.065s]
Masking low complexity seeds...  [0.024s]
Searching alignments...  [2.369s]
Processing query block 1, reference block 1/1, shape 3/16, index chunk 1/4.
Building reference seed array...  [0.083s]
Building query seed array...  [0.087s]
Computing hash join...  [0.066s]
Masking low complexity seeds...  [0.025s]
Searching alignments...  [2.825s]
Processing query block 1, reference block 1/1, shape 3/16, index chunk 2/4.
Building reference seed array...  [0.1s]
Building query seed array...  [0.104s]
Computing hash join...  [0.066s]
Masking low complexity seeds...  [0.025s]
Searching alignments...  [2.579s]
Processing query block 1, reference block 1/1, shape 3/16, index chunk 3/4.
Building reference seed array...  [0.105s]
Building query seed array...  [0.109s]
Computing hash join...  [0.066s]
Masking low complexity seeds...  [0.025s]
Searching alignments...  [2.491s]
Processing query block 1, reference block 1/1, shape 3/16, index chunk 4/4.
Building reference seed array...  [0.084s]
Building query seed array...  [0.087s]
Computing hash join...  [0.066s]
Masking low complexity seeds...  [0.025s]
Searching alignments...  [2.389s]
Processing query block 1, reference block 1/1, shape 4/16, index chunk 1/4.
Building reference seed array...  [0.085s]
Building query seed array...  [0.086s]
Computing hash join...  [0.066s]
Masking low complexity seeds...  [0.025s]
Searching alignments...  [2.805s]
Processing query block 1, reference block 1/1, shape 4/16, index chunk 2/4.
Building reference seed array...  [0.1s]
Building query seed array...  [0.101s]
Computing hash join...  [0.066s]
Masking low complexity seeds...  [0.025s]
Searching alignments...  [2.57s]
Processing query block 1, reference block 1/1, shape 4/16, index chunk 3/4.
Building reference seed array...  [0.103s]
Building query seed array...  [0.104s]
Computing hash join...  [0.066s]
Masking low complexity seeds...  [0.025s]
Searching alignments...  [2.469s]
Processing query block 1, reference block 1/1, shape 4/16, index chunk 4/4.
Building reference seed array...  [0.082s]
Building query seed array...  [0.087s]
Computing hash join...  [0.065s]
Masking low complexity seeds...  [0.025s]
Searching alignments...  [2.38s]
Processing query block 1, reference block 1/1, shape 5/16, index chunk 1/4.
Building reference seed array...  [0.083s]
Building query seed array...  [0.086s]
Computing hash join...  [0.065s]
Masking low complexity seeds...  [0.024s]
Searching alignments...  [2.785s]
Processing query block 1, reference block 1/1, shape 5/16, index chunk 2/4.
Building reference seed array...  [0.101s]
Building query seed array...  [0.099s]
Computing hash join...  [0.065s]
Masking low complexity seeds...  [0.024s]
Searching alignments...  [2.556s]
Processing query block 1, reference block 1/1, shape 5/16, index chunk 3/4.
Building reference seed array...  [0.1s]
Building query seed array...  [0.104s]
Computing hash join...  [0.065s]
Masking low complexity seeds...  [0.024s]
Searching alignments...  [2.451s]
Processing query block 1, reference block 1/1, shape 5/16, index chunk 4/4.
Building reference seed array...  [0.08s]
Building query seed array...  [0.083s]
Computing hash join...  [0.065s]
Masking low complexity seeds...  [0.024s]
Searching alignments...  [2.421s]
Processing query block 1, reference block 1/1, shape 6/16, index chunk 1/4.
Building reference seed array...  [0.081s]
Building query seed array...  [0.087s]
Computing hash join...  [0.066s]
Masking low complexity seeds...  [0.024s]
Searching alignments...  [2.789s]
Processing query block 1, reference block 1/1, shape 6/16, index chunk 2/4.
Building reference seed array...  [0.096s]
Building query seed array...  [0.1s]
Computing hash join...  [0.066s]
Masking low complexity seeds...  [0.024s]
Searching alignments...  [2.546s]
Processing query block 1, reference block 1/1, shape 6/16, index chunk 3/4.
