# HG changeset patch
# User iuc
# Date 1663577262 0
# Node ID 2b6e795b22a978f2c87af9441a59aedb2912c6be

planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/plasmidfinder commit 32b1446d0da698b945d7f8b5df6d251b9989d3b1

diff -r 000000000000 -r 2b6e795b22a9 macro.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macro.xml	Mon Sep 19 08:47:42 2022 +0000
@@ -0,0 +1,23 @@
+
+<macros>
+  <token name="@TOOL_VERSION@">2.1.6</token>
+  <token name="@VERSION_SUFFIX@">0</token>
+  <token name="@PROFILE@">21.05</token>
+  <token name="@THREADS@">\${GALAXY_SLOTS:-7}</token>
+
+  <xml name="xrefs">
+    <xrefs>
+      <xref type='bio.tools'>PlasmidFinder</xref>
+    </xrefs>
+  </xml>
+  <xml name="requirements">
+    <requirements>
+      <requirement type="package" version="@TOOL_VERSION@">plasmidfinder</requirement>
+    </requirements>
+  </xml>
+  <xml name="citations">
+      <citations>
+          <citation type="doi">10.1007/978-1-4939-9877-7_20</citation>
+      </citations>
+  </xml>
+</macros>
diff -r 000000000000 -r 2b6e795b22a9 plasmidfinder.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/plasmidfinder.xml	Mon Sep 19 08:47:42 2022 +0000
@@ -0,0 +1,149 @@
+<tool id="plasmidfinder" name="PlasmidFinder" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+    <description>
+        Plasmid identification in bacteria.
+    </description>
+    <macros>
+        <import>macro.xml</import>
+    </macros>
+    <expand macro='xrefs'/>
+    <expand macro="requirements" />
+    <command detect_errors="aggressive"><![CDATA[
+        mkdir output_dir &&
+        mkdir temp_dir &&
+        plasmidfinder.py
+        -i '$input.input_file'
+        -p '$input.database_name.fields.path'
+        -l '$options.min_cov'
+        -t '$options.threshold'
+        #if $input.input_file.ext == 'fasta' or $input.input_file.ext == 'fasta.gz'
+            -mp blastn
+        #else if $input.input_file.ext == 'fastqsanger.gz' or $input.input_file.ext == 'fastqsanger'
+            -mp kma
+        #end if
+        -x
+        -o output_dir
+        -tmp temp_dir
+        #*======================================
+                            LOG file
+        ======================================*#
+        | tee '$log_file'
+        ]]>
+    </command>
+    <inputs>
+        <section name="input" title="Input parameters" expanded="true">
+            <param name="input_file" type="data" format="fasta,fastq,fasta.gz,fastq.gz" label="Choose a fasta or fastq file" help="File to be analyzed"/>
+            <param name="database_name" type="select" label="PlasmidFinder database">
+                <options from_data_table="plasmidfinder_db">
+                    <validator message="No PlasmidFinder database is available" type="no_options"/>
+                </options>
+            </param>
+        </section>
+        <section name="options" title="Options">
+            <param name="min_cov" type="float" min="0" max="1" value="0.6" label="Minimal coverage" help="Choose a minimum coverage value (default: 0.6)"/>
+            <param name="threshold" type="float" min="0" max="1" value="0.95" label="Minimal identity" help="Choose a minimum identity value (default: 0.95)"/>
+        </section>
+        <section name="output_files" title="Output file selection">
+            <param name="output_selection" type="select" display="checkboxes" multiple="true" label="Output files selection">
+              <option value="data_json">JSON file result</option>
+              <option value="hit_fasta" selected="true">Hits in genome</option>
+              <option value="plasmid_fasta" selected="true">Plasmid hits</option>
+              <option value="result_tsv" selected="true">Plasmid results</option>
+              <option value="result_txt" selected="true">Raw results</option>
+              <option value="logfile">Log file</option>
+            </param>
+        </section>
+    </inputs>
+    <outputs>
+        <data name="json_file" format="json" from_work_dir="output_dir/data.json" label="${tool.name} on ${on_string}: data.json">
+            <filter>  "data_json" in output_files['output_selection'] </filter>
+        </data>
+        <data name="hit_file" format="fasta" from_work_dir="output_dir/Hit_in_genome_seq.fsa" label="${tool.name} on ${on_string}: hit_in_genome.fasta">
+            <filter>  "hit_fasta" in output_files['output_selection'] </filter>
+        </data>
+        <data name="plasmid_file" format="fasta" from_work_dir="output_dir/Plasmid_seqs.fsa" label="${tool.name} on ${on_string}: plasmid.fasta">
+            <filter> "plasmid_fasta" in output_files['output_selection'] </filter>
+        </data>
+        <data name="result_file" format="tabular" from_work_dir="output_dir/results_tab.tsv" label="${tool.name} on ${on_string}: results.tsv">
+            <filter>  "result_tsv" in output_files['output_selection'] </filter>
+        </data>
+        <data name="raw_file" format="txt" from_work_dir="output_dir/results.txt" label="${tool.name} on ${on_string}: raw_result.txt">
+            <filter>  "result_txt" in output_files['output_selection'] </filter>
+        </data>
+        <data name="log_file" format="txt" from_work_dir="output_dir" label="${tool.name} on ${on_string}: log file">
+            <filter>  "logfile" in output_files['output_selection'] </filter>
+        </data>
+    </outputs>
+    <tests>
+        <!--test_1 with default value and all output files for contigs -->
+        <test expect_num_outputs="6">
+              <section name="input">
+                  <param name="input_file" value="contigs.fasta"/>
+                  <param name="input_type" value="genome"/>
+                  <param name="database_name" value="test-plasmindfinder-db"/>
+              </section>
+              <section name="output_files">
+                  <param name="output_selection" value="data_json,hit_fasta,plasmid_fasta,result_tsv,result_txt,logfile"/>
+              </section>
+              <output name="json_file" value="test_1/data_test1.json" ftype="json" compare="sim_size"/>
+              <output name="hit_file" value="test_1/Hit_in_genome_seq_test1.fsa" ftype="fasta"/>
+              <output name="plasmid_file" value="test_1/Plasmid_seqs_test1.fsa" ftype="fasta"/>
+              <output name="result_file" value="test_1/results_tab_test1.tsv"/>
+              <output name="raw_file" value="test_1/results_test1.txt" lines_diff="2"/>
+              <output name="log_file" value="test_1/logfile_test1.log" lines_diff="7"/>
+        </test>
+        <!--test_2 with default value and for fastq file -->
+        <test expect_num_outputs="4">
+              <section name="input">
+                  <param name="input_file" value="data.fastq.gz"/>
+                  <param name="input_type" value="raw"/>
+                  <param name="database_name" value="test-plasmindfinder-db"/>
+              </section>
+              <section name="output_files">
+                  <param name="output_selection" value="data_json,result_tsv,result_txt,logfile"/>
+              </section>
+              <output name="json_file" value="test_2/data_test2.json" ftype="json" compare="sim_size"/>
+              <output name="result_file" value="test_2/results_tab_test2.tsv"/>
+              <output name="raw_file" value="test_2/results_test2.txt" lines_diff="2"/>
+              <output name="log_file" value="test_2/logfile_test2.log" lines_diff="7"/>
+        </test>
+        <!--test_3 with default value and for fastq file -->
+        <test expect_num_outputs="3">
+              <section name="input">
+                  <param name="input_file" value="contigs.fasta"/>
+                  <param name="input_type" value="genome"/>
+                  <param name="database_name" value="test-plasmindfinder-db"/>
+              </section>
+              <section name="options">
+                  <param name="min_cov" value="0.2" />
+                  <param name="threshold" value="0.6"/>
+              </section>
+              <section name="output_files">
+                  <param name="output_selection" value="hit_fasta,plasmid_fasta,result_tsv"/>
+              </section>
+              <output name="hit_file" value="test_3/Hit_in_genome_seq_test3.fsa" ftype="fasta"/>
+              <output name="plasmid_file" value="test_3/Plasmid_seqs_test3.fsa" ftype="fasta"/>
+              <output name="result_file" value="test_3/results_tab_test3.tsv"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+      **What it does**
+      PlasmidFinder characterize plasmid sequences into whole genome sequencing.
+      It is based on [plasmidfinder database](https://bitbucket.org/genomicepidemiology/plasmidfinder_db/) with hundreds sequences.
+      **Input**
+      It can analyse raw data using a k-mer approach based on KMA or a blastn for genome assembly.
+      A database is need obtained from the plasmidfinder database.
