# HG changeset patch
# User menegidio
# Date 1622044914 0
# Node ID 8813044f72bf6b51aebf625e5b452332ccfd33a3

Uploaded

diff -r 000000000000 -r 8813044f72bf mito-prokka/.shed.yml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mito-prokka/.shed.yml	Wed May 26 16:01:54 2021 +0000
@@ -0,0 +1,13 @@
+name: mito-prokka
+owner: menegidio
+remote_repository_url: "github.com/menegidio-lab/mitogalaxy/tree/master/tools-shed/mito-prokka"
+homepage_url: "https://github.com/tseemann/prokka"
+type: unrestricted
+description: Mito-Prokka - Rapid annotation of bacteria, archaeal, viral and mitochondria genomes
+long_description: |
+  Prokka is a software tool to rapidly annotate bacterial, archaeal and viral
+  genomes, and produce output files that require only minor tweaking to submit
+  to GenBank/ENA/DDBJ. Mito-Prokka is a version adapted for annotation of 
+  mitochondria and chloroplasts.
+categories:
+- "Sequence Analysis"
diff -r 000000000000 -r 8813044f72bf mito-prokka/mito-prokka.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mito-prokka/mito-prokka.xml	Wed May 26 16:01:54 2021 +0000
@@ -0,0 +1,249 @@
+<tool id="prokka" name="Prokka" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
+    <description>Prokaryotic genome annotation</description>
+    <macros>
+        <token name="@TOOL_VERSION@">1.14.6</token>
+        <token name="@VERSION_SUFFIX@">0</token>
+    </macros>
+    <requirements>
+        <requirement type="package" version="@TOOL_VERSION@">prokka</requirement>
+    </requirements>
+
+    <version_command>prokka --version</version_command>
+    <command detect_errors="exit_code"><![CDATA[
+prokka
+--cpus \${GALAXY_SLOTS:-8}
+--quiet ## to avoid non-error messages written to stderr
+--outdir outdir --prefix prokka ## used in outputs section
+#if $locustag
+    --locustag '$locustag'
+#end if
+#if str($increment)
+    --increment $increment
+#end if
+--gffver $gffver
+#if $compliant.compliant_select == "no"
+    #if $compliant.addgenes
+        --addgenes
+    #end if
+    #if str($compliant.mincontig)
+        --mincontig $compliant.mincontig
+    #end if
+#else
+    --compliant
+#end if
+#if $centre
+    --centre '$centre'
+#end if
+#if $genus
+    --genus '$genus'
+#end if
+#if $species
+    --species '$species'
+#end if
+#if $strain
+    --strain '$strain'
+#end if
+#if $plasmid
+    --plasmid '$plasmid'
+#end if
+--kingdom $kingdom.kingdom_select
+#if str($kingdom.gcode)
+    --gcode $kingdom.gcode
+#end if
+#if $usegenus
+    --usegenus
+#end if
+#if $proteins
+    --proteins '$proteins'
+#end if
+#if $metagenome
+    --metagenome
+#end if
+#if $fast
+    --fast
+#end if
+#if str($evalue)
+    --evalue $evalue
+#end if
+#if $rfam
+    --rfam
+#end if
+#if $norrna
+    --norrna
+#end if
+#if $notrna
+    --notrna
+#end if
+$input
+    ]]></command>
+    <inputs>
+        <param name="input" type="data" format="fasta" label="Contigs to annotate" help="FASTA format" />
+        <param argument="--locustag" type="text" value="" label="Locus tag prefix" />
+        <param argument="--increment" type="integer" value="1" min="1" optional="true" label="Locus tag counter increment" />
+        <param argument="--gffver" type="select" label="GFF version">
+            <option value="3">3</option>
+            <option value="2">2</option>
+            <option value="1">1</option>
+        </param>
+        <conditional name="compliant">
+            <param name="compliant_select" type="select" label="Force GenBank/ENA/DDJB compliance"
+                help="Equivalent to --addgenes --mincontiglen 200 --centre Prokka (or other centre specified below) (--compliant)">
+                <option value="no">No</option>
+                <option value="yes">Yes</option>
+            </param>
+            <when value="no">
+                <param name="addgenes" type="boolean" checked="false" label="Add 'gene' features for each 'CDS' feature (--addgenes)" />
+                <param name="mincontig" type="integer" value="200" optional="true" label="Minimum contig size (--mincontiglen)" help="NCBI needs 200" />
+            </when>
+            <when value="yes" />
+        </conditional>
+        <param argument="--centre" type="text" value="" label="Sequencing centre ID" />
+        <param argument="--genus" type="text" value="" label="Genus name" help="May be used to aid annotation, see --usegenus below" />
+        <param argument="--species" type="text" value="" label="Species name" />
+        <param argument="--strain" type="text" value="" label="Strain name" />
+        <param argument="--plasmid" type="text" value="" label="Plasmid name or identifier" />
+        <conditional name="kingdom">
+            <param name="kingdom_select" type="select" label="Kingdom" help="(--kingdom)">
+                <option value="Archaea">Archaea</option>
+		<option value="Bacteria">Bacteria</option>
+		<option value="Mitochondria" selected="true">Mitochondria</option>
+                <option value="Viruses">Viruses</option>
+            </param>
+            <when value="Archaea">
+                <param argument="--gcode" type="integer" value="11" min="1" max="23" optional="true" label="Genetic code (transl_table)" /><!-- max should be 25, but prodigal would crash -->
+            </when>
+            <when value="Bacteria">
+                <param argument="--gcode" type="integer" value="11" min="1" max="23" optional="true" label="Genetic code (transl_table)" /><!-- max should be 25, but prodigal would crash -->
+                <!-- <param name="gram" type="select" display="radio" label="Gram (- -gram)">
+                    <option selected="true" value="none">N/A</option>
+                    <option value="pos">positive</option>
+                    <option value="neg">negative</option>
+                </param> SignalP is not FOSS -->
+		</when>
+	    <when value="Mitochondria">
+                <param argument="--gcode" type="integer" value="1" min="1" max="23" optional="true" label="Genetic code (transl_table)" /><!-- max should be 25, but prodigal would crash -->
+            </when>
+            <when value="Viruses">
+                <param argument="--gcode" type="integer" value="1" min="1" max="23" optional="true" label="Genetic code (transl_table)" /><!-- max should be 25, but prodigal would crash -->
+            </when>
+        </conditional>
+        <param argument="--usegenus" type="boolean" checked="false" label="Use genus-specific BLAST database" help="Will use the BLAST database for the genus specified above, if installed" />
+        <param argument="--proteins" type="data" format="fasta" optional="true" label="Optional FASTA file of trusted proteins to first annotate from" />
+        <param argument="--metagenome" type="boolean" checked="false" label="Improve gene predictions for highly fragmented genomes" help="Will set --meta option for Prodigal" />
+        <param argument="--fast" type="boolean" checked="false" label="Fast mode" help="Skip CDS /product searching" />
+        <param argument="--evalue" type="float" value="1e-06" min="0" optional="true" label="Similarity e-value cut-off" />
+        <param argument="--rfam" type="boolean" checked="false" label="Enable searching for ncRNAs with Infernal+Rfam (SLOW!)" />
+        <param argument="--norrna" type="boolean" checked="false" label="Don't run rRNA search with Barrnap" />
+        <param argument="--notrna" type="boolean" checked="false" label="Don't run tRNA search with Aragorn" />
+
+        <param name="outputs" type="select" multiple="true" display="checkboxes" label="Additional outputs">
+            <option value="gff" selected="True">Annotation in GFF3 format, containing both sequences and annotations (.gff)</option>
+            <option value="gbk" selected="True">Standard GenBank file. If the input was a multi-FASTA, then this will be a multi-GenBank, with one record for each sequence (.gbk)</option>
+            <option value="fna" selected="True">Nucleotide FASTA file of the input contig sequences (.fna)</option>
+            <option value="faa" selected="True">Protein FASTA file of the translated CDS sequences (.faa)</option>
+            <option value="ffn" selected="True">Nucleotide FASTA file of all the annotated sequences, not just CDS (.ffn)</option>
+            <option value="sqn" selected="True">An ASN1 format "Sequin" file for submission to GenBank. It needs to be edited to set the correct taxonomy, authors, related publication, etc. (.sqn)</option>
+            <option value="fsa" selected="True">Nucleotide FASTA file of the input contig sequences, with extra Sequin tags in the sequence description lines (.fsa)</option>
+            <option value="tbl" selected="True">Feature Table file (.tbl)</option>
+            <option value="tsv" selected="True">Annotations in tabular format including COGs etc.</option>
+            <option value="err" selected="True">Unacceptable annotations - the NCBI discrepancy report (.err)</option>
+            <option value="txt" selected="True">Statistics relating to the annotated features found (.txt)</option>
+        </param>
+
+    </inputs>
+    <outputs>
+        <data name="out_gff" format="gff" label="${tool.name} on ${on_string}: gff" from_work_dir="outdir/prokka.gff">
+            <filter>outputs and 'gff' in outputs</filter>
+        </data>
+        <data name="out_gbk" format="genbank" label="${tool.name} on ${on_string}: gbk" from_work_dir="outdir/prokka.gbk">
+            <filter>outputs and 'gbk' in outputs</filter>
+        </data>
+        <data name="out_fna" format="fasta" label="${tool.name} on ${on_string}: fna" from_work_dir="outdir/prokka.fna">
+            <filter>outputs and 'fna' in outputs</filter>
+        </data>
+        <data name="out_faa" format="fasta" label="${tool.name} on ${on_string}: faa" from_work_dir="outdir/prokka.faa">
+            <filter>outputs and 'faa' in outputs</filter>
+        </data>
+        <data name="out_ffn" format="fasta" label="${tool.name} on ${on_string}: ffn" from_work_dir="outdir/prokka.ffn">
+             <filter>outputs and 'ffn' in outputs</filter>
+        </data>
+        <data name="out_sqn" format="asn1" label="${tool.name} on ${on_string}: sqn" from_work_dir="outdir/prokka.sqn">
+             <filter>outputs and 'sqn' in outputs</filter>
+        </data>
+        <data name="out_fsa" format="fasta" label="${tool.name} on ${on_string}: fsa" from_work_dir="outdir/prokka.fsa">
+             <filter>outputs and 'fsa' in outputs</filter>
+        </data>
+        <data name="out_tbl" format="txt" label="${tool.name} on ${on_string}: tbl" from_work_dir="outdir/prokka.tbl">
+             <filter>outputs and 'tbl' in outputs</filter>
+        </data>
+        <data name="out_tsv" format="tabular" label="${tool.name} on ${on_string}: tsv" from_work_dir="outdir/prokka.tsv">
+             <filter>outputs and 'tsv' in outputs</filter>
+        </data>
+        <data name="out_err" format="txt" label="${tool.name} on ${on_string}: err" from_work_dir="outdir/prokka.err">
+             <filter>outputs and 'err' in outputs</filter>
+        </data>
+        <data name="out_txt" format="txt" label="${tool.name} on ${on_string}: txt" from_work_dir="outdir/prokka.txt">
+             <filter>outputs and 'txt' in outputs</filter>
+        </data>
+        <data name="out_log" format="txt" label="${tool.name} on ${on_string}: log" from_work_dir="outdir/prokka.log" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="input" ftype="fasta" value="phiX174.fasta" />
+            <param name="outputs" value="gff,gbk,fna,faa,ffn,sqn,fsa,tbl,tsv,err,txt" />
+            <output name="out_gff" file="out.gff" />
+            <output name="out_gbk" >
+                <assert_contents>
+                    <has_text_matching expression="LOCUS" />
+                    <has_text_matching expression="//" />
+                </assert_contents>
+            </output>
+            <output name="out_fna" file="out.fna" />
+            <output name="out_faa" file="out.faa" />
+            <output name="out_ffn" file="out.ffn" />
+            <output name="out_sqn" >
+                <assert_contents>
+                    <has_text_matching expression="Seq-entry" />
+                    <has_text_matching expression="contig2" />
+                </assert_contents>
+            </output>
+            <output name="out_fsa" file="out.fsa" />
+            <output name="out_tbl" file="out.tbl" />
+            <output name="out_tsv" file="out.tsv" />
+            <output name="out_err" file="out.err" lines_diff="14" />
+            <output name="out_txt" file="out.txt" />
+            <output name="out_log">
+                <assert_contents>
+                    <has_text text="Type 'prokka --citation' for more details." />
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+**What it does**
+
+Prokka_ is a software tool to rapidly annotate bacterial, archaeal and viral genomes, and produce output files that require only minor tweaking to submit to GenBank/ENA/DDBJ.
+
+.. _Prokka: http://github.com/tseemann/prokka
+
+**Output files**
+
+Prokka creates several output files, which are described in the **Additional outputs** section above.
+
+**License and citation**
+
+This Galaxy tool is Copyright © 2013 Lionel Guy, © 2013-2014 `CRS4 Srl.`_, © 2015-2016 `Earlham Institute`_, 2018 `Galaxy IUC` and is released under the `MIT license`_.
+
+.. _CRS4 Srl.: http://www.crs4.it/
+.. _Earlham Institute: http://earlham.ac.uk/
+.. _MIT license: https://opensource.org/licenses/MIT
+
+You can use this tool only if you agree to the license terms of: `Prokka`_.
+
+.. _Prokka: http://github.com/tseemann/prokka
+    ]]></help>
+    <citations>
+        <citation type="doi">10.1093/bioinformatics/btu135</citation>
+        <citation type="doi">10.1093/bioinformatics/btu153</citation>
+    </citations>
+</tool>
diff -r 000000000000 -r 8813044f72bf mito-prokka/test-data/out.err
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mito-prokka/test-data/out.err	Wed May 26 16:01:54 2021 +0000
@@ -0,0 +1,144 @@
+Discrepancy Report Results
+
+Summary
+DISC_PROTEIN_NAMES:All proteins have same name "hypothetical protein"
+FATAL: MISSING_PROTEIN_ID:5 proteins have invalid IDs.
+DISC_SOURCE_QUALS_ASNDISC:strain (all present, all same)
+DISC_SOURCE_QUALS_ASNDISC:taxname (all present, all same)
+DISC_FEATURE_COUNT:CDS: 5 present
+DISC_COUNT_NUCLEOTIDES:7 nucleotide Bioseqs are present
+FEATURE_LOCATION_CONFLICT:5 features have inconsistent gene locations.
+NO_ANNOTATION:3 bioseqs have no features
+DISC_QUALITY_SCORES:Quality scores are missing on all sequences.
+ONCALLER_COMMENT_PRESENT:7 comment descriptors were found (all same)
+SHORT_PROT_SEQUENCES:2 protein sequences are shorter than 50 aa.
+MISSING_GENOMEASSEMBLY_COMMENTS:7 bioseqs are missing GenomeAssembly structured comments
+MOLTYPE_NOT_MRNA:7 molecule types are not set as mRNA.
+TECHNIQUE_NOT_TSA:7 technique are not set as TSA
+MISSING_STRUCTURED_COMMENT:7 sequences do not include structured comments.
+MISSING_PROJECT:12 sequences do not include project.
+DISC_INCONSISTENT_MOLINFO_TECH:Molinfo Technique Report (some missing, all same)
+
+
+Detailed Report
+
+DiscRep_ALL:DISC_PROTEIN_NAMES::All proteins have same name "hypothetical protein"
+
+FATAL: DiscRep_ALL:MISSING_PROTEIN_ID::5 proteins have invalid IDs.
+outdir/prokka:contig2_1 (length 152)
+outdir/prokka:contig2_2 (length 38)
+outdir/prokka:contig4_1 (length 287)
+outdir/prokka:contig5_1 (length 43)
+outdir/prokka:contig6_1 (length 253)
+
+DiscRep_ALL:DISC_SOURCE_QUALS_ASNDISC::strain (all present, all same)
+DiscRep_SUB:DISC_SOURCE_QUALS_ASNDISC::7 sources have 'strain' for strain
+DiscRep_ALL:DISC_SOURCE_QUALS_ASNDISC::taxname (all present, all same)
+DiscRep_SUB:DISC_SOURCE_QUALS_ASNDISC::7 sources have 'Genus species' for taxname
+DiscRep_ALL:DISC_FEATURE_COUNT::CDS: 5 present
+DiscRep_ALL:DISC_COUNT_NUCLEOTIDES::7 nucleotide Bioseqs are present
+outdir/prokka:contig1 (length 350)
+outdir/prokka:contig2 (length 840)
+outdir/prokka:contig3 (length 210)
+outdir/prokka:contig4 (length 1260)
+outdir/prokka:contig5 (length 490)
+outdir/prokka:contig6 (length 1960)
+outdir/prokka:contig7 (length 276)
+
+DiscRep_ALL:FEATURE_LOCATION_CONFLICT::5 features have inconsistent gene locations.
+DiscRep_SUB:FEATURE_LOCATION_CONFLICT::Coding region xref gene does not exist
+outdir/prokka:CDS	hypothetical protein	contig2:40-498	HMJLFLJH_00001
+
+DiscRep_SUB:FEATURE_LOCATION_CONFLICT::Coding region xref gene does not exist
+outdir/prokka:CDS	hypothetical protein	contig2:498-614	HMJLFLJH_00002
+
+DiscRep_SUB:FEATURE_LOCATION_CONFLICT::Coding region xref gene does not exist
+outdir/prokka:CDS	hypothetical protein	contig4:21-884	HMJLFLJH_00003
+
+DiscRep_SUB:FEATURE_LOCATION_CONFLICT::Coding region xref gene does not exist
+outdir/prokka:CDS	hypothetical protein	contig5:275-406	HMJLFLJH_00004
+
+DiscRep_SUB:FEATURE_LOCATION_CONFLICT::Coding region xref gene does not exist
+outdir/prokka:CDS	hypothetical protein	contig6:6-767	HMJLFLJH_00005
+
+DiscRep_ALL:NO_ANNOTATION::3 bioseqs have no features
+outdir/prokka:contig1 (length 350)
+outdir/prokka:contig3 (length 210)
+outdir/prokka:contig7 (length 276)
+
+DiscRep_ALL:DISC_QUALITY_SCORES::Quality scores are missing on all sequences.
+
+DiscRep_ALL:ONCALLER_COMMENT_PRESENT::7 comment descriptors were found (all same)
+outdir/prokka:contig1:Annotated using prokka 1.14.5 from https://github.com/tseemann/prokka
+outdir/prokka:contig2:Annotated using prokka 1.14.5 from https://github.com/tseemann/prokka
+outdir/prokka:contig3:Annotated using prokka 1.14.5 from https://github.com/tseemann/prokka
+outdir/prokka:contig4:Annotated using prokka 1.14.5 from https://github.com/tseemann/prokka
+outdir/prokka:contig5:Annotated using prokka 1.14.5 from https://github.com/tseemann/prokka
+outdir/prokka:contig6:Annotated using prokka 1.14.5 from https://github.com/tseemann/prokka
+outdir/prokka:contig7:Annotated using prokka 1.14.5 from https://github.com/tseemann/prokka
+
+DiscRep_ALL:SHORT_PROT_SEQUENCES::2 protein sequences are shorter than 50 aa.
+outdir/prokka:contig2_2 (length 38)
+outdir/prokka:contig5_1 (length 43)
+
+DiscRep_ALL:MISSING_GENOMEASSEMBLY_COMMENTS::7 bioseqs are missing GenomeAssembly structured comments
+outdir/prokka:contig1 (length 350)
+outdir/prokka:contig2 (length 840)
+outdir/prokka:contig3 (length 210)
+outdir/prokka:contig4 (length 1260)
+outdir/prokka:contig5 (length 490)
+outdir/prokka:contig6 (length 1960)
+outdir/prokka:contig7 (length 276)
+
+DiscRep_ALL:MOLTYPE_NOT_MRNA::7 molecule types are not set as mRNA.
+outdir/prokka:contig1 (length 350)
+outdir/prokka:contig2 (length 840)
+outdir/prokka:contig3 (length 210)
+outdir/prokka:contig4 (length 1260)
+outdir/prokka:contig5 (length 490)
+outdir/prokka:contig6 (length 1960)
+outdir/prokka:contig7 (length 276)
+
+DiscRep_ALL:TECHNIQUE_NOT_TSA::7 technique are not set as TSA
+outdir/prokka:contig1 (length 350)
+outdir/prokka:contig2 (length 840)
+outdir/prokka:contig3 (length 210)
+outdir/prokka:contig4 (length 1260)
+outdir/prokka:contig5 (length 490)
+outdir/prokka:contig6 (length 1960)
+outdir/prokka:contig7 (length 276)
+
+DiscRep_ALL:MISSING_STRUCTURED_COMMENT::7 sequences do not include structured comments.
+outdir/prokka:contig1 (length 350)
+outdir/prokka:contig2 (length 840)
+outdir/prokka:contig3 (length 210)
+outdir/prokka:contig4 (length 1260)
+outdir/prokka:contig5 (length 490)
+outdir/prokka:contig6 (length 1960)
+outdir/prokka:contig7 (length 276)
+
+DiscRep_ALL:MISSING_PROJECT::12 sequences do not include project.
+outdir/prokka:contig1 (length 350)
+outdir/prokka:contig2 (length 840)
+outdir/prokka:contig2_1 (length 152)
+outdir/prokka:contig2_2 (length 38)
+outdir/prokka:contig3 (length 210)
+outdir/prokka:contig4 (length 1260)
+outdir/prokka:contig4_1 (length 287)
+outdir/prokka:contig5 (length 490)
+outdir/prokka:contig5_1 (length 43)
+outdir/prokka:contig6 (length 1960)
+outdir/prokka:contig6_1 (length 253)
+outdir/prokka:contig7 (length 276)
+
+DiscRep_ALL:DISC_INCONSISTENT_MOLINFO_TECH::Molinfo Technique Report (some missing, all same)
+DiscRep_SUB:DISC_INCONSISTENT_MOLINFO_TECH::technique (all missing)
+DiscRep_SUB:DISC_INCONSISTENT_MOLINFO_TECH::7 Molinfos are missing field technique
+outdir/prokka:contig1 (length 350)
+outdir/prokka:contig2 (length 840)
+outdir/prokka:contig3 (length 210)
+outdir/prokka:contig4 (length 1260)
+outdir/prokka:contig5 (length 490)
+outdir/prokka:contig6 (length 1960)
+outdir/prokka:contig7 (length 276)
+
diff -r 000000000000 -r 8813044f72bf mito-prokka/test-data/out.faa
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mito-prokka/test-data/out.faa	Wed May 26 16:01:54 2021 +0000
@@ -0,0 +1,20 @@
+>HMJLFLJH_00001 hypothetical protein
+MSQVTEQSVRFQTALASIKLIQASAVLDLTEDDFDFLTSNKVWIATDRSRARRCVEACVY
+GTLDFVGYPRFPAPVEFIAAVIAYYVHPVNIQTACLIMEGAEFTENIINGVERPVKAAEL
+FAFTLRVRAGNTDVLTDAEENVRQKLRAEGVM
+>HMJLFLJH_00002 hypothetical protein
+MSKGKKRSGARPGRPQPLRGTKGKRKGARLWYVGGQQF
+>HMJLFLJH_00003 hypothetical protein
+MPDRTEANPNELNQDDARYGFRCCHLKNIWTAPLPPETELSRQMTTSTTSIDIMGLQAAY
+ANLHTDQERDYFMQRYHDVISSFGGKTSYDADNRPLLVMRSNLWASGYDVDGTDQTSLGQ
+FSGRVQQTYKHSVPRFFVPEHGTMFTLALVRFPPTATKEIQYLNAKGALTYTDIAGDPVL
+YGNLPPREISMKDVFRSGDSSKKFKIAEGQWYRYAPSYVSPAYHLLEGFPFIQEPPSGDL
+QERVLIRHHDYDQCFQSVQLLQWNSQVKFNVTVYRNLPTTRDSIMTS
+>HMJLFLJH_00004 hypothetical protein
+MVLLLAVLLLLLLVAPCLNCLEAVKKPPPVAFKVMCLLPITIL
+>HMJLFLJH_00005 hypothetical protein
+MAKAGKGLLEGTLQAGTSAVSDKLLDLVGLGGKSAADKGKDTRDYLAAAFPELNAWERAG
+ADASSAGMVDAGFENQKELTKMQLDNQKEIAEMQNETQKEIAGIQSATSRQNTKDQVYAQ
+NEMLAYQQKESTARVASIMENTNLSKQQQVSEIMRQMLTQAQTAGQYFTNDQIKEMTRKV
+SAEVDLVHQQTQNQRYGSSHIGATAKDISNVVTDAASGVVDIFHGIDKAVADTWNNFWKD
+GKADGIGSNLSRK
diff -r 000000000000 -r 8813044f72bf mito-prokka/test-data/out.ffn
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mito-prokka/test-data/out.ffn	Wed May 26 16:01:54 2021 +0000
@@ -0,0 +1,46 @@
+>HMJLFLJH_00001 hypothetical protein
+ATGAGTCAAGTTACTGAACAATCCGTACGTTTCCAGACCGCTTTGGCCTCTATTAAGCTC
+ATTCAGGCTTCTGCCGTTTTGGATTTAACCGAAGATGATTTCGATTTTCTGACGAGTAAC
+AAAGTTTGGATTGCTACTGACCGCTCTCGTGCTCGTCGCTGCGTTGAGGCTTGCGTTTAT
+GGTACGCTGGACTTTGTGGGATACCCTCGCTTTCCTGCTCCTGTTGAGTTTATTGCTGCC
+GTCATTGCTTATTATGTTCATCCCGTCAACATTCAAACGGCCTGTCTCATCATGGAAGGC
+GCTGAATTTACGGAAAACATTATTAATGGCGTCGAGCGTCCGGTTAAAGCCGCTGAATTG
+TTCGCGTTTACCTTGCGTGTACGCGCAGGAAACACTGACGTTCTTACTGACGCAGAAGAA
+AACGTGCGTCAAAAATTACGTGCGGAAGGAGTGATGTAA
+>HMJLFLJH_00002 hypothetical protein
+ATGTCTAAAGGTAAAAAACGTTCTGGCGCTCGCCCTGGTCGTCCGCAGCCGTTGCGAGGT
+ACTAAAGGCAAGCGTAAAGGCGCTCGTCTTTGGTATGTAGGTGGTCAACAATTTTAA
+>HMJLFLJH_00003 hypothetical protein
+ATGCCTGACCGTACCGAGGCTAACCCTAATGAGCTTAATCAAGATGATGCTCGTTATGGT
+TTCCGTTGCTGCCATCTCAAAAACATTTGGACTGCTCCGCTTCCTCCTGAGACTGAGCTT
+TCTCGCCAAATGACGACTTCTACCACATCTATTGACATTATGGGTCTGCAAGCTGCTTAT
+GCTAATTTGCATACTGACCAAGAACGTGATTACTTCATGCAGCGTTACCATGATGTTATT
+TCTTCATTTGGAGGTAAAACCTCTTATGACGCTGACAACCGTCCTTTACTTGTCATGCGC
+TCTAATCTCTGGGCATCTGGCTATGATGTTGATGGAACTGACCAAACGTCGTTAGGCCAG
+TTTTCTGGTCGTGTTCAACAGACCTATAAACATTCTGTGCCGCGTTTCTTTGTTCCTGAG
+CATGGCACTATGTTTACTCTTGCGCTTGTTCGTTTTCCGCCTACTGCGACTAAAGAGATT
+CAGTACCTTAACGCTAAAGGTGCTTTGACTTATACCGATATTGCTGGCGACCCTGTTTTG
+TATGGCAACTTGCCGCCGCGTGAAATTTCTATGAAGGATGTTTTCCGTTCTGGTGATTCG
+TCTAAGAAGTTTAAGATTGCTGAGGGTCAGTGGTATCGTTATGCGCCTTCGTATGTTTCT
+CCTGCTTATCACCTTCTTGAAGGCTTCCCATTCATTCAGGAACCGCCTTCTGGTGATTTG
+CAAGAACGCGTACTTATTCGCCACCATGATTATGACCAGTGTTTCCAGTCCGTTCAGTTG
+TTGCAGTGGAATAGTCAGGTTAAATTTAATGTGACCGTTTATCGCAATCTGCCGACCACT
+CGCGATTCAATCATGACTTCGTGA
+>HMJLFLJH_00004 hypothetical protein
+TTGGTGCTATTGCTGGCGGTATTGCTTCTGCTCTTGCTGGTGGCGCCATGTCTAAATTGT
+TTGGAGGCGGTCAAAAAGCCGCCTCCGGTGGCATTCAAGGTGATGTGCTTGCTACCGATA
+ACAATACTGTAG
+>HMJLFLJH_00005 hypothetical protein
+ATGGCTAAAGCTGGTAAAGGACTTCTTGAAGGTACGTTGCAGGCTGGCACTTCTGCCGTT
+TCTGATAAGTTGCTTGATTTGGTTGGACTTGGTGGCAAGTCTGCCGCTGATAAAGGAAAG
+GATACTCGTGATTATCTTGCTGCTGCATTTCCTGAGCTTAATGCTTGGGAGCGTGCTGGT
+GCTGATGCTTCCTCTGCTGGTATGGTTGACGCCGGATTTGAGAATCAAAAAGAGCTTACT
+AAAATGCAACTGGACAATCAGAAAGAGATTGCCGAGATGCAAAATGAGACTCAAAAAGAG
+ATTGCTGGCATTCAGTCGGCGACTTCACGCCAGAATACGAAAGACCAGGTATATGCACAA
+AATGAGATGCTTGCTTATCAACAGAAGGAGTCTACTGCTCGCGTTGCGTCTATTATGGAA
+AACACCAATCTTTCCAAGCAACAGCAGGTTTCCGAGATTATGCGCCAAATGCTTACTCAA
+GCTCAAACGGCTGGTCAGTATTTTACCAATGACCAAATCAAAGAAATGACTCGCAAGGTT
+AGTGCTGAGGTTGACTTAGTTCATCAGCAAACGCAGAATCAGCGGTATGGCTCTTCTCAT
+ATTGGCGCTACTGCAAAGGATATTTCTAATGTCGTCACTGATGCTGCTTCTGGTGTGGTT
+GATATTTTTCATGGTATTGATAAAGCTGTTGCCGATACTTGGAACAATTTCTGGAAAGAC
+GGTAAAGCTGATGGTATTGGCTCTAATTTGTCTAGGAAATAA
diff -r 000000000000 -r 8813044f72bf mito-prokka/test-data/out.fna
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mito-prokka/test-data/out.fna	Wed May 26 16:01:54 2021 +0000
@@ -0,0 +1,99 @@
+>contig1
+GAGTTTTATCGCTTCCATGACGCAGAAGTTAACACTTTCGGATATTTCTGATGAGTCGAA
+AAATTATCTTGATAAAGCAGGAATTACTACTGCTTGTTTACGAATTAAATCGAAGTGGAC
+TGCTGGCGGAAAATGAGAAAATTCGACCTATCCTTGCGCAGCTCGAGAAGCTCTTACTTT
+GCGACCTTTCGCCATCAACTAACGATTCTGTCAAAAACTGACGCGTTGGATGAGGAGAAG
+TGGCTTAATATGCTTGGCACGTTCGTCAAGGACTGGTTTAGATATGAGTCACATTTTGTT
+CATGGTAGAGATTCTCTTGTTGACATTTTAAAAGAGCGTGGATTACTATC
+>contig2
+TGAGTCCGATGCTGTTCAACCACTAATAGGTAAGAAATCATGAGTCAAGTTACTGAACAA
+TCCGTACGTTTCCAGACCGCTTTGGCCTCTATTAAGCTCATTCAGGCTTCTGCCGTTTTG
+GATTTAACCGAAGATGATTTCGATTTTCTGACGAGTAACAAAGTTTGGATTGCTACTGAC
+CGCTCTCGTGCTCGTCGCTGCGTTGAGGCTTGCGTTTATGGTACGCTGGACTTTGTGGGA
+TACCCTCGCTTTCCTGCTCCTGTTGAGTTTATTGCTGCCGTCATTGCTTATTATGTTCAT
+CCCGTCAACATTCAAACGGCCTGTCTCATCATGGAAGGCGCTGAATTTACGGAAAACATT
+ATTAATGGCGTCGAGCGTCCGGTTAAAGCCGCTGAATTGTTCGCGTTTACCTTGCGTGTA
+CGCGCAGGAAACACTGACGTTCTTACTGACGCAGAAGAAAACGTGCGTCAAAAATTACGT
+GCGGAAGGAGTGATGTAATGTCTAAAGGTAAAAAACGTTCTGGCGCTCGCCCTGGTCGTC
+CGCAGCCGTTGCGAGGTACTAAAGGCAAGCGTAAAGGCGCTCGTCTTTGGTATGTAGGTG
+GTCAACAATTTTAATTGCAGGGGCTTCGGCCCCTTACTTGAGGATAAATTATGTCTAATA
+TTCAAACTGGCGCCGAGCGTATGCCGCATGACCTTTCCCATCTTGGCTTCCTTGCTGGTC
+AGATTGGTCGTCTTATTACCATTTCAACTACTCCGGTTATCGCTGGCGACTCCTTCGAGA
+TGGACGCCGTTGGCGCTCTCCGTCTTTCTCCATTGCGTCGTGGCCTTGCTATTGACTCTA
+>contig3
+CTGTAGACATTTTTACTTTTTATGTCCCTCATCGTCACGTTTATGGTGAACAGTGGATTA
+AGTTCATGAAGGATGGTGTTAATGCCACTCCTCTCCCGACTGTTAACACTACTGGTTATA
+TTGACCATGCCGCTTTTCTTGGCACGATTAACCCTGATACCAATAAAATCCCTAAGCATT
+TGTTTCAGGGTTATTTGAATATCTATAACA
+>contig4
+ACTATTTTAAAGCGCCGTGGATGCCTGACCGTACCGAGGCTAACCCTAATGAGCTTAATC
+AAGATGATGCTCGTTATGGTTTCCGTTGCTGCCATCTCAAAAACATTTGGACTGCTCCGC
+TTCCTCCTGAGACTGAGCTTTCTCGCCAAATGACGACTTCTACCACATCTATTGACATTA
+TGGGTCTGCAAGCTGCTTATGCTAATTTGCATACTGACCAAGAACGTGATTACTTCATGC
+AGCGTTACCATGATGTTATTTCTTCATTTGGAGGTAAAACCTCTTATGACGCTGACAACC
+GTCCTTTACTTGTCATGCGCTCTAATCTCTGGGCATCTGGCTATGATGTTGATGGAACTG
+ACCAAACGTCGTTAGGCCAGTTTTCTGGTCGTGTTCAACAGACCTATAAACATTCTGTGC
+CGCGTTTCTTTGTTCCTGAGCATGGCACTATGTTTACTCTTGCGCTTGTTCGTTTTCCGC
+CTACTGCGACTAAAGAGATTCAGTACCTTAACGCTAAAGGTGCTTTGACTTATACCGATA
+TTGCTGGCGACCCTGTTTTGTATGGCAACTTGCCGCCGCGTGAAATTTCTATGAAGGATG
+TTTTCCGTTCTGGTGATTCGTCTAAGAAGTTTAAGATTGCTGAGGGTCAGTGGTATCGTT
+ATGCGCCTTCGTATGTTTCTCCTGCTTATCACCTTCTTGAAGGCTTCCCATTCATTCAGG
+AACCGCCTTCTGGTGATTTGCAAGAACGCGTACTTATTCGCCACCATGATTATGACCAGT
+GTTTCCAGTCCGTTCAGTTGTTGCAGTGGAATAGTCAGGTTAAATTTAATGTGACCGTTT
+ATCGCAATCTGCCGACCACTCGCGATTCAATCATGACTTCGTGATAAAAGATTGAGTGTG
+AGGTTATAACGCCGAAGCGGTAAAAATTTTAATTTTTGCCGCTGAGGGGTTGACCAAGCG
+AAGCGCGGTAGGTTTTCTGCTTAGGAGTTTAATCATGTTTCAGACTTTTATTTCTCGCCA
+TAATTCAAACTTTTTTTCTGATAAGCTGGTTCTCACTTCTGTTACTCCAGCTTCTTCGGC
+ACCTGTTTTACAGACACCTAAAGCTACATCGTCAACGTTATATTTTGATAGTTTGACGGT
+TAATGCTGGTAATGGTGGTTTTCTTCATTGCATTCAGATGGATACATCTGTCAACGCCGC
+TAATCAGGTTGTTTCTGTTGGTGCTGATATTGCTTTTGATGCCGACCCTAAATTTTTTGC
+>contig5
+CTGTTTGGTTCGCTTTGAGTCTTCTTCGGTTCCGACTACCCTCCCGACTGCCTATGATGT
+TTATCCTTTGAATGGTCGCCATGATGGTGGTTATTATACCGTCAAGGACTGTGTGACTAT
+TGACGTCCTTCCCCGTACGCCGGGCAATAACGTTTATGTTGGTTTCATGGTTTGGTCTAA
+CTTTACCGCTACTAAATGCCGCGGATTGGTTTCGCTGAATCAGGTTATTAAAGAGATTAT
+TTGTCTCCAGCCACTTAAGTGAGGTGATTTATGTTTGGTGCTATTGCTGGCGGTATTGCT
+TCTGCTCTTGCTGGTGGCGCCATGTCTAAATTGTTTGGAGGCGGTCAAAAAGCCGCCTCC
+GGTGGCATTCAAGGTGATGTGCTTGCTACCGATAACAATACTGTAGGCATGGGTGATGCT
+GGTATTAAATCTGCCATTCAAGGCTCTAATGTTCCTAACCCTGATGAGGCCGCCCCTAGT
+TTTGTTTCTG
+>contig6
+GTGCTATGGCTAAAGCTGGTAAAGGACTTCTTGAAGGTACGTTGCAGGCTGGCACTTCTG
+CCGTTTCTGATAAGTTGCTTGATTTGGTTGGACTTGGTGGCAAGTCTGCCGCTGATAAAG
+GAAAGGATACTCGTGATTATCTTGCTGCTGCATTTCCTGAGCTTAATGCTTGGGAGCGTG
+CTGGTGCTGATGCTTCCTCTGCTGGTATGGTTGACGCCGGATTTGAGAATCAAAAAGAGC
+TTACTAAAATGCAACTGGACAATCAGAAAGAGATTGCCGAGATGCAAAATGAGACTCAAA
+AAGAGATTGCTGGCATTCAGTCGGCGACTTCACGCCAGAATACGAAAGACCAGGTATATG
+CACAAAATGAGATGCTTGCTTATCAACAGAAGGAGTCTACTGCTCGCGTTGCGTCTATTA
+TGGAAAACACCAATCTTTCCAAGCAACAGCAGGTTTCCGAGATTATGCGCCAAATGCTTA
+CTCAAGCTCAAACGGCTGGTCAGTATTTTACCAATGACCAAATCAAAGAAATGACTCGCA
+AGGTTAGTGCTGAGGTTGACTTAGTTCATCAGCAAACGCAGAATCAGCGGTATGGCTCTT
+CTCATATTGGCGCTACTGCAAAGGATATTTCTAATGTCGTCACTGATGCTGCTTCTGGTG
+TGGTTGATATTTTTCATGGTATTGATAAAGCTGTTGCCGATACTTGGAACAATTTCTGGA
+AAGACGGTAAAGCTGATGGTATTGGCTCTAATTTGTCTAGGAAATAACCGTCAGGATTGA
+CACCCTCCCAATTGTATGTTTTCATGCCTCCAAATCTTGGAGGCTTTTTTATGGTTCGTT
+CTTATTACCCTTCTGAATGTCACGCTGATTATTTTGACTTTGAGCGTATCGAGGCTCTTA
+AACCTGCTATTGAGGCTTGTGGCATTTCTACTCTTTCTCAATCCCCAATGCTTGGCTTCC
+ATAAGCAGATGGATAACCGCATCAAGCTCTTGGAAGAGATTCTGTCTTTTCGTATGCAGG
+GCGTTGAGTTCGATAATGGTGATATGTATGTTGACGGCCATAAGGCTGCTTCTGACGTTC
+GTGATGAGTTTGTATCTGTTACTGAGAAGTTAATGGATGAATTGGCACAATGCTACAATG
+TGCTCCCCCAACTTGATATTAATAACACTATAGACCACCGCCCCGAAGGGGACGAAAAAT
+GGTTTTTAGAGAACGAGAAGACGGTTACGCAGTTTTGCCGCAAGCTGGCTGCTGAACGCC
+CTCTTAAGGATATTCGCGATGAGTATAATTACCCCAAAAAGAAAGGTATTAAGGATGAGT
+GTTCAAGATTGCTGGAGGCCTCCACTATGAAATCGCGTAGAGGCTTTGCTATTCAGCGTT
+TGATGAATGCAATGCGACAGGCTCATGCTGATGGTTGGTTTATCGTTTTTGACACTCTCA
+CGTTGGCTGACGACCGATTAGAGGCGTTTTATGATAATCCCAATGCTTTGCGTGACTATT
+TTCGTGATATTGGTCGTATGGTTCTTGCTGCCGAGGGTCGCAAGGCTAATGATTCACACG
+CCGACTGCTATCAGTATTTTTGTGTGCCTGAGTATGGTACAGCTAATGGCCGTCTTCATT
+TCCATGCGGTGCACTTTATGCGGACACTTCCTACAGGTAGCGTTGACCCTAATTTTGGTC
+GTCGGGTACGCAATCGCCGCCAGTTAAATAGCTTGCAAAATACGTGGCCTTATGGTTACA
+GTATGCCCATCGCAGTTCGCTACACGCAGGACGCTTTTTCACGTTCTGGTTGGTTGTGGC
+CTGTTGATGCTAAAGGTGAGCCGCTTAAAGCTACCAGTTATATGGCTGTTGGTTTCTATG
+TGGCTAAATACGTTAACAAAAAGTCAGATATGGACCTTGCTGCTAAAGGTCTAGGAGCTA
+AAGAATGGAACAACTCACTAAAAACCAAGCTGTCGCTACT
+>contig7
+TCCCAAGAAGCTGTTCAGAATCAGAATGAGCCGCAACTTCGGGATGAAAATGCTCACAAT
+GACAAATCTGTCCACGGAGTGCTTAATCCAACTTACCAAGCTGGGTTACGACGCGACGCC
+GTTCAACCAGATATTGAAGCAGAACGCAAAAAGAGAGATGAGATTGAGGCTGGGAAAAGT
+TACTGTAGCCGACGTTTTGGCGGCGCAACCTGTGACGACAAATCTGCTCAAATTTATGCG
+CGCTTCGATAAAAATGATTGGCGTATCCAACCTGCA
diff -r 000000000000 -r 8813044f72bf mito-prokka/test-data/out.fsa
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mito-prokka/test-data/out.fsa	Wed May 26 16:01:54 2021 +0000
@@ -0,0 +1,99 @@
+>contig1 [gcode=11] [organism=Genus species] [strain=strain]
+GAGTTTTATCGCTTCCATGACGCAGAAGTTAACACTTTCGGATATTTCTGATGAGTCGAA
+AAATTATCTTGATAAAGCAGGAATTACTACTGCTTGTTTACGAATTAAATCGAAGTGGAC
+TGCTGGCGGAAAATGAGAAAATTCGACCTATCCTTGCGCAGCTCGAGAAGCTCTTACTTT
+GCGACCTTTCGCCATCAACTAACGATTCTGTCAAAAACTGACGCGTTGGATGAGGAGAAG
+TGGCTTAATATGCTTGGCACGTTCGTCAAGGACTGGTTTAGATATGAGTCACATTTTGTT
+CATGGTAGAGATTCTCTTGTTGACATTTTAAAAGAGCGTGGATTACTATC
+>contig2 [gcode=11] [organism=Genus species] [strain=strain]
+TGAGTCCGATGCTGTTCAACCACTAATAGGTAAGAAATCATGAGTCAAGTTACTGAACAA
+TCCGTACGTTTCCAGACCGCTTTGGCCTCTATTAAGCTCATTCAGGCTTCTGCCGTTTTG
+GATTTAACCGAAGATGATTTCGATTTTCTGACGAGTAACAAAGTTTGGATTGCTACTGAC
+CGCTCTCGTGCTCGTCGCTGCGTTGAGGCTTGCGTTTATGGTACGCTGGACTTTGTGGGA
+TACCCTCGCTTTCCTGCTCCTGTTGAGTTTATTGCTGCCGTCATTGCTTATTATGTTCAT
+CCCGTCAACATTCAAACGGCCTGTCTCATCATGGAAGGCGCTGAATTTACGGAAAACATT
+ATTAATGGCGTCGAGCGTCCGGTTAAAGCCGCTGAATTGTTCGCGTTTACCTTGCGTGTA
+CGCGCAGGAAACACTGACGTTCTTACTGACGCAGAAGAAAACGTGCGTCAAAAATTACGT
+GCGGAAGGAGTGATGTAATGTCTAAAGGTAAAAAACGTTCTGGCGCTCGCCCTGGTCGTC
+CGCAGCCGTTGCGAGGTACTAAAGGCAAGCGTAAAGGCGCTCGTCTTTGGTATGTAGGTG
+GTCAACAATTTTAATTGCAGGGGCTTCGGCCCCTTACTTGAGGATAAATTATGTCTAATA
+TTCAAACTGGCGCCGAGCGTATGCCGCATGACCTTTCCCATCTTGGCTTCCTTGCTGGTC
+AGATTGGTCGTCTTATTACCATTTCAACTACTCCGGTTATCGCTGGCGACTCCTTCGAGA
+TGGACGCCGTTGGCGCTCTCCGTCTTTCTCCATTGCGTCGTGGCCTTGCTATTGACTCTA
+>contig3 [gcode=11] [organism=Genus species] [strain=strain]
+CTGTAGACATTTTTACTTTTTATGTCCCTCATCGTCACGTTTATGGTGAACAGTGGATTA
+AGTTCATGAAGGATGGTGTTAATGCCACTCCTCTCCCGACTGTTAACACTACTGGTTATA
+TTGACCATGCCGCTTTTCTTGGCACGATTAACCCTGATACCAATAAAATCCCTAAGCATT
+TGTTTCAGGGTTATTTGAATATCTATAACA
+>contig4 [gcode=11] [organism=Genus species] [strain=strain]
+ACTATTTTAAAGCGCCGTGGATGCCTGACCGTACCGAGGCTAACCCTAATGAGCTTAATC
+AAGATGATGCTCGTTATGGTTTCCGTTGCTGCCATCTCAAAAACATTTGGACTGCTCCGC
+TTCCTCCTGAGACTGAGCTTTCTCGCCAAATGACGACTTCTACCACATCTATTGACATTA
+TGGGTCTGCAAGCTGCTTATGCTAATTTGCATACTGACCAAGAACGTGATTACTTCATGC
+AGCGTTACCATGATGTTATTTCTTCATTTGGAGGTAAAACCTCTTATGACGCTGACAACC
+GTCCTTTACTTGTCATGCGCTCTAATCTCTGGGCATCTGGCTATGATGTTGATGGAACTG
+ACCAAACGTCGTTAGGCCAGTTTTCTGGTCGTGTTCAACAGACCTATAAACATTCTGTGC
+CGCGTTTCTTTGTTCCTGAGCATGGCACTATGTTTACTCTTGCGCTTGTTCGTTTTCCGC
+CTACTGCGACTAAAGAGATTCAGTACCTTAACGCTAAAGGTGCTTTGACTTATACCGATA
+TTGCTGGCGACCCTGTTTTGTATGGCAACTTGCCGCCGCGTGAAATTTCTATGAAGGATG
+TTTTCCGTTCTGGTGATTCGTCTAAGAAGTTTAAGATTGCTGAGGGTCAGTGGTATCGTT
+ATGCGCCTTCGTATGTTTCTCCTGCTTATCACCTTCTTGAAGGCTTCCCATTCATTCAGG
+AACCGCCTTCTGGTGATTTGCAAGAACGCGTACTTATTCGCCACCATGATTATGACCAGT
+GTTTCCAGTCCGTTCAGTTGTTGCAGTGGAATAGTCAGGTTAAATTTAATGTGACCGTTT
+ATCGCAATCTGCCGACCACTCGCGATTCAATCATGACTTCGTGATAAAAGATTGAGTGTG
+AGGTTATAACGCCGAAGCGGTAAAAATTTTAATTTTTGCCGCTGAGGGGTTGACCAAGCG
+AAGCGCGGTAGGTTTTCTGCTTAGGAGTTTAATCATGTTTCAGACTTTTATTTCTCGCCA
+TAATTCAAACTTTTTTTCTGATAAGCTGGTTCTCACTTCTGTTACTCCAGCTTCTTCGGC
+ACCTGTTTTACAGACACCTAAAGCTACATCGTCAACGTTATATTTTGATAGTTTGACGGT
+TAATGCTGGTAATGGTGGTTTTCTTCATTGCATTCAGATGGATACATCTGTCAACGCCGC
+TAATCAGGTTGTTTCTGTTGGTGCTGATATTGCTTTTGATGCCGACCCTAAATTTTTTGC
+>contig5 [gcode=11] [organism=Genus species] [strain=strain]
+CTGTTTGGTTCGCTTTGAGTCTTCTTCGGTTCCGACTACCCTCCCGACTGCCTATGATGT
+TTATCCTTTGAATGGTCGCCATGATGGTGGTTATTATACCGTCAAGGACTGTGTGACTAT
+TGACGTCCTTCCCCGTACGCCGGGCAATAACGTTTATGTTGGTTTCATGGTTTGGTCTAA
+CTTTACCGCTACTAAATGCCGCGGATTGGTTTCGCTGAATCAGGTTATTAAAGAGATTAT
+TTGTCTCCAGCCACTTAAGTGAGGTGATTTATGTTTGGTGCTATTGCTGGCGGTATTGCT
+TCTGCTCTTGCTGGTGGCGCCATGTCTAAATTGTTTGGAGGCGGTCAAAAAGCCGCCTCC
+GGTGGCATTCAAGGTGATGTGCTTGCTACCGATAACAATACTGTAGGCATGGGTGATGCT
+GGTATTAAATCTGCCATTCAAGGCTCTAATGTTCCTAACCCTGATGAGGCCGCCCCTAGT
+TTTGTTTCTG
+>contig6 [gcode=11] [organism=Genus species] [strain=strain]
+GTGCTATGGCTAAAGCTGGTAAAGGACTTCTTGAAGGTACGTTGCAGGCTGGCACTTCTG
+CCGTTTCTGATAAGTTGCTTGATTTGGTTGGACTTGGTGGCAAGTCTGCCGCTGATAAAG
+GAAAGGATACTCGTGATTATCTTGCTGCTGCATTTCCTGAGCTTAATGCTTGGGAGCGTG
+CTGGTGCTGATGCTTCCTCTGCTGGTATGGTTGACGCCGGATTTGAGAATCAAAAAGAGC
+TTACTAAAATGCAACTGGACAATCAGAAAGAGATTGCCGAGATGCAAAATGAGACTCAAA
+AAGAGATTGCTGGCATTCAGTCGGCGACTTCACGCCAGAATACGAAAGACCAGGTATATG
+CACAAAATGAGATGCTTGCTTATCAACAGAAGGAGTCTACTGCTCGCGTTGCGTCTATTA
+TGGAAAACACCAATCTTTCCAAGCAACAGCAGGTTTCCGAGATTATGCGCCAAATGCTTA
+CTCAAGCTCAAACGGCTGGTCAGTATTTTACCAATGACCAAATCAAAGAAATGACTCGCA
+AGGTTAGTGCTGAGGTTGACTTAGTTCATCAGCAAACGCAGAATCAGCGGTATGGCTCTT
+CTCATATTGGCGCTACTGCAAAGGATATTTCTAATGTCGTCACTGATGCTGCTTCTGGTG
+TGGTTGATATTTTTCATGGTATTGATAAAGCTGTTGCCGATACTTGGAACAATTTCTGGA
+AAGACGGTAAAGCTGATGGTATTGGCTCTAATTTGTCTAGGAAATAACCGTCAGGATTGA
+CACCCTCCCAATTGTATGTTTTCATGCCTCCAAATCTTGGAGGCTTTTTTATGGTTCGTT
+CTTATTACCCTTCTGAATGTCACGCTGATTATTTTGACTTTGAGCGTATCGAGGCTCTTA
+AACCTGCTATTGAGGCTTGTGGCATTTCTACTCTTTCTCAATCCCCAATGCTTGGCTTCC
+ATAAGCAGATGGATAACCGCATCAAGCTCTTGGAAGAGATTCTGTCTTTTCGTATGCAGG
+GCGTTGAGTTCGATAATGGTGATATGTATGTTGACGGCCATAAGGCTGCTTCTGACGTTC
+GTGATGAGTTTGTATCTGTTACTGAGAAGTTAATGGATGAATTGGCACAATGCTACAATG
+TGCTCCCCCAACTTGATATTAATAACACTATAGACCACCGCCCCGAAGGGGACGAAAAAT
+GGTTTTTAGAGAACGAGAAGACGGTTACGCAGTTTTGCCGCAAGCTGGCTGCTGAACGCC
+CTCTTAAGGATATTCGCGATGAGTATAATTACCCCAAAAAGAAAGGTATTAAGGATGAGT
+GTTCAAGATTGCTGGAGGCCTCCACTATGAAATCGCGTAGAGGCTTTGCTATTCAGCGTT
+TGATGAATGCAATGCGACAGGCTCATGCTGATGGTTGGTTTATCGTTTTTGACACTCTCA
+CGTTGGCTGACGACCGATTAGAGGCGTTTTATGATAATCCCAATGCTTTGCGTGACTATT
+TTCGTGATATTGGTCGTATGGTTCTTGCTGCCGAGGGTCGCAAGGCTAATGATTCACACG
+CCGACTGCTATCAGTATTTTTGTGTGCCTGAGTATGGTACAGCTAATGGCCGTCTTCATT
+TCCATGCGGTGCACTTTATGCGGACACTTCCTACAGGTAGCGTTGACCCTAATTTTGGTC
+GTCGGGTACGCAATCGCCGCCAGTTAAATAGCTTGCAAAATACGTGGCCTTATGGTTACA
+GTATGCCCATCGCAGTTCGCTACACGCAGGACGCTTTTTCACGTTCTGGTTGGTTGTGGC
+CTGTTGATGCTAAAGGTGAGCCGCTTAAAGCTACCAGTTATATGGCTGTTGGTTTCTATG
+TGGCTAAATACGTTAACAAAAAGTCAGATATGGACCTTGCTGCTAAAGGTCTAGGAGCTA
+AAGAATGGAACAACTCACTAAAAACCAAGCTGTCGCTACT
+>contig7 [gcode=11] [organism=Genus species] [strain=strain]
+TCCCAAGAAGCTGTTCAGAATCAGAATGAGCCGCAACTTCGGGATGAAAATGCTCACAAT
+GACAAATCTGTCCACGGAGTGCTTAATCCAACTTACCAAGCTGGGTTACGACGCGACGCC
+GTTCAACCAGATATTGAAGCAGAACGCAAAAAGAGAGATGAGATTGAGGCTGGGAAAAGT
+TACTGTAGCCGACGTTTTGGCGGCGCAACCTGTGACGACAAATCTGCTCAAATTTATGCG
+CGCTTCGATAAAAATGATTGGCGTATCCAACCTGCA
diff -r 000000000000 -r 8813044f72bf mito-prokka/test-data/out.gbk
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mito-prokka/test-data/out.gbk	Wed May 26 16:01:54 2021 +0000
@@ -0,0 +1,257 @@
+LOCUS       contig1                  350 bp    DNA     linear       27-MAR-2018
+DEFINITION  Genus species strain strain.
+ACCESSION   
+VERSION
+KEYWORDS    .
+SOURCE      Genus species
+  ORGANISM  Genus species
+            Unclassified.
+COMMENT     Annotated using prokka 1.13 from
+            https://github.com/tseemann/prokka.
+FEATURES             Location/Qualifiers
+     source          1..350
+                     /organism="Genus species"
+                     /mol_type="genomic DNA"
+                     /strain="strain"
+ORIGIN      
+        1 gagttttatc gcttccatga cgcagaagtt aacactttcg gatatttctg atgagtcgaa
+       61 aaattatctt gataaagcag gaattactac tgcttgttta cgaattaaat cgaagtggac
+      121 tgctggcgga aaatgagaaa attcgaccta tccttgcgca gctcgagaag ctcttacttt
+      181 gcgacctttc gccatcaact aacgattctg tcaaaaactg acgcgttgga tgaggagaag
+      241 tggcttaata tgcttggcac gttcgtcaag gactggttta gatatgagtc acattttgtt
+      301 catggtagag attctcttgt tgacatttta aaagagcgtg gattactatc
+//
+LOCUS       contig2                  840 bp    DNA     linear       27-MAR-2018
+DEFINITION  Genus species strain strain.
+ACCESSION   
+VERSION
+KEYWORDS    .
+SOURCE      Genus species
+  ORGANISM  Genus species
+            Unclassified.
+COMMENT     Annotated using prokka 1.13 from
+            https://github.com/tseemann/prokka.
+FEATURES             Location/Qualifiers
+     source          1..840
+                     /organism="Genus species"
+                     /mol_type="genomic DNA"
+                     /strain="strain"
+     CDS             40..498
+                     /locus_tag="HMJLFLJH_00001"
+                     /inference="ab initio prediction:Prodigal:2.6"
+                     /codon_start=1
+                     /transl_table=11
+                     /product="hypothetical protein"
+                     /translation="MSQVTEQSVRFQTALASIKLIQASAVLDLTEDDFDFLTSNKVWI
+                     ATDRSRARRCVEACVYGTLDFVGYPRFPAPVEFIAAVIAYYVHPVNIQTACLIMEGAE
+                     FTENIINGVERPVKAAELFAFTLRVRAGNTDVLTDAEENVRQKLRAEGVM"
+     CDS             498..614
+                     /locus_tag="HMJLFLJH_00002"
+                     /inference="ab initio prediction:Prodigal:2.6"
+                     /codon_start=1
+                     /transl_table=11
+                     /product="hypothetical protein"
+                     /translation="MSKGKKRSGARPGRPQPLRGTKGKRKGARLWYVGGQQF"
+ORIGIN      
+        1 tgagtccgat gctgttcaac cactaatagg taagaaatca tgagtcaagt tactgaacaa
+       61 tccgtacgtt tccagaccgc tttggcctct attaagctca ttcaggcttc tgccgttttg
+      121 gatttaaccg aagatgattt cgattttctg acgagtaaca aagtttggat tgctactgac
+      181 cgctctcgtg ctcgtcgctg cgttgaggct tgcgtttatg gtacgctgga ctttgtggga
+      241 taccctcgct ttcctgctcc tgttgagttt attgctgccg tcattgctta ttatgttcat
+      301 cccgtcaaca ttcaaacggc ctgtctcatc atggaaggcg ctgaatttac ggaaaacatt
+      361 attaatggcg tcgagcgtcc ggttaaagcc gctgaattgt tcgcgtttac cttgcgtgta
+      421 cgcgcaggaa acactgacgt tcttactgac gcagaagaaa acgtgcgtca aaaattacgt
+      481 gcggaaggag tgatgtaatg tctaaaggta aaaaacgttc tggcgctcgc cctggtcgtc
+      541 cgcagccgtt gcgaggtact aaaggcaagc gtaaaggcgc tcgtctttgg tatgtaggtg
+      601 gtcaacaatt ttaattgcag gggcttcggc cccttacttg aggataaatt atgtctaata
+      661 ttcaaactgg cgccgagcgt atgccgcatg acctttccca tcttggcttc cttgctggtc
+      721 agattggtcg tcttattacc atttcaacta ctccggttat cgctggcgac tccttcgaga
+      781 tggacgccgt tggcgctctc cgtctttctc cattgcgtcg tggccttgct attgactcta
+//
+LOCUS       contig3                  210 bp    DNA     linear       27-MAR-2018
+DEFINITION  Genus species strain strain.
+ACCESSION   
+VERSION
+KEYWORDS    .
+SOURCE      Genus species
+  ORGANISM  Genus species
+            Unclassified.
+COMMENT     Annotated using prokka 1.13 from
+            https://github.com/tseemann/prokka.
+FEATURES             Location/Qualifiers
+     source          1..210
+                     /organism="Genus species"
+                     /mol_type="genomic DNA"
+                     /strain="strain"
+ORIGIN      
+        1 ctgtagacat ttttactttt tatgtccctc atcgtcacgt ttatggtgaa cagtggatta
+       61 agttcatgaa ggatggtgtt aatgccactc ctctcccgac tgttaacact actggttata
+      121 ttgaccatgc cgcttttctt ggcacgatta accctgatac caataaaatc cctaagcatt
+      181 tgtttcaggg ttatttgaat atctataaca
+//
+LOCUS       contig4                 1260 bp    DNA     linear       27-MAR-2018
+DEFINITION  Genus species strain strain.
+ACCESSION   
+VERSION
+KEYWORDS    .
+SOURCE      Genus species
+  ORGANISM  Genus species
+            Unclassified.
+COMMENT     Annotated using prokka 1.13 from
+            https://github.com/tseemann/prokka.
+FEATURES             Location/Qualifiers
+     source          1..1260
+                     /organism="Genus species"
+                     /mol_type="genomic DNA"
+                     /strain="strain"
+     CDS             21..884
+                     /locus_tag="HMJLFLJH_00003"
+                     /inference="ab initio prediction:Prodigal:2.6"
+                     /codon_start=1
+                     /transl_table=11
+                     /product="hypothetical protein"
+                     /translation="MPDRTEANPNELNQDDARYGFRCCHLKNIWTAPLPPETELSRQM
+                     TTSTTSIDIMGLQAAYANLHTDQERDYFMQRYHDVISSFGGKTSYDADNRPLLVMRSN
+                     LWASGYDVDGTDQTSLGQFSGRVQQTYKHSVPRFFVPEHGTMFTLALVRFPPTATKEI
+                     QYLNAKGALTYTDIAGDPVLYGNLPPREISMKDVFRSGDSSKKFKIAEGQWYRYAPSY
+                     VSPAYHLLEGFPFIQEPPSGDLQERVLIRHHDYDQCFQSVQLLQWNSQVKFNVTVYRN
+                     LPTTRDSIMTS"
+ORIGIN      
+        1 actattttaa agcgccgtgg atgcctgacc gtaccgaggc taaccctaat gagcttaatc
+       61 aagatgatgc tcgttatggt ttccgttgct gccatctcaa aaacatttgg actgctccgc
+      121 ttcctcctga gactgagctt tctcgccaaa tgacgacttc taccacatct attgacatta
+      181 tgggtctgca agctgcttat gctaatttgc atactgacca agaacgtgat tacttcatgc
+      241 agcgttacca tgatgttatt tcttcatttg gaggtaaaac ctcttatgac gctgacaacc
+      301 gtcctttact tgtcatgcgc tctaatctct gggcatctgg ctatgatgtt gatggaactg
+      361 accaaacgtc gttaggccag ttttctggtc gtgttcaaca gacctataaa cattctgtgc
+      421 cgcgtttctt tgttcctgag catggcacta tgtttactct tgcgcttgtt cgttttccgc
+      481 ctactgcgac taaagagatt cagtacctta acgctaaagg tgctttgact tataccgata
+      541 ttgctggcga ccctgttttg tatggcaact tgccgccgcg tgaaatttct atgaaggatg
+      601 ttttccgttc tggtgattcg tctaagaagt ttaagattgc tgagggtcag tggtatcgtt
+      661 atgcgccttc gtatgtttct cctgcttatc accttcttga aggcttccca ttcattcagg
+      721 aaccgccttc tggtgatttg caagaacgcg tacttattcg ccaccatgat tatgaccagt
+      781 gtttccagtc cgttcagttg ttgcagtgga atagtcaggt taaatttaat gtgaccgttt
+      841 atcgcaatct gccgaccact cgcgattcaa tcatgacttc gtgataaaag attgagtgtg
+      901 aggttataac gccgaagcgg taaaaatttt aatttttgcc gctgaggggt tgaccaagcg
+      961 aagcgcggta ggttttctgc ttaggagttt aatcatgttt cagactttta tttctcgcca
+     1021 taattcaaac tttttttctg ataagctggt tctcacttct gttactccag cttcttcggc
+     1081 acctgtttta cagacaccta aagctacatc gtcaacgtta tattttgata gtttgacggt
+     1141 taatgctggt aatggtggtt ttcttcattg cattcagatg gatacatctg tcaacgccgc
+     1201 taatcaggtt gtttctgttg gtgctgatat tgcttttgat gccgacccta aattttttgc
+//
+LOCUS       contig5                  490 bp    DNA     linear       27-MAR-2018
+DEFINITION  Genus species strain strain.
+ACCESSION   
+VERSION
+KEYWORDS    .
+SOURCE      Genus species
+  ORGANISM  Genus species
+            Unclassified.
+COMMENT     Annotated using prokka 1.13 from
+            https://github.com/tseemann/prokka.
+FEATURES             Location/Qualifiers
+     source          1..490
+                     /organism="Genus species"
+                     /mol_type="genomic DNA"
+                     /strain="strain"
+     CDS             275..406
+                     /locus_tag="HMJLFLJH_00004"
+                     /inference="ab initio prediction:Prodigal:2.6"
+                     /codon_start=1
+                     /transl_table=11
+                     /product="hypothetical protein"
+                     /translation="MVLLLAVLLLLLLVAPCLNCLEAVKKPPPVAFKVMCLLPITIL"
+ORIGIN      
+        1 ctgtttggtt cgctttgagt cttcttcggt tccgactacc ctcccgactg cctatgatgt
+       61 ttatcctttg aatggtcgcc atgatggtgg ttattatacc gtcaaggact gtgtgactat
+      121 tgacgtcctt ccccgtacgc cgggcaataa cgtttatgtt ggtttcatgg tttggtctaa
+      181 ctttaccgct actaaatgcc gcggattggt ttcgctgaat caggttatta aagagattat
+      241 ttgtctccag ccacttaagt gaggtgattt atgtttggtg ctattgctgg cggtattgct
+      301 tctgctcttg ctggtggcgc catgtctaaa ttgtttggag gcggtcaaaa agccgcctcc
+      361 ggtggcattc aaggtgatgt gcttgctacc gataacaata ctgtaggcat gggtgatgct
+      421 ggtattaaat ctgccattca aggctctaat gttcctaacc ctgatgaggc cgcccctagt
+      481 tttgtttctg
+//
+LOCUS       contig6                 1960 bp    DNA     linear       27-MAR-2018
+DEFINITION  Genus species strain strain.
+ACCESSION   
+VERSION
+KEYWORDS    .
+SOURCE      Genus species
+  ORGANISM  Genus species
+            Unclassified.
+COMMENT     Annotated using prokka 1.13 from
+            https://github.com/tseemann/prokka.
+FEATURES             Location/Qualifiers
+     source          1..1960
+                     /organism="Genus species"
+                     /mol_type="genomic DNA"
+                     /strain="strain"
+     CDS             6..767
+                     /locus_tag="HMJLFLJH_00005"
+                     /inference="ab initio prediction:Prodigal:2.6"
+                     /codon_start=1
+                     /transl_table=11
+                     /product="hypothetical protein"
+                     /translation="MAKAGKGLLEGTLQAGTSAVSDKLLDLVGLGGKSAADKGKDTRD
+                     YLAAAFPELNAWERAGADASSAGMVDAGFENQKELTKMQLDNQKEIAEMQNETQKEIA
+                     GIQSATSRQNTKDQVYAQNEMLAYQQKESTARVASIMENTNLSKQQQVSEIMRQMLTQ
+                     AQTAGQYFTNDQIKEMTRKVSAEVDLVHQQTQNQRYGSSHIGATAKDISNVVTDAASG
+                     VVDIFHGIDKAVADTWNNFWKDGKADGIGSNLSRK"
+ORIGIN      
+        1 gtgctatggc taaagctggt aaaggacttc ttgaaggtac gttgcaggct ggcacttctg
+       61 ccgtttctga taagttgctt gatttggttg gacttggtgg caagtctgcc gctgataaag
+      121 gaaaggatac tcgtgattat cttgctgctg catttcctga gcttaatgct tgggagcgtg
+      181 ctggtgctga tgcttcctct gctggtatgg ttgacgccgg atttgagaat caaaaagagc
+      241 ttactaaaat gcaactggac aatcagaaag agattgccga gatgcaaaat gagactcaaa
+      301 aagagattgc tggcattcag tcggcgactt cacgccagaa tacgaaagac caggtatatg
+      361 cacaaaatga gatgcttgct tatcaacaga aggagtctac tgctcgcgtt gcgtctatta
+      421 tggaaaacac caatctttcc aagcaacagc aggtttccga gattatgcgc caaatgctta
+      481 ctcaagctca aacggctggt cagtatttta ccaatgacca aatcaaagaa atgactcgca
+      541 aggttagtgc tgaggttgac ttagttcatc agcaaacgca gaatcagcgg tatggctctt
+      601 ctcatattgg cgctactgca aaggatattt ctaatgtcgt cactgatgct gcttctggtg
+      661 tggttgatat ttttcatggt attgataaag ctgttgccga tacttggaac aatttctgga
+      721 aagacggtaa agctgatggt attggctcta atttgtctag gaaataaccg tcaggattga
+      781 caccctccca attgtatgtt ttcatgcctc caaatcttgg aggctttttt atggttcgtt
+      841 cttattaccc ttctgaatgt cacgctgatt attttgactt tgagcgtatc gaggctctta
+      901 aacctgctat tgaggcttgt ggcatttcta ctctttctca atccccaatg cttggcttcc
+      961 ataagcagat ggataaccgc atcaagctct tggaagagat tctgtctttt cgtatgcagg
+     1021 gcgttgagtt cgataatggt gatatgtatg ttgacggcca taaggctgct tctgacgttc
+     1081 gtgatgagtt tgtatctgtt actgagaagt taatggatga attggcacaa tgctacaatg
+     1141 tgctccccca acttgatatt aataacacta tagaccaccg ccccgaaggg gacgaaaaat
+     1201 ggtttttaga gaacgagaag acggttacgc agttttgccg caagctggct gctgaacgcc
+     1261 ctcttaagga tattcgcgat gagtataatt accccaaaaa gaaaggtatt aaggatgagt
+     1321 gttcaagatt gctggaggcc tccactatga aatcgcgtag aggctttgct attcagcgtt
+     1381 tgatgaatgc aatgcgacag gctcatgctg atggttggtt tatcgttttt gacactctca
+     1441 cgttggctga cgaccgatta gaggcgtttt atgataatcc caatgctttg cgtgactatt
+     1501 ttcgtgatat tggtcgtatg gttcttgctg ccgagggtcg caaggctaat gattcacacg
+     1561 ccgactgcta tcagtatttt tgtgtgcctg agtatggtac agctaatggc cgtcttcatt
+     1621 tccatgcggt gcactttatg cggacacttc ctacaggtag cgttgaccct aattttggtc
+     1681 gtcgggtacg caatcgccgc cagttaaata gcttgcaaaa tacgtggcct tatggttaca
+     1741 gtatgcccat cgcagttcgc tacacgcagg acgctttttc acgttctggt tggttgtggc
+     1801 ctgttgatgc taaaggtgag ccgcttaaag ctaccagtta tatggctgtt ggtttctatg
+     1861 tggctaaata cgttaacaaa aagtcagata tggaccttgc tgctaaaggt ctaggagcta
+     1921 aagaatggaa caactcacta aaaaccaagc tgtcgctact
+//
+LOCUS       contig7                  276 bp    DNA     linear       27-MAR-2018
+DEFINITION  Genus species strain strain.
+ACCESSION   
+VERSION
+KEYWORDS    .
+SOURCE      Genus species
+  ORGANISM  Genus species
+            Unclassified.
+COMMENT     Annotated using prokka 1.13 from
+            https://github.com/tseemann/prokka.
+FEATURES             Location/Qualifiers
+     source          1..276
+                     /organism="Genus species"
+                     /mol_type="genomic DNA"
+                     /strain="strain"
+ORIGIN      
+        1 tcccaagaag ctgttcagaa tcagaatgag ccgcaacttc gggatgaaaa tgctcacaat
+       61 gacaaatctg tccacggagt gcttaatcca acttaccaag ctgggttacg acgcgacgcc
+      121 gttcaaccag atattgaagc agaacgcaaa aagagagatg agattgaggc tgggaaaagt
+      181 tactgtagcc gacgttttgg cggcgcaacc tgtgacgaca aatctgctca aatttatgcg
+      241 cgcttcgata aaaatgattg gcgtatccaa cctgca
+//
diff -r 000000000000 -r 8813044f72bf mito-prokka/test-data/out.gff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mito-prokka/test-data/out.gff	Wed May 26 16:01:54 2021 +0000
@@ -0,0 +1,113 @@
+##gff-version 3
+##sequence-region contig1 1 350
+##sequence-region contig2 1 840
+##sequence-region contig3 1 210
+##sequence-region contig4 1 1260
+##sequence-region contig5 1 490
+##sequence-region contig6 1 1960
+##sequence-region contig7 1 276
+contig2	Prodigal:002006	CDS	40	498	.	+	0	ID=HMJLFLJH_00001;inference=ab initio prediction:Prodigal:002006;locus_tag=HMJLFLJH_00001;product=hypothetical protein
+contig2	Prodigal:002006	CDS	498	614	.	+	0	ID=HMJLFLJH_00002;inference=ab initio prediction:Prodigal:002006;locus_tag=HMJLFLJH_00002;product=hypothetical protein
+contig4	Prodigal:002006	CDS	21	884	.	+	0	ID=HMJLFLJH_00003;inference=ab initio prediction:Prodigal:002006;locus_tag=HMJLFLJH_00003;product=hypothetical protein
+contig5	Prodigal:002006	CDS	275	406	.	+	0	ID=HMJLFLJH_00004;inference=ab initio prediction:Prodigal:002006;locus_tag=HMJLFLJH_00004;product=hypothetical protein
+contig6	Prodigal:002006	CDS	6	767	.	+	0	ID=HMJLFLJH_00005;inference=ab initio prediction:Prodigal:002006;locus_tag=HMJLFLJH_00005;product=hypothetical protein
+##FASTA
+>contig1
+GAGTTTTATCGCTTCCATGACGCAGAAGTTAACACTTTCGGATATTTCTGATGAGTCGAA
+AAATTATCTTGATAAAGCAGGAATTACTACTGCTTGTTTACGAATTAAATCGAAGTGGAC
+TGCTGGCGGAAAATGAGAAAATTCGACCTATCCTTGCGCAGCTCGAGAAGCTCTTACTTT
+GCGACCTTTCGCCATCAACTAACGATTCTGTCAAAAACTGACGCGTTGGATGAGGAGAAG
+TGGCTTAATATGCTTGGCACGTTCGTCAAGGACTGGTTTAGATATGAGTCACATTTTGTT
+CATGGTAGAGATTCTCTTGTTGACATTTTAAAAGAGCGTGGATTACTATC
+>contig2
+TGAGTCCGATGCTGTTCAACCACTAATAGGTAAGAAATCATGAGTCAAGTTACTGAACAA
+TCCGTACGTTTCCAGACCGCTTTGGCCTCTATTAAGCTCATTCAGGCTTCTGCCGTTTTG
+GATTTAACCGAAGATGATTTCGATTTTCTGACGAGTAACAAAGTTTGGATTGCTACTGAC
+CGCTCTCGTGCTCGTCGCTGCGTTGAGGCTTGCGTTTATGGTACGCTGGACTTTGTGGGA
+TACCCTCGCTTTCCTGCTCCTGTTGAGTTTATTGCTGCCGTCATTGCTTATTATGTTCAT
+CCCGTCAACATTCAAACGGCCTGTCTCATCATGGAAGGCGCTGAATTTACGGAAAACATT
+ATTAATGGCGTCGAGCGTCCGGTTAAAGCCGCTGAATTGTTCGCGTTTACCTTGCGTGTA
+CGCGCAGGAAACACTGACGTTCTTACTGACGCAGAAGAAAACGTGCGTCAAAAATTACGT
+GCGGAAGGAGTGATGTAATGTCTAAAGGTAAAAAACGTTCTGGCGCTCGCCCTGGTCGTC
+CGCAGCCGTTGCGAGGTACTAAAGGCAAGCGTAAAGGCGCTCGTCTTTGGTATGTAGGTG
+GTCAACAATTTTAATTGCAGGGGCTTCGGCCCCTTACTTGAGGATAAATTATGTCTAATA
+TTCAAACTGGCGCCGAGCGTATGCCGCATGACCTTTCCCATCTTGGCTTCCTTGCTGGTC
+AGATTGGTCGTCTTATTACCATTTCAACTACTCCGGTTATCGCTGGCGACTCCTTCGAGA
+TGGACGCCGTTGGCGCTCTCCGTCTTTCTCCATTGCGTCGTGGCCTTGCTATTGACTCTA
+>contig3
+CTGTAGACATTTTTACTTTTTATGTCCCTCATCGTCACGTTTATGGTGAACAGTGGATTA
+AGTTCATGAAGGATGGTGTTAATGCCACTCCTCTCCCGACTGTTAACACTACTGGTTATA
+TTGACCATGCCGCTTTTCTTGGCACGATTAACCCTGATACCAATAAAATCCCTAAGCATT
+TGTTTCAGGGTTATTTGAATATCTATAACA
+>contig4
+ACTATTTTAAAGCGCCGTGGATGCCTGACCGTACCGAGGCTAACCCTAATGAGCTTAATC
+AAGATGATGCTCGTTATGGTTTCCGTTGCTGCCATCTCAAAAACATTTGGACTGCTCCGC
+TTCCTCCTGAGACTGAGCTTTCTCGCCAAATGACGACTTCTACCACATCTATTGACATTA
+TGGGTCTGCAAGCTGCTTATGCTAATTTGCATACTGACCAAGAACGTGATTACTTCATGC
+AGCGTTACCATGATGTTATTTCTTCATTTGGAGGTAAAACCTCTTATGACGCTGACAACC
+GTCCTTTACTTGTCATGCGCTCTAATCTCTGGGCATCTGGCTATGATGTTGATGGAACTG
+ACCAAACGTCGTTAGGCCAGTTTTCTGGTCGTGTTCAACAGACCTATAAACATTCTGTGC
+CGCGTTTCTTTGTTCCTGAGCATGGCACTATGTTTACTCTTGCGCTTGTTCGTTTTCCGC
+CTACTGCGACTAAAGAGATTCAGTACCTTAACGCTAAAGGTGCTTTGACTTATACCGATA
+TTGCTGGCGACCCTGTTTTGTATGGCAACTTGCCGCCGCGTGAAATTTCTATGAAGGATG
+TTTTCCGTTCTGGTGATTCGTCTAAGAAGTTTAAGATTGCTGAGGGTCAGTGGTATCGTT
+ATGCGCCTTCGTATGTTTCTCCTGCTTATCACCTTCTTGAAGGCTTCCCATTCATTCAGG
+AACCGCCTTCTGGTGATTTGCAAGAACGCGTACTTATTCGCCACCATGATTATGACCAGT
+GTTTCCAGTCCGTTCAGTTGTTGCAGTGGAATAGTCAGGTTAAATTTAATGTGACCGTTT
+ATCGCAATCTGCCGACCACTCGCGATTCAATCATGACTTCGTGATAAAAGATTGAGTGTG
+AGGTTATAACGCCGAAGCGGTAAAAATTTTAATTTTTGCCGCTGAGGGGTTGACCAAGCG
+AAGCGCGGTAGGTTTTCTGCTTAGGAGTTTAATCATGTTTCAGACTTTTATTTCTCGCCA
+TAATTCAAACTTTTTTTCTGATAAGCTGGTTCTCACTTCTGTTACTCCAGCTTCTTCGGC
+ACCTGTTTTACAGACACCTAAAGCTACATCGTCAACGTTATATTTTGATAGTTTGACGGT
+TAATGCTGGTAATGGTGGTTTTCTTCATTGCATTCAGATGGATACATCTGTCAACGCCGC
+TAATCAGGTTGTTTCTGTTGGTGCTGATATTGCTTTTGATGCCGACCCTAAATTTTTTGC
+>contig5
+CTGTTTGGTTCGCTTTGAGTCTTCTTCGGTTCCGACTACCCTCCCGACTGCCTATGATGT
+TTATCCTTTGAATGGTCGCCATGATGGTGGTTATTATACCGTCAAGGACTGTGTGACTAT
+TGACGTCCTTCCCCGTACGCCGGGCAATAACGTTTATGTTGGTTTCATGGTTTGGTCTAA
+CTTTACCGCTACTAAATGCCGCGGATTGGTTTCGCTGAATCAGGTTATTAAAGAGATTAT
+TTGTCTCCAGCCACTTAAGTGAGGTGATTTATGTTTGGTGCTATTGCTGGCGGTATTGCT
+TCTGCTCTTGCTGGTGGCGCCATGTCTAAATTGTTTGGAGGCGGTCAAAAAGCCGCCTCC
+GGTGGCATTCAAGGTGATGTGCTTGCTACCGATAACAATACTGTAGGCATGGGTGATGCT
+GGTATTAAATCTGCCATTCAAGGCTCTAATGTTCCTAACCCTGATGAGGCCGCCCCTAGT
+TTTGTTTCTG
+>contig6
+GTGCTATGGCTAAAGCTGGTAAAGGACTTCTTGAAGGTACGTTGCAGGCTGGCACTTCTG
+CCGTTTCTGATAAGTTGCTTGATTTGGTTGGACTTGGTGGCAAGTCTGCCGCTGATAAAG
+GAAAGGATACTCGTGATTATCTTGCTGCTGCATTTCCTGAGCTTAATGCTTGGGAGCGTG
+CTGGTGCTGATGCTTCCTCTGCTGGTATGGTTGACGCCGGATTTGAGAATCAAAAAGAGC
+TTACTAAAATGCAACTGGACAATCAGAAAGAGATTGCCGAGATGCAAAATGAGACTCAAA
+AAGAGATTGCTGGCATTCAGTCGGCGACTTCACGCCAGAATACGAAAGACCAGGTATATG
+CACAAAATGAGATGCTTGCTTATCAACAGAAGGAGTCTACTGCTCGCGTTGCGTCTATTA
+TGGAAAACACCAATCTTTCCAAGCAACAGCAGGTTTCCGAGATTATGCGCCAAATGCTTA
+CTCAAGCTCAAACGGCTGGTCAGTATTTTACCAATGACCAAATCAAAGAAATGACTCGCA
+AGGTTAGTGCTGAGGTTGACTTAGTTCATCAGCAAACGCAGAATCAGCGGTATGGCTCTT
+CTCATATTGGCGCTACTGCAAAGGATATTTCTAATGTCGTCACTGATGCTGCTTCTGGTG
+TGGTTGATATTTTTCATGGTATTGATAAAGCTGTTGCCGATACTTGGAACAATTTCTGGA
+AAGACGGTAAAGCTGATGGTATTGGCTCTAATTTGTCTAGGAAATAACCGTCAGGATTGA
+CACCCTCCCAATTGTATGTTTTCATGCCTCCAAATCTTGGAGGCTTTTTTATGGTTCGTT
+CTTATTACCCTTCTGAATGTCACGCTGATTATTTTGACTTTGAGCGTATCGAGGCTCTTA
+AACCTGCTATTGAGGCTTGTGGCATTTCTACTCTTTCTCAATCCCCAATGCTTGGCTTCC
+ATAAGCAGATGGATAACCGCATCAAGCTCTTGGAAGAGATTCTGTCTTTTCGTATGCAGG
+GCGTTGAGTTCGATAATGGTGATATGTATGTTGACGGCCATAAGGCTGCTTCTGACGTTC
+GTGATGAGTTTGTATCTGTTACTGAGAAGTTAATGGATGAATTGGCACAATGCTACAATG
+TGCTCCCCCAACTTGATATTAATAACACTATAGACCACCGCCCCGAAGGGGACGAAAAAT
+GGTTTTTAGAGAACGAGAAGACGGTTACGCAGTTTTGCCGCAAGCTGGCTGCTGAACGCC
+CTCTTAAGGATATTCGCGATGAGTATAATTACCCCAAAAAGAAAGGTATTAAGGATGAGT
+GTTCAAGATTGCTGGAGGCCTCCACTATGAAATCGCGTAGAGGCTTTGCTATTCAGCGTT
+TGATGAATGCAATGCGACAGGCTCATGCTGATGGTTGGTTTATCGTTTTTGACACTCTCA
+CGTTGGCTGACGACCGATTAGAGGCGTTTTATGATAATCCCAATGCTTTGCGTGACTATT
+TTCGTGATATTGGTCGTATGGTTCTTGCTGCCGAGGGTCGCAAGGCTAATGATTCACACG
+CCGACTGCTATCAGTATTTTTGTGTGCCTGAGTATGGTACAGCTAATGGCCGTCTTCATT
+TCCATGCGGTGCACTTTATGCGGACACTTCCTACAGGTAGCGTTGACCCTAATTTTGGTC
+GTCGGGTACGCAATCGCCGCCAGTTAAATAGCTTGCAAAATACGTGGCCTTATGGTTACA
+GTATGCCCATCGCAGTTCGCTACACGCAGGACGCTTTTTCACGTTCTGGTTGGTTGTGGC
+CTGTTGATGCTAAAGGTGAGCCGCTTAAAGCTACCAGTTATATGGCTGTTGGTTTCTATG
+TGGCTAAATACGTTAACAAAAAGTCAGATATGGACCTTGCTGCTAAAGGTCTAGGAGCTA
+AAGAATGGAACAACTCACTAAAAACCAAGCTGTCGCTACT
+>contig7
+TCCCAAGAAGCTGTTCAGAATCAGAATGAGCCGCAACTTCGGGATGAAAATGCTCACAAT
+GACAAATCTGTCCACGGAGTGCTTAATCCAACTTACCAAGCTGGGTTACGACGCGACGCC
+GTTCAACCAGATATTGAAGCAGAACGCAAAAAGAGAGATGAGATTGAGGCTGGGAAAAGT
+TACTGTAGCCGACGTTTTGGCGGCGCAACCTGTGACGACAAATCTGCTCAAATTTATGCG
+CGCTTCGATAAAAATGATTGGCGTATCCAACCTGCA
diff -r 000000000000 -r 8813044f72bf mito-prokka/test-data/out.sqn
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mito-prokka/test-data/out.sqn	Wed May 26 16:01:54 2021 +0000
@@ -0,0 +1,836 @@
+Seq-entry ::= set {
+  class genbank ,
+  seq-set {
+    seq {
+      id {
+        local
+          str "contig1" } ,
+      descr {
+        source {
+          org {
+            taxname "Genus species" ,
+            orgname {
+              mod {
+                {
+                  subtype strain ,
+                  subname "strain" } } ,
+              gcode 11 } } } ,
+        molinfo {
+          biomol genomic } ,
+        comment "Annotated using prokka 1.13 from
+ https://github.com/tseemann/prokka" ,
+        user {
+          type
+            str "NcbiCleanup" ,
+          data {
+            {
+              label
+                str "method" ,
+              data
+                str "SeriousSeqEntryCleanup" } ,
+            {
+              label
+                str "version" ,
+              data
+                int 8 } ,
+            {
+              label
+                str "month" ,
+              data
+                int 3 } ,
+            {
+              label
+                str "day" ,
+              data
+                int 27 } ,
+            {
+              label
+                str "year" ,
+              data
+                int 2018 } } } ,
+        create-date
+          std {
+            year 2018 ,
+            month 3 ,
+            day 27 } } ,
+      inst {
+        repr raw ,
+        mol dna ,
+        length 350 ,
+        seq-data
+          iupacna "GAGTTTTATCGCTTCCATGACGCAGAAGTTAACACTTTCGGATATTTCTGATGAGTCGA
+AAAATTATCTTGATAAAGCAGGAATTACTACTGCTTGTTTACGAATTAAATCGAAGTGGACTGCTGGCGGAAAATGAG
+AAAATTCGACCTATCCTTGCGCAGCTCGAGAAGCTCTTACTTTGCGACCTTTCGCCATCAACTAACGATTCTGTCAAA
+AACTGACGCGTTGGATGAGGAGAAGTGGCTTAATATGCTTGGCACGTTCGTCAAGGACTGGTTTAGATATGAGTCACA
+TTTTGTTCATGGTAGAGATTCTCTTGTTGACATTTTAAAAGAGCGTGGATTACTATC" } } ,
+    set {
+      class nuc-prot ,
+      descr {
+        source {
+          org {
+            taxname "Genus species" ,
+            orgname {
+              mod {
+                {
+                  subtype strain ,
+                  subname "strain" } } ,
+              gcode 11 } } } ,
+        comment "Annotated using prokka 1.13 from
+ https://github.com/tseemann/prokka" ,
+        user {
+          type
+            str "NcbiCleanup" ,
+          data {
+            {
+              label
+                str "method" ,
+              data
+                str "SeriousSeqEntryCleanup" } ,
+            {
+              label
+                str "version" ,
+              data
+                int 8 } ,
+            {
+              label
+                str "month" ,
+              data
+                int 3 } ,
+            {
+              label
+                str "day" ,
+              data
+                int 27 } ,
+            {
+              label
+                str "year" ,
+              data
+                int 2018 } } } ,
+        create-date
+          std {
+            year 2018 ,
+            month 3 ,
+            day 27 } } ,
+      seq-set {
+        seq {
+          id {
+            local
+              str "contig2" } ,
+          descr {
+            molinfo {
+              biomol genomic } } ,
+          inst {
+            repr raw ,
+            mol dna ,
+            length 840 ,
+            seq-data
+              iupacna "TGAGTCCGATGCTGTTCAACCACTAATAGGTAAGAAATCATGAGTCAAGTTACTG
+AACAATCCGTACGTTTCCAGACCGCTTTGGCCTCTATTAAGCTCATTCAGGCTTCTGCCGTTTTGGATTTAACCGAAG
+ATGATTTCGATTTTCTGACGAGTAACAAAGTTTGGATTGCTACTGACCGCTCTCGTGCTCGTCGCTGCGTTGAGGCTT
+GCGTTTATGGTACGCTGGACTTTGTGGGATACCCTCGCTTTCCTGCTCCTGTTGAGTTTATTGCTGCCGTCATTGCTT
+ATTATGTTCATCCCGTCAACATTCAAACGGCCTGTCTCATCATGGAAGGCGCTGAATTTACGGAAAACATTATTAATG
+GCGTCGAGCGTCCGGTTAAAGCCGCTGAATTGTTCGCGTTTACCTTGCGTGTACGCGCAGGAAACACTGACGTTCTTA
+CTGACGCAGAAGAAAACGTGCGTCAAAAATTACGTGCGGAAGGAGTGATGTAATGTCTAAAGGTAAAAAACGTTCTGG
+CGCTCGCCCTGGTCGTCCGCAGCCGTTGCGAGGTACTAAAGGCAAGCGTAAAGGCGCTCGTCTTTGGTATGTAGGTGG
+TCAACAATTTTAATTGCAGGGGCTTCGGCCCCTTACTTGAGGATAAATTATGTCTAATATTCAAACTGGCGCCGAGCG
+TATGCCGCATGACCTTTCCCATCTTGGCTTCCTTGCTGGTCAGATTGGTCGTCTTATTACCATTTCAACTACTCCGGT
+TATCGCTGGCGACTCCTTCGAGATGGACGCCGTTGGCGCTCTCCGTCTTTCTCCATTGCGTCGTGGCCTTGCTATTGA
+CTCTA" } } ,
+        seq {
+          id {
+            local
+              str "contig2_1" } ,
+          descr {
+            title "hypothetical protein HMJLFLJH_00001 [Genus species]" ,
+            molinfo {
+              biomol peptide ,
+              tech concept-trans } } ,
+          inst {
+            repr raw ,
+            mol aa ,
+            length 152 ,
+            seq-data
+              ncbieaa "MSQVTEQSVRFQTALASIKLIQASAVLDLTEDDFDFLTSNKVWIATDRSRARRCV
+EACVYGTLDFVGYPRFPAPVEFIAAVIAYYVHPVNIQTACLIMEGAEFTENIINGVERPVKAAELFAFTLRVRAGNTD
+VLTDAEENVRQKLRAEGVM" } ,
+          annot {
+            {
+              data
+                ftable {
+                  {
+                    id
+                      local
+                        id 3 ,
+                    data
+                      prot {
+                        name {
+                          "hypothetical protein" } } ,
+                    location
+                      int {
+                        from 0 ,
+                        to 151 ,
+                        id
+                          local
+                            str "contig2_1" } } } } } } ,
+        seq {
+          id {
+            local
+              str "contig2_2" } ,
+          descr {
+            title "hypothetical protein HMJLFLJH_00002 [Genus species]" ,
+            molinfo {
+              biomol peptide ,
+              tech concept-trans } } ,
+          inst {
+            repr raw ,
+            mol aa ,
+            length 38 ,
+            seq-data
+              ncbieaa "MSKGKKRSGARPGRPQPLRGTKGKRKGARLWYVGGQQF" } ,
+          annot {
+            {
+              data
+                ftable {
+                  {
+                    id
+                      local
+                        id 4 ,
+                    data
+                      prot {
+                        name {
+                          "hypothetical protein" } } ,
+                    location
+                      int {
+                        from 0 ,
+                        to 37 ,
+                        id
+                          local
+                            str "contig2_2" } } } } } } } ,
+      annot {
+        {
+          data
+            ftable {
+              {
+                id
+                  local
+                    id 1 ,
+                data
+                  cdregion {
+                    frame one ,
+                    code {
+                      id 11 } } ,
+                product
+                  whole
+                    local
+                      str "contig2_1" ,
+                location
+                  int {
+                    from 39 ,
+                    to 497 ,
+                    strand plus ,
+                    id
+                      local
+                        str "contig2" } ,
+                qual {
+                  {
+                    qual "inference" ,
+                    val "ab initio prediction:Prodigal:2.6" } } ,
+                xref {
+                  {
+                    data
+                      gene {
+                        locus-tag "HMJLFLJH_00001" } } } } ,
+              {
+                id
+                  local
+                    id 2 ,
+                data
+                  cdregion {
+                    frame one ,
+                    code {
+                      id 11 } } ,
+                product
+                  whole
+                    local
+                      str "contig2_2" ,
+                location
+                  int {
+                    from 497 ,
+                    to 613 ,
+                    strand plus ,
+                    id
+                      local
+                        str "contig2" } ,
+                qual {
+                  {
+                    qual "inference" ,
+                    val "ab initio prediction:Prodigal:2.6" } } ,
+                xref {
+                  {
+                    data
+                      gene {
+                        locus-tag "HMJLFLJH_00002" } } } } } } } } ,
+    seq {
+      id {
+        local
+          str "contig3" } ,
+      descr {
+        source {
+          org {
+            taxname "Genus species" ,
+            orgname {
+              mod {
+                {
+                  subtype strain ,
+                  subname "strain" } } ,
+              gcode 11 } } } ,
+        molinfo {
+          biomol genomic } ,
+        comment "Annotated using prokka 1.13 from
+ https://github.com/tseemann/prokka" ,
+        user {
+          type
+            str "NcbiCleanup" ,
+          data {
+            {
+              label
+                str "method" ,
+              data
+                str "SeriousSeqEntryCleanup" } ,
+            {
+              label
+                str "version" ,
+              data
+                int 8 } ,
+            {
+              label
+                str "month" ,
+              data
+                int 3 } ,
+            {
+              label
+                str "day" ,
+              data
+                int 27 } ,
+            {
+              label
+                str "year" ,
+              data
+                int 2018 } } } ,
+        create-date
+          std {
+            year 2018 ,
+            month 3 ,
+            day 27 } } ,
+      inst {
+        repr raw ,
+        mol dna ,
+        length 210 ,
+        seq-data
+          iupacna "CTGTAGACATTTTTACTTTTTATGTCCCTCATCGTCACGTTTATGGTGAACAGTGGATT
+AAGTTCATGAAGGATGGTGTTAATGCCACTCCTCTCCCGACTGTTAACACTACTGGTTATATTGACCATGCCGCTTTT
+CTTGGCACGATTAACCCTGATACCAATAAAATCCCTAAGCATTTGTTTCAGGGTTATTTGAATATCTATAACA" } } ,
+    set {
+      class nuc-prot ,
+      descr {
+        source {
+          org {
+            taxname "Genus species" ,
+            orgname {
+              mod {
+                {
+                  subtype strain ,
+                  subname "strain" } } ,
+              gcode 11 } } } ,
+        comment "Annotated using prokka 1.13 from
+ https://github.com/tseemann/prokka" ,
+        user {
+          type
+            str "NcbiCleanup" ,
+          data {
+            {
+              label
+                str "method" ,
+              data
+                str "SeriousSeqEntryCleanup" } ,
+            {
+              label
+                str "version" ,
+              data
+                int 8 } ,
+            {
+              label
+                str "month" ,
+              data
+                int 3 } ,
+            {
+              label
+                str "day" ,
+              data
+                int 27 } ,
+            {
+              label
+                str "year" ,
+              data
+                int 2018 } } } ,
+        create-date
+          std {
+            year 2018 ,
+            month 3 ,
+            day 27 } } ,
+      seq-set {
+        seq {
+          id {
+            local
+              str "contig4" } ,
+          descr {
+            molinfo {
+              biomol genomic } } ,
+          inst {
+            repr raw ,
+            mol dna ,
+            length 1260 ,
+            seq-data
+              iupacna "ACTATTTTAAAGCGCCGTGGATGCCTGACCGTACCGAGGCTAACCCTAATGAGCT
+TAATCAAGATGATGCTCGTTATGGTTTCCGTTGCTGCCATCTCAAAAACATTTGGACTGCTCCGCTTCCTCCTGAGAC
+TGAGCTTTCTCGCCAAATGACGACTTCTACCACATCTATTGACATTATGGGTCTGCAAGCTGCTTATGCTAATTTGCA
+TACTGACCAAGAACGTGATTACTTCATGCAGCGTTACCATGATGTTATTTCTTCATTTGGAGGTAAAACCTCTTATGA
+CGCTGACAACCGTCCTTTACTTGTCATGCGCTCTAATCTCTGGGCATCTGGCTATGATGTTGATGGAACTGACCAAAC
+GTCGTTAGGCCAGTTTTCTGGTCGTGTTCAACAGACCTATAAACATTCTGTGCCGCGTTTCTTTGTTCCTGAGCATGG
+CACTATGTTTACTCTTGCGCTTGTTCGTTTTCCGCCTACTGCGACTAAAGAGATTCAGTACCTTAACGCTAAAGGTGC
+TTTGACTTATACCGATATTGCTGGCGACCCTGTTTTGTATGGCAACTTGCCGCCGCGTGAAATTTCTATGAAGGATGT
+TTTCCGTTCTGGTGATTCGTCTAAGAAGTTTAAGATTGCTGAGGGTCAGTGGTATCGTTATGCGCCTTCGTATGTTTC
+TCCTGCTTATCACCTTCTTGAAGGCTTCCCATTCATTCAGGAACCGCCTTCTGGTGATTTGCAAGAACGCGTACTTAT
+TCGCCACCATGATTATGACCAGTGTTTCCAGTCCGTTCAGTTGTTGCAGTGGAATAGTCAGGTTAAATTTAATGTGAC
+CGTTTATCGCAATCTGCCGACCACTCGCGATTCAATCATGACTTCGTGATAAAAGATTGAGTGTGAGGTTATAACGCC
+GAAGCGGTAAAAATTTTAATTTTTGCCGCTGAGGGGTTGACCAAGCGAAGCGCGGTAGGTTTTCTGCTTAGGAGTTTA
+ATCATGTTTCAGACTTTTATTTCTCGCCATAATTCAAACTTTTTTTCTGATAAGCTGGTTCTCACTTCTGTTACTCCA
+GCTTCTTCGGCACCTGTTTTACAGACACCTAAAGCTACATCGTCAACGTTATATTTTGATAGTTTGACGGTTAATGCT
+GGTAATGGTGGTTTTCTTCATTGCATTCAGATGGATACATCTGTCAACGCCGCTAATCAGGTTGTTTCTGTTGGTGCT
+GATATTGCTTTTGATGCCGACCCTAAATTTTTTGC" } } ,
+        seq {
+          id {
+            local
+              str "contig4_1" } ,
+          descr {
+            title "hypothetical protein HMJLFLJH_00003 [Genus species]" ,
+            molinfo {
+              biomol peptide ,
+              tech concept-trans } } ,
+          inst {
+            repr raw ,
+            mol aa ,
+            length 287 ,
+            seq-data
+              ncbieaa "MPDRTEANPNELNQDDARYGFRCCHLKNIWTAPLPPETELSRQMTTSTTSIDIMG
+LQAAYANLHTDQERDYFMQRYHDVISSFGGKTSYDADNRPLLVMRSNLWASGYDVDGTDQTSLGQFSGRVQQTYKHSV
+PRFFVPEHGTMFTLALVRFPPTATKEIQYLNAKGALTYTDIAGDPVLYGNLPPREISMKDVFRSGDSSKKFKIAEGQW
+YRYAPSYVSPAYHLLEGFPFIQEPPSGDLQERVLIRHHDYDQCFQSVQLLQWNSQVKFNVTVYRNLPTTRDSIMTS" } ,
+          annot {
+            {
+              data
+                ftable {
+                  {
+                    id
+                      local
+                        id 6 ,
+                    data
+                      prot {
+                        name {
+                          "hypothetical protein" } } ,
+                    location
+                      int {
+                        from 0 ,
+                        to 286 ,
+                        id
+                          local
+                            str "contig4_1" } } } } } } } ,
+      annot {
+        {
+          data
+            ftable {
+              {
+                id
+                  local
+                    id 5 ,
+                data
+                  cdregion {
+                    frame one ,
+                    code {
+                      id 11 } } ,
+                product
+                  whole
+                    local
+                      str "contig4_1" ,
+                location
+                  int {
+                    from 20 ,
+                    to 883 ,
+                    strand plus ,
+                    id
+                      local
+                        str "contig4" } ,
+                qual {
+                  {
+                    qual "inference" ,
+                    val "ab initio prediction:Prodigal:2.6" } } ,
+                xref {
+                  {
+                    data
+                      gene {
+                        locus-tag "HMJLFLJH_00003" } } } } } } } } ,
+    set {
+      class nuc-prot ,
+      descr {
+        source {
+          org {
+            taxname "Genus species" ,
+            orgname {
+              mod {
+                {
+                  subtype strain ,
+                  subname "strain" } } ,
+              gcode 11 } } } ,
+        comment "Annotated using prokka 1.13 from
+ https://github.com/tseemann/prokka" ,
+        user {
+          type
+            str "NcbiCleanup" ,
+          data {
+            {
+              label
+                str "method" ,
+              data
+                str "SeriousSeqEntryCleanup" } ,
+            {
+              label
+                str "version" ,
+              data
+                int 8 } ,
+            {
+              label
+                str "month" ,
+              data
+                int 3 } ,
+            {
+              label
+                str "day" ,
+              data
+                int 27 } ,
+            {
+              label
+                str "year" ,
+              data
+                int 2018 } } } ,
+        create-date
+          std {
+            year 2018 ,
+            month 3 ,
+            day 27 } } ,
+      seq-set {
+        seq {
+          id {
+            local
+              str "contig5" } ,
+          descr {
+            molinfo {
+              biomol genomic } } ,
+          inst {
+            repr raw ,
+            mol dna ,
+            length 490 ,
+            seq-data
+              iupacna "CTGTTTGGTTCGCTTTGAGTCTTCTTCGGTTCCGACTACCCTCCCGACTGCCTAT
+GATGTTTATCCTTTGAATGGTCGCCATGATGGTGGTTATTATACCGTCAAGGACTGTGTGACTATTGACGTCCTTCCC
+CGTACGCCGGGCAATAACGTTTATGTTGGTTTCATGGTTTGGTCTAACTTTACCGCTACTAAATGCCGCGGATTGGTT
+TCGCTGAATCAGGTTATTAAAGAGATTATTTGTCTCCAGCCACTTAAGTGAGGTGATTTATGTTTGGTGCTATTGCTG
+GCGGTATTGCTTCTGCTCTTGCTGGTGGCGCCATGTCTAAATTGTTTGGAGGCGGTCAAAAAGCCGCCTCCGGTGGCA
+TTCAAGGTGATGTGCTTGCTACCGATAACAATACTGTAGGCATGGGTGATGCTGGTATTAAATCTGCCATTCAAGGCT
+CTAATGTTCCTAACCCTGATGAGGCCGCCCCTAGTTTTGTTTCTG" } } ,
+        seq {
+          id {
+            local
+              str "contig5_1" } ,
+          descr {
+            title "hypothetical protein HMJLFLJH_00004 [Genus species]" ,
+            molinfo {
+              biomol peptide ,
+              tech concept-trans } } ,
+          inst {
+            repr raw ,
+            mol aa ,
+            length 43 ,
+            seq-data
+              ncbieaa "MVLLLAVLLLLLLVAPCLNCLEAVKKPPPVAFKVMCLLPITIL" } ,
+          annot {
+            {
+              data
+                ftable {
+                  {
+                    id
+                      local
+                        id 8 ,
+                    data
+                      prot {
+                        name {
+                          "hypothetical protein" } } ,
+                    location
+                      int {
+                        from 0 ,
+                        to 42 ,
+                        id
+                          local
+                            str "contig5_1" } } } } } } } ,
+      annot {
+        {
+          data
+            ftable {
+              {
+                id
+                  local
+                    id 7 ,
+                data
+                  cdregion {
+                    frame one ,
+                    code {
+                      id 11 } } ,
+                product
+                  whole
+                    local
+                      str "contig5_1" ,
+                location
+                  int {
+                    from 274 ,
+                    to 405 ,
+                    strand plus ,
+                    id
+                      local
+                        str "contig5" } ,
+                qual {
+                  {
+                    qual "inference" ,
+                    val "ab initio prediction:Prodigal:2.6" } } ,
+                xref {
+                  {
+                    data
+                      gene {
+                        locus-tag "HMJLFLJH_00004" } } } } } } } } ,
+    set {
+      class nuc-prot ,
+      descr {
+        source {
+          org {
+            taxname "Genus species" ,
+            orgname {
+              mod {
+                {
+                  subtype strain ,
+                  subname "strain" } } ,
+              gcode 11 } } } ,
+        comment "Annotated using prokka 1.13 from
+ https://github.com/tseemann/prokka" ,
+        user {
+          type
+            str "NcbiCleanup" ,
+          data {
+            {
+              label
+                str "method" ,
+              data
+                str "SeriousSeqEntryCleanup" } ,
+            {
+              label
+                str "version" ,
+              data
+                int 8 } ,
+            {
+              label
+                str "month" ,
+              data
+                int 3 } ,
+            {
+              label
+                str "day" ,
+              data
+                int 27 } ,
+            {
+              label
+                str "year" ,
+              data
+                int 2018 } } } ,
+        create-date
+          std {
+            year 2018 ,
+            month 3 ,
+            day 27 } } ,
+      seq-set {
+        seq {
+          id {
+            local
+              str "contig6" } ,
+          descr {
+            molinfo {
+              biomol genomic } } ,
+          inst {
+            repr raw ,
+            mol dna ,
+            length 1960 ,
+            seq-data
+              iupacna "GTGCTATGGCTAAAGCTGGTAAAGGACTTCTTGAAGGTACGTTGCAGGCTGGCAC
+TTCTGCCGTTTCTGATAAGTTGCTTGATTTGGTTGGACTTGGTGGCAAGTCTGCCGCTGATAAAGGAAAGGATACTCG
+TGATTATCTTGCTGCTGCATTTCCTGAGCTTAATGCTTGGGAGCGTGCTGGTGCTGATGCTTCCTCTGCTGGTATGGT
+TGACGCCGGATTTGAGAATCAAAAAGAGCTTACTAAAATGCAACTGGACAATCAGAAAGAGATTGCCGAGATGCAAAA
+TGAGACTCAAAAAGAGATTGCTGGCATTCAGTCGGCGACTTCACGCCAGAATACGAAAGACCAGGTATATGCACAAAA
+TGAGATGCTTGCTTATCAACAGAAGGAGTCTACTGCTCGCGTTGCGTCTATTATGGAAAACACCAATCTTTCCAAGCA
+ACAGCAGGTTTCCGAGATTATGCGCCAAATGCTTACTCAAGCTCAAACGGCTGGTCAGTATTTTACCAATGACCAAAT
+CAAAGAAATGACTCGCAAGGTTAGTGCTGAGGTTGACTTAGTTCATCAGCAAACGCAGAATCAGCGGTATGGCTCTTC
+TCATATTGGCGCTACTGCAAAGGATATTTCTAATGTCGTCACTGATGCTGCTTCTGGTGTGGTTGATATTTTTCATGG
+TATTGATAAAGCTGTTGCCGATACTTGGAACAATTTCTGGAAAGACGGTAAAGCTGATGGTATTGGCTCTAATTTGTC
+TAGGAAATAACCGTCAGGATTGACACCCTCCCAATTGTATGTTTTCATGCCTCCAAATCTTGGAGGCTTTTTTATGGT
+TCGTTCTTATTACCCTTCTGAATGTCACGCTGATTATTTTGACTTTGAGCGTATCGAGGCTCTTAAACCTGCTATTGA
+GGCTTGTGGCATTTCTACTCTTTCTCAATCCCCAATGCTTGGCTTCCATAAGCAGATGGATAACCGCATCAAGCTCTT
+GGAAGAGATTCTGTCTTTTCGTATGCAGGGCGTTGAGTTCGATAATGGTGATATGTATGTTGACGGCCATAAGGCTGC
+TTCTGACGTTCGTGATGAGTTTGTATCTGTTACTGAGAAGTTAATGGATGAATTGGCACAATGCTACAATGTGCTCCC
+CCAACTTGATATTAATAACACTATAGACCACCGCCCCGAAGGGGACGAAAAATGGTTTTTAGAGAACGAGAAGACGGT
+TACGCAGTTTTGCCGCAAGCTGGCTGCTGAACGCCCTCTTAAGGATATTCGCGATGAGTATAATTACCCCAAAAAGAA
+AGGTATTAAGGATGAGTGTTCAAGATTGCTGGAGGCCTCCACTATGAAATCGCGTAGAGGCTTTGCTATTCAGCGTTT
+GATGAATGCAATGCGACAGGCTCATGCTGATGGTTGGTTTATCGTTTTTGACACTCTCACGTTGGCTGACGACCGATT
+AGAGGCGTTTTATGATAATCCCAATGCTTTGCGTGACTATTTTCGTGATATTGGTCGTATGGTTCTTGCTGCCGAGGG
+TCGCAAGGCTAATGATTCACACGCCGACTGCTATCAGTATTTTTGTGTGCCTGAGTATGGTACAGCTAATGGCCGTCT
+TCATTTCCATGCGGTGCACTTTATGCGGACACTTCCTACAGGTAGCGTTGACCCTAATTTTGGTCGTCGGGTACGCAA
+TCGCCGCCAGTTAAATAGCTTGCAAAATACGTGGCCTTATGGTTACAGTATGCCCATCGCAGTTCGCTACACGCAGGA
+CGCTTTTTCACGTTCTGGTTGGTTGTGGCCTGTTGATGCTAAAGGTGAGCCGCTTAAAGCTACCAGTTATATGGCTGT
+TGGTTTCTATGTGGCTAAATACGTTAACAAAAAGTCAGATATGGACCTTGCTGCTAAAGGTCTAGGAGCTAAAGAATG
+GAACAACTCACTAAAAACCAAGCTGTCGCTACT" } } ,
+        seq {
+          id {
+            local
+              str "contig6_1" } ,
+          descr {
+            title "hypothetical protein HMJLFLJH_00005 [Genus species]" ,
+            molinfo {
+              biomol peptide ,
+              tech concept-trans } } ,
+          inst {
+            repr raw ,
+            mol aa ,
+            length 253 ,
+            seq-data
+              ncbieaa "MAKAGKGLLEGTLQAGTSAVSDKLLDLVGLGGKSAADKGKDTRDYLAAAFPELNA
+WERAGADASSAGMVDAGFENQKELTKMQLDNQKEIAEMQNETQKEIAGIQSATSRQNTKDQVYAQNEMLAYQQKESTA
+RVASIMENTNLSKQQQVSEIMRQMLTQAQTAGQYFTNDQIKEMTRKVSAEVDLVHQQTQNQRYGSSHIGATAKDISNV
+VTDAASGVVDIFHGIDKAVADTWNNFWKDGKADGIGSNLSRK" } ,
+          annot {
+            {
+              data
+                ftable {
+                  {
+                    id
+                      local
+                        id 10 ,
+                    data
+                      prot {
+                        name {
+                          "hypothetical protein" } } ,
+                    location
+                      int {
+                        from 0 ,
+                        to 252 ,
+                        id
+                          local
+                            str "contig6_1" } } } } } } } ,
+      annot {
+        {
+          data
+            ftable {
+              {
+                id
+                  local
+                    id 9 ,
+                data
+                  cdregion {
+                    frame one ,
+                    code {
+                      id 11 } } ,
+                product
+                  whole
+                    local
+                      str "contig6_1" ,
+                location
+                  int {
+                    from 5 ,
+                    to 766 ,
+                    strand plus ,
+                    id
+                      local
+                        str "contig6" } ,
+                qual {
+                  {
+                    qual "inference" ,
+                    val "ab initio prediction:Prodigal:2.6" } } ,
+                xref {
+                  {
+                    data
+                      gene {
+                        locus-tag "HMJLFLJH_00005" } } } } } } } } ,
+    seq {
+      id {
+        local
+          str "contig7" } ,
+      descr {
+        source {
+          org {
+            taxname "Genus species" ,
+            orgname {
+              mod {
+                {
+                  subtype strain ,
+                  subname "strain" } } ,
+              gcode 11 } } } ,
+        molinfo {
+          biomol genomic } ,
+        comment "Annotated using prokka 1.13 from
+ https://github.com/tseemann/prokka" ,
+        user {
+          type
+            str "NcbiCleanup" ,
+          data {
+            {
+              label
+                str "method" ,
+              data
+                str "SeriousSeqEntryCleanup" } ,
+            {
+              label
+                str "version" ,
+              data
+                int 8 } ,
+            {
+              label
+                str "month" ,
+              data
+                int 3 } ,
+            {
+              label
+                str "day" ,
+              data
+                int 27 } ,
+            {
+              label
+                str "year" ,
+              data
+                int 2018 } } } ,
+        create-date
+          std {
+            year 2018 ,
+            month 3 ,
+            day 27 } } ,
+      inst {
+        repr raw ,
+        mol dna ,
+        length 276 ,
+        seq-data
+          iupacna "TCCCAAGAAGCTGTTCAGAATCAGAATGAGCCGCAACTTCGGGATGAAAATGCTCACAA
+TGACAAATCTGTCCACGGAGTGCTTAATCCAACTTACCAAGCTGGGTTACGACGCGACGCCGTTCAACCAGATATTGA
+AGCAGAACGCAAAAAGAGAGATGAGATTGAGGCTGGGAAAAGTTACTGTAGCCGACGTTTTGGCGGCGCAACCTGTGA
+CGACAAATCTGCTCAAATTTATGCGCGCTTCGATAAAAATGATTGGCGTATCCAACCTGCA" } } } }
diff -r 000000000000 -r 8813044f72bf mito-prokka/test-data/out.tbl
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mito-prokka/test-data/out.tbl	Wed May 26 16:01:54 2021 +0000
@@ -0,0 +1,27 @@
+>Feature contig1
+>Feature contig2
+40	498	CDS
+			inference	ab initio prediction:Prodigal:002006
+			locus_tag	HMJLFLJH_00001
+			product	hypothetical protein
+498	614	CDS
+			inference	ab initio prediction:Prodigal:002006
+			locus_tag	HMJLFLJH_00002
+			product	hypothetical protein
+>Feature contig3
+>Feature contig4
+21	884	CDS
+			inference	ab initio prediction:Prodigal:002006
+			locus_tag	HMJLFLJH_00003
+			product	hypothetical protein
+>Feature contig5
+275	406	CDS
+			inference	ab initio prediction:Prodigal:002006
+			locus_tag	HMJLFLJH_00004
+			product	hypothetical protein
+>Feature contig6
+6	767	CDS
+			inference	ab initio prediction:Prodigal:002006
+			locus_tag	HMJLFLJH_00005
+			product	hypothetical protein
+>Feature contig7
diff -r 000000000000 -r 8813044f72bf mito-prokka/test-data/out.tsv
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mito-prokka/test-data/out.tsv	Wed May 26 16:01:54 2021 +0000
@@ -0,0 +1,6 @@
+locus_tag	ftype	length_bp	gene	EC_number	COG	product
+HMJLFLJH_00001	CDS	459				hypothetical protein
+HMJLFLJH_00002	CDS	117				hypothetical protein
+HMJLFLJH_00003	CDS	864				hypothetical protein
+HMJLFLJH_00004	CDS	132				hypothetical protein
+HMJLFLJH_00005	CDS	762				hypothetical protein
diff -r 000000000000 -r 8813044f72bf mito-prokka/test-data/out.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mito-prokka/test-data/out.txt	Wed May 26 16:01:54 2021 +0000
@@ -0,0 +1,4 @@
+organism: Genus species strain 
+contigs: 7
+bases: 5386
+CDS: 5
diff -r 000000000000 -r 8813044f72bf mito-prokka/test-data/phiX174.fasta
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mito-prokka/test-data/phiX174.fasta	Wed May 26 16:01:54 2021 +0000
@@ -0,0 +1,85 @@
+>contig1
+GAGTTTTATCGCTTCCATGACGCAGAAGTTAACACTTTCGGATATTTCTGATGAGTCGAAAAATTATCTT
+GATAAAGCAGGAATTACTACTGCTTGTTTACGAATTAAATCGAAGTGGACTGCTGGCGGAAAATGAGAAA
+ATTCGACCTATCCTTGCGCAGCTCGAGAAGCTCTTACTTTGCGACCTTTCGCCATCAACTAACGATTCTG
+TCAAAAACTGACGCGTTGGATGAGGAGAAGTGGCTTAATATGCTTGGCACGTTCGTCAAGGACTGGTTTA
+GATATGAGTCACATTTTGTTCATGGTAGAGATTCTCTTGTTGACATTTTAAAAGAGCGTGGATTACTATC
+>contig2
+TGAGTCCGATGCTGTTCAACCACTAATAGGTAAGAAATCATGAGTCAAGTTACTGAACAATCCGTACGTT
+TCCAGACCGCTTTGGCCTCTATTAAGCTCATTCAGGCTTCTGCCGTTTTGGATTTAACCGAAGATGATTT
+CGATTTTCTGACGAGTAACAAAGTTTGGATTGCTACTGACCGCTCTCGTGCTCGTCGCTGCGTTGAGGCT
+TGCGTTTATGGTACGCTGGACTTTGTGGGATACCCTCGCTTTCCTGCTCCTGTTGAGTTTATTGCTGCCG
+TCATTGCTTATTATGTTCATCCCGTCAACATTCAAACGGCCTGTCTCATCATGGAAGGCGCTGAATTTAC
+GGAAAACATTATTAATGGCGTCGAGCGTCCGGTTAAAGCCGCTGAATTGTTCGCGTTTACCTTGCGTGTA
+CGCGCAGGAAACACTGACGTTCTTACTGACGCAGAAGAAAACGTGCGTCAAAAATTACGTGCGGAAGGAG
+TGATGTAATGTCTAAAGGTAAAAAACGTTCTGGCGCTCGCCCTGGTCGTCCGCAGCCGTTGCGAGGTACT
+AAAGGCAAGCGTAAAGGCGCTCGTCTTTGGTATGTAGGTGGTCAACAATTTTAATTGCAGGGGCTTCGGC
+CCCTTACTTGAGGATAAATTATGTCTAATATTCAAACTGGCGCCGAGCGTATGCCGCATGACCTTTCCCA
+TCTTGGCTTCCTTGCTGGTCAGATTGGTCGTCTTATTACCATTTCAACTACTCCGGTTATCGCTGGCGAC
+TCCTTCGAGATGGACGCCGTTGGCGCTCTCCGTCTTTCTCCATTGCGTCGTGGCCTTGCTATTGACTCTA
+>contig3
+CTGTAGACATTTTTACTTTTTATGTCCCTCATCGTCACGTTTATGGTGAACAGTGGATTAAGTTCATGAA
+GGATGGTGTTAATGCCACTCCTCTCCCGACTGTTAACACTACTGGTTATATTGACCATGCCGCTTTTCTT
+GGCACGATTAACCCTGATACCAATAAAATCCCTAAGCATTTGTTTCAGGGTTATTTGAATATCTATAACA
+>contig4
+ACTATTTTAAAGCGCCGTGGATGCCTGACCGTACCGAGGCTAACCCTAATGAGCTTAATCAAGATGATGC
+TCGTTATGGTTTCCGTTGCTGCCATCTCAAAAACATTTGGACTGCTCCGCTTCCTCCTGAGACTGAGCTT
+TCTCGCCAAATGACGACTTCTACCACATCTATTGACATTATGGGTCTGCAAGCTGCTTATGCTAATTTGC
+ATACTGACCAAGAACGTGATTACTTCATGCAGCGTTACCATGATGTTATTTCTTCATTTGGAGGTAAAAC
+CTCTTATGACGCTGACAACCGTCCTTTACTTGTCATGCGCTCTAATCTCTGGGCATCTGGCTATGATGTT
+GATGGAACTGACCAAACGTCGTTAGGCCAGTTTTCTGGTCGTGTTCAACAGACCTATAAACATTCTGTGC
+CGCGTTTCTTTGTTCCTGAGCATGGCACTATGTTTACTCTTGCGCTTGTTCGTTTTCCGCCTACTGCGAC
+TAAAGAGATTCAGTACCTTAACGCTAAAGGTGCTTTGACTTATACCGATATTGCTGGCGACCCTGTTTTG
+TATGGCAACTTGCCGCCGCGTGAAATTTCTATGAAGGATGTTTTCCGTTCTGGTGATTCGTCTAAGAAGT
+TTAAGATTGCTGAGGGTCAGTGGTATCGTTATGCGCCTTCGTATGTTTCTCCTGCTTATCACCTTCTTGA
+AGGCTTCCCATTCATTCAGGAACCGCCTTCTGGTGATTTGCAAGAACGCGTACTTATTCGCCACCATGAT
+TATGACCAGTGTTTCCAGTCCGTTCAGTTGTTGCAGTGGAATAGTCAGGTTAAATTTAATGTGACCGTTT
+ATCGCAATCTGCCGACCACTCGCGATTCAATCATGACTTCGTGATAAAAGATTGAGTGTGAGGTTATAAC
+GCCGAAGCGGTAAAAATTTTAATTTTTGCCGCTGAGGGGTTGACCAAGCGAAGCGCGGTAGGTTTTCTGC
+TTAGGAGTTTAATCATGTTTCAGACTTTTATTTCTCGCCATAATTCAAACTTTTTTTCTGATAAGCTGGT
+TCTCACTTCTGTTACTCCAGCTTCTTCGGCACCTGTTTTACAGACACCTAAAGCTACATCGTCAACGTTA
+TATTTTGATAGTTTGACGGTTAATGCTGGTAATGGTGGTTTTCTTCATTGCATTCAGATGGATACATCTG
+TCAACGCCGCTAATCAGGTTGTTTCTGTTGGTGCTGATATTGCTTTTGATGCCGACCCTAAATTTTTTGC
+>contig5
+CTGTTTGGTTCGCTTTGAGTCTTCTTCGGTTCCGACTACCCTCCCGACTGCCTATGATGTTTATCCTTTG
+AATGGTCGCCATGATGGTGGTTATTATACCGTCAAGGACTGTGTGACTATTGACGTCCTTCCCCGTACGC
+CGGGCAATAACGTTTATGTTGGTTTCATGGTTTGGTCTAACTTTACCGCTACTAAATGCCGCGGATTGGT
+TTCGCTGAATCAGGTTATTAAAGAGATTATTTGTCTCCAGCCACTTAAGTGAGGTGATTTATGTTTGGTG
+CTATTGCTGGCGGTATTGCTTCTGCTCTTGCTGGTGGCGCCATGTCTAAATTGTTTGGAGGCGGTCAAAA
+AGCCGCCTCCGGTGGCATTCAAGGTGATGTGCTTGCTACCGATAACAATACTGTAGGCATGGGTGATGCT
+GGTATTAAATCTGCCATTCAAGGCTCTAATGTTCCTAACCCTGATGAGGCCGCCCCTAGTTTTGTTTCTG
+>contig6
+GTGCTATGGCTAAAGCTGGTAAAGGACTTCTTGAAGGTACGTTGCAGGCTGGCACTTCTGCCGTTTCTGA
+TAAGTTGCTTGATTTGGTTGGACTTGGTGGCAAGTCTGCCGCTGATAAAGGAAAGGATACTCGTGATTAT
+CTTGCTGCTGCATTTCCTGAGCTTAATGCTTGGGAGCGTGCTGGTGCTGATGCTTCCTCTGCTGGTATGG
+TTGACGCCGGATTTGAGAATCAAAAAGAGCTTACTAAAATGCAACTGGACAATCAGAAAGAGATTGCCGA
+GATGCAAAATGAGACTCAAAAAGAGATTGCTGGCATTCAGTCGGCGACTTCACGCCAGAATACGAAAGAC
+CAGGTATATGCACAAAATGAGATGCTTGCTTATCAACAGAAGGAGTCTACTGCTCGCGTTGCGTCTATTA
+TGGAAAACACCAATCTTTCCAAGCAACAGCAGGTTTCCGAGATTATGCGCCAAATGCTTACTCAAGCTCA
+AACGGCTGGTCAGTATTTTACCAATGACCAAATCAAAGAAATGACTCGCAAGGTTAGTGCTGAGGTTGAC
+TTAGTTCATCAGCAAACGCAGAATCAGCGGTATGGCTCTTCTCATATTGGCGCTACTGCAAAGGATATTT
+CTAATGTCGTCACTGATGCTGCTTCTGGTGTGGTTGATATTTTTCATGGTATTGATAAAGCTGTTGCCGA
+TACTTGGAACAATTTCTGGAAAGACGGTAAAGCTGATGGTATTGGCTCTAATTTGTCTAGGAAATAACCG
+TCAGGATTGACACCCTCCCAATTGTATGTTTTCATGCCTCCAAATCTTGGAGGCTTTTTTATGGTTCGTT
+CTTATTACCCTTCTGAATGTCACGCTGATTATTTTGACTTTGAGCGTATCGAGGCTCTTAAACCTGCTAT
+TGAGGCTTGTGGCATTTCTACTCTTTCTCAATCCCCAATGCTTGGCTTCCATAAGCAGATGGATAACCGC
+ATCAAGCTCTTGGAAGAGATTCTGTCTTTTCGTATGCAGGGCGTTGAGTTCGATAATGGTGATATGTATG
+TTGACGGCCATAAGGCTGCTTCTGACGTTCGTGATGAGTTTGTATCTGTTACTGAGAAGTTAATGGATGA
+ATTGGCACAATGCTACAATGTGCTCCCCCAACTTGATATTAATAACACTATAGACCACCGCCCCGAAGGG
+GACGAAAAATGGTTTTTAGAGAACGAGAAGACGGTTACGCAGTTTTGCCGCAAGCTGGCTGCTGAACGCC
+CTCTTAAGGATATTCGCGATGAGTATAATTACCCCAAAAAGAAAGGTATTAAGGATGAGTGTTCAAGATT
+GCTGGAGGCCTCCACTATGAAATCGCGTAGAGGCTTTGCTATTCAGCGTTTGATGAATGCAATGCGACAG
+GCTCATGCTGATGGTTGGTTTATCGTTTTTGACACTCTCACGTTGGCTGACGACCGATTAGAGGCGTTTT
+ATGATAATCCCAATGCTTTGCGTGACTATTTTCGTGATATTGGTCGTATGGTTCTTGCTGCCGAGGGTCG
+CAAGGCTAATGATTCACACGCCGACTGCTATCAGTATTTTTGTGTGCCTGAGTATGGTACAGCTAATGGC
+CGTCTTCATTTCCATGCGGTGCACTTTATGCGGACACTTCCTACAGGTAGCGTTGACCCTAATTTTGGTC
+GTCGGGTACGCAATCGCCGCCAGTTAAATAGCTTGCAAAATACGTGGCCTTATGGTTACAGTATGCCCAT
+CGCAGTTCGCTACACGCAGGACGCTTTTTCACGTTCTGGTTGGTTGTGGCCTGTTGATGCTAAAGGTGAG
+CCGCTTAAAGCTACCAGTTATATGGCTGTTGGTTTCTATGTGGCTAAATACGTTAACAAAAAGTCAGATA
+TGGACCTTGCTGCTAAAGGTCTAGGAGCTAAAGAATGGAACAACTCACTAAAAACCAAGCTGTCGCTACT
+>contig7
+TCCCAAGAAGCTGTTCAGAATCAGAATGAGCCGCAACTTCGGGATGAAAATGCTCACAATGACAAATCTG
+TCCACGGAGTGCTTAATCCAACTTACCAAGCTGGGTTACGACGCGACGCCGTTCAACCAGATATTGAAGC
+AGAACGCAAAAAGAGAGATGAGATTGAGGCTGGGAAAAGTTACTGTAGCCGACGTTTTGGCGGCGCAACC
+TGTGACGACAAATCTGCTCAAATTTATGCGCGCTTCGATAAAAATGATTGGCGTATCCAACCTGCA
+