Building reference seed array...  [0.103s]
Building query seed array...  [0.107s]
Computing hash join...  [0.065s]
Masking low complexity seeds...  [0.024s]
Searching alignments...  [2.456s]
Processing query block 1, reference block 1/1, shape 6/16, index chunk 4/4.
Building reference seed array...  [0.081s]
Building query seed array...  [0.084s]
Computing hash join...  [0.066s]
Masking low complexity seeds...  [0.024s]
Searching alignments...  [2.399s]
Processing query block 1, reference block 1/1, shape 7/16, index chunk 1/4.
Building reference seed array...  [0.082s]
Building query seed array...  [0.085s]
Computing hash join...  [0.064s]
Masking low complexity seeds...  [0.025s]
Searching alignments...  [2.72s]
Processing query block 1, reference block 1/1, shape 7/16, index chunk 2/4.
Building reference seed array...  [0.099s]
Building query seed array...  [0.1s]
Computing hash join...  [0.065s]
Masking low complexity seeds...  [0.025s]
Searching alignments...  [2.554s]
Processing query block 1, reference block 1/1, shape 7/16, index chunk 3/4.
Building reference seed array...  [0.099s]
Building query seed array...  [0.106s]
Computing hash join...  [0.065s]
Masking low complexity seeds...  [0.025s]
Searching alignments...  [2.437s]
Processing query block 1, reference block 1/1, shape 7/16, index chunk 4/4.
Building reference seed array...  [0.078s]
Building query seed array...  [0.082s]
Computing hash join...  [0.065s]
Masking low complexity seeds...  [0.025s]
Searching alignments...  [2.381s]
Processing query block 1, reference block 1/1, shape 8/16, index chunk 1/4.
Building reference seed array...  [0.083s]
Building query seed array...  [0.086s]
Computing hash join...  [0.065s]
Masking low complexity seeds...  [0.024s]
Searching alignments...  [2.772s]
Processing query block 1, reference block 1/1, shape 8/16, index chunk 2/4.
Building reference seed array...  [0.098s]
Building query seed array...  [0.102s]
Computing hash join...  [0.065s]
Masking low complexity seeds...  [0.024s]
Searching alignments...  [2.559s]
Processing query block 1, reference block 1/1, shape 8/16, index chunk 3/4.
Building reference seed array...  [0.103s]
Building query seed array...  [0.106s]
Computing hash join...  [0.065s]
Masking low complexity seeds...  [0.024s]
Searching alignments...  [2.451s]
Processing query block 1, reference block 1/1, shape 8/16, index chunk 4/4.
Building reference seed array...  [0.081s]
Building query seed array...  [0.085s]
Computing hash join...  [0.065s]
Masking low complexity seeds...  [0.024s]
Searching alignments...  [2.399s]
Processing query block 1, reference block 1/1, shape 9/16, index chunk 1/4.
Building reference seed array...  [0.084s]
Building query seed array...  [0.087s]
Computing hash join...  [0.066s]
Masking low complexity seeds...  [0.024s]
Searching alignments...  [2.81s]
Processing query block 1, reference block 1/1, shape 9/16, index chunk 2/4.
Building reference seed array...  [0.101s]
Building query seed array...  [0.103s]
Computing hash join...  [0.065s]
Masking low complexity seeds...  [0.024s]
Searching alignments...  [2.556s]
Processing query block 1, reference block 1/1, shape 9/16, index chunk 3/4.
Building reference seed array...  [0.105s]
Building query seed array...  [0.108s]
Computing hash join...  [0.066s]
Masking low complexity seeds...  [0.024s]
Searching alignments...  [2.487s]
Processing query block 1, reference block 1/1, shape 9/16, index chunk 4/4.
Building reference seed array...  [0.081s]
Building query seed array...  [0.085s]
Computing hash join...  [0.066s]
Masking low complexity seeds...  [0.024s]
Searching alignments...  [2.401s]
Processing query block 1, reference block 1/1, shape 10/16, index chunk 1/4.
Building reference seed array...  [0.083s]
Building query seed array...  [0.086s]
Computing hash join...  [0.064s]
