I have recently downloaded Roary to try and use some of the pan-genome comparison features but I wanted to familiarize myself with this a little bit first by completing the tutorial. I got this message "'GCA_000008285.1_ASM828v1_genomic.fna' is not a readable non-empty FASTA file". I downloaded and ran everything according to the tutorial. I am not sure how to convert this into a readable FASTA file or why it is not reading it as one. Thank you in advance.
Here is the whole chunk of output if that helps.
[09:50:18] This is prokka 1.11
[09:50:18] Written by Torsten Seemann torsten.seemann@monash.edu
[09:50:18] Victorian Bioinformatics Consortium - http://www.vicbioinformatics.com
[09:50:18] Local time is Wed Apr 19 09:50:18 2023
[09:50:18] You are benturner
[09:50:18] Operating system is darwin
[09:50:18] You have BioPerl 1.007002
[09:50:18] System has 8 cores.
[09:50:18] Will use maximum of 8 cores.
[09:50:18] Annotating as >>> Bacteria <<<
[09:50:18] Creating new output folder: prokka_GCA_000008285
[09:50:18] Running: mkdir -p prokka_GCA_000008285
[09:50:18] Using filename prefix: GCA_000008285_04192023.XXX
[09:50:18] Setting HMMER_NCPU=1
[09:50:18] Writing log to: prokka_GCA_000008285/GCA_000008285_04192023.log
[09:50:18] Command: --kingdom Bacteria --outdir prokka_GCA_000008285 --genus Listeria --locustag GCA_000008285 GCA_000008285.1_ASM828v1_genomic.fna
[09:50:18] Looking for 'aragorn' - found /Users/benturner/miniconda3/bin/aragorn
[09:50:18] Determined aragorn version is 1.2
[09:50:18] Looking for 'barrnap' - found /Users/benturner/miniconda3/bin/barrnap
[09:50:18] Determined barrnap version is 0.9
[09:50:18] Looking for 'blastp' - found /Users/benturner/miniconda3/bin/blastp
[09:50:19] Determined blastp version is 2.6
[09:50:19] Looking for 'cmpress' - found /Users/benturner/miniconda3/bin/cmpress
[09:50:19] Determined cmpress version is 1.1
[09:50:19] Looking for 'cmscan' - found /Users/benturner/miniconda3/bin/cmscan
[09:50:19] Determined cmscan version is 1.1
[09:50:19] Looking for 'egrep' - found /usr/bin/egrep
[09:50:19] Looking for 'find' - found /usr/bin/find
[09:50:19] Looking for 'grep' - found /usr/bin/grep
[09:50:19] Looking for 'hmmpress' - found /Users/benturner/miniconda3/bin/hmmpress
[09:50:19] Determined hmmpress version is 3.3
[09:50:19] Looking for 'hmmscan' - found /Users/benturner/miniconda3/bin/hmmscan
[09:50:19] Determined hmmscan version is 3.3
[09:50:19] Looking for 'less' - found /usr/bin/less
[09:50:19] Looking for 'makeblastdb' - found /Users/benturner/miniconda3/bin/makeblastdb
[09:50:19] Determined makeblastdb version is 2.6
[09:50:19] Looking for 'minced' - found /Users/benturner/miniconda3/bin/minced
[09:50:19] Determined minced version is 3.0
[09:50:19] Looking for 'parallel' - found /Users/benturner/miniconda3/bin/parallel
[09:50:20] Determined parallel version is 20230322
[09:50:20] Looking for 'prodigal' - found /Users/benturner/miniconda3/bin/prodigal
[09:50:20] Determined prodigal version is 2.6
[09:50:20] Looking for 'prokka-genbank_to_fasta_db' - found /Users/benturner/miniconda3/bin/prokka-genbank_to_fasta_db
[09:50:20] Looking for 'sed' - found /usr/bin/sed
[09:50:20] Looking for 'tbl2asn' - found /Users/benturner/miniconda3/bin/tbl2asn
[09:50:20] Determined tbl2asn version is 25.8
[09:50:20] Using genetic code table 11.
[09:50:20] 'GCA_000008285.1_ASM828v1_genomic.fna' is not a readable non-empty FASTA file"
I have recently downloaded Roary to try and use some of the pan-genome comparison features but I wanted to familiarize myself with this a little bit first by completing the tutorial. I got this message "'GCA_000008285.1_ASM828v1_genomic.fna' is not a readable non-empty FASTA file". I downloaded and ran everything according to the tutorial. I am not sure how to convert this into a readable FASTA file or why it is not reading it as one. Thank you in advance.
Here is the whole chunk of output if that helps.
[09:50:18] This is prokka 1.11 [09:50:18] Written by Torsten Seemann torsten.seemann@monash.edu [09:50:18] Victorian Bioinformatics Consortium - http://www.vicbioinformatics.com [09:50:18] Local time is Wed Apr 19 09:50:18 2023 [09:50:18] You are benturner [09:50:18] Operating system is darwin [09:50:18] You have BioPerl 1.007002 [09:50:18] System has 8 cores. [09:50:18] Will use maximum of 8 cores. [09:50:18] Annotating as >>> Bacteria <<< [09:50:18] Creating new output folder: prokka_GCA_000008285 [09:50:18] Running: mkdir -p prokka_GCA_000008285 [09:50:18] Using filename prefix: GCA_000008285_04192023.XXX [09:50:18] Setting HMMER_NCPU=1 [09:50:18] Writing log to: prokka_GCA_000008285/GCA_000008285_04192023.log [09:50:18] Command: --kingdom Bacteria --outdir prokka_GCA_000008285 --genus Listeria --locustag GCA_000008285 GCA_000008285.1_ASM828v1_genomic.fna [09:50:18] Looking for 'aragorn' - found /Users/benturner/miniconda3/bin/aragorn [09:50:18] Determined aragorn version is 1.2 [09:50:18] Looking for 'barrnap' - found /Users/benturner/miniconda3/bin/barrnap [09:50:18] Determined barrnap version is 0.9 [09:50:18] Looking for 'blastp' - found /Users/benturner/miniconda3/bin/blastp [09:50:19] Determined blastp version is 2.6 [09:50:19] Looking for 'cmpress' - found /Users/benturner/miniconda3/bin/cmpress [09:50:19] Determined cmpress version is 1.1 [09:50:19] Looking for 'cmscan' - found /Users/benturner/miniconda3/bin/cmscan [09:50:19] Determined cmscan version is 1.1 [09:50:19] Looking for 'egrep' - found /usr/bin/egrep [09:50:19] Looking for 'find' - found /usr/bin/find [09:50:19] Looking for 'grep' - found /usr/bin/grep [09:50:19] Looking for 'hmmpress' - found /Users/benturner/miniconda3/bin/hmmpress [09:50:19] Determined hmmpress version is 3.3 [09:50:19] Looking for 'hmmscan' - found /Users/benturner/miniconda3/bin/hmmscan [09:50:19] Determined hmmscan version is 3.3 [09:50:19] Looking for 'less' - found /usr/bin/less [09:50:19] Looking for 'makeblastdb' - found /Users/benturner/miniconda3/bin/makeblastdb [09:50:19] Determined makeblastdb version is 2.6 [09:50:19] Looking for 'minced' - found /Users/benturner/miniconda3/bin/minced [09:50:19] Determined minced version is 3.0 [09:50:19] Looking for 'parallel' - found /Users/benturner/miniconda3/bin/parallel [09:50:20] Determined parallel version is 20230322 [09:50:20] Looking for 'prodigal' - found /Users/benturner/miniconda3/bin/prodigal [09:50:20] Determined prodigal version is 2.6 [09:50:20] Looking for 'prokka-genbank_to_fasta_db' - found /Users/benturner/miniconda3/bin/prokka-genbank_to_fasta_db [09:50:20] Looking for 'sed' - found /usr/bin/sed [09:50:20] Looking for 'tbl2asn' - found /Users/benturner/miniconda3/bin/tbl2asn [09:50:20] Determined tbl2asn version is 25.8 [09:50:20] Using genetic code table 11. [09:50:20] 'GCA_000008285.1_ASM828v1_genomic.fna' is not a readable non-empty FASTA file"
Ben Turner