+      **Options**
+      You can modify the coverage value (% of matching sequence on the total target sequence)
+      You can modify the identity threshold (% of shared nucleotide on the match)
+      **Output**
+      Some output files are availables
+      - A fasta file with all available hits detected in the genome
+      - A fasta file with all plasmid sequences from the database
+      - A summary of the analysis in tabular format
+      - A Raw result file in text format
+      - A JSON file could be use for other boinformatic analaysis
+      - A log file with analysis parameters
+
+    ]]></help>
+      <expand macro="citations"/>
+</tool>
diff -r 000000000000 -r 2b6e795b22a9 test-data/contigs.fasta
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/contigs.fasta	Mon Sep 19 08:47:42 2022 +0000
@@ -0,0 +1,603 @@
+>contig00001 len=5513 cov=11.7 corr=0 origname=NODE_1_length_5513_cov_11.741181_pilon sw=shovill-spades/1.1.0 date=20220302
+CAGCATCGGACTCAGATAGTAATCCACGCTCTTTTAAAATGTCAACAAGAGAATCTCTAC
+CATGAACAAAATGTGACTCATATCTAAACCAGTCCTTGACGAACGTGCCAAGCATATTAA
+GCCACTTCTCCTCATCCAACGCGTCAGTTTTTGACAGAATCGTTAGTTGATGGCGAAAGG
+TCGCAAAGTAAGAGCTTCTCGAGCTGCGCAAGGATAGGTCGAATTTTCTCATTTTCCGCC
+AGCAGTCCACTTCGATTTAATTCGTAAACAAGCAGTAGTAATTCCTGCTTTATCAAGATA
+ATTTTTCGACTCATCAGAAATATCCGAAAGTGTTAACTTCTGCGTCATGGAAGCGATAAA
+ACTCTGCAGGTTGGATACGCCAATCATTTTTATCGAAGCGCGCATAAATTTGAGCAGATT
+TGTCGTCACAGGTTGCGCCGCCAAAACGTCGGCTACAGTAACTTTTCCCAGCCTCAATCT
+CATCTCTCTTTTTGCGTTCTGCTTCAATATCTGGTTGAACGGCGTCGCGTCGTAACCCAG
+CTTGGTAAGTTGGATTAAGCACTCCGTGGACAGATTTGTCATTGTGAGCATTTTCATCCC
+GAAGTTGCGGCTCATTCTGATTCTGAACAGCTTCTTGGGAAGTAGCGACAGCTTGGTTTT
+TAGTGAGTTGTTCCATTCTTTAGCTCCTAGACCTTTAGCAGCAAGGTCCATATCTGACTT
+TTTGTTAACGTATTTAGCCACATAGAAACCAACAGCCATATAACTGGTAGCTTTAAGCGG
+CTCACCTTTAGCATCAACAGGCCACAACCAACCAGAACGTGAAAAAGCGTCCTGCGTGTA
+GCGAACTGCGATGGGCATACTGTAACCATAAGGCCACGTATTTTGCAAGCTATTTAACTG
+GCGGCGATTGCGTACCCGACGACCAAAATTAGGGTCAACGCTACCTGTAGGAAGTGTCCG
+CATAAAGTGCACCGCATGGAAATGAAGACGGCCATTAGCTGTACCATACTCAGGCACACA
+AAAATACTGATAGCAGTCGGCGTGTGAATCATTAGCCTTGCGACCCTCGGCAGCAAGAAC
+CATACGACCAATATCACGAAAATAGTCACGCAAAGCATTGGGATTATCATAAAACGCCTC
+TAATCGGTCGTCAGCCAACGTGAGAGTGTCAAAAACGATAAACCAACCATCAGCATGAGC
+CTGTCGCATTGCATTCATCAAACGCTGAATAGCAAAGCCTCTACGCGATTTCATAGTGGA
+GGCCTCCAGCAATCTTGAACACTCATCCTTAATACCTTTCTTTTTGGGGTAATTATACTC
+ATCGCGAATATCCTTAAGAGGGCGTTCAGCAGCCAGCTTGCGGCAAAACTGCGTAACCGT
+CTTCTCGTTCTCTAAAAACCATTTTTCGTCCCCTTCGGGGCGGTGGTCTATAGTGTTATT
+AATATCAAGTTGGGGGAGCACATTGTAGCATTGTGCCAATTCATCCATTAACTTCTCAGT
+AACAGATACAAACTCATCACGAACGTCAGAAGCAGCCTTATGGCCGTCAACATACATATC
+ACCATTATCGAACTCAACGCCCTGCATACGAAAAGACAGAATCTCTTCCAAGAGCTTGAT
+GCGGTTATCCATCTGCTTATGGAAGCCAAGCATTGGGGATTGAGAAAGAGTAGAAATGCC
+ACAAGCCTCAATAGCAGGTTTAAGAGCCTCGATACGCTCAAAGTCAAAATAATCAGCGTG
+ACATTCAGAAGGGTAATAAGAACGAACCATAAAAAAGCCTCCAAGATTTGGAGGCATGAA
+AACATACAATTGGGAGGGTGTCAATCCTGACGGTTATTTCCTAGACAAATTAGAGCCAAT
+ACCATCAGCTTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCAACAGCTTTATCAAT
+ACCATGAAAAATATCAACCACACCAGAAGCAGCATCAGTGACGACATTAGAAATATCCTT
+TGCAGTAGCGCCAATATGAGAAGAGCCATACCGCTGATTCTGCGTTTGCTGATGAACTAA
+GTCAACCTCAGCACTAACCTTGCGAGTCATTTCTTTGATTTGGTCATTGGTAAAATACTG
+ACCAGCCGTTTGAGCTTGAGTAAGCATTTGGCGCATAATCTCGGAAACCTGCTGTTGCTT
+GGAAAGATTGGTGTTTTCCATAATAGACGCAACGCGAGCAGTAGACTCCTTCTGTTGATA
+AGCAAGCATCTCATTTTGTGCATATACCTGGTCTTTCGTATTCTGGCGTGAAGTCGCCGA
+CTGAATGCCAGCAATCTCTTTTTGAGTCTCATTTTGCATCTCGGCAATCTCTTTCTGATT
+GTCCAGTTGCATTTTAGTAAGCTCTTTTTGATTCTCAAATCCGGCGTCAACCATACCAGC
+AGAGGAAGCATCAGCACCAGCACGCTCCCAAGCATTAAGCTCAGGAAATGCAGCAGCAAG
+ATAATCACGAGTATCCTTTCCTTTATCAGCGGCAGACTTGCCACCAAGTCCAACCAAATC
+AAGCAACTTATCAGAAACGGCAGAAGTGCCAGCCTGCAACGTACCTTCAAGAAGTCCTTT
+ACCAGCTTTAGCCATAGCACCAGAAACAAAACTAGGGACGGCCTCATCAGGGTTAGGAAC
+ATTAGAGCCTTGAATGGCAGATTTAATACCAGCATCACCCATGCCTACAGTATTGTTATC
+GGTAGCAAGCACATCACCTTGAATGCCACCGGAGGCGGCTTTTTGACCGCCTCCAAACAA
+TTTAGACATGGCGCCACCAGCAAGAGCAGAAGCAATACCGCCAGCAATAGCACCAAACAT
+AAATCACCTCACTTAAGTGGCTGGAGACAAATAATCTCTTTAATAACCTGATTCAGCGAA
+ACCAATCCGCGGCATTTAGTAGCGGTAAAGTTAGACCAAACCATGAAACCAACATAAACA
+TTATTGCCCGGCGTACGGGGAAGGACGTCAATAGTCACACAGTCCTTGACGGTATAATAA
+CCACCATCATGGCGACCATCCAAAGGATAAACATCATAGGCAGTCGGGAGGGTAGTCGGA
+ACCGAAGAAGACTCAAAGCGAACCAAACAGGCAAAAAATTTAGGGTCGGCATCAAAAGCA
+ATATCAGCACCAACAGAAACAACCTGATTAGCGGCGTTGACAGATGTATCCATCTGAATG
+CAATGAAGAAAACCACCATTACCAGCATTAACCGTCAAACTATCAAAATATAACGTTGAC
+GATGTAGCTTTAGGTGTCTGTAAAACAGGTGCCGAAGAAGCTGGAGTAACAGAAGTGAGA
+ACCAGCTTATCAGAAAAAAAGTTTGAATTATGGCGAGAAATAAAAGTCTGAAACATGATT
+AAACTCCTAAGCAGAAAACCTACCGCGCTTCGCTTGGTCAACCCCTCAGCGGCAAAAATT
+AAAATTTTTACCGCTTCGGCGTTATAACCTCACACTCAATCTTTTATCACGAAGTCATGA
+TTGAATCGCGAGTGGTCGGCAGATTGCGATAAACGGTCACATTAAATTTAACCTGACTAT
+TCCACTGCAACAACTGAACGGACTGGAAACACTGGTCATAATCATGGTGGCGAATAAGTA
+CGCGTTCTTGCAAATCACCAGAAGGCGGTTCCTGAATGAATGGGAAGCCTTCAAGAAGGT
+GATAAGCAGGAGAAACATACGAAGGCGCATAACGATACCACTGACCCTCAGCAATCTTAA
+ACTTCTTAGACGAATCACCAGAACGGAAAACATCCTTCATAGAAATTTCACGCGGCGGCA
+AGTTGCCATACAAAACAGGGTCGCCAGCAATATCGGTATAAGTCAAAGCACCTTTAGCGT
+TAAGGTACTGAATCTCTTTAGTCGCAGTAGGCGGAAAACGAACAAGCGCAAGAGTAAACA
+TAGTGCCATGCTCAGGAACAAAGAAACGCGGCACAGAATGTTTATAGGTCTGTTGAACAC
+GACCAGAAAACTGGCCTAACGACGTTTGGTCAGTTCCATCAACATCATAGCCAGATGCCC
+AGAGATTAGAGCGCATGACAAGTAAAGGACGGTTGTCAGCGTCATAAGAGGTTTTACCTC
+CAAATGAAGAAATAACATCATGGTAACGCTGCATGAAGTAATCACGTTCTTGGTCAGTAT
+GCAAATTAGCATAAGCAGCTTGCAGACCCATAATGTCAATAGATGTGGTAGAAGTCGTCA
+TTTGGCGAGAAAGCTCAGTCTCAGGAGGAAGCGGAGCAGTCCAAATGTTTTTGAGATGGC
+AGCAACGGAAACCATAACGAGCATCATCTTGATTAAGCTCATTAGGGTTAGCCTCGGTAC
+GGTCAGGCATCCACGGCGCTTTAAAATAGTTGTTATAGATATTCAAATAACCCTGAAACA
+AATGCTTAGGGATTTTATTGGTATCAGGGTTAATCGTGCCAAGAAAAGCGGCATGGTCAA
+TATAACCAGTAGTGTTAACAGTCGGGAGAGGAGTGGCATTAACACCATCCTTCATGAACT
+TAATCCACTGTTCACCATAAACGTGACGATGAGGGACATAAAAAGTAAAAATGTCTACAG
+TAGAGTCAATAGCAAGGCCACGACGCAATGGAGAAAGACGGAGAGCGCCAACGGCGTCCA
+TCTCGAAGGAGTCGCCAGCGATAACCGGAGTAGTTGAAATGGTAATAAGACGACCAATCT
+GACCAGCAAGGAAGCCAAGATGGGAAAGGTCATGCGGCATACGCTCGGCGCCAGTTTGAA
+TATTAGACATAATTTATCCTCAAGTAAGGGGCCGAAGCCCCTGCAATTAAAATTGTTGAC
+CACCTACATACCAAAGACGAGCGCCTTTACGCTTGCCTTTAGTACCTCGCAACGGCTGCG
+GACGACCAGGGCGAGCGCCAGAACGTTTTTTACCTTTAGACATTACATCACTCCTTCTGC
+ACGTAATTTTTGACGCACGTTTTCTTCTGCGTCAGTAAGAACGTCAGTGTTTCCTGCGCG
+TACACGCAAGGTAAACGCGAACAATTCAGCGGCTTTAACCGGACGCTCGACGCCATTAAT
+AATGTTTTCCGTAAATTCAGCGCCTTCCATGATGAGACAGGCCGTTTGAATGTTGACGGG
+ATGAACATAATAAGCAATGACGGCAGCAATAAACTCAACAGGAGCAGGAAAGCGAGGGTA
+TCCTACAAAGTCCAGCGTACCATAAACGCAAGCCTCAACGCAGCGACGAGCACGAGAGCG
+GTCAGTAGCAATCCAAACTTTGTTACTCGTCAGAAAATCGAAATCATCTTCGGTTAAATC
+CAAAACGGCAGAAGCCTGAATGAGCTTAATAGAGGCCAAAGCGGTCTGGAAACGTACGGA
+TTGTTCAGTAACTTGACTCATGATTTCTTACCTATTAGTGGTTGAACAGCATCGGACTCA
+GATAGTAATCCACGCTCTTTTAAAATGTCAACAAGAGAATCTCTACCATGAACAAAATGT
+GACTCATATCTAAACCAGTCCTTGACGAACGTGCCAAGCATATTAAGCCACTT
+>contig00002 len=3532 cov=5.1 corr=0 origname=NODE_2_length_3532_cov_5.072834_pilon sw=shovill-spades/1.1.0 date=20220302
+CGGACTACCGTCCCGAAATACTCATATAAATGCCAAAAACCATTTGCTGTCAAAACGGCG
+TAACAATTTCCTACTGTCAGTTTCTTTTTAATTTCTGCTTTACTGGAACCATATTTATGT
+TGAGCATATTGGTCCCACTCTGCAAACTCATTTCCCTTGATCATCTGATTGAATGTATTG
+TCAGAAACAAAATAATAATCCTCTTGATCTTTTTCCCCAGGTCTTGGTGATCGATTCGTG
+TAAGTAATGATCTTTTGTTCCGGCTGAAAAATAGCTTCTGCGAGTGAAGTTTTTCCAGAA
+CCAGAAGGACCGATAAATACATAGCAATAATTCATTGTCATTTCTCCTTTGATGATTGAA
+CAAGTGAAAAAGCTTTGGAAAATATTTCCAAAGCTTTTAAAAGTAACTTTGCTTTTTTGT
+ATATTATACCAGCAAGCCAGTCACAATAGCACTTAAAAAGCTGACTAAAGTCGCTGTTAG
+CAAAATTTTCAATCCGTGTTTTGCGACAAGATTTCCTTTTTCTTCATTTAATCCCTTCAT
+CGCACCAGAAATGATCCCGATAGAAGAGAAGTTGGCAAATGAAACGAGGAAGACAGATAT
+AATTGCTGTTGTACGCTCAGTAAAATGGAAAGATTTTCTGTAGTTGCTTCTTTCCGTTTC
+TTTGTGAATTTTTACCAGTCATTTTTTACTGGATTGTTATTTTTTATAAAATATGATAAA
+ATTTTGGTAGCGCTTTATAAGCGCGTTGCTTTTTCAAGAATAAACTCTCATTATTTTTTT
+AACTGGCTGCTCGAAAGAGCAGTCTTTTTTATTATTTATCCGTCTCTTTTACAAACAATT
+CTTCGTTAGGACTGTTGTAATAATTTGAATTTAATTTAAGTTCTCCGTTGGAATTGTTTT
+TTCCAATTACGGATAATAGCATGGGGCTAAAACCTAATATTCCTAGAGAAATAGAACCCA
+GTACCAACACAGTTTTTTTTAACATAGGTTATACCTCCACTTTTTTTAACGCTACCACTT
+GTATACACATTTTAAATACTAGCCTTCAGTTTATCAAATGTTTAAATTGAACGGATATAA
+ATCAAAATTAAATTTTCAAAAGTTGTTCTAAAAAATTTTTCTTTTTTGGAAGTTACTCTA
+ACTTTTTTTGCTTGTGGTGCTTGGTATGTTTTCTTCGCCGACCGTTTAGGTTCTTGACCA
+TTTTCTCTTATAAGTGGGATTTTTACCACGTTGAGAGAAAATGGTCAAGAACCTGGGAGG
+CGGAGAATGCCCTTAATACCAAGCACCGCAAGCCTTTCCCATACTTTATTCGATGATCCC
+ACGATGATCTCATAATGATTCTACAATGACCCTACGATGATCAAAATTCTCAAAAAAAAT
+AAACGAAATTTCAAACGATTTTTTTGAAATTTTGTTAAAATCACATTTGTTTTTTTATGA
+CTTTTTCAACAAAATCGATTAGAATTTATTTTGTTTTTCCACCAAAAATTGAGTGAGATT
+TCAACCTATTTTAAGCAATAAGTCACCATATAGTTTGATAGTTTACAACTATAAACATTG
+ATTGTTTACAGTTGTAAACTATTTTTTCTTTCTCATAAAAATTTGAGTGATCTCCCCATC
+AGGTAGTACAACTTTTTCCTCTACTATCCGAACTAACTTCTAGAAAATTTTAGAGATTGG
+TTCTATTAGATTTCCAAATTTGCCACCACTTTTTTTCAATAAGTGGTTGTGTATTGTCTG
+CTTTTTTTTCAGAAAAGGCAGTTGATTCGGTTGTTGGAGTTTCTTCTGTATAAGTTAAAT
+GGAGCTGTTCTTGTAGGTTCTCAATTTGTTGGTTCGCTTGTAGAGTGAGTTGTTGTTGCT
+GGTCGAGTAATTTTTGCATTTGTTTTATTTGATTATCTTTTTCTTGTAGCTGTATATCTT
+TTCGATTTAACTGTTTTTCTAGGAAAGAAAGGAGTTTTAATTCGGAAACTTGGTTGGTGT
+TTTTATGGTTTTTGGTTTTTGATTTTTCGCCAACTAGTTTTCGATTTAAGTTTGCGTTAT
+CGACTAAAAACATTGATTTTATAGCTTTTTGACCGGTTTCGTTAATCACAAACTTGTTTC
+CGTTTTTTGCAAACCAAAGTTTTCGATTTTTGTCAGAAACTTTTTTGTTAATTGCTGTTT
+TACTAACTCCTAATTCTTCCGCAAGTTCTTTGATTGTTTTATCTGCCATAAATACTCCTT
+AAGCTTAATCGAATAAGTTTTGTAAATTTCCTAGTAAATCTTGTTTGAGTTTGTTTGAAA
+GTTCTCGTTTTTCTGCCTGTTTTTCTTCAGTTTGTTGTTGTTGTTTAAAATCAGCTTCAT
+GAGTGCCTAAGGGAAGATTTAGTATTCGATCTTTAGCGCGCCATTTTTCTTCTCGTGTTA
+ATTCTCCATTGTGATCAATATTAAATAATTTGGTTCTGTTGCAAAGTTTTAAATAAAGAA
+TAAAATCCCTTACGGTATCTATGATTTAAGCTGGGATTCCCAATAATACCTTGATTTCAG
+TACAGACCGAAAACCCGAAGAGAGTGCCTTCTTTTCGGGTTTTCTTATATAATCCTCGAA
+TGGCTTCCATGCCTTTAATCGTGGTAGAGGCAGTGCGTAAACTTCGATAGAATTTATTGC
+GTCTCTTTACTGGACGATGGTCTTGTTCAATCAAATTATTCAGGTATTTAATGGTACGAT
+GTTCTGTCCCTTGATAAAAGCCGTATTCTTTTAGTTTCTTAAAGGCACTTGTAATAGAGG
+GGGCTTTATCTGTGACTACAACCTTCGGTTCATCAAACTGCTTCACTAACCGCTTAAGAA
+AAGCATAGGCTGCTTGTGTGTCCCGTTTTTTACGTAACCAAATATCCAAGGTTAAACCAT
+CTGCATCGATGGCTCGATACAAATAATGCCATTTTCCTTTAATTTTGATGTACGTTTCAT
+CCATTTTCCATGAATAAAAGGATTTTTTATTTTTCTTTTTCCAAATTTGATAGAGTAGTT
+TGCCATATTCTTGCACCCAACGATAAATCGTCGTATGAGAAACGTTAATGCCACGATCAT
+ATAAGATTTCTTGAACTTCACGATAGCTAAGGTTATAACGAAGATAGTAGCCCACGGCTA
+CAATAATCACATCCTGCTGAAATTGCTTTCCTTTAAAATGATTCATCGTCATTCCTCCTG
+CTATCTTTTTCTATTATTCTACCTTATTTGATAGTAGATTTAAAACTTTGCAACAGAACC
+GATAATCTTATACGTGGGGAATTTCATTTCCTTTCTGAAAAAGATATGAACATAATCCCC
+TCGTTTAAAGATTCAGGTTATATTCCTGATACGAAGGCTATGCTTATTTACGATGAAACA
+GGGCAATTAGAAAATTATTTATCAGAGATAAGTGGTGCAAGACCAAATAGACTTACTGAA
+GAAAATGCTAATTTTTTGTTGTGTAATTTCTCTAATCTATGGTTGATGGGAATCAACGTT
+CTAAAAAGAGGAGAATATGCTCGTTCATTAGAACTCTTATCACAACTTCAAA
+>contig00003 len=3227 cov=2.2 corr=0 origname=NODE_3_length_3227_cov_2.232903_pilon sw=shovill-spades/1.1.0 date=20220302
+GATGGGCGACTTCTGCCTAATTCTGTTAAAGAAAAAAGAAGTGGTTTTTAGGCGGGAAAA
+TTAGCCCCCCTCTTTTTATATCTCTTTTTAAACCTCTTTTTAAACCTCTTTACCGTAAGC
+TGTGTCCTTACTCTACCAATGGATACAGAATGTTATGAAGGACATTTTGTCTGTTTATGA
+AGGACATTTTGTCTGTTTATGAAGGACATTTTGTCTGTTTATGAAGGACATTTTGTCTGT
+TTGAACGTCAAATATGAATGTCTTGACATTTAAAAAATGTCATTCATAATTGGATTGAGG
+TGATTATATGGCTAATGAGATTGTAAAATACCACCATGAGTTAAATACAATTCCTTTAAG
+AAAATTTACACCGGTTGAAATGAATTTGTTTTTTTCCATCGTGTCTAGAATGCGTGAAAA
+AGGGGATAAGACAGTTCGTTTTACGTTTGACCAACTAAAAGATTTAAGTAACTACAAAGC
+AACTGCAAATGTACGATTTGTAGAAGATTTAAAAGCAACTTATGAAAAAATCTTATCTTT
+ACGCTTTGGTCGTAGAAGTGAGTCTGGGCTTTCTTACGATATGTTTGTAATGTTTACAGA
+ATTTAAAATCAACGGGGACGTAGAAAATCCTTACGTAGATATACGAATTTACGAAAAAGC
+ACTGCCTTTGTTAAATAATTTAGACGAGTGGGTACGCTATTCTTTACAACAATTCAACGA
+GCTACAAAGTGGCTATGCAAAGACTATGTTTCGTCTGTTAAAGCAATACAGAACCAAAGG
+TTTCGCATATTTCTCCAAAGAAGACTTTCTTGAATTATTAGATATTCCTAAAAGTTATAA
+GCAACCTGATATAGATAAACGAGTTATAAAACCTATACGTCAAGAACTAACTGCAATCTT
+CAAAGGACTAACAATCAAAAAGAAATACGGAAAAGGACGGGGAAAACCTGTTATTGGCTA
+TCAATTTACGTTCAAACCTGAGATCAAAAAAGCAGACGACTTTAACAAACATGCACCAAC
+CAAAGAAGACCAAAATAAAGCATTGGCTTTAGCTGATAAACAAAAAGAATACGAAGAACC
+CGCTACAACAATTAACGAAAAAATCAAACAGAAGAAACGAGAACTTGAACTCCTCCAACA
+AATCAAACAACTAGAAAAAGAGAAAAAAGCTCTTGAAAAACAAACAGAGTCCGCACTTTC
+GGAAAAAGAGAAAAAAAGTTTATTATCTGATTTAGATAATTTATTCCAGTAGCAACCTAG
+GAGGCAACCAGTATGCAACCACAAGAAACCTTTACAATAAAGGAATTGTCAGATCTTTTT
+AAGATGAGTAGGCAAGCAATATCGAAACATATCCAAAAATTAGATTCTTCCATGATAGCT
+AAAAATGAGCGTGGTTATAAGGTTGTATTGCGTTCTGGAGTATTGCAACTTGCTCGCAAC
+TTAGACAATCAAAGGTTGCTAGATAAGTTGCATAAACATGAACAAAACAACGATAAAAAT
+GCTTATATACCAAACAAAAACGTGGTTGCAAACAAGTTGCTAGATCAGTTGCGTGAAGAA
+AATGAATTTTTACGAGAACAACTTGCCCTCAAAGAGCAAAATAATTCTCATATACAAAAA
+CTACTCGACCAGCAACAACAACTCACCCTGCAAGCCAACCAACAAATCGAAAAACTTCAG
+GAGCAACTGCAGTTGACTTATACGGAAGAGTCTTCAGAGAATAGTTCAACGACTCTTTCT
+GAAGCAACAGAAACAATGGACGAACAAACAAAGAATTGGAAAAAATGGTGGCAGCTATGG
+AAATGAAGAAGGAAATACTTATGACAAAAAAACACTTGCTATTCGGTTCTATCCTACTAG
+GAATATTAAGCTTTAGCCCAATGTTATTATCAGTGGCCAACAAAGGAAATAAAAAAGGGG
+AACTAAAACTCAATCCTAATTACTACAACAGTCAAAATGAGGAAGTATTTGTAGAAAAAC
+TTGATAAATAAGAAAAGACTGCTCGTACGAGCAGTCTTTCTGAAAGAGATTATCCTATTA
+TTAACCTTAGAAAAGAATAATAAATGAATATGAGATATGTAAAAAGCATAACAAACACAA
+ACAAAAATAACAAGTATTTAAAAAATGACCGATCAATATTCACAAAGAATTAGAAAGAAA
+CAACCGCAGAAAACCAAGCCTTAAAAAGAGCTTTTAACCTAGACCAATAAAAATTCACAA
+AATCAGCGCCTGGATCCCTTGGTACAGGCGTTACTTGGTAGTATACACATTATGTCTACT
+AGCTGTTTAAATAACTGATCTTATAATTTTATTTAAACGATTATGAATTCAAAACTACTT
+TTTATGACGTTAATCATTGTTATATAATAAAATGTTATATAATAAAATTACTAAGATTAT
+TTAATATAACAAGCAATTTTAAAAAAACGAAAAGGAAAAACAATCATGAAAAAGAAAGTA
+TTAAAACATTGTGTTATTCTAGGAATATTAGGAACTTGTCTAGCTGGCATCGGTACAGGA
+ATAAAAGTTGATGCAGCTACTTACTATGGAAATGGTCTTTATTGTAACAAAGAAAAATGT
+TGGGTAGATTGGAATCAAGCTAAAGGAGAAATTGGAAAAATTATTGTTAATGGTTGGGTT
+AATCATGGTCCATGGGCACCTAGAAGGTAGTGGTAGGGAGGTTATTATAATGGATTTTAC
+TAAAGAAGAAAAACTTTTAAATGCAATTAGTAAAGTATACAATGAAGCAACTATAGATGA
+CTATCCTGACTTAAAAGAAAAGCTCTTTCTTTATTCTAAAGAAATCAGTGAGGGAAAAAG
+TGTTGGTGAAGTTAGTATGAAATTAAGTAGTTTTCTTGGAAGATATATTTTAAAACATAA
+ATTTGGATTACCTAAATCTTTAATAGAATTACAAGAAATTGTTAGTAAGGAATCTCAAGT
+ATATAGAGGATGGGCTTCTATTGGTATTTGGAGTTAATTCTTTGGAATAAAATGAAAATG
+GGACTGAAGAATCAATTCTGATTCATCAGTCCCATAAATTATAGAGCCGAAAAATTATCA
+TATTTATAGATTTATTAATAGTAAATGGCATAAGAATCTTTGAACAACGAAAAAAATGTA
+GCTCTACCTAATTATTGATTTGCAACAATTTCACCGAAGGTGAAACAAGCGAAACTTTAC
+AAAAAGTGGCTAGCATTTGCTAGTCTTTTTTGTATTGTGGAGAGTGG
+>contig00004 len=3138 cov=2.3 corr=1 origname=NODE_4_length_3138_cov_2.261375_pilon sw=shovill-spades/1.1.0 date=20220302
+TTTTTTTCCGATATAATTTGCTGGTAAATCTATCACAGCCAATGAGAGTCCGGGATTGCT
+TTCTTCCTGATAATCTTTCCGTTGGTATAAAATCTTTTCGCCTAGATATACAGTAATCCA
+TTGATGGTTTCCTTTGATTAGTAAATTTGCTTCGTCCAACGGTTTTTCAAGTGTCGTTTC
+CATAATGAATGTTTCGTCTTTATCCACGGTAGGAATCGTACGAGTGTACTTGCTGTCAAA
+CTTAAAATCAGGATCATCTTTTGTATAGAAAACCCACGAATCTTTTATTTCTTTCATTTG
+ATTGCTGTCCGCAGGAGAAAAAATAAAATAAAAGAAATAAGCAATTCCTGTTAAAAATAA
+CAATGATAATATAATGATTATGCTCCACTTTATACGTAAATAAAAAGATTCTTTTTTATT
+ATATATGTTATTAAAAAAAGACATAAAGGTATTCCTTTGAGAGTATAAAATATTTTGTGT
+AAATGAAAAAATCCATACAAAAAAGGAAGTCCCTTCTGTAGAATAAAGTTAACGACAACC
+AATTCACAGAAAAGAGGACTTCCCTATGAATGATTTTACTACAGAAATTGTGCAAACTCT
+AGTCACTAAAGGCGATTTAAATGAATTATTCCGTTCGCACTTAGAAAAAGCGATAAACAC
+ACTCCTACGGACTGAATTAACGGCTTTTTTAGATTACGAAAAATATGATCGCACTGGTTT
+TAATTCAGGTAATTCGAGAAACGGTTCTTACTTTCGATCAATCAAAACCGAATATGGTGA
+ATTAACATTGGAAATACCTAGAGATCGTAATGGTGAGTTTAAACAACAAACTTTACCAGC
+CTACAAAAGAACAAACGATACATTGGAAACCACTATTATCCATTTATTCGAAAAAGGTGT
+TACGATGTCTGAAATTGCTGATTTGATCGAAAAAATGTACGGTCATCACTATACTCCACA
+AACCATGTCCAACATGACTAAAGTTCTGACTGAAGAAGTAAATGCCTTTAAATCCAGAGC
+CTTAAATGATAAGTATGTCGCTATTTTTATGGACGTTACTTACATTCCACTAAAACGTCA
+AACTGTATCCAAAGAAGCGATTTATATTGCCATTGGTATACGAGAAGACGGCACTAAAGA
+AGTACTGAGTTATGCGATTGCTCCAACTGAATCAACATACGTTTGGAATGAGCTGCTACA
+GGATATTAACTCCAGAGGAGTTCAAGAAGTCTTGCTTTTTATTACGGACGGCTTAAAAGG
+CATGAAAGATACTATCCATCAAATTTATCCTAAAGCAAAATATCAGCATTGTTGTATCCA
+TGTATCTCGTAACATCGCTCATAAAGTACGTGTCAAAGACCGAAAAGAAATCTGTGATGA
+CTTTAAGGCTGTTTATCAAGCTAACTCAAAAGAAGAAGCGAATACCTTCTTATCCGGCAT
+GATTGAGAAATGGAAGAAAAACTATCCTAAAGTGACGCAGTCACTCATAGAAAACCAAGA
+CTTATTAACTTTTTATGATTTTCCACCTAGCATTCGTAGAACCATTTACTCAACCAATCT