Masking low complexity seeds...  [0.025s]
Searching alignments...  [2.746s]
Processing query block 1, reference block 1/1, shape 10/16, index chunk 2/4.
Building reference seed array...  [0.098s]
Building query seed array...  [0.102s]
Computing hash join...  [0.064s]
Masking low complexity seeds...  [0.025s]
Searching alignments...  [2.546s]
Processing query block 1, reference block 1/1, shape 10/16, index chunk 3/4.
Building reference seed array...  [0.102s]
Building query seed array...  [0.106s]
Computing hash join...  [0.064s]
Masking low complexity seeds...  [0.025s]
Searching alignments...  [2.451s]
Processing query block 1, reference block 1/1, shape 10/16, index chunk 4/4.
Building reference seed array...  [0.081s]
Building query seed array...  [0.084s]
Computing hash join...  [0.064s]
Masking low complexity seeds...  [0.025s]
Searching alignments...  [2.385s]
Processing query block 1, reference block 1/1, shape 11/16, index chunk 1/4.
Building reference seed array...  [0.084s]
Building query seed array...  [0.086s]
Computing hash join...  [0.066s]
Masking low complexity seeds...  [0.025s]
Searching alignments...  [2.794s]
Processing query block 1, reference block 1/1, shape 11/16, index chunk 2/4.
Building reference seed array...  [0.101s]
Building query seed array...  [0.103s]
Computing hash join...  [0.065s]
Masking low complexity seeds...  [0.025s]
Searching alignments...  [2.593s]
Processing query block 1, reference block 1/1, shape 11/16, index chunk 3/4.
Building reference seed array...  [0.102s]
Building query seed array...  [0.107s]
Computing hash join...  [0.065s]
Masking low complexity seeds...  [0.025s]
Searching alignments...  [2.466s]
Processing query block 1, reference block 1/1, shape 11/16, index chunk 4/4.
Building reference seed array...  [0.091s]
Building query seed array...  [0.084s]
Computing hash join...  [0.065s]
Masking low complexity seeds...  [0.025s]
Searching alignments...  [2.434s]
Processing query block 1, reference block 1/1, shape 12/16, index chunk 1/4.
Building reference seed array...  [0.082s]
Building query seed array...  [0.085s]
Computing hash join...  [0.068s]
Masking low complexity seeds...  [0.025s]
Searching alignments...  [2.755s]
Processing query block 1, reference block 1/1, shape 12/16, index chunk 2/4.
Building reference seed array...  [0.096s]
Building query seed array...  [0.101s]
Computing hash join...  [0.065s]
Masking low complexity seeds...  [0.024s]
Searching alignments...  [2.534s]
Processing query block 1, reference block 1/1, shape 12/16, index chunk 3/4.
Building reference seed array...  [0.105s]
Building query seed array...  [0.107s]
Computing hash join...  [0.064s]
Masking low complexity seeds...  [0.024s]
Searching alignments...  [2.449s]
Processing query block 1, reference block 1/1, shape 12/16, index chunk 4/4.
Building reference seed array...  [0.082s]
Building query seed array...  [0.085s]
Computing hash join...  [0.064s]
Masking low complexity seeds...  [0.024s]
Searching alignments...  [2.391s]
Processing query block 1, reference block 1/1, shape 13/16, index chunk 1/4.
Building reference seed array...  [0.084s]
Building query seed array...  [0.086s]
Computing hash join...  [0.064s]
Masking low complexity seeds...  [0.025s]
Searching alignments...  [2.749s]
Processing query block 1, reference block 1/1, shape 13/16, index chunk 2/4.
Building reference seed array...  [0.098s]
Building query seed array...  [0.102s]
Computing hash join...  [0.064s]
Masking low complexity seeds...  [0.025s]
Searching alignments...  [2.551s]
Processing query block 1, reference block 1/1, shape 13/16, index chunk 3/4.
Building reference seed array...  [0.103s]
Building query seed array...  [0.107s]
Computing hash join...  [0.064s]
Masking low complexity seeds...  [0.025s]
Searching alignments...  [2.472s]
Processing query block 1, reference block 1/1, shape 13/16, index chunk 4/4.
