CAMI-challenge/CAMISIM

Issues

• Missing main.nf

  #195 opened 2 months ago by mortonjt
  2

• [MetagenomeSimulationPipeline] Empty bam file list in line 106

  #150 opened 2 years ago by Louis-MG
  8

• Skipping genomes and empty bam file list in line 106

  #198 opened a month ago by SMontesinos
  2

• Simulating 16S metabarcoding reads?

  #196 opened 2 months ago by marieleoz
  3

• Hi,

  #197 opened 2 months ago by HAJRA-sys
  0

• Guidance on Simulating Metatranscriptomes for CAMI 2 Challenge Short-Read Metagenomes

  #194 opened 3 months ago by ohickl
  1

• Changing read lengths from the default 150bp

  #193 opened 5 months ago by cberta11
  1

• Could not find workflow.nf in the repo.

  #184 opened 5 months ago by ravinpoudel
  5

• camisim encountered an error when specifying the --hmm_model parameter in pbsim2

  #183 opened 5 months ago by zwh82
  3

• ERROR: [MetagenomeSimulationPipeline] 'M' in line 122

  #175 opened 5 months ago by kangxiongbin
  4

• metagenomesimulation.py raising "ERROR: [MetagenomeSimulationPipeline] 'gb|*********.1|:1-****' in line 117" Error

  #192 opened 5 months ago by cberta11
  3

• NoneType path error when trying to run metagenome_from_profile.py from default_config.ini

  #191 opened 5 months ago by cberta11
  3

• Is profile-based design with custom genomes possible?

  #177 opened 6 months ago by CassandraHjo
  11

• How can I simulate reads data when I manually designed an OTU table?

  #179 opened 6 months ago by fanqiedantang
  4

• How to map relevant genomes to OTU through scientific names？

  #185 opened 6 months ago by fanqiedantang
  11

• Confused by the abundance values in the CAMI2 toy datasets

  #189 opened 6 months ago by TakacsBertalan
  1

• Controlling the rate of error

  #187 opened 6 months ago by mahmudhera
  1

• Handling coverage

  #190 opened 6 months ago by CorvusVaine
  0

• Generation from different genome for same specie

  #186 opened 6 months ago by CorvusVaine
  4

• Changing temp_directory in config file

  #173 opened a year ago by CassandraHjo
  4

• the data type of CAMISIM long read dataset

  #188 opened 9 months ago by zwh82
  1

• ERROR: [MetagenomeSimulationPipeline] 'utf-8' codec can't decode byte 0x8b in position 1: invalid start byte in line 49？

  #180 opened a year ago by fanqiedantang
  3

• No file found for all the reads of the sample in the output

  #182 opened a year ago by shussin245
  2

• how to increase the size of the simulated dataset?

  #181 opened a year ago by fanqiedantang
  1

• should i download all the reference genomes of the species involved in the BIOM file？

  #171 opened a year ago by fanqiedantang
  1

• Hi,I still cant understand what "adundance" means …………

  #170 opened a year ago by NickShanyt
  1

• some error when i try the command ---- "python metagenome_form_profile.py -p defaults/mini.biom "

  #172 opened a year ago by fanqiedantang
  1

• Meaning of community parameters in config file

  #176 opened a year ago by CassandraHjo
  1

• Input genomes

  #174 opened a year ago by CassandraHjo
  3

• Errors when running from_profile default

  #178 opened a year ago by CassandraHjo
  8

• the details in simulating the madness dataset of CAMI II by CAMISIM

  #165 opened a year ago by fanqiedantang
  12

• Some problems occur when I run “python metagenomesimulation.py defaults/mini_config.ini”

  #162 opened a year ago by fanqiedantang
  8

• Error running simulation using custom genomes

  #169 opened a year ago by CassandraHjo
  1

• Question, is there any existing repository.

  #167 opened a year ago by shanoudi
  7

• metagenome simulation

  #168 opened a year ago by lcamelo10
  2

• Problem trying to run metagenome_from_profile.py with docker. Is python3 update completed?

  #149 opened 2 years ago by MateDuda
  2

• A problem in testing one commond in the wiki

  #161 opened a year ago by fanqiedantang
  1

• How to speed up the microbiome simulation process using CamiSim

  #163 opened a year ago by YunyunGao374
  4

• 2023-10-10 23:40:29 ERROR: [MetagenomeSimulationPipeline] 'Salmonella_enterica_Typhimurium_1898' in line 83

  #166 opened a year ago by icbarron
  4

• attempting to simulate viral community, continue to encounter an error

  #164 opened a year ago by icbarron
  5

• "ncbi_taxdump=tools/ncbi-taxonomy_20170222.tar.gz" Unsupported newer version.

  #160 opened a year ago by NickShanyt
  10

• Error free illumina reads

  #158 opened 2 years ago by Paupiera
  1

• Create Python package and conda recipe?

  #159 opened 2 years ago by vinisalazar
  2

• Unable to download Mouse Toy dataset

  #157 opened 2 years ago by richardlett
  1

• ERROR: [MetagenomeSimulationPipeline] could not convert string to float: 'abundance' in line 80

  #155 opened 2 years ago by prototaxites
  2

• Data availability for CAMISIM Figure 3

  #156 opened 2 years ago by paulinetrinh
  2

• "Population must be a sequence. For dicts or sets, use sorted(d). in line 83" [Python 3.11 compatibility?]

  #154 opened 2 years ago by prototaxites
  4

• Question about {out}/anonymous_gsa_pooled.fasta file and its corresponding bam file

  #153 opened 2 years ago by Steven-GUHK
  4

• ERROR: [MetagenomeSimulationPipeline] 'MGV-GENOME-0364315' in line 117

  #152 opened 2 years ago by Steven-GUHK
  2

• [MetagenomeSimulationPipeline] Required file not found! Was design of communities not completed?

  #151 opened 2 years ago by Louis-MG
  1