jolespin/veba

Issues

• [Error] BUSCO fails to find database at --download_path

  #120 opened 14 days ago by abissett
  3

• EnvironmentLocationNotFound error for installation on HPC with sudo rights

  #113 opened 2 months ago by joao1980
  2

• [Feature Request] Walkthrough for running the cluster module on genomes sourced from NCBI

  #111 opened 2 months ago by 411an13
  3

• [Question] Where have all the mRNAs gone?

  #110 opened 3 months ago by bheimbu
  5

• [Feature Request] bioconda recipe

  #95 opened 4 months ago by cmkobel
  3

• [Question] Is it possible to use the VEBA Microeukaryotic database with MMSEQS2 taxonomy?

  #35 opened 10 months ago by franlat
  19

• How do I start with pre-filtered data ready to assemble?

  #85 opened 4 months ago by kellyu01
  2

• [Question] <Is there documentation on how to run VEBA using the docker containers?>

  #86 opened 4 months ago by grendon
  2

• [Question] VEBA-biosynthetic_env/bin/mmseqs: No such file or directory

  #84 opened 6 months ago by javiercnav
  3

• [Bug] DAS_Tool starts but fails after calculating contig lengths (binning-prokaryotic.py)

  #45 opened 7 months ago by abissett
  14

• [Bug] featureCounts error in binning-eukaryotic.py | ERROR: failed to find the gene identifier attribute in the 9th column of the provided GTF file.

  #47 opened 8 months ago by javiercnav
  6

• [Bug] classify-prokaryotic.py excludes archaeal genomes (Downstream Issue in building custom HUMAnN db)

  #48 opened 8 months ago by nicolazarte
  5

• Issue: Broken pipe error in kofamscan step

  #46 opened 8 months ago by nicolazarte
  3

• [Question] ERROR: Paired-end reads were detected in single-end read library" at the featurecounts step. How do I indicate that there are paired-end r

  #22 opened a year ago by MACampbell91
  11

• Question - Length mismatch during merging step of annotation

  #34 opened 10 months ago by MACampbell91
  0

• [Question] CHECKVDB environment variable NOT set

  #28 opened 10 months ago by javiercnav
  9

• [Question] What does the homogenity value mean in the output taxonomy.tsv file of classify-eukaryotic

  #29 opened 10 months ago by franlat
  7

• Duplicate scaffold/contig identifiers are not allowed

  #25 opened a year ago by MACampbell91
  8

• [Question] Why isn't `binning-eukaryotic.py` finding any eukaryotic bins and why are the output files empty?

  #30 opened a year ago by franlat
  9

• [Bug] different number of reads in paired input files; repair.sh does not seem to be working in preprocess.py

  #27 opened a year ago by yangchen2
  5

• [Question] Why do I get permission error for binning-prokaryotic.py only and not for binning-viral modules?

  #26 opened a year ago by the-eon-flux
  1

• [Feature Request] Expanding Viral Identification & Analysis Toolset

  #9 opened a year ago by erfanshekarriz
  7

• VEBA-binning-prokaryotic module - step 7_dastool error: /bin/sh: 1: Syntax error: redirection unexpected

  #23 opened a year ago by MACampbell91
  23

• Installation error. bash install_veba.sh

  #24 opened a year ago by RazaRaza
  4

• [Bug] binning-prokaryotic.py module fails with scaffolds_to_bins.tsv file missing (penultimate step)

  #4 opened 2 years ago by hyphaltip
  16

• Issue with --skip_maxbin2 and --skip_concoct params

  #21 opened 2 years ago by jdilme
  2

• [Feature Request] Assembly-level Eukaryotic Metatranscriptomic Functional Annotation & Read-count Mapping

  #19 opened 2 years ago by erfanshekarriz
  6

• [Bug] Error when creating VEBA environments

  #20 opened 2 years ago by andressamv
  2

• [Feature Request] Adding MEGAHIT to assembly module

  #5 opened 2 years ago by erfanshekarriz
  7

• [Feature Request] Add checkpoint after 1__assembly assembly (before index building)

  #18 opened 2 years ago by erfanshekarriz
  5

• [Bug] ModuleNotFoundError: No module named 'Bio'

  #17 opened 2 years ago by erfanshekarriz
  2

• [Typo] Installation Guide bash update_environment_variables.sh

  #16 opened 2 years ago by erfanshekarriz
  2

• [Bug] v1.0.3* conda installation error VEBA-assembly_env perl-xml-parser-2.44-4

  #15 opened 2 years ago by erfanshekarriz
  5

• [Typo] Typo in installation README.md

  #14 opened 2 years ago by erfanshekarriz
  1

• [Bug] `Error: unexpected input in "_"` when running `VirFinder_wrapper.R` via `binning-viral.py` module

  #13 opened 2 years ago by jolespin
  1

• [Bug] Empty `identifier_mapping.metaeuk.tsv` file generated from `filter_busco_results.py` of `binning-eukaryotic.py`

  #12 opened 2 years ago by jolespin
  1

• [Bug] IndexError: Replacement index 1 out of range for positional args tuple when running `binning-eukaryotic.py`

  #11 opened 2 years ago by jolespin
  1

• [Bug] Package conflicts for VEBA-process_env.yml environment installation

  #10 opened 2 years ago by jolespin
  2

• [Question] Retaining k-mer and non-kmer hits in the bbduk.sh step of preprocess.py

  #7 opened 2 years ago by erfanshekarriz
  2

• [Typo] In Viral Metatranscriptomics Tutorial

  #8 opened 2 years ago by erfanshekarriz
  1

• [Question] Why did I get a KeyError: 'TMPDIR' when running binning-prokaryotic.py?

  #6 opened 2 years ago by erfanshekarriz
  3

• [Bug] Misspelling "itermediate" -> "intermediate" in binning-eukaryotic.py

  #2 opened 2 years ago by hyphaltip
  2

• [Database] Delete compressed human reference after decompression

  #1 opened 2 years ago by hyphaltip
  2