GMSMetaPost

Prerequisites

Metadata files

Two metadata files are required assets/samples.csv and assets/samplesheet.csv. Here are examples of how they may look like:

• assets/samples.csv

sample,path,pairing,read1,read2
SRR12875558_se-SRR12875558,assets/SRR12875558_se-SRR12875558.tsv,single_end,assets/input/se/SRR12875558_1.fastq.gz
SRR12875570_pe-SRR12875570,assets/SRR12875570_pe-SRR12875570.tsv,paired_end,assets/input/pe/SRR12875570_1.fastq.gz,assets/input/pe/SRR12875570_2.fastq.gz

• assets/samplesheet.csv

sample,kraken2,centrifuge,kaiju
sample1,assets/tsvs/SRR12875570_pe-SRR12875570-kraken2.kraken2.report.tsv,assets/tsvs/SRR12875570_pe-SRR12875570-centrifuge.report.tsv,assets/tsvs/SRR12875570_pe-SRR12875570-kaiju.tsv
sample2,assets/tsvs/SRR12875558_se-SRR12875558-kraken2.kraken2.report.tsv,assets/tsvs/SRR12875558_se-SRR12875558-centrifuge.report.tsv,assets/tsvs/SRR12875558_se-SRR12875558-kaiju.tsv

The path to assets/samples.csv should be defined in filtered_hits parameter in nextflow.config or on the command line.

BLAST nt database

GMSMetaPost requires a local version of BLAST nt database. The easiest way to aqcuire it is by downloading with blast v.2.13.0 utility update_blastdb.pl:

update_blastdb.pl \
--decompress \
nt

In addition the latest taxonomy database is required as well. It should be downloaded into the same directory:

wget --continue https://ftp.ncbi.nlm.nih.gov/blast/db/taxdb.tar.gz
rm taxdb.btd taxdb.bti
tar xvf taxdb.tar.gz
rm -f taxdb.tar.gz

It is also recommended to update regularly the local BLAST nt database with command:

update_blastdb.pl \
nt

Finally, the user should define the path to the database by either defining blast_db parameter in nextflow.config or on the command line.

Running GMSMetaPost

GMSMetaPost can be run with command:

nextflow run main.nf \
--input assets/samplesheet.csv \
--outdir test \
-profile conda

conda profile can also be replaced by singularity or docker.

Troubleshooting

• If you get the following error message: no space left on device, make sure that that you are using:

  singularity.cacheDir = "/path/to/cache"

• If you get the following error message for singularity:

  FATAL: While getting image info: error decoding image: invalid ObjectId in JSON

  You are likely using an older version of singularity. You can update it with the command:

  conda install -c conda-forge singularity

Acknowledgements

This pipeline uses code and infrastructure developed and maintained by the nf-core community, reused here under the MIT license.

The nf-core framework for community-curated bioinformatics pipelines.

Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.

Nat Biotechnol. 2020 Feb 13. doi: 10.1038/s41587-020-0439-x. In addition, references of tools and data used in this pipeline are as follows: