Antismash on Fasta files

Question

[szb6246]

I am looking at the cluster of secondary metabolites in Pseudomonas. I have assembled genomes and all files are fasta files. When I run these in the web interface of antismash I do get output. But I need to do further cluster analysis using BigSCAPE and need to run antismah in the command line using conda.

This is what I have done so far

conda create -n antismash antismash
conda activate antismash
download-antismash-databases

Everything looks good and I am ready to call antismash and run

conda activate antismash
antismash my_input.gbk

Now here is the issue. It needs gbk files as input and I have fasta files of assemblies. Even when I went ahead and annotated these with RAST, the output is not a gbk file. How do I run antismash on fasta files. Is there any alternate way.

[liorglic]

Please don't use "urgent" unless you work in a hospital and a patient's life is on the line...

[Ram]

Correction: Nothing posted on online technical/scientific fora can be urgent. If something needs urgent attention, this is not the place for it. I'll be removing the words conveying urgency from the post.

Answer 1

[patrickdm]

Hello, you can provide FASTA files to it

########### antiSMASH 6.1.1 #############

usage: antismash [--taxon {bacteria,fungi}] [--output-dir OUTPUT_DIR] [--output-basename OUTPUT_BASENAME] [--reuse-results PATH] [--limit LIMIT] [--minlength MINLENGTH] [--start START] [--end END] [--databases PATH]
                 [--write-config-file PATH] [--without-fimo] [--executable-paths EXECUTABLE=PATH,EXECUTABLE2=PATH2,...] [--allow-long-headers] [-v] [-d] [--logfile PATH] [--list-plugins] [--check-prereqs]
                 [--limit-to-record RECORD_ID] [-V] [--profiling] [--skip-sanitisation] [--skip-zip-file] [--minimal] [--enable-genefunctions] [--enable-lanthipeptides] [--enable-lassopeptides] [--enable-nrps-pks]
                 [--enable-sactipeptides] [--enable-t2pks] [--enable-thiopeptides] [--enable-tta] [--enable-html] [--fullhmmer] [--fullhmmer-pfamdb-version FULLHMMER_PFAMDB_VERSION] [--hmmdetection-strictness {strict,relaxed,loose}]
                 [--sideload JSON] [--sideload-simple ACCESSION:START-END] [--sideload-by-cds LOCUS1,LOCUS2,...] [--sideload-size-by-cds NUCLEOTIDES] [--cassis] [--clusterhmmer]
                 [--clusterhmmer-pfamdb-version CLUSTERHMMER_PFAMDB_VERSION] [--tigrfam] [--asf] [--cc-mibig] [--cc-custom-dbs FILE1,FILE2,...] [--cb-general] [--cb-subclusters] [--cb-knownclusters] [--cb-nclusters count]
                 [--cb-min-homology-scale LIMIT] [--pfam2go] [--rre] [--rre-cutoff RRE_CUTOFF] [--rre-minlength RRE_MIN_LENGTH] [--smcog-trees] [--tta-threshold TTA_THRESHOLD] [--html-title HTML_TITLE]
                 [--html-description HTML_DESCRIPTION] [--html-start-compact] [--genefinding-tool {glimmerhmm,prodigal,prodigal-m,none,error}] [--genefinding-gff3 GFF3_FILE] [-h] [--help-showall] [-c CPUS]
                 [SEQUENCE [SEQUENCE ...]]


arguments:
  SEQUENCE  GenBank/EMBL/FASTA file(s) containing DNA.

and also specify which gene prediction tool to use, with the option:

--genefinding-tool {glimmerhmm,prodigal,prodigal-m,none,error}
Specify algorithm used for gene finding: GlimmerHMM, Prodigal, Prodigal Metagenomic/Anonymous mode, or none.

or specify the GFF3 file to extract features from, with the option

--genefinding-gff3 GFF3_FILE

hth

P.S. I'd refrain myself from opening a help request with the word 'urgent', as it usually triggers a sudden loss of interest in answering to it.

[Debut]

Hello, I didn't understand how to put a FASTA file, can you write an example please!

Answer 2

[v.berriosfarias]

Hello, using the web browser you can click on the download button at the top of the page, search the gbk files in the downloaded folder.