AnantharamanLab ViWrap issues

AnantharamanLab / ViWrap

A wrapper to identify, bin, classify, and predict host-viral relationship for viruses

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issues

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VS2 issue

#52 drob2727 opened 2 weeks ago
3
custom_MAGs

#50 Charles-Lou opened 3 weeks ago
0
Sklearn issue?

#49 drob2727 opened 3 weeks ago
0
download all the necessary databases, package them together, and then provide a unified download link

#48 tynot opened 1 month ago
3
HELP Step 4 Set up ViWrap database

#47 Rap0ss0 closed 1 month ago
1
Is it possible to run the entire pipeline w/out paired reads ?

#46 eechase opened 2 months ago
0
The annotation result of geNomad and run_annotate_by_VIBRANT_db.py

#45 quliping closed 4 months ago
0
vRhyme is unable to make bins

#44 aritrarc15 opened 4 months ago
1
geNomad failure (solution provided)

#43 jamesck2 closed 3 months ago
0
code issues about master_run.py

#42 beaPhD opened 5 months ago
0
No module named 'pandas'

#41 MHolden3 closed 5 months ago
0
FileNotFoundError: [Errno 2] No such file or directory: *.phages_lytic.fna

#40 clementcoclet opened 6 months ago
0
FileNotFoundError: [Errno 2] No such file or directory: 'test_metaG_ViWrap_out/03_vConTACT2_outdir/genome_by_genome_overview.csv'

#39 ChiLiubio closed 6 months ago
0
conda env path is not present!

#38 yyyangzd closed 6 months ago
1
FileNotFoundError: [Errno 2] No such file or directory: 'Host_prediction_to_genome_m90.csv'

#37 CynthiaChibani opened 7 months ago
1
FileNotFoundError: [Errno 2] No such file or directory: '/home/user/ViWrap_conda_environments/example_datatest_metaG_ViWrap_out5/02_vRhyme_outdir/vRhyme_best_bins_fasta_CheckV_result/CheckV_quality_summary.txt'

#36 MAXzbh opened 7 months ago
2
CheckV error

#35 tenguzame opened 7 months ago
3
Nanopore reads, no input files detected

#34 jonbakerlab opened 8 months ago
0
result issues

#33 AndAvia opened 8 months ago
0
Can't download databases

#32 SaraOliva closed 8 months ago
1
[Errno 2] No such file or directory: '/public/home/02_vRhyme_outdir/vRhyme_best_bins_fasta_CheckV_result/CheckV_quality_summary.txt'

#31 BigtigerLi closed 8 months ago
0
FileNotFoundError: [Errno 2] No such file or directory: '/lustre/isaac/proj/UTK0002/PALAVAS/PALAVAS_ViWrap/00_VIBRANT_VirSorter_PHYCOVIR_MEGAVIROME.contigs/VirSorter_PHYCOVIR_MEGAVIROME.contigs/pass/final-viral-score.tsv'

#30 eechase opened 8 months ago
4
FileNotFoundError: [Errno 2] No such file or directory:'/public/home/test/viwrap_test2/00_VIBRANT_VirSorter_test_metaG/VirSorter_test_metaG/CheckV_result/quality_summary.tsv'

#29 BigtigerLi closed 8 months ago
1
Databases manually setup & Virus identification tools

#28 Jiulong-Zhao opened 9 months ago
1
geNomad and ViWrap are not connected correctly

#27 lungphage closed 7 months ago
1
FileNotFoundError: [Errno 2] No such file or directory: '/data4/machuang/test1/ViWrap_outdir/00_VIBRANT_test_metaG/VIBRANT_phages_test_metaG/test_metaG.phages_lytic.fna'

#26 AndAvia opened 10 months ago
3
Run error: No such file or directory (final-viral-score.tsv)

#25 maocheng2020 closed 9 months ago
3
syntax error in master_run.py

#24 nitishnih opened 11 months ago
1
Logic error for 'custom_MAGs_dir'

#23 quliping closed 9 months ago
0
Logic error for 'custom_MAGs_dir'

#22 quliping closed 9 months ago
1
Linux

#21 XiaomengWang0413 closed 9 months ago
0
Bug report about vcontact2, test data, and a summary of bug found before.

#20 quliping closed 9 months ago
3
Error when running mapping_metaG_reads.py

#19 quliping closed 1 year ago
1
No such file or directory: 'genome_by_genome_overview.csv'

#18 Noob-Monkey closed 1 year ago
6
No results were produced by virsorter2

#17 quliping closed 1 year ago
5
ViWrap-DVF conda env path is not present!

#16 Timmywang1 opened 1 year ago
1
`FileNotFoundError` ViWrap_out/02_vRhyme_outdir/vRhyme_best_bins_fasta_CheckV_result/CheckV_quality_summary.txt'

#15 Sidduppal opened 1 year ago
2
🐎 ⬆️ Split assembly and speed up Vibrant

#14 Sidduppal closed 9 months ago
1
A suggestion about the operation of the software

#13 lungphage closed 7 months ago
1
Error: ConnectionError: could not open index file /path/to/dir/reads_R1.fastq.gz.fxi

#12 SharonLab opened 1 year ago
1
Error with mapping_metaG_reads.py step

#11 ilnamkang opened 1 year ago
0
About the update problem about the script "downloadDB.py"

#10 lungphage closed 7 months ago
2
A failure in CheckV download

#9 ilnamkang opened 1 year ago
0
Vcontact2 error

#8 CynthiaChibani closed 1 year ago
1
Problem with iPHoP step

#7 BenMinch opened 1 year ago
11
Error in the step "Run vRhyme to bin viral scaffolds. In processing... "

#6 WoCer2019 opened 1 year ago
11
Allowing for specific location of `custom_db` to solve permission and multi-users problems.

#5 patriciatran closed 1 year ago
1
Problem after the step "[2023-02-09 15:16:41] | Get virus genome abundance. Finished"

#4 rdenise closed 9 months ago
1
:bug: Missing a space after create

#3 rdenise opened 1 year ago
0
Header issues in some cases

#2 michoug closed 9 months ago
2