genome_by_genome.csv is missing!

[Rap0ss0]

Hi, I'm trying to run ViWrap and after reinstall and check dependencies several times I'm getting the same problem. After check the vcontact2 itself the vcontact2 starts to run and enters in loop resulting in the process fail and don't generate the genome_by_genome_overview.csv

(ViWrap) labmicro@metagenome:~/caio/teste_v$ ViWrap run --input_metagenome test_metaG.fasta --input_reads reads_1.fastq.gz,reads_2.fastq.gz --out_dir screen_test --db_dir /home/labmicro/ViWrap_db/ --identify_method vb --conda_env_dir /home/labmicro/programs/miniconda3/ViWrap/ViWrap_envs/ --threads 140 --input_length_limit 1000

Welcome to ViWrap

The issued command is:
/home/labmicro/programs/miniconda3/ViWrap/ViWrap run --input_metagenome test_metaG.fasta --input_reads reads_1.fastq.gz,reads_2.fastq.gz --out_dir screen_test --db_dir /home/labmicro/ViWrap_db/ --identify_method vb --conda_env_dir /home/labmicro/programs/miniconda3/ViWrap/ViWrap_envs/ --threads 140 --input_length_limit 1000

[2025-07-23 20:09:55] | Pre-check inputings. In processing...
[2025-07-23 20:09:55] | Looks like the input metagenome and reads, database, and custom MAGs dir (if option used) are now set up well, start up to run ViWrap pipeline
[2025-07-23 20:09:55] | Run VIBRANT to identify and annotate viruses from input metagenome. In processing...
[2025-07-23 20:12:23] | Run VIBRANT to identify and annotate viruses from input metagenome. Finished
[2025-07-23 20:12:23] | Map reads to metagenome. In processing...
Renaming screen_test/01_Mapping_result_outdir/test_metaG.bowtie2_idx.3.bt2.tmp to screen_test/01_Mapping_result_outdir/test_metaG.bowtie2_idx.3.bt2
Renaming screen_test/01_Mapping_result_outdir/test_metaG.bowtie2_idx.4.bt2.tmp to screen_test/01_Mapping_result_outdir/test_metaG.bowtie2_idx.4.bt2
Renaming screen_test/01_Mapping_result_outdir/test_metaG.bowtie2_idx.1.bt2.tmp to screen_test/01_Mapping_result_outdir/test_metaG.bowtie2_idx.1.bt2
Renaming screen_test/01_Mapping_result_outdir/test_metaG.bowtie2_idx.2.bt2.tmp to screen_test/01_Mapping_result_outdir/test_metaG.bowtie2_idx.2.bt2
Renaming screen_test/01_Mapping_result_outdir/test_metaG.bowtie2_idx.rev.1.bt2.tmp to screen_test/01_Mapping_result_outdir/test_metaG.bowtie2_idx.rev.1.bt2
Renaming screen_test/01_Mapping_result_outdir/test_metaG.bowtie2_idx.rev.2.bt2.tmp to screen_test/01_Mapping_result_outdir/test_metaG.bowtie2_idx.rev.2.bt2
[2025-07-23T23:12:43Z INFO coverm] CoverM version 0.6.1
[2025-07-23T23:12:43Z INFO coverm] Using min-read-percent-identity 97%
[2025-07-23T23:12:43Z INFO coverm] CoverM version 0.6.1
[2025-07-23T23:12:43Z INFO coverm] Setting single read percent identity threshold at 0.97 for MetaBAT adjusted coverage, and not filtering out supplementary, secondary and improper pair alignments
[2025-07-23T23:12:43Z INFO coverm] Using min-covered-fraction 0%
[2025-07-23T23:12:44Z INFO coverm::contig] In sample 'reads.filtered', found 172038 reads mapped out of 174248 total (98.73%)

[2025-07-23 20:12:44] | Map reads to metagenome. Finished
[2025-07-23 20:12:44] | Run vRhyme to bin viral scaffolds. In processing...
[2025-07-23 20:13:58] | Run vRhyme to bin viral scaffolds. Finished
[2025-07-23 20:13:58] | Run vContact2 to cluster viral genomes. In processing...
Traceback (most recent call last):
File "/home/labmicro/programs/miniconda3/ViWrap/ViWrap", line 173, in
output = cli()
File "/home/labmicro/programs/miniconda3/ViWrap/ViWrap", line 167, in cli
args"func"
File "/home/labmicro/programs/miniconda3/ViWrap/scripts/master_run.py", line 510, in main
scripts.module.get_genus_cluster_info(genome_by_genome_file, genus_cluster_info, ref_pro2viral_gn_map)
File "/home/labmicro/programs/miniconda3/ViWrap/scripts/module.py", line 419, in get_genus_cluster_info
with open(genome_by_genome_file,"r") as file_lines:
FileNotFoundError: [Errno 2] No such file or directory: 'screen_test/03_vConTACT2_outdir/genome_by_genome_overview.csv'