Building reference seed array...  [0.08s]
Building query seed array...  [0.083s]
Computing hash join...  [0.064s]
Masking low complexity seeds...  [0.025s]
Searching alignments...  [2.389s]
Processing query block 1, reference block 1/1, shape 14/16, index chunk 1/4.
Building reference seed array...  [0.085s]
Building query seed array...  [0.088s]
Computing hash join...  [0.065s]
Masking low complexity seeds...  [0.024s]
Searching alignments...  [2.77s]
Processing query block 1, reference block 1/1, shape 14/16, index chunk 2/4.
Building reference seed array...  [0.101s]
Building query seed array...  [0.104s]
Computing hash join...  [0.064s]
Masking low complexity seeds...  [0.024s]
Searching alignments...  [2.584s]
Processing query block 1, reference block 1/1, shape 14/16, index chunk 3/4.
Building reference seed array...  [0.105s]
Building query seed array...  [0.11s]
Computing hash join...  [0.065s]
Masking low complexity seeds...  [0.024s]
Searching alignments...  [2.473s]
Processing query block 1, reference block 1/1, shape 14/16, index chunk 4/4.
Building reference seed array...  [0.083s]
Building query seed array...  [0.086s]
Computing hash join...  [0.064s]
Masking low complexity seeds...  [0.024s]
Searching alignments...  [2.4s]
Processing query block 1, reference block 1/1, shape 15/16, index chunk 1/4.
Building reference seed array...  [0.081s]
Building query seed array...  [0.083s]
Computing hash join...  [0.065s]
Masking low complexity seeds...  [0.024s]
Searching alignments...  [2.793s]
Processing query block 1, reference block 1/1, shape 15/16, index chunk 2/4.
Building reference seed array...  [0.1s]
Building query seed array...  [0.103s]
Computing hash join...  [0.065s]
Masking low complexity seeds...  [0.024s]
Searching alignments...  [2.557s]
Processing query block 1, reference block 1/1, shape 15/16, index chunk 3/4.
Building reference seed array...  [0.104s]
Building query seed array...  [0.107s]
Computing hash join...  [0.065s]
Masking low complexity seeds...  [0.024s]
Searching alignments...  [2.468s]
Processing query block 1, reference block 1/1, shape 15/16, index chunk 4/4.
Building reference seed array...  [0.081s]
Building query seed array...  [0.084s]
Computing hash join...  [0.065s]
Masking low complexity seeds...  [0.024s]
Searching alignments...  [2.435s]
Processing query block 1, reference block 1/1, shape 16/16, index chunk 1/4.
Building reference seed array...  [0.081s]
Building query seed array...  [0.085s]
Computing hash join...  [0.064s]
Masking low complexity seeds...  [0.024s]
Searching alignments...  [2.752s]
Processing query block 1, reference block 1/1, shape 16/16, index chunk 2/4.
Building reference seed array...  [0.098s]
Building query seed array...  [0.102s]
Computing hash join...  [0.064s]
Masking low complexity seeds...  [0.024s]
Searching alignments...  [2.529s]
Processing query block 1, reference block 1/1, shape 16/16, index chunk 3/4.
Building reference seed array...  [0.103s]
Building query seed array...  [0.105s]
Computing hash join...  [0.064s]
Masking low complexity seeds...  [0.024s]
Searching alignments...  [2.429s]
Processing query block 1, reference block 1/1, shape 16/16, index chunk 4/4.
Building reference seed array...  [0.082s]
Building query seed array...  [0.084s]
Computing hash join...  [0.064s]
Masking low complexity seeds...  [0.024s]
Searching alignments...  [2.402s]
Deallocating buffers...  [0.004s]
Clearing query masking...  [0.005s]
Computing alignments...  [42.947s]
Deallocating reference...  [0.003s]
Loading reference sequences...  [0s]
Deallocating buffers...  [0.004s]
Deallocating queries...  [0.002s]
Loading query sequences...  [0s]
Closing the input file...  [0s]
Closing the output file...  [0.002s]
Cleaning up...  [0s]
Total time = 228.434s
Reported 4038385 pairwise alignments, 4038385 HSPs.
270568 queries aligned.


-------------------------------Protein clustering-------------------------------
INFO:vcontact2: Loading proteins...
INFO:vcontact2: Merging ProkaryoticViralRefSeq94-Merged to user gene-to-genome mapping...
.................................................. 1M
.................................................. 2M
.................................................. 3M
......................................
[mclIO] writing <./Documents/Adhip/vcontact2/vc2_nchoe_02/merged.self-diamond.tab.mci>
.......................................
[mclIO] wrote native interchange 241042x241042 matrix with 4652476 entries to stream <./Documents/Adhip/vcontact2/vc2_nchoe_02/merged.self-diamond.tab.mci>
[mclIO] wrote 241042 tab entries to stream <./Documents/Adhip/vcontact2/vc2_nchoe_02/merged.self-diamond.tab_mcxload.tab>
[mcxload] tab has 241042 entries
[mclIO] reading <./Documents/Adhip/vcontact2/vc2_nchoe_02/merged.self-diamond.tab.mci>
.......................................
[mclIO] read native interchange 241042x241042 matrix with 4652476 entries
[mcl] pid 19358
 ite -------------------  chaos  time hom(avg,lo,hi) m-ie m-ex i-ex fmv
  1  ...................  37.70  1.29 0.98/0.23/3.52 2.33 2.20 2.20   0
  2  ...................  57.50  6.04 0.88/0.14/5.08 3.17 0.88 1.95   2
  3  ...................  31.00  3.60 0.84/0.14/6.01 2.12 0.75 1.47   0
  4  ...................  21.25  1.66 0.83/0.09/6.92 1.47 0.74 1.09   0
  5  ...................  15.16  0.81 0.82/0.14/5.31 1.21 0.72 0.78   0
  6  ...................  10.98  0.42 0.82/0.11/4.13 1.08 0.74 0.57   0
  7  ...................   9.18  0.26 0.83/0.20/2.55 1.03 0.78 0.45   0
  8  ...................   6.50  0.19 0.84/0.20/2.10 1.01 0.81 0.36   0
  9  ...................   5.23  0.16 0.86/0.20/1.27 1.00 0.82 0.30   0
 10  ...................   5.41  0.13 0.89/0.22/1.29 1.00 0.82 0.24   0
 11  ...................   4.31  0.11 0.92/0.19/1.32 1.00 0.82 0.20   0
 12  ...................   4.50  0.09 0.95/0.19/1.05 1.00 0.83 0.17   0
 13  ...................   4.73  0.08 0.97/0.22/1.00 1.00 0.86 0.14   0
 14  ...................   5.19  0.07 0.98/0.20/1.00 1.00 0.89 0.13   0
 15  ...................   4.09  0.07 0.99/0.24/1.00 1.00 0.92 0.12   0
 16  ...................   4.28  0.07 0.99/0.19/1.00 1.00 0.95 0.11   0
 17  ...................   4.21  0.06 1.00/0.23/1.00 1.00 0.97 0.11   0
 18  ...................   5.36  0.06 1.00/0.36/1.00 1.00 0.98 0.11   0
 19  ...................   2.49  0.06 1.00/0.39/1.00 1.00 0.99 0.10   0
 20  ...................   0.67  0.06 1.00/0.57/1.00 1.00 0.99 0.10   0
 21  ...................   0.49  0.06 1.00/0.64/1.00 1.00 1.00 0.10   0
 22  ...................   0.39  0.06 1.00/0.70/1.00 1.00 1.00 0.10   0
 23  ...................   0.30  0.06 1.00/0.75/1.00 1.00 1.00 0.10   0
 24  ...................   0.24  0.06 1.00/0.79/1.00 1.00 1.00 0.10   0
 25  ...................   0.22  0.06 1.00/0.78/1.00 1.00 1.00 0.10   0
 26  ...................   0.08  0.06 1.00/0.93/1.00 1.00 1.00 0.10   0
 27  ...................   0.14  0.06 1.00/0.93/1.00 1.00 1.00 0.10   0
 28  ...................   0.22  0.06 1.00/0.83/1.00 1.00 1.00 0.10   0
 29  ...................   0.24  0.06 1.00/0.76/1.00 1.00 1.00 0.10   0
 30  ...................   0.12  0.06 1.00/0.88/1.00 1.00 1.00 0.10   0
 31  ...................   0.01  0.06 1.00/0.99/1.00 1.00 1.00 0.10   0
 32  ...................   0.00  0.06 1.00/1.00/1.00 1.00 1.00 0.10   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 ./Documents/Adhip/vcontact2/vc2_nchoe_02/merged.self-diamond.tab_mcl20.clusters
[mcl] 31100 clusters found
[mcl] output is in ./Documents/Adhip/vcontact2/vc2_nchoe_02/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: Building the cluster and profiles (this may take some time...)
If it fails, try re-running using --blast-fp flag and specifiying merged.self-diamond.tab (or merged.self-blastp.tab)
INFO:vcontact2: Saving intermediate files...


----------------------------------Loading data----------------------------------
INFO:vcontact2: Read 233640 entries (dropped 2626 singletons) from ./Documents/Adhip/vcontact2/vc2_nchoe_02/vConTACT_profiles.csv


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


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


------------------------Contig Clustering & Affiliation-------------------------
Loaded graph with 2634 nodes and 96104 edges
[====================] 100% Growing clusters from seeds...
[====================] 100% Finding highly overlapping clusters...
[====================] 100% Merging highly overlapping clusters...
Detected 362 complexes


--------------------------------Protein modules---------------------------------
.................................................. 1M
.................................................. 2M
...............
[mcl] new tab created
[mcl] pid 19686
 ite -------------------  chaos  time hom(avg,lo,hi) m-ie m-ex i-ex fmv
  1  ...................  99.19  0.82 1.04/0.01/9.75 5.47 1.81 1.81  72
  2  ...................  49.59  1.67 0.72/0.04/4.18 10.33 0.11 0.20  91
  3  ...................   7.42  0.09 0.87/0.08/11.03 2.06 0.22 0.04  13
  4  ...................   7.14  0.01 0.96/0.14/11.33 1.04 0.58 0.03   0
  5  ...................   1.35  0.01 0.99/0.30/1.23 1.00 0.80 0.02   0
  6  ...................   0.30  0.01 1.00/0.76/1.22 1.00 0.91 0.02   0
  7  ...................   0.25  0.01 1.00/0.77/1.16 1.00 0.98 0.02   0
  8  ...................   0.75  0.01 1.00/0.54/1.03 1.00 1.00 0.02   0
  9  ...................   0.01  0.01 1.00/1.00/1.00 1.00 1.00 0.02   0
 10  ...................   0.00  0.01 1.00/1.00/1.00 1.00 1.00 0.02   0
[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 ./Documents/Adhip/vcontact2/vc2_nchoe_02/modules_mcl_5.0.clusters
[mcl] 707 clusters found
[mcl] output is in ./Documents/Adhip/vcontact2/vc2_nchoe_02/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)



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


----------------------------Exporting results files-----------------------------
There were 687 genomes (including refs) that were singleton, outlier or overlaps.
Still identifying genome substrings. Consider adjusting input genomes naming.
'nchoe_02_contig_11'
(vcontact2) virology@virology:~$

‌

[Ben Bolduc]

Similar mentions of this genome affecting runs have been reported elsewhere. This seems to be an issue where vContact2 can’t identify a specific genome within the network because the name is contained within another name, e.g. Pseudomonas Phage P1 is a subset of Pseudomonas Phage P10. A fix for this was implemented quite some time ago - but that seems to only affect user genomes, not the reference database.

We’ll be updating the reference DB to deal with this sequence.