+AATCGAGTCTTTCAATAAGCAAATTAAAAGATACAGCCGTAGAAAAGAGCAGTTTCAAAA
+TGAAGAATCACTAGAACGCTTTCTAGTCAGCATTTTTGATACATACAATCAAAAATTTCT
+AAACAGAAGCCATAAAGGTTTTCAACAGGTAACCGATACATTAGTTTCAATGTTTACTGA
+GTAACTAATTATTTTGCAGGAGGACAATTTATTTACACAAAATTATTGACGCTCCCTAAC
+AAAATCCCACCTACTTTATCTTATAACTTGTTTTTTTGCATAAAAACTAAATAAAGAGTG
+CGGCATTTCGCACTTTTTTATTATATATTATTTGTCAAATTAAGCGAGACAAAACTTTCC
+ATTTACGTAACTCAAAAAAACTTCTAATGGTGTTTGGTAATTTAGTGATTTTCTAGGGAT
+ATGGTTTCTTTTGGACGCAACGGATGAGATGAATCCTTGATTGACTTGGTGGAAGTCCAT
+TTCTTTTGGTAGTCCATCTTTTCGGAGGAGTCCGTTTGAATGTTCATTTAATCCCCGTTG
+GGAAGGCGTTCCTGGGTCTGCGAAATAAATATCAATATCATTCGTATTACTAATACTTTT
+CCAATTAGAGAATTCTTTTCCACAATCAAAGGTAATTGATTTGAAAAGATTTTTGGGTAC
+GGATTGAAGCCATTCATTAATCGAATTTTCAATATCAACTGCCTTACGGCCTTCTGGTTT
+CAAGGCGATAATGGCTTTTGAAAGTCGCTCAACGAGTGTGATGACGGCACTTTTATGGTG
+GATGCCGACAATCGTATCACCCTCTAAATGTCCAAATTCTTCTTCGAAAACGACATAATC
+TTTTTTACGTTCAGAAATATTTCTTTTGAATGCCTGTTTTCCACGTTTTTCCTTATAACC
+ATTTGGTTTTCGTTTTCCTTGCATCGGTAAATGTAAAACATTGAATTCTCCCGTCTTAAA
+CCGGCGATAGAGGGTACTTACTGAACAAGAGAAGGTTCGCTCTGCACGGCCAATAATGAC
+GTCTGGGGTCCAACCTTCAGTTGATCTTTTTGCAATGTATTCTTTTTCCTCAGCAGGAAA
+AATGATTTCGGTTCTCCCACAACGTCGCTTATTTTCTTTGTATTGTTCAAAGTATTCAAG
+TGCTGTTCCACCACATTTGAGAAAGTTATAGACATTGTAAATTGTTTGGCGTCCACGTTT
+AAGCTGCTTCGCAACGATAGCAACCGGAGTTTCTTGATGAAAATATGCTTCTATCATTAC
+AAGCTCGTTTGGTGTAAGATGGGTATAAGTCATTTATGTTCACTCTCCTTGTATGCTTTA
+GCGGGTATTACAATTGGAGTGTAACATAAATGGCTTTTTTATTTGTCTCGCTTAATTATA
+CAAACGGCGTTGTTAAATAAATAGGAACAAAAAAATTAAATTATTTAATACACACATTAG
+GGATCATTCATTGAAGGATTAGAAGACAACGAGGATGGCGAAAAATATGATTACAATAGA
+AAAGTCGTTCTAAACCAATCAGTTCCTAGTATCACACAACGCAAGCCAGTCGATTTGGTG
+AGATTAGAGGAGTGAAAG
+>contig00005 len=3026 cov=4.4 corr=0 origname=NODE_5_length_3026_cov_4.409452_pilon sw=shovill-spades/1.1.0 date=20220302
+AATGATTTTTCCGGTGTAATCGTGATTGCTGTATTTAGCATAACTTCGCCGACTCTTGTC
+GCATTTGGCTTGGCTTGTAGTAGGCGATCTTCTCCAATCAACTCTTCTACGAAATCGTTT
+GCAGGATGACGTAAAATATTTTCTGGTGTATCAAATTGGATCACACGGCCTTCACTCATG
+ATGGCGATACGGCTTGCTAGTTTAACAGAATTAGGCAGAAGTCGCCCATCCTCTATAGGT
+GGGTGATGAATGCCGTTCGGTATGAGGGTTACCGTTGGTAACTCGAAGACCGACAACTAA
+GGCGTATTGCCTTTTTATTTTGTTCCATGTTACAATCAGTCTATACAAGAAATGAGTTGA
+TATAACATGGAATTAGATACAAATAATCATTCAGTATTTCTTCTTTATTACCACCTTGTT
+TTAGTAACGAAATATCGTAGACAAGTGATTGATGATGAAATATCTGATTATGCCAAAACT
+ACTTTTGAAAGAATTTCAGAATCGTATCACATTACTTTAGTGGAGTGGAATCATGATAAA
+GACCACGTTCATATTATGTTCAAAGCTCAACCTAAAACAGAATTGACAAAATTCATCAAT
+GCCTATAAAAGTGCCAGCTCAAGATTGATAAAACGTGACTTTCCAAGAGTCAAACAATTT
+CTTTGGAAAGAAATGTTCTGGTCTAAAAGTTTTTGTCTTCTGACAACTGGTGGCGCACCA
+ATTGATGTGATTAAGAAGTATATCCAAAATCAAGGAAACAATCATAAATAGAAAGTAGGT
+GAACTTTATGGAACAACTAAAAGCATACAAATTCAGAATCTATCCAACAGAGGAACAAGA
+AATCTTCTTTGCCAAATCTTTTGGTTGTGTCCGTAAGGTCTACAATCTAATGCTTGATGA
+CCGAAAAAAGGCGTATGAAGAAGTTAAAAATGATTCTTCTAAAAAAATGACTTTTCCGAC
+ACCAGCTAAATACAAGAAAGAATTTCCGTTTTTGAAAGAAATTGATAGCCTTGCTTTAGC
+CAATGCCCAACTTAATTTAGATAAAGCATACAAGAATTTTTTTCGGGATAAATCCGTTGG
+ATTTCCACGTTTCAAAAGTAAGAAAAATCCTGTTCAGAGTTATACAACGAATAATCAAAA
+TGGTACAGTTGCTTTGATTGATAGTAAATTCATCAAAGTTCCTAAATTGAAGTCATTAGT
+AAGAATTAAGCTTCATAGACAACCAAAAGGGATTATCAAATCTGCTACAATATCACGTCA
+TTCTAGCGGTAAATACTATATTTCTTTGTTGTGTAAAGAAGAAATTATCGAATTACCTAA
+AACTAATTCCACAATTGGTATTGACTTAGGTATTATGGACTTTGCGATTCTTTCTGATGG
+ACAAAAAATTGATAATAATAAATTCACGTCCAAAATGGAAAAGAAACTAAAGCGTGAACA
+ACGCAAATTGTCTAGGCGTGCTTTATTGGCTAAAAATAAAGGTACCAATCTATTTGAAGC
+TAAAAATTATCAAAAACAAAAACGCAAAGTAGCTAGATTGCATGAAAAAGTAATGAATCA
+ACGTACTGATTTTCTGAATAAGTTGAGTACAGAAATGATCAAAAATCACGATATTATCTG
+TATTGAAGACTTAAACACAAAAGGTATGTTGCGAAATCATAAATTAGCTAAAAGTATTTC
+TGATGTTTCTTGGTCAAAGTTTGTGACTAAATTACAATACAAGGCTGACTGGTATGGACG
+AAAAATCATCAAAGTAGATAAATGGTTTCCGTCTAGTCAGATTTGTTCAGAGTGCGGACA
+TAAAGATGGCAAGAAATCTCTTGAAATTCGAGAATGGACTTGTCCTGTTTGTCATACTCA
+TCATGATCGTGATATCAATGCTAGTATCAATATTCTGACCGAAGGTCTAAGACTACATTC
+TATGGGATTGGCTTAGATCCAATCATCAAGAACCGTAGGAACTACGGGGATAGCTTGGTA
+AATAAGAGACACCGCTGTTAGTAAAGAAATACGCTATCAAGTATGCTCTATTCCCAAGAA
+GCTCCCACTTCAAGCGTTAAGAACCGTCAGGTTTAGCTAAGTGGTGAGTAGTTCACACAG
+GTTCGCGCATTTTTCAAAACTGCCAATCCAAAACCTTGCTTCCTACGGTCGCCAAAAAGG
+TGTGATCGCTACGCTCTCACATTGTACTGCGCAGTCGCCTAAAGGCTCCTTTGCTAAAAA
+CATGTTGGTAAAGAGGCCTTTGAGCGGTTCTGAATGCTTATCTAAGCCGTTTTAAGACAG
+TCTTGGATAAAAATCCTTATCTAGCTTTAAAGCGCCTTACAGGCGGTCAGGGCAAGCCCT
+AACAACCCTAAAATAAGCGATACTTAAAAACACCACACAAGTTTAATTTTTTAAGATATA
+ATAACTTGTCGCCTATCCGACAGTCTTGCGACTGGAAGGAGGTGTATCTAATGTTTGAAT
+TGTTCATTTGCCCCCTTCTTATAGAAGTTTGTGTCTCTTTATTCAGTTATTGGTTGAATA
+ACCGAAACAAGAAGTAAAATCAATAAAGGCGACATCAACCTGAAAAAAAGCCCCAGAGAA
+TCCGACCTCTCTGGGGATTTCGTGTGTTTCGTGTTCACTTATTTGCAATCAAATTATAAC
+AGAAATAAATATTTATTTCAAAAATATCCTACAAAAGTCTAAAATCCGTAATTATTTCTT
+ATATGCAACATTTACAAATAAAGTCGCTCTGAGAGCTCGTATTTTTCGATTTAAGACGTT
+TTATTTAGTTTTTGGTGTATTTCATTGGTCCAAGCTAAAAAACTCTTAGAAGCGATTTTA
+GAGCCATTTAAACCCACTTAATTATATTCTCCATGAAATTCGCTCCATGCGTCAAAAGCT
+GCGTCTGAAATTCCGCCGTCTTCGTTCACTAGTTGCATTAATTTTTCCAACGATCGTTTT
+CTTTCGGGTGTCATATTTTTATATTCCAACAATTTTTCGTCTGTTAAATTTGGTTATCGA
+TTACACGTGCAGCACTCCCCCCCGAA
+>contig00006 len=2973 cov=2.6 corr=1 origname=NODE_6_length_2973_cov_2.590302_pilon sw=shovill-spades/1.1.0 date=20220302
+TACAGTCATCCATCATGTATTCGATGGAGATGCTTATTTTCCACCTGTTGACTGGTCTGA
+TTGGTCACTGATCAATACTAGTCAAGGAGAAATGGATGAAAAAAATCGTTATCCGCATCA
+ATTTGAAACGTATCAGCGTAATGAGAATCCTGTAAAAAGCGGGACAGGCGAATTGACGAT
+ATAAAAAGATTCCCGAATCCAATGCTTCTTCCACAATAAACTGGATCGTTGGTTTATCCA
+CGATTGGAAGCATTTCTTTTGCCATGGCTTTTGTTGCCGGCAAAAAACGTGTTCCTAGCC
+CAGCGGCAGGAATGACTGCTTTTTTGACCTTCACTTGCTGTTCCTCCTCGTAAAATATCA
+TTTTTCTAATAGTTTTTATTCAAAATGTTTCTAGATTATAAAATTTATTGAATAACACAT
+TCCTAACGGAATTTGTTTCGATATTGTGTGATTTCTCAGAGTACAATGGATGTATGGAAA
+GGATCCAACGGGAATTTGCTATTTCCTCCTGTAGCGTTTGTCTACCCTGTTTAGTCTGTT
+ACCCGAACCACTGTTATCACTACCAACTCATTAGCTGTTTCGATAATGGACTAGACTTTC
+AAATAGTAGTTTGGAAGGCAGCTTCTAGCTCTTTTATCACCGTATTCTATTAGGCGAGGT
+TGTGGCTATACAGTGAGTTTCTGGGAAATCCCACAGTATCGAAGCATTTTCCAAAATTTA
+TATCGAAAGGAGGTCCTTCTTCCATGAAATTATTTGTCGGTATTGACGTTAGCTCTGAAA
+AACTAGATGTTTGTTTTTTAACAGACGACAATCAATTGTCTATCTTATCTGAAATCTCTG
+TTGCCAATGACATCGAAGGTGCTTCATTCATACGAGAAACAATTCTTGAATTCAATGACA
+GCTACCACTTTGATCAAATTGTGATTGGCATGGAGTCAACGTCCATGTACAGCTTCCATC
+CTTCCATGTTTTTTCATGAAGATGAGAAACTAAAGAAGCTCAACACACTTGTAACGATTG
+AAAATCCTTTTCGGGTGAAACAATTTAGTCGCATGTTTGATGAGAATAAAACTGATCGAA
+ACGATGCATTAAGAATCGCTGATTTCTTGCGTATTCAACGATTCACAACTTCCCCTATCA
+AAGAAGAGAAATACATGGCCTTACAGCGTTTAACACGTACTCGCTATCAACTTATTAAGC
+AATTGATTCGTACAAAGCAACATTTTCTTGAAAATCTAACGTACAAATGTAATACGCTTG
+CTCGAGAAATGCGAGACGAATCGACGAGTCTTTTTAGTGCAACCCTCATTTCACTCATGA
+CGGAAGATTTCACATTGGATGAACTTGCTGAGCTTCCTTTAGAAGCTTTCTGTGATTTAC
+TTCAAGAAAAAGGAAAAGGCCGTTTCAAGCAACCAGAAAAAATCGCTAAAGCAATTCAAC
+GTGCAATTACCATGAGTTACCGCCTAGGTGCTCTTGCACAAGAATCAATTAATGTTGTTT
+TAAGTGTTCTCGTACGAGAAATACGAGCACTTGAAAAAAATATCAAAGAATTAGATAAAG
+CCATCGAACAAGTAATTGTTGTCATTCCAGAATATCAATGCTTAACCAGTATTCCAGGCG
+TTGGTAAAGTCTATGCTGCCGGTTTAATCGCTGAAATTGGTCAAATCGAAAGATTTGAAG
+ATCAGACAAAATTGGCAAAATACGCTGGATTAAGTTGGAAAGTGAACCAATCTGGAAACT
+ATCAGTCGCAAAATACACCTCTGACAAAACAAGGAAATCGATATTTTAGATACTACTTAG
+TTGAAGCTGCCAACTCTGTAAAAAATTATCTTCCTGAATACAAAGCTTTTTATCAAAGTA
+AATATAAGGAGGTTCCAAAGCATCAACACAAACGTGCACTCGTCCTAACCGCAAGAAAAT
+TTACGCGTCTGGTGGATACGCTACTACGTAAACACCAACTCTATACGCCACCAAGGAGTG
+TGATAGAGAAATAACAATCCGTTATTGACGCAAATCCTTGAATCAACCCGAAAAAAATTT
+GATTTTGATCGGGTCTAGTTTCGTGCGCTTCAAAACATATTACTCAATAAAGAAAATCTT
+AAATTTCATCTTGACTTATCACCATTAGACTAAATAAATTCCTTACTCAATGCCTAAGGT
+AATACTACCTTTTTATTAATCGTCGTGACTCCTTCTAAGCCTTTATCTGTAAAATTTATT
+CCTCCAGTTTTTATTCTTCTTTATCCGCTACAAATTCAATGATTTCAAAGCTGACAATAT
+AATCACTCAAATATGACCAAGTATCTTCAACAGATAATTCGTCTCCATTATCATTCATAA
+GCGTCATTTTAAACCATTCATTACCTTCATCATCTTCAGGTAGCAAGCCGAATCCAATTG
+GATTATCAGTCAATGTTTGATCGTATAAATCATCCTCGTCTAATGCTAAAACATCTAATC
+CTTTACAATTTCCGCCCCTTCTAAACGTCACAAATCCTTTGTAATCCCAACGTTGGAAAG
+AAACCTTAATAGTATGTGTGCCCAATCGTATATTCGGATCATAATTTTTCATTTGTCATT
+CCTCCATTACGTAAATTTCATTTTCTCTATGCTTTATATTAATTTTTTCACTTTATTCAG
+GACTTGTTCATATTTTATCGTTTTTCGTTTACTTAAAAATACATAAAAAATTTCGACTCG
+TTTATGGCGTCCGAAACGAGAAACCCTAGACAGCGGTAAATGCTCGATTGATCCAATAAT
+CAACGTCCTCGCAAGTATCTACATGTACTGCAGCACACGACACAATTTCTTGTGCGTCCT
+CCCCATTACGAGAAGACCTACTCCTTATTCCATGAGTTTGCGTCAAAGTCTAGATCCCTT
+AGTAGCTGCTCATGATTAATCTAGACGCTATTCTAACTTGTCTAACTTCTAAATTCCCTC
+TTGTTTACTCTGCGCTTATTATTTACACAAATT
+>contig00007 len=2947 cov=4.2 corr=0 origname=NODE_7_length_2947_cov_4.215957_pilon sw=shovill-spades/1.1.0 date=20220302
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+AAAAAAATTAAAAAAAAAGCAGAAGAAGGCATACGAGATAAGATGTAGTGACAGGAGTTC
+AGACGTGTGCAATTCCGATCTACGATCAGTATAATCAATTCCGGAGATAAAAACATAATA
+GCCATATAATAATACCAAACACAAAAATACAGTAAATAAAGATACCAAAAGAAGATAAAA
+AAAACAAGAAGAACAAAAAAAAACTGTTCCTTGCATTCTAAAACCTTAAATACCAGAAAA
+CAGCTTTTTCAAAGTTGTTTTCAAAGTTGGCGTATAACATAGTATCGACGGAGCCGATTT
+TGAAACCACAATTATGATAGAATTTACAAGCTATAAGGTTATTGTCCTGGGTTTCAAGCA
+TTAGTCCATGCAAGTTTTTATGCTTTGCCCATTCTATAGATATATTGATAAGCGCGCTGC
+CTATGCCTTGCCCCCTGAAATCCTTACATACGGCGATATCTTCTATATAAAAGATAACCC
+GTGGTGCTAGTTAATTTTTTCCTAGAGGAAAATGTCTAAACATGTTGGTAAATCAACAAA
+AAAACGCATATAGTAGTCTCAAAACTCCCAAGAAATGGGCTCTATAATTTATGGGACTGA
+TGAATCAGAATTGATTCTTCAGCCCCATTTTCATTTTAGGTATTAAAAAACATATCGTTC
+TCTAGTATGATTAAATCACCACAAAATAAACAACTGAGAGGACGATACGCTATATGAATG
+ATTCTATCAAAAAAATGCTGAGAATAACAGAGAAAGATTTGATGATTACAGAGGTCTCTT
+ACGAGACCCTTCAGAAGAAAAAGACGTTGGTCGTCGATGCTGTTCTCTCGCCTACTCCTC
+GTGCTTGTAGAAGTTGTGGTTCTACTGTGGTAGATGGAAACGGGAAAGCAATTATAGTGA
+AAAATGGAAAAAAGGAAACGATTGTCCGTTTTGAACAATACAATCATATGCCTTTGGTTA
+TGCGCCTAAAAAAGCAACGCTATACCTGTAAAAACTGTCGCACCCATTGGACGGCTCAAA
+GTTATTTTGTCCAACCCAGACATTCAATCGCAAATCATGTTAGATATAAAATTGCTTCTT
+TACTGACTGAAAAAGTATCTTTATCTTTTATTGCGAAAAGCTGTCAGGTATCTTTGACCA
+CCGTTATTCGTACATTGAAAGAGTTTAAAAGCTATTTACCAAAGCAATCTAAGAAGATCC
+TCCCCAGAGTATTGATGGTTGACGAATTTCGTTCGCATGCTTCCATAGAAGATAAGATGA
+GCTTTATTTGCGCGGATGGCGAAACAGGAAAATTAATAGATGTTTTGCCTACGCGTAAAT
+TACCTCGATTAACAAGCTATTTCTTAGGTTGTACCAATCCAGAAGAAGTAGAATTCTTGG
+TGACAGACATGAACGCCGCCTACTTCCAGCTCACCAAACGTGTTCTGCCAAATGCGAAAG
+TCGTGATTGATCGGTTTCATATTGTCAAACACATGAATCAAGCGTTCAATGAGTTGCGTA
+TCCGTGAAATGAATGAACTTCGTAAAGCCGGACAGAAAAGCCAGGCAGAAAAACTGAAAA
+AGAACTGGCGCTTTTTGCTAAAAAATCGTGCAAACATCAACCATTATGAATACAAAACAT
+GGAAAAGTTTCCGAGCACCAAAATACCCATTTCTTACTGAAGCAATGATGATTGATCGAT
+TGCTTGAGTTTTCTCCGCCCCTAAAGGAGGCGTATCCCTTTTTTCATGAATTAGTTGAAG
+CCTTTCGAGACAAAGACCCTGACTTATTTTTCTCCTTATTGGCAGAACTTCCCGAAACGT
+TAGATGACAGCTTTCGGGAAAAGCTTCAAAACCTTCTGACCTATGAAGAAGGCATCACCA
+ACGCAATGATCTATCCTTATTCCAATGGAAAAATAGAAGCGAAGAATACCCACATAAAGA
+CAATGAAACGAGTATCCTACGGATTTAAATCATTTGAGAACATGAGAATTAGAATCTTTT
+TGATCAATCAATTAATCAATGTAAGATAACAAAAAATCTGAGCCAGAATGTGGTTCATTC
+TGACTCAGATTTGATTTTGCACAACTCATCAGTCCTTATTGACAAAGAGCCTATTTAATT
+AACTTATAATATAGCAGACAAAATTTTATAAACAAAGAAACCTTTTATCTCTTTTCTTCT
+AGAAAGGATAAAAGGCTTTTTTGTTTTTCCTATTTGCTTCTCATAGCTAGTCAGCCAAGA
+TTTCTATCGTATCCCCAACGCAATCCGTGCATAACGGCTCATCTTATCTGTCGTCCATGC
+TGGATACCAGACTAGTTTGACTTCTGCTTTCGTTACTTCTGGCACTTCTTTTAATGCGTC
+ATGGATAGATTCTGTTAAAATATCTGCTAATGGACAGCCCATAGTTGTTAGAGTCATCTT
+AATGACTGTTTCTCCATTTTCAGGATTGAATTCTATATCATAAATCAAGCCTAAATTGAC
+GATGTCGATTCCTAATTCAGGATCAATCACCATTTCCAAGGCAGCAAGAATACGTTCTTT
+GATTAGTTCTATTTCTTGTCCAGACCGTTCTTGGTTTGCTTCGCTCATCGTACGACACTC
+CTTAACACGATTTTTATTTATCATACTCTTTTTTTAGCTGCTTGTAAATGAGAATTTAGA
+AGTAAGATTCTCGTTTAAATTTATAAAAATGTTCTTATTAGATGTAATAGATTAAATTTA
+TTCTAAAATAAACCTGATTCCTCATTTTTTTTGTGAACGATTTTTTATTTCTGGCAATAC
+GCCAGTTGTTCGATACATTTTTTGTTCGTTTTCATTTGCAAACCGGCCAAATACTGAATG
+AGTTGGTAAAATATTGATAAATGCATCGTCGTCGATTTCATGAACGATCTGATCAAGATC
+ATACATT
+>contig00008 len=2292 cov=2.6 corr=0 origname=NODE_11_length_2292_cov_2.631409_pilon sw=shovill-spades/1.1.0 date=20220302
+CTGATGAATTGAAGATCTCGGGGATCCTACGCGTGAAATCTTCTTCTACAATGAATCTCT
+TATCTCCAGGAATCGCTTATAGCGATCAATTAACGACTCAAATCGTCAACGAAAACAAAG
+AATCAGAAATCGTCAAAGCTCAAAGAGACAGTGGTGTAAATGTCTTAACTACTGAAAAAG
+TTGACGAAAATGCCAAACAAACATTGCTTAGTTATTTAGGTGGAGACAGCTTGCCTTCAA
+GTATCATGATTTATCCGAACAATTTTGAAGACAAAGAAAAGATCTTGGATTATCTAGATG
+ATTACAATAAAGGCAAATCAGATGAAGATAAAATCATTTATACTGATTTAGCTGGAACGA
+TGACTGAACTGACTGGCGGATTGATGGATGCTATCACTTATGTCCTTATTGCTTTTGCAG
+GGATCTCTTTAGTAACAAGTATGATCATGATCAGTATCATTACTTATACATCTGTGATTG
+AACGGACAAAAGAAATCGGTGTACTAAAAGCTTTAGGTGCACGTAAAAAAGACATCACTC
+GCGTATTTGACGTAGAAACGTGTATTTTAGGTATTTCTTCTGGGATATTAGGTGTGTTTA
+TTGCATGGCTAGCTACGTTCCCTATCAATAGCATCTTATACAACATGACGGATCTAAAAA
+ATGTTGCTCAACTAAATCCTGTCCATGCGATTATTCTAGTGATCGTCTCTACTATATTGA
+CGATGCTTGGCGGTCATCTTCCTGCACGAATGGCAGGGCGGAGGAAAACTGACCGATCTA
+GTGGGTTATAGTGCCAATCTTGCAAGAATCGATTTCGGAGTCATCCCTACTTTAGCTAGT
+AATTGTGCTCCATGGACACCTCTTGCTGTCATGTATAAGGAGAATGGACAAGCAGAAGGG
+AAAACAGAACACTTTTACAGACAAGCTGCTTTTTTTATAACAGATCCCCAATTAGTGATT
+GATTCCCCTGTTCCATATTTCATTGCCGGGTTAGCAGATACACTAGCAAAATGGTATGAA
+TCTGAGCTCATCTTAGAACAAGATTTTTTGCAAGATGAATCATTTTTGAAGCTAGCACAA
+GATACTGCGAAGATCTGCAAAGAAGAGATTTTGAATCATACTGCTAAAGCAATCCAAGAT
+ATGGCACAAAGAAAACTGACATCGGAGTTCAAACAGCTTTCAGAGATTATCTTTGCTGTT
+GCTGGTTTAGTTGGAGGATTAGGAGATAAATACGCAAGAAATGTGGCAGCACATGCTATG
+CATGACGCTATCAGTAAATATATTCCGGAAAGCCATCGTTTTCTACATGGAGAAAAAGTA
+GCGTATGGGATTTTCTATCAACTGGCACTAGAAGGTCGCTGGGAAAAAATAGACGAGTTA
+TATCCTTTGTATCGGGAATTAGAAATATGGAGAAGATATTGCGTATATCGAAATACTTAA
+ATTTCATGAAGGAAAAGGTCGTATTGATTTTAATCCGAATAAGATAGGCCAGTTTTTAGC
+TAGTTCCATGAAAGGATTCATTCATGACCTATTTTTAGATCCGCATTTTTCCCGGGCGGA
+TATTGCCTGCGATATTGTAGATGTGCCGGATGACTTTATTACTCAGTATCGTATTGTAGA
+CCCGATTTCTTTTAAGCCAATCTACGGCCGTTCTGGCAAGCTAGAAACAGCGTACTGGGG
+CAGTCGTGCCAGTGAGCGCCAAGTGCGACTGTACAACAAAAAGCTAGAGCAGGAACGAAA
+AAAAGTAATCGTGCCAAAAGAAATCGATACGTGGTGGCGGTTAGAAATGCAGCTAAGACG
+TGGCAAAGCAACGGATTGGCATGCGATGGTTCAGGAAAGCTTAGATAGTTTTGCAAGCCC
+GCATTTTTTGCCGATTGATATAAAACCTATTGATAAAATAGTTATTGATGGTTTGATAGC
+TGAGCCTTCTAATTGGTCGATAATTGCTAGACATACAAAATATAAATATCGGAATTTGCT
+GAAGCAAGAAAGTCAAAATGATGAGTTAACGAATCATTTACGAGAGACTTTTAAGGAATC
+TGCAGACGAATTAAAAAAAGAATTGGATACGTGGCTTTTGGGGTTGGATGTGACAGAGAA
+GTGATACCGAATAAGAAAAGTCAGATGAGTGAGAGTAAATTTACGTCAATGTTTAATGAC
+GTGGATTTACGATAAGCGATTATTTTGCGTGAAGCAAAATAAAGCGTAAAAGGAGTTGAG
+AGCGTGACACGCTTTCGGCTCCTTTTTTCGTTGTCACTTGTGACAGCGAATACCCTCGGA
+GAGCATTTGGAA
+>contig00009 len=2060 cov=9.4 corr=0 origname=NODE_14_length_2060_cov_9.400414_pilon sw=shovill-spades/1.1.0 date=20220302
+TTTACGATAAGCGATTATTTTGCGTGAAGCAAAATAAAGCGTAAAAGGAGTTGAGAGCGT
+GACACGCTTTCGGCTCCTTTTTTCGTTGTCACTTGTGACAGCGAATACCCTCGGAGAGCA
+TTTGGAATTGTGACAGCCATGTCACAATTAGGAAAATATTACTCTTTGTCAAAGAGTAAC
+AGAAAGGTTTACACTCTTTTTATTGGCGACAGCGCGAAGGAGGGGTTTAACTTGGGGTTT
+AGTATTTCGTTCAAAAAGGGAACAAAAAATACAAGCATTTCTCATAATAATCGTGAGTTA
+ACTGATAGCCAAAAAATCAATGGTTTGTCTGGTAGAAAATAATTAGCAGATTTACAAGTG
+GGAAATAAAAAGCTGAAAGAAGAAAATTGCATTTCAAACTACATTTTCTACAATAGCTCT
+AAAATGGCATATTTTGCGTTCTGAGCGGTTTTAGCGTTTATTTCGTTTAGTTATCGGCAC
+AATCGGTGAAACACGTTAGAGGAGCGAAAATGGAGCCTGTAAGGCGACTGGTAGCGGAAC
+GGTCGTGTTAGATTGTGTAGCCGATAGCTGAACGAAATAAATGCTGGCAGCGCCATTCTA
+TTTCGGCAGGAGGAGGCTCAAGGGGTTCGGGGAATGAAATTCCCTGAGGTCTTTTTATTT
+TTTCTAGAGGAGTGCTATAATCAAAGAAAATGAGAAAAAAGAGTAAAAAAATAGTCGAGC
+AGTGTTGACGCACTCTCGACCTTTACGGAAACTAATCACACTAGCTCCGTAACTTCTTAA
+TCATTATACGAATATTTTTAGGTTTCTTCAAGACTAGAGATTTTTTGGTAATGAATTTTT
+AAGAGTTACGTGAACTTTTGAAAATTCTTTCCAGAAGTCTCTTTTTTCTTTGAGGAGGAA
+CTAAATTTGAGTAAAAAAGGCACGATCATAAATGAGTGGGAAAAATTAACAGCCCCCTCT
+AACAGGCGGTTAAGTGTTGACGATAAGGTACACCCCCTAAAATTAAGTTGGTCAATCGAT
+CGAATTACAATCGTCGGAAAACTGAAAGAAAATATTTATTATCACACTCCAAATGATGTG
+TTGATTTTAGATTTTGAACAGCTTATGCGCCTAAATGAAGGTAACGGTTATTTAAGATCT
+GTTAGTAATAATGGTTGGCAGTTGTTAGACCAACATGAAGAGAATATTGCTTATATTGAA
+ATTTTAAAATGGCAAGAGGGGAAAGGGCGTATAGACTTCAATCCGAATAAGATTAGTCAA
+TTCTTAGCTAGTTCCATGAAAAATTTTATTCATGATTTGTTTATCGAACCTCACTTTTCA
+CGTGCAGATATTGCTTGCGACATTATCGATGTACCTGATGAGTTTATTACACAATATCGG
+GTAGTTGATCCAGTTTCTTTTAAGCCTATTTATGGACGGAATGGAAAATTAGAGACGGCA
+TATTGGGGATCTCGCTCTTCTGAACGTCAAATTCGGATGTATAATAAAAAACTGGAACAA
+GAGAAGAAAAGAAAAATTGTGCCAAAAGAAATCGTGAGTTGGTGGCGGTTAGAAATGCAG
+CTAAGACGTGGCAAAGCAACAGATTGGCATGCGATGGTTCGGGAAAGTTTAGATAGCTTT
+GCAAGTCCTCATTACTTGCCTGGAGATGTAAAACCTGTTGATAGAATTATGATAAAAGGG
+CTGAATCAAGATCATTCAGAGTGGGCGTATATTAGCAGAAATTTGAAATATAGATTGCGC
+AAATTGTTGAAAGAAGAAAGCCAAAATGATGAATTGACGAATCATTTGCGAGAAACCTTT
+GCAGAATCGGCAGACGATTTAAAAAAAGAATTAGACACATGGCTTCTAGGGCTAGACGTA
+ACAGAGGAGTGATACCGAATAAGAAAAGTCAGATGAGTGAGAGTAAATTTACGTCAATGT
+TTAATGACGTGAGTTTACGATAAGCGATTATTTTGCGTGAAGCAAAATAAAGCGTAAAAG
+GAGTTGAGAGCGTGACACGCTTTCGGCTCCTTTTTTCGTTGTCACTTGTGACAGCGAATA
+CCCTCGGAGAGCATTTGGAA
+>contig00010 len=1718 cov=2.0 corr=0 origname=NODE_18_length_1718_cov_2.041483_pilon sw=shovill-spades/1.1.0 date=20220302
+TATACTTAAAAATATAGGAATCCCCTTACATTTTTTAGGAAATAAATGCTAAAAATATGC
+AAAAAAAGGGACTGAGACAAAAGTCTTGTCGCAGTCCCTTATTCCAAATAAAGGCTCTAT
+ACTTTTTGATGTTGGTGAACTTCACCAACATCTTTTTTGTATAAAAAAATATAGAAAAGA
+CACCCTGAAATCCTTTAGAATTAATTTGGCTACCAATTCATAGGAGGATTCAAGATGTCT
+CATACTCAGCTTATCAAAGATACCCTAAATATTCTAGACCTAAATATCTATTTCGAGGAA
+AATTGTTTAACTAAAGAAAAATACAAAGGGCAAATTTGCTTGATTTACAAAGGAACTCTT
+CTGTACAAGCCAGAAGAGTGTTCCCATTGTCTTTGTGTCGTCCCCTCTAGGATCATTCGT
+TGGGGGACGACAACCGTTCGGTTGTTACTGAATGATGTGTCTGAGTATCGCACTTATCTG
+GAGCTGAAGAAACAACGATTTAAATGTAAGTCTTGCCAAAGAACATTCGTAGCGGATACC
+TCTGTTGCTGAAAAACACTGTTTCATTAGTCAAAAAGTTCGTTGGTCTGTCATTGCTCGC
+TTAAAAGAGAATACTTCCATGACGGAAATCGCTCGTCAGAAAAATATTTCCACTTCTTCG
+GTCTATCTTGTCATGAAGCGATTCTACCGCCCATTGAATCCTTTCAAACAGACTTTGCCA
+AAGGTCTTATGCTTTGATGAATTCAAATCGGTTCGAAGTGTTGCCAGTGCAATGAGTTTT
+ATCATGATGGACGGACAAAGCCATGCATTATTGGATATTGTCGAAAATCGACGCTTGCCT
+TATTTAGAACGCTATTTTTCTCGGTTTTCATTAGCGACTCGTGAAGCCGTTCAATTGATT
+GTTATTGATATGTATGCGCCTTATGTTTCGTTGGTGAAAAAGCTTTTCCCGAATGCTCAG
+TTGATCATCGATCGTTTCCACATCGTCCAACATATTGGCAGAACTTTCTTGAATCATCGA
+GTGAAAGAAACCACGGTACGACTTAAAGGAAATTCCCACTCTCAACGAGGGTTAGGGAAA
+AAATTGAAGCGCTATTGGAAACTCCTACAAAAAGAAGAAGCAAAGTTAAACTATGAAAAA
+CGGGTTTGGCGTGCCAGTTTTAAAGATTATTTGACTGAAAGTGAGATTGCCGATCGACTG
+TTAGCTGCTTGTCCCAACTTACGCCAAGGCTATCAGTTATACCAAGACATTCTTTATGCG
+GTAAAGAAAAGAGATCAGTCACTATTTGAGGATTGTTTAACTAGAGACATTAGCGGTCTG
+CCAGAAACCTATACAACCACTTTACGAACGTTTAAAAAGTTTCTGCCACAGATCCAAAAT
+GCGCTTCACTACAGCTATTCAAACGGACCATTGGAATGCTTAAACAACCACATCAAAGTA
+TTAAAACGCAATGCGTACGGCTTTCGCAACTTTTACAATTTCAAACTACGAATTATGATT
+CGTCATGGCAAAACATTTTTAACCAAATAAACAGAACAGAAAGAGGTTTTCTTCTTTCTG
+TTCTGTCCAAATTATTCTAAGATTTCTCTTTACCAACATCATTTGACAAAGAGCCCGTTT
+TTCATACATGTTTATCTGTCTCAACCATACATATATGGAGACGGCGGGAGTCGAACCCGC
+GTCCAAACACATCGCCACTTAAAAATCTACGTTCATAG
+>contig00011 len=1047 cov=2.1 corr=0 origname=NODE_82_length_1047_cov_2.069565_pilon sw=shovill-spades/1.1.0 date=20220302
+ACTTATGATACACTTTTGAAACTCGCATTACGGCATCGTCCAGACTTGCTAATCATTGGC
+GAGATAAGAGATGAATCAACTGCACATGCTGCGGTAAGAGCAGCACTAACAGGGCACCGG
+GTTTTTGCAACCGTACATGCACGCAATCTTGAAGGTACATTGGTCAGAATCCATGAACTG
+ACAAAGAAAAAAGAAGAGCTATCTGAATGTTTAGCTGGTGTCATTTATCAAGAACTTTTG
+GAAGATGCCAATCACCATCCTTCTGTTTTATGGAGTTATCAATTTATGGAGGAAGAATCA
+GTAAAAAAATCATGGGAGGAAAGTTATGAAGAAGCTCAGGAAAATATTTGGCAGTCAGAA
+CTATTCTAAAGGATTAACAAGAAGCCAGCAAAACCAGTTTGCACAAACCATGGGAGAACT
+GCTTTTATCTGGTTTTAGTCTGCAAGAATCCCTTTATTTATTACTCACGATCCGTTCGTT
+TCCACCTGTTATTTTGGCAAATATCCAACATCAGCTAAAGGAAGGGCAAGCGTTTAGTGA
+GGTACTTTCGCAAATAGGATATGGAGCAGAGCAACTGGTACAGATCGAGTTAGCTGAACG
+TCATGGGAATCTGCCGACAACTTTGTTGGAAATTGCCAAACAGTTTCGGCTTGTTGAAGG
+ATTTCGCAATGATTTGAAAAAGCTGCTTGCATATCCGATGCTATTGCTCACCTTTTTGCT
+AGGTATCTTGTTTAGTATGCGGTTGTTCGTTTTGCCTCAGCTTATTGGTTCAGGAATGGT
+CATGCAAGAGCATTGGGGTATTCAGCTGATACAAGTCTTTCATTGGTATGTTCTACTATT
+CATCCTAGCGGTTACTCTATTGGCTTTACTAGTAAGGTATCGTCTGATGAAGTTGTCTCC
+TGTTGATCAGAGTGAATGGATAAGCAGACAATTATTGATTGGACCGATATATTCCTTGTA
+TCAATCGGCTTATTTGTCACTAGAGATTGGAAAGCTTTTTCATGAAGGTTTCGAATTAAG
+GCAAATCATAGTCTGCTTAAAGGAAAC
+>contig00012 len=887 cov=2.0 corr=0 origname=NODE_144_length_887_cov_2.006579_pilon sw=shovill-spades/1.1.0 date=20220302
+AATCGATATCGATGCGTCAAAATTTGGACGACGCCATGAAACATCTTTGTCGATCCTCGG
+TGATGCAAACACAGCTTTGCAAAGACTTGTCGAGTTAGGGGATGCTCGCCCTGCTGATAG
+CTGGTACCTAGCAAATCAAGAAAATAAAGAAAAATGGGTAAATTGGTTGAAATCTTTTGA
+AGATCGAGAGGAAGAACCGATTCGTCCAGAGGCTGTCTATAAAGAAATCAATCGTATTGC
+TGAAGACGATGCGATTTTCGTCACAGATGTCGGTAACACGACTATCCATTCTATTCGTTT
+ATTGAATATGAACGGTAAACAAAAACATACGACATCTGGATGGTTCGCAACTATGGGTAA
+TGGTGTGCCAGGAGGAATTGCCGCACAACTAAGCTACCCAGAAAAACAAGTATTTACCTT
+AAGTGGTGATGGCGGGTTTGCTATGGTCATGCAAGATATCATTACACAAGTCAAATATCA
+GCTTCCAATTATTAATGTTGTCTTTTCGAATGATTCTTTTGGTTTCATCGAAGCAGAACA
+AGAAGATACGGAACAAAAGAAATTTGGTGTATTTTTAGAAGATGCAGATTTCGGTAAAGT
+TGGAGAAGCGCTCGGGGCAAATAGCTTTACAGTCACAGAATACTCGCAACTTCGATTTGC
+CTTTGATGCAGCTGCAAAATCAGATCGTCCTGTAGTAATCGATGTGAAGATCAATAACAA
+GCGCCCATTGCCAGTAGAAGATCTGCATTTAGATCCAAGAAAATATTCTGAAGAAGAAAT
+CCAAGCATTCAAAGAAAAATATGAAGTCCATGATTTGCCAGTATTGAATGAATTATATGA
+AAAGAGGTTGTGACAACTGCGCTATGCTTCGAGTATTAAGATAAAAT
+>contig00013 len=886 cov=2.2 corr=0 origname=NODE_146_length_886_cov_2.193676_pilon sw=shovill-spades/1.1.0 date=20220302
+ATCGACAATGTAGGTATTCGCCGTAAAATAGGTGTGGCAGCCACGACAGTGGTAGCGTTG
+TTTCGCTAAAGCAAGATAAGTCAGTTGGTTCGCACATTTATTAAGTTGAATGAGCGATTT
+TTTCTTTCCGTTCTTAACGATCATGCCTTCATGATTCATCTGTTTACACAAAGGACAGCG
+ACGAATTTCTTTACTTAACGTCGCAGAAACAACAAGACTCTTGATATTCTTAATGCTCTT
+CGATTCCACATTTGTGATGAAAATGTTTTTATCTTTGATTCCAAGTAGTAGTTTGATATG
+ATGAAGATCAGGCATACAGAACGCTCCTTTGATTGTGTTGTGGTGATTCAATTCTAACGG
+AGCTTCTGTATGTTTTGTTTTTTCATGCTCAAAAGGGACCGATAGAATGATTTTCTATCA
+GTCCTAGAAATTATAGAGCCTTTTTTATTTGGTCTTGAAGAAGAAAAGTAAGCGCCCCAT
+AGAACAGTACCTGTACGTCAAATAACCCGACCTATAGAATAGAATCGGGAATGTTTGGCG
+TTTTTAGTTACGAGAAAAATGTTGTTGTACATCCTTGTTCCAAGGCAACAGTTGATCTAA
+AGTTTCTGCTGAAAGTACGGGAAGATTTGGