Files that may be or may not be present are shown in italic.

Due to the sanitization of input files, your initial uploaded files may have been rewritten, leading to extra GenBank files in your "uploads" folder. In some cases however, the original input file is also present.

General

Folder	Filename	Description
logs	CAGECAT_version.txt	The version of CAGECAT when your job was executed. Used for backtracking of errors.
logs	{job_id}.log	Log file which stores information about the executed analysis. Output from the executed programs/tools is stored in this file. May contain sanitization (from antiSmash tool) information. Can be inspected to get an impression of the steps that have been executed.
logs	{job_id}_command.txt	Command line interface command that was executed on CAGECAT's servers. Can be inspected to learn how submitted parameters are used in a command, executed using the command line interface.
logs	{job_id}_options.txt	Overview of submitted parameters and their values.

cblaster

Search

Folder	Filename	Description
logs	query_headers.csv	Overview of headers of the submitted queries. Used when trying to recompute a job.
results	{job_id}_binary.txt	An absence/presence matrix of input queries vs. cluster hits. Shows the total number of hits in detected clusters per query sequence.
results	{job_id}_plot.html	Cluster heatmap visualization. Interactive HTML plot visualizing your input queries per scaffold hit.
results	{job_id}_session.json	Stores all information about found hit clusters and query sequences. Used when trying to execute a subsequent cblaster analysis.
results	{job_id}_summary.txt	Detailed overview of hit details/scores of input queries per scaffold hit.
uploads	your_input_file.gbk	The file you uploaded and what will be used as input file for the analysis.

Recompute

The cblaster recompute module has the same output files as the cblaster search analysis.

Gene neighbourhood estimation

Folder	Filename	Description
results	{job_id}_plot.html	Interactive HTML visualization of mean and median hit cluster sizes (bp) at different gap sizes and total clusters at different gap sizes. Helpful for a visual interpretation of robustness of cluster prediction.
results	{job_id}_summary.txt	Overview of GNE statistics

Extract sequences

Folder	Filename	Description
results	{job_id}_sequences.txt	Overview of where query genes hit on which scaffolds and positions. Is created when the "Download sequences" option was not checked.
results	{job_id}_sequences.fasta	Nucleotide FASTA of scaffold sequences where the query genes hit. Is created when the "Download sequences" option was checked.

Extract clusters

Folder	Filename	Description
results	{prefix}{job_id}_cluster{number}.gbk	GenBank files of selected cluster hits. {prefix} is only used when a value was entered for the "Prefix" option. {number} is inherent to the number of extracted clusters.

Visualize cluster hits compared to queries

Folder	Filename	Description
results	{job_id}_plot.html	Similar to a clinker plot, but comparisons are only available for your query cluster vs. individual hit cluster.

clinker

Folder	Filename	Description
results	alignments.txt	Overview of identity and similarity percentages between genes in clusters.
results	{job_id}_plot.html	The clinker visualisation enabling visual comparison of the submitted clusters and creation of such figures.
results	{job_id}_session.json	Stores all information about the cluster alignments.
uploads	your_input_fie.gbk	Your uploaded files which have been used as input files.