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dadasnake is a Snakemake workflow to process amplicon sequencing data, from raw fastq-files to taxonomically assigned "OTU" tables, based on the DADA2 method. Running dadasnake could not be easier: it is called by a single command from the command line. With a human-readable configuration file and a simple sample table, its steps are adjustable to a wide array of input data and requirements. It is designed to run on a computing cluster using a single conda environment in multiple jobs triggered by Snakemake. dadasnake reports on intermediary steps and statistics in intuitive figures and tables. Final data output formats include biom format, phyloseq objects, and flexible text files or R data sets for easy integration in microbial ecology analysis scripts.

Installing dadasnake

For dadasnake to work, you need conda.

  1. Clone this repository to your disk:
git clone https://github.com/a-h-b/dadasnake.git

Change into the dadasnake directory:

cd dadasnake

At this point, you have all the scripts you need to run the workflow using snakemake, and you'd just need to get some data and databases (see point 8). If you want to use the comfortable dadasnake wrapper, follow the points 2-6.

  1. Decide how you want to run dadasnake, if you let it submit jobs to the cluster: Only do one of the two:
  • if you want to submit the process running snakemake to the cluster:
cp auxiliary_files/dadasnake_allSubmit dadasnake
chmod 755 dadasnake
  • if you want to keep the process running snakemake on the frontend using tmux:
cp auxiliary_files/dadasnake_tmux dadasnake
chmod 755 dadasnake

If you don't submit jobs to the cluster, but want to run the whole workflow interactively, e.g. on a laptop, it doesn't matter which wrapper you use. Just copy one of them, as described above.

  1. Adjust the file VARIABLE_CONFIG to your requirements (have a tab between the variable name and your setting):
  • SNAKEMAKE_VIA_CONDA - set this to true, if you don't have snakemake in your path and want to install it via conda. Leave empty, if you don't need an additional snakemake.
  • SNAKEMAKE_EXTRA_ARGUMENTS - if you want to pass additional arguments to snakemake, put them here (e.g. --latency-wait=320 for slower file systems). Leave empty usually.
  • LOADING_MODULES - insert a bash command to load modules, if you need them to run conda. Leave empty, if you don't need to load a module.
  • SUBMIT_COMMAND - insert the bash command you'll usually use to submit a job to your cluster to run on a single cpu for a few days. You only need this, if you want to have the snakemake top instance running in a submitted job. You alternatively have the option to run it on the frontend via tmux. Leave empty, if you want to use this frontend version and have tmux installed. You don't need to set this, if you are wanting to run the workflow interactively / on a laptop.
  • BIND_JOBS_TO_MAIN - if you use the option to run the snakemake top instance in a submitted job and need to bind the other jobs to the same node, you can set this option to true. See FAQ below for more details. You don't need to set this, if you are wanting to run the workflow interactively / on a laptop.
  • NODENAME_VAR - if you use the BIND_JOBS_TO_MAIN option, you need to let dadasnake know, how to access the node name (e.g.SLURMD_NODENAME on slurm). You don't need to set this, if you are wanting to run the workflow interactively / on a laptop.
  • SCHEDULER - insert the name of the scheduler you want to use (currently slurm or uge). This determines the cluster config given to snakemake, e.g. the cluster config file for slurm is config/slurm.config.yaml . Also check that the settings in this file is correct. If you have a different system, contact us ( https://github.com/a-h-b/dadasnake/issues ). You don't need to set this, if you are wanting to run the workflow interactively / on a laptop.
  • MAX_THREADS - set this to the maximum number of cores you want to be using in a run. If you don't set this, the default will be 50. Users can override this setting at runtime.
  • NORMAL_MEM_EACH - set the size of the RAM of one core of your normal copute nodes (e.g. 8G). If you're not planning to use dadasnake to submit to a cluster, you don't need to set this.
  • BIGMEM_MEM_EACH - set the size of the RAM of one core of your bigmem (or highmem) compute nodes. If you're not planning to use dadasnake to submit to a cluster or don't have separate bigmem nodes, you don't need to set this.
  • BIGMEM_CORES - set this to the maximum number of bigmem cores you want to require for a task. Set to 0, if you don't have separate bigmem nodes. You don't need to set this, if you're not planning to use dadasnake to submit to a cluster.
  • LOCK_SETTINGS - set this to true, if you don't want users to choose numbers and sizes of compute nodes at run time. If you're not planning to use dadasnake to submit to a cluster, you don't need to set this. Setting LOCK_SETTINGS makes the workflow slightly less flexible, as all large data sets will be run with the maximum number of bigmem nodes you set up here (see big_data settings below). On the other hand, it can be helpful, if you're setting up dadasnake for inexperienced users or have only one possible setting anyhow. If you're not locking, it's advised to set useful settings in the config/config.default.yaml file for normalMem, bigMem, and bigCores.
  1. optional, but highly recommended: Install snakemake via conda: If you want to use snakemake via conda (and you've set SNAKEMAKE_VIA_CONDA to true), install the environment, as recommended by Snakemake:
conda install -c conda-forge mamba
mkdir -p conda
mamba create --prefix $PWD/conda/snakemake_env
conda activate $PWD/conda/snakemake_env
mamba install -c conda-forge -c bioconda snakemake=6.9.1 mamba
conda deactivate

Alternatively, if the above does not work, you can install a fixed snakemake version without mamba like so:

conda env create -f workflow/envs/snakemake_env.yml --prefix $PWD/conda/snakemake_env

Dadasnake will run with Snakemake version >= 5.9.1 and hasn't been tested with any previous versions.

  1. Set permissions / PATH: Dadasnake is meant to be used by multiple users. Set the permissions accordingly. I'd suggest:
  • to have read access for all files for the users plus
  • execution rights for the dadasnake file and the .sh scripts in the subfolder submit_scripts
  • read, write and execution rights for the conda subfolder
  • Add the dadasnake directory to your path.
  • It can also be useful to make the VARIABLE_CONFIG file not-writable, because you will always need it. The same goes for config.default.yaml once you've set the paths to the databases you want to use (see below).
  1. Initialize conda environments: This run sets up the conda environments that will be usable by all users:
./dadasnake -i config/config.init.yaml 

This step will take several minutes. It will also create a folder with the name "dadasnake_initialized". You can safely remove it or keep it. I strongly suggest to remove one line from the activation script after the installation, namely the one reading: R CMD javareconf > /dev/null 2>&1 || true, because you don't need this line later and if two users run this at the same time it can cause trouble. You can do this by running:

sed -i "s/R CMD javareconf/#R CMD javareconf/" conda/*/etc/conda/activate.d/activate-r-base.sh
  1. Optional test run: The test run does not need any databases. You should be able to start it by running
./dadasnake -l -n "TESTRUN" -r config/config.test.yaml

If all goes well, dadasnake will run in the current session, load the conda environment, and make and fill a directory called testoutput. A completed run contains a file "workflow.done". If you don't want to see dadasnake's guts at this point, you can also run this with the -c or -f settings to submit to your cluster or start a tmux session (see How to run dadasnake below).

  1. Databases: The dadasnake does not supply databases. I'd suggest to use the SILVA database for 16S data and UNITE for ITS.
  • dadasnake can use mothur to do the classification, as it's faster and likely more accurate than the legacy DADA2 option. You need to format the database like for mothur (see here).
  • dadasnake can alternatively use the DADA2 implementation of the same classifier. You can find some databases maintained by Michael R. McLaren here. More information on the format is in the DADA2 tutorial.
  • In addition to the bayesian classifier, dadasnake implements DECIPHER. You can find decipher databases on the decipher website or build them yourself.
  • dadasnake can use fungal traits to assign traits to fungal genere. Download the latest table from here - dadasnake has been tested with v1.2.
  • You can also use dadasnake to blast and to annotate fungal taxonomy with guilds via funguild, if you have suitable databases. Have a look at the NCBI's ftp.
  • You can also use tax4fun2 within dadasnake, and you need to set up suitable databases, as described here. You need to set the path to the databases of your choice in the config file. By default, dadasnake looks for databases in the directory above where it was called. It makes sense to change this for your system in the config.default.yaml file upon installation, if all users access databases in the same place.
  1. Fasttree: dadasnake comes with fasttree for treeing, but if you have a decent number of sequences, it is likely to be relatively slow. If you have fasttreeMP, you can give the path to it in the config file.

How to cite dadasnake

Christina Weißbecker, Beatrix Schnabel, Anna Heintz-Buschart, Dadasnake, a Snakemake implementation of DADA2 to process amplicon sequencing data for microbial ecology, GigaScience, Volume 9, Issue 12, December 2020, giaa135. Please also cite DADA2: Callahan, B., McMurdie, P., Rosen, M. et al. DADA2: High-resolution sample inference from Illumina amplicon data. Nat Methods 13, 581–583 (2016), and any other tools you use within dadasnake, e.g. mothur, DECIPHER, ITSx, Fasttree, FUNGuild, BASTA, tax4fun2.

overview

How to run dadasnake

To run the dadasnake, you need a config file and a sample table, plus data:

  • The config file (in yaml format) is read by Snakemake to determine the inputs, steps, arguments and outputs.
  • The sample table (tab-separated text) always gives sample names and file names, with column headers named library and r1_file (and r2_file for paired-end data sets). The path to the sample table has to be mentioned in the config file. You can add columns labeled run and sample to indicate libraries that should be combined into one final column and different sequencing runs (see the section about the sample table below).
  • All raw data (usually fastq files) need to be in one directory (which has to be given in the config file).
  • It is possible (and the best way to do this) to have one config file per run, which defines all settings that differ from the default config file.

Using the dadasnake wrapper

As shown in the installation description above, dadasnake can be run in a single step, by calling dadasnake. Since most of the configuration is done via the config file, the options are very limited. You can either:

  • -c run (submit to a cluster) dadasnake and make a report (-r), or
  • -l run (in the current terminal) dadasnake and make a report (-r), or
  • -f run (in a tmux session on the frontend) dadasnake only available in the tmux installation and make a report (-r), or
  • just make a report (-r), or
  • run a dryrun (-d), or
  • unlock a working directory, if a run was killed (-u)
  • initialize the conda environmnets only (-i) - you should only need this during the installation. It is strongly recommended to first run a dryrun on a new configuration, which will tell you within a few seconds and without submission to a cluster whether your chosen steps work together, the input files are where you want them, and your sample file is formatted correctly. In all cases you need the config file as the last argument.
dadasnake -d -r config.yaml

You can also set the number of cpus to maximally run at the same time with -t. The defaults (1 for local/frontend runs and 50 for clusters) are reasonable for many settings and if you don't know what this means, you probably don't have to worry. But you may want to increase the numbers for larger datasets or bigger infrastructure, or decrease the numbers to match your environment's constraints. You can add a name for your main job (-n NAME), e.g.:

dadasnake -c -n RUNNAME -r config.yaml

Note that spaces in RUNNAME are not allowed and dots will be replaced by underscores.

If you use the tmux version, you can see the tmux process running by typing tmux ls. You can also see the progress by checking the stdandard error file tail RUNNAME_XXXXXXXXXX.stderr.

Depending on your dataset and settings and your cluster's scheduler, the workflow will take a few minutes to days to finish.

Running snakemake manually

Once raw data, config file and sample file are present, the workflow can be started from the dadasnake directory by the snakemake command:

snakemake -s Snakefile --configfile /PATH/TO/YOUR/CONFIGFILE --use-conda

If you're using a computing cluster, add your cluster's submission command and the number of jobs you want to maximally run at the same time, e.g.:

snakemake -j 50 -s Snakefile --cluster "qsub -l h_rt={resources.runtime},h_vmem=8G -pe smp {threads} -cwd" --configfile /PATH/TO/YOUR/CONFIGFILE --use-conda 

This will submit most steps as their own job to your cluster's queue. The same can be achieved with a cluster configuration:

snakemake -j 50 -s Snakefile --cluster-config PATH/TO/SCHEDULER.config.yaml --cluster "{cluster.call} {cluster.runtime}{resources.runtime} {cluster.mem_per_cpu}{resources.mem} {cluster.threads}{threads} {cluster.partition}" --configfile /PATH/TO/YOUR/CONFIGFILE --use-conda

If you want to share the conda installation with colleagues, use the --conda-prefix argument of Snakemake

snakemake -j 50 -s Snakefile --cluster-config PATH/TO/SCHEDULER.config.yaml --cluster "{cluster.call} {cluster.runtime}{params.runtime} {cluster.mem_per_cpu}{resources.mem} {cluster.threads}{threads} {cluster.partition}" --use-conda --conda-prefix /PATH/TO/YOUR/COMMON/CONDA/DIRECTORY

Depending on your dataset and settings, and your cluster's queue, the workflow will take a few minutes to days to finish.

What does the dadasnake do?

  • primer removal - using cutadapt
  • quality filtering and trimming - using DADA2
  • optional downsampling of reads per sample - using seqtk
  • error estimation & denoising - using DADA2
  • paired-ends assembly - using DADA2
  • OTU table generation - using DADA2
  • chimera removal - using DADA2
  • taxonomic classification - using mothur and/or DECIPHER (& ITS detection - using ITSx & blastn + BASTA)
  • functional annotation - using funguild, fungalTraits, or tax4fun2
  • length check - in R
  • treeing - using clustal omega and fasttree
  • hand-off in biom-format, as R object, as R phyloseq object, and as fasta and tab-separated tables
  • keeping tabs on number of reads in each step, and read quality control - using fastqc & multiQC You can control the settings for each step in a config file.

steps

The configuration

The config file must be in .yaml format. The order within the yaml file does not matter, but the hierarchy has to be kept. Here are some explanations.

top-level parameters sub-parameters subsub-parameters default value possible values used in stage explanation comments / recommendations
email "" "" or a valid email address all email address for mail notification keep empty if you don't want emails. Check spelling, it's not tested.
sessionName "" "" or a single word all session name only read, if you're not using the dadasnake wrapper
normalMem "" "" or a number and letter all size of the RAM of one core of your normal copute nodes (e.g. 8G) may be fixed during installation, only necessary for cluster submission
bigMem "" "" or a number and letter all size of the RAM of one core of your high memory copute nodes (e.g. 30G) may be fixed during installation, only necessary for cluster submission
bigCores "" "" or a number all maximum number of high memory copute nodes to use (e.g. 4) 0 means all nodes have the same (normal) size may be fixed during installation, only necessary for cluster submission
sessionKind "" a string all automatically set by dadasnake wrapper keep ""
settingsLocked false a boolean or string all automatically set by dadasnake wrapper it doesn't matter what you do
big_data false a boolean dada, taxonomy, post whether to use big data settings set to true, if you have extra high memory nodes and more than 1000 samples
tmp_dir "/work/$USER/tmp" any path that you have permissions for writing to all directory for temporary, intermediate files that shouldn't be kept keep this in your /work so you don't need to worry about removing its contents
raw_directory "/work/$USER" any one path where you might have your raw data all directory with all raw data you will usually have this somewhere in a project folder
sample_table "/work/$USER/samples.tsv" any one location of your samples table all path to the samples table you can keep this in your /work, because the dadasnake will copy it to your output directory
outputdir "dadasnake_output" any path that you have permissions for writing to all directory where all the output will go change this; a scratch-type place works best (e.g. subdirectory of /work/$USER), but remember to move to a steady location afterwards; each output directory can hold the results of one completed pipeline run only
do_primers true true or false all should primers be cut?
do_dada true true or false all should DADA2 be run?
do_taxonomy true true or false all should taxonomic classification be done?
do_postprocessing true true or false all should some more steps be done (e.g. functional annotation)
primers primers information on primers
  fwd primers information on forward primer
  sequence GTGYCAGCMGCCGCGGTAA any sequence of IUPAC DNA code primers sequence of forward primer
  name 515F anything primers name of forward primer for your reference only
  rvs primers information on reverse primer
  sequence GGACTACNVGGGTWTCTAAT any sequence of IUPAC DNA code primers sequence of reverse primer
  name 806R anything primers name of reverse primer
paired true true or false primers and dada do you want to use paired-end sequencing data? if true, you have to give r1_file and r2_file in the samples table, if false only r1_file is read (if you want to use only R2 files from a paired-end sequencing run, put their name in the r1_file column)
sequencing_direction "unknown" fwd_1, rvs_1 or unknown primers fwd_1: fwd primer in read 1; rvs_1: rvs primer in read 1; unknown: you don't know the sequencing direction or the direction is mixed if you want to run single-end data and don't know the direction, dadasnake will re-orient the primers
primer_cutting primers arguments for primer cutting by cutadapt
  overlap 10 1-length of primer primers minimum length of detected primer
  count 2 a positive integer primers maximum number of primers removed from each end
  filter_if_not_match any any or both primers reads are discarded if primer is not found on both or any end any is the more strict setting; not used in single-end mode
  perc_mismatch 0.2 0-1 primers % mismatch between read and each primer don't set this to 1
  indels "--no-indels" "--no-indels" or "" primers whether indels in the primer sequence are allowed
  both_primers_in_read false false or true primers whether both primers are expected to be in the read only used in single-end mode
filtering dada settings for quality / length filtering; note on terminology: for paired sequencing fwd read refers to reads that had fwd primer or were declared as such (if no primer cutting was done); for single-end workflow, only the fwd setting is used, no matter the sequencing direction
  trunc_length dada length to truncate to (shorter reads are discarded)
  fwd 0 a positive integer dada length after which fwd read is cut - shorter reads are discarded 0: no truncation by length; if you've cut the primers, this number refers to the length left after primer cutting
  rvs 0 a positive integer dada length after which rvs read is cut - shorter reads are discarded 0: no truncation by length; ignored in single-ende mode; if you've cut the primers, this number refers to the length left after primer cutting
  trunc_qual 2 0-40 dada reads are cut before the first position with this quality
  fwd 2 0-40 dada fwd reads are cut before the first position with this quality
  rvs 2 0-40 dada rvs reads are cut before the first position with this quality ignored in single-ende mode
  max_EE dada filtering by maximum expected error after truncation: Expected errors are calculated from the nominal definition of the quality score: EE = sum(10^(-Q/10))
  fwd 2 a positive number dada After truncation, read pairs with higher than maxEE "expected errors" in fwd read will be discarded use with trunc_length and/or truncQ; note that low truncQ or high trunc_length make it difficult to reach low maxEE values
  rvs 2 a positive number dada After truncation, read pairs with higher than maxEE "expected errors" in rvs read will be discarded ignored in single-ende mode; use with trunc_length and/or truncQ; note that low truncQ or high trunc_length make it difficult to reach low maxEE values
  minLen dada filtering by mimum length
  fwd 20 a positive integer dada Remove reads with length less than minLen on fwd read. minLen is enforced after trimming and truncation. use with truncQ
  rvs 20 a positive integer dada Remove reads with length less than minLen on rvs read. minLen is enforced after trimming and truncation. ignored in single-ende mode; use with truncQ
  maxLen dada filtering by maximum length
  fwd Inf a positive integer or Inf dada Remove reads with length of fwd read greater than maxLen. maxLen is enforced before trimming and truncation.
  rvs Inf a positive integer or Inf dada Remove reads with length of rvs read greater than maxLen. maxLen is enforced before trimming and truncation. ignored in single-ende mode
  minQ dada filtering by minimum quality after tuncation
  fwd 0 0 or a positive number dada read pairs that contain a quality score lower than this in the fwd read after truncation will be discarded use with trunc_length
  rvs 0 0 or a positive number dada read pairs that contain a quality score lower than this in the rvs read after truncation will be discarded ignored in single-ende mode; use with trunc_length
  trim_left dada
  fwd 0 0 or a positive number dada this many bases will be cut from the 5' end of fwd reads filtered reads will have length truncLen-trimLeft
  rvs 0 0 or a positive number dada this many bases will be cut from the 5' end of rvs reads filtered reads will have length truncLen-trimLeft
  rm_phix true true or false dada remove phiX useful with Illumina sequencing
error_seed 100 any positive integer dada seed for error models keep constant in re-runs
downsampling dada
  do false true or false dada set to true if you want to downsample before DADA2 ASV construction
  number 50000 positive integer dada number of reads to keep per sample
  min true true or false dada true to keep only samples with that many reads samples with less reads are discarded
  seed 123 any positive integer dada seed for downsampling keep constant in re-runs
dada dada special DADA2 settings - default is good for Illumina
  band_size 16 a positive integer dada Banding restricts the net cumulative number of insertion of one sequence relative to the other. default is good for Illumina; set to 32 for 454 or PacBio
  homopolymer_gap_penalty NULL NULL or a negative integer dada The cost of gaps in homopolymer regions (>=3 repeated bases). Default is NULL, which causes homopolymer gaps to be treated as normal gaps. default is good for Illumina; set to -1 for 454
  pool false true, false, "pseudo", or "within_run" dada Should DADA2 be run per sample (default) or in a pool, or should pseudo-pooling be done? default is good for Illumina and much more efficient for large data sets; set to true for 454, pacbio and nanopore; set to pseudo for non-huge datasets, if you're interested in rare ASVs. You can also have within-run pools, but this setting is rarely useful.
  omega_A 1e-40 number between 0 and 1 dada Threshold to start new partition based on abundance in ASV finding. default is good for Illumina; set lower for 454; according to the DADA2 authors, it's an underused feature - it can also kill your analysis
  priors "" "" or the absolute path to a fasta file with prior sequence data dada You can give DADA2 sequences to look out for in your dataset. Don't change unless you know what you're doing.
  omega_P 1e-4 number between 0 and 1 dada Like omega_A, but for sequences matched by priors. Only does anything, if you gave priors.
  omega_C 1e-40 number between 0 and 1 dada Threshold to start new partition based on quality in ASV finding. Don't change unless you know what you're doing.
  selfConsist false true or false dada Should DADA2 do multiple rounds of ASV inference based on the normal error estimation? Don't change unless you know what you're doing.
  no_error_assumptions false true or false dada If you've set selfConsist to true, you can make DADA2 not start from the normal error estimation. Don't change unless you know what you're doing.
  errorEstimationFunction loessErrfun loessErrfun, PacBioErrfun or noqualErrfun dada The error estimation method within the DADA2 inference step. default is good for Illumina; set to PacBioErrfun for pacbio and possibly to noqualErrfun if your hacking data without real quality values
  use_quals true true or false dada DADA2 can be run without caring about quality. Don't change unless you know what you're doing.
  gapless true true or false dada In the pre-screening, Kmers are employed to find gaps. Don't change unless you know what you're doing - might help with 454 data and the like.
  kdist_cutoff 0.42 a number between 0 and 1 dada After the pre-screening, sequences of Kmers with this similarity are checked for actual matches. Don't change unless you know what you're doing.
  match 4 a number dada Score for match in Needleman-Wunsch-Alignment (the check for matching sequences). Don't change unless you know what you're doing.
  mismatch -5 a number dada Penaltiy for mismatch in Needleman-Wunsch-Alignment (the check for matching sequences). Don't change unless you know what you're doing.
  gap_penalty -8 a number dada Penaltiy for gaps in Needleman-Wunsch-Alignment (the check for matching sequences), unless the gaps are part of homopolymers - these are handled separately, see above. Don't change unless you know what you're doing.
pair_merging dada settings for merging of read pairs
  min_overlap 12 a positive integer dada The minimum length of the overlap required for merging the forward and reverse reads. ignored in single-ende mode
  max_mismatch 0 0 or a positive integer dada The maximum mismatches allowed in the overlap region. ignored in single-ende mode
  just_concatenate false true or false dada whether reads should be concatenated rather than overlapped ignored in single-ende mode; If TRUE, the forward and reverse-complemented reverse read are concatenated rather than merged, with a NNNNNNNNNN (10 Ns) spacer inserted between them.
  trim_overhang true true or false dada whether overhangs should be trimmed off after merging ignored in single-ende mode; usually, overhangs should have been removed with the primer cutting step
chimeras dada settings for chimera removal
  remove true true or false dada whether chimeras should be removed
  method consensus consensus, pooled or per-sample dada how chimeras are detected consensus: samples are checked individually and sequences are removed by consensus; pooled: the samples are pooled and chimeras are inferred from pool; samples are checked individually and sequence counts of chimeras are set to 0 in individual samples
  minFoldParentOverAbundance 2 a number > 1 dada how overabundant do parents have to be to consider a read chimeric? Should be higher for long amplicons (e.g. pacbio 3.5)
  minParentAbundance 8 a number > 1 dada how abundant do parents have to be to consider a read chimeric? Don't change unless you know what you're doing.
  allowOneOff false true or false dada should sequences with a mismatch be flagged as potential chimera? Don't change unless you know what you're doing.
  minOneOffParentDistance 4 a number > 1 dada if flagging sequences with one mismatch as potential one-off parents, how many mismatches are needed Don't change unless you know what you're doing.
  maxShift 16 a number dada maximum shift when aligning to potential parents Don't change unless you know what you're doing.
taxonomy taxonomy settings for taxonomic annotation
  dada taxonomy settings for DADA2 implementation of bayesian classifier
  do false true or false taxonomy whether DADA2 should be used for taxonomic annotation the DADA2 implementation may work less well than the mothur classifier, and it may be slower
  post_ITSx false true or false taxonomy whether the classifier should be run before or after ITSx if you set this to true, you also have to set ITSx[do] to true; the DB isn't cut to a specific ITS region
  db_path "../DBs/DADA2" taxonomy directory where the database sits change when setting up dadasnake on a new system
  refFasta "silva_nr99_v138_train_set.fa.gz" taxonomy training database name
  db_short_names "silva_v138_nr99" taxonomy short name(s) to label database(s) in the output, separated by a whitespace; should be as many items as in ref_dbs_full if your give less database names than databases, not all databases will be used
  ref_dbs_full "" taxonomy full path and database file name(s) (without suffix), separated by a whitespace if your give less database names than databases, not all databases will be used
  minBoot 50 1-100 taxonomy bootstrap value for classification see DADA2 documentation for details
  tryRC false false or true taxonomy if your reads are in the direction of the database (false), or reverse complement or you don't know (true) true takes longer than false
  seed 101 a positive integer taxonomy seed for DADA2 taxonomy classifier keep constant in re-runs
  look_for_species false true or false taxonomy whether you want to run a species-level annotation species is an overkill for 16S data; if you set this, you need to have a specialised database (currently available for 16S silva 132)
  spec_db "../DBs/DADA2/silva_species_assignment_v138.fa.gz" taxonomy a DADA2-formatted species assignment database with path change when setting up dadasnake on a new system
  decipher taxonomy settings for DECIPHER
  do false true or false taxonomy whether DECIPHER should be used for taxonomic annotation DECIPHER can work better than the mothur classifier, but it is slower and we don't have many databases for this software; you can run both DECIPHER and mothur (in parallel)
  post_ITSx false true or false taxonomy whether DECIPHER should be run before or after ITSx if you set this to true, you also have to set ITSx[do] to true; the DB isn't cut to a specific ITS region
  db_path "../DBs/decipher" taxonomy directory where the database sits change when setting up dadasnake on a new system
  tax_db "SILVA_SSU_r138_2019.RData" taxonomy decipher database name
  db_short_names "SILVA_138_SSU" taxonomy short name(s) to label database(s) in the output, separated by a whitespace; should be as many items as in ref_dbs_full if your give less database names than databases, not all databases will be used
  ref_dbs_full "" taxonomy full path and database file name(s) (without suffix), separated by a whitespace if your give less database names than databases, not all databases will be used
  threshold 60 1-100 taxonomy threshold for classification see DECIPHER documentation for details
  strand bottom bottom, top or both taxonomy if your reads are in the direction of the database (top), reverse complement (bottom) or you don't know (both) both takes roughly twice as long as the others
  bootstraps 100 a positive integer taxonomy number of bootstraps
  seed 100 a positive integer taxonomy seed for DECIPHER run keep constant in re-runs
  look_for_species false true or false taxonomy whether you want to run a species-level annotation after DECIPHER species is an overkill for 16S data; if you set this, you need to have a specialised database (currently available for 16S silva 132)
  spec_db "../DBs/DADA2/silva_species_assignment_v138.fa.gz" taxonomy a DADA2-formatted species assignment database with path change when setting up dadasnake on a new system
  mothur taxonomy settings for Bayesian classifier (mothur implementation)
  do true true or false taxonomy whether mothur's classify.seqs should be used for taxonomix annotation we have more and more specific databases for mothur (and can make new ones), it's faster than DECIPHER, but potentially less correct; you can run both mothur and DECIPHER (in parallel)
  post_ITSx false true or false taxonomy whether mothur's classify.seqs should be run before or after ITSx if you set this to true, you also have to set ITSx[do] to true; use an ITSx-cut database if run afterwards
  db_path "../DBs/amplicon" taxonomy directory where the database sits change when setting up dadasnake on a new system
  tax_db "SILVA_138_SSURef_NR99_prok.515F.806R" taxonomy the beginning of the filename of a mothur-formatted database don't add .taxonomy or .fasta
  db_short_names "SILVA_138_SSU_NR99" taxonomy short name(s) to label database(s) in the output, separated by a whitespace; should be as many items as in ref_dbs_full if your give less database names than databases, not all databases will be used
  ref_dbs_full "" taxonomy full path and database file name(s) (without suffix), separated by a whitespace if your give less database names than databases, not all databases will be used
  cutoff 60 1-100 taxonomy cut-off for classification
blast taxonomy
  do false true or false taxonomy whether blast should be run
  db_path "../DBs/ncbi_16SMicrobial" taxonomy path to blast database
  tax_db 16S_ribosomal_RNA taxonomy name (without suffix) of blast database
  e_val 0.01 taxonomy e-value for blast
  tax2id "" "tax2id table or "none" taxonomy whether taxonomic data is available in a tax2id table this also assumes there is a taxdb file in the db_path; you don't need it, if you have a blast5 database
  all true taxonomy whether blastn should also be run on sequences that have been classified already
  run_basta true true or false taxonomy whether BASTA should be run on the BLASTn output
  basta_path "../bin/basta" taxonomy path to the basta binary basta needs to be installed manually
  basta_db "../DBs/ncbi_taxonomy" taxonomy path to the NCBI-taxonomy database that is prepared when basta is installed make sure you run these steps during installation of basta
  basta_e_val 0.00001 taxonomy e-value for hit selection
  basta_alen 100 taxonomy minimum alignment length of hits
  basta_number 0 0 or a positive integer taxonomy maximum number of hits to use for classification if set to 0 all hits will be considered
  basta_min 3 a positive number taxonomy minimum number of hits a sequence must have to be assigned an LCA needs to be smaller or equal to max_targets
  basta_id 80 1-100 taxonomy minimum identity of hit to be considered good
  basta_besthit true true or false taxonomy if set the final taxonomy will contain an additional column containing the taxonomy of the best (first) hit with defined taxonomy
  basta_perchits 99 an odd number greater than 50 taxonomy percentage of hits that are used for LCA estimation
ITSx taxonomy settings for ITSx
  do false true or false taxonomy whether ITSx should be run only makes sense for analyses targetting an ITS region
  min_regions 1 1-4 taxonomy minimum number of detected regions counting includes SSU, LSU and 5.8 next to the ITS regions
  region ITS2 ITS1 or ITS2 taxonomy which region to extract
  e_val 1.00E-05 0-1 taxonomy e-value for ITS detection
hand_off dada, taxonomy, postprocessing settings deciding if additional formats should be given
  biom true true or false dada, taxonomy whether a biome format output should be written biome contains OTU table or OTU table and taxonomy (if taxonomy was run); biome table is never filtered
  phyloseq false true or false taxonomy, postprocessing whether a phyloseq object should be returned contains OTU table and taxonomy and tree (if each was run; if tree is run on pruned OTU table, phyloseq object contains filtered dataset)
final_table_filtering postprocessing settings for filtering the final OTU table (before postprocessing, if postprocessing is done)
  do true true or false postprocessing whether a filtered version of the OTU table and sequences should be made and used for the post-processing steps
  keep_target_taxa "." "." or a regular expression for taxa to keep, e.g. "Bacteria" postprocessing pattern to look for in the taxstrings done based on mothur and DECIPHER result; "." means all are kept; both taxstrings are searched, if both classifiers were used
  target_min_length 0 postprocessing minimal length sequence doesn't care for ITSx results
  target_max_length Inf postprocessing maximum length of sequence doesn't care for ITSx results
postprocessing postprocessing settings for postprocessing
  fungalTraits postprocessing settings for fungalTraits
  do false true or false postprocessing whether fungalTraits should be assigned
  db "../DBs/functions/FungalTraits_1.2_ver_16Dec_2020_V.1.2.tsv" postprocessing path to fungalTraits DB change when setting up dadasnake on a new system
  classifier mothur.SILVA_138_SSURef_NR99_cut postprocessing which classifier to use can only be one
  funguild postprocessing settings for funguild
  do false true or false postprocessing whether funguild should be run
  funguild_db "../DBs/functions/funguild_db.json" postprocessing path to funguild DB change when setting up dadasnake on a new system
  classifier mothur mothur or decipher, depending on what was used postprocessing which classifier to use can only be one
  tax4fun2 postprocessing settings for tax4fun2
  do false true or false postprocessing whether tax4fun2 should be used
  db "../DBs/functions/Tax4Fun2_ReferenceData_v2" postprocessing path to tax4fun2 DB change when setting up dadasnake on a new system
  database_mod Ref99NR Ref99NR or Ref100NR postprocessing which database to use
  normalize_by_copy_number true true or false postprocessing whether to normalize tax4fun2 results by copy number normalization of pathway results is not possible
  min_identity_to_reference 0.97 90 to 100 or 0.9 to 1.0 postprocessing minimum similarity between ASV sequence and tax4fun DB
  user_data false true or false postprocessing whether user database should be used
  user_dir "../DBs/Functions/GTDB_202_tax4fun2" postprocessing path to user database
  user_db GTDB_fun postprocessing path to user database
  treeing true or false postprocessing
  do true postprocessing whether a phylogenetic tree should be made
  fasttreeMP "" postprocessing path to fasttreeMP executable change when setting up dadasnake on a new system
  rarefaction_curve true true or false postprocessing whether a rarefaction curve should be made

The samples table

Every samples table needs sample names (under header library) and file names (just the names, the path should be in the config file under header r1_file and potentially r2_file). Since DADA2 estimates run-specific errors, it can be helpful to give run IDs (under header run). If you have many (>500 samples), it is also useful to split them into runs for the analysis, as some of the most memory-intensive steps are done by run.
If several fastq files should end up in the same column of the OTU table, you can indicate this by giving these libraries the same sample name (under header sample). Libraries from different runs are combined in the final OTU table (example 1). Libraries from the same run are combined after primer-processing (example 2). Example 1: overview Example 2: overview

What if something goes wrong?

If you gave dadasnake your email address and your system supports mailing (to that address), you will receive an email upon start and if the workflow encountered a problem or after the successful run. If there was a problem, you have to check the output and logs.

  • Use the -d option of dadasnake or the --dryrun option of Snakemake before the run to check that your input files are where you want them and that you have permissions to write to your target directory. This will also do some checks on the configuration and samples table, so it discovers the majority of errors on a suitable combination of dataset and configuration.
  • You can not make two runs of dadasnake write to the same output directory. If you start the second run while the first is still running, you will get an error either indicating that the directory can't be locked, or that the metadata is incomplete. If you've finished the first run already, the dadasnake will tell you that there's nothing to be done. Change the output directory in the config file to be unique for each run.
  • A common reason for errors are misformatted inputs, e.g. the databases for the classification or the read files.
  • dadasnake should catch most errors related to empty outputs. For example: the filtering is too stringent and no sequences are left; the primers you expected to find are not present; the sequences were truncated too short to be merged. Please report issues where this didn't happen.
  • The best way to pinpoint those errors is to first check the .stderr file made by dadasnake (or the Snakemake output, if you run the workflow outside dadasnake). This will tell you which rule encountered the error, and, if you use the cluster submission, the job ID. You may have to search for the error a bit, because dadasnake will try to finish as much as possible of your run before dying. Hint: you can find errors by colour or by searching for "Error in rule".
  • If you use the cluster submission, log files for every rule are written into the output directory and you can check the one with the job ID for additional information, otherwise the same information is written to the Snakemake output.
  • The logs directory in the output directory contains log files for all steps that can produce comments. They are named with the step and then the name of the rule, so you can check the log file of the step that sent the error. Depending on the tool that sent the error, this will be easy to understand or cryptic. Don't hesitate to raise an issue in this repository if you get stuck.

How to ...?

I don't have primers on my reads, what do I do? Set do_primers: false in the configuration file, but make sure that orientation of the reads is the same.

I did paired end sequencing, but my reads are too short to overlap You have two options:

  1. use only one read (usually the first) by setting paired: false in the config file and providing only the read you want to use in the samples table. This will run a single-end workflow. The makers of DADA2 would probably recommend this option in most cases.
  2. use both reads, set a truncation length for filtering to make sure the sequences have the same lengths and use DADA2's option to "merge" reads without overlap e.g.
filtering:
  trunc_length:
    fwd: 250
    rvs: 200
pair_merging:
  min_overlap: 0
  just_concatenate: true

I need to set further parameters for job submission You can change the cluster configs and add the parameter, for example directly as part of the call field.

I need to bind the jobs to the same node as the main job Yes, you can. If you use the submission-based wrapper, you can provide the flag for choosing a node as part of the SUBMIT_COMMAND variable in the VARIABLE_CONFIG file. Also, specify BIND_JOBS_TO_MAIN as true. You also need to set the variable that holds the node's name in your submission system as NODENAME_VAR. All jobs will then be submitted to the same node as the one that runs the main snakemake, if you include the flag for choosing a node as part of the call field in the cluster config. You can also specify that one, using -b. Example: VARIABLE_CONFIG file:

...
SUBMIT_COMMAND	slurm --nodelist=
BIND_JOBS_TO_MAIN	true
NODENAME_VAR	SLURMD_NODENAME
SCHEDULER	slurm_simple
...

slurm_simple.config:

__default__:
  call: "sbatch --nodelist="
  mem_per_cpu: "--mem-per-cpu "
  partition: ""
  runtime: "-t"
  threads: "-c"
  stdout: "-o dadasnake.{rule}.{wildcards}.stdout"

call:

./dadasnake -c -b favorite_node -n TESTRUN config/config.test.yaml

I have a very large dataset Great, if you have the computing power to match it, dadasnake will help you. It has successfully processed >27,000 samples in the same run. If you run out of memory in your run, set big_data to true in the config file and allow the use of multiple bigmem cores (we needed 360GB RAM for the 27,000 dataset). Disable highly memory intensive steps, such as treeing, chimera removal, plotting of rarefaction curves. If you didn't use the grouping by runs in your sample table, invent some runs of approx 100 samples each - these will be treated separately for some of the heavier DADA2 steps (error estimation).

How do I restart a failed run? Depends on why it failed...

  • If you ran into a time limit or similar, you can just run dadasnake on the same config with the -u option and then again with the -c option. This will make Snakemake pick up where it left off.
  • For most other situations, it's probably best to fix what caused the error in your config file and delete the output directory to start from scratch. If you're going to be loosing a lot of run time to that, and you're quite certain the problem is only in the last attempted step, you can try to restart. Ask us, if in doubt.

Can I restart from a certain step? If you're familiar with Snakemake, you can use it to force re-running the steps you need. It's not (yet) part of the dadasnake to do this more comfortably.

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