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Running an analysis

Running AuriClass on only the forward reads gives the best results, as the reverse reads are usually more noisy:

auriclass Candida_auris_R1.fq.gz

But it can also be run on an arbitrary number of fastq files of the same sample:

auriclass Candida_auris_R1.fq.gz Candida_auris_R2.fq.gz Candida_auris_unpaired.fq.gz

or with a fasta file:

auriclass Candida_auris.fasta.gz

Note

All input files are treated as a single sample, so running auriclass input_genomes/*.fasta will try to do a single clade prediction for all fasta files in input_genomes. To run AuriClass on multiple samples, check out Running multiple samples in parallel

A standard analysis creates two files: - report.tsv which contains the clade prediction, closest reference sample and QC checks. The report contains the default "isolate" as sample name. - report.YYYY-mm-dd_HH-MM-SS.log which contains messages written to STDERR with additional data.

Specifying output

This will create report_Candida_auris.tsv and report_Candida_auris.log. The report will contain the sample name "Candida_auris".

auriclass --name Candida_auris -o report_Candida_auris.tsv Candida_auris_R1.fq.gz

Forcing full analysis

This forces AuriClass to perform the full analysis on a sample, even if the species quality check fails.

auriclass --non_candida_threshold 1 Candida_auris_R1.fq.gz

Warning

This will cause some QC checks to always pass, so use with caution.

Running multiple samples in parallel

AuriClass currently does not support multithreaded analysis. For both Fastq and Fasta input, multi-threading mash commands where possible makes minimal difference. Additionally, peak memory usage is typically 100-200 Mb RAM according to /usr/bin/time -v. Therefore, the best option if you have to analyse a lot of files is to run multiple AuriClass analyses concurrently.

Two good options are either:

An example how to run AuriClass using parallel on a set of assemblies in the directory fasta_input:

parallel auriclass --fasta -n {/.} -o report.{/.}.tsv {} ::: fasta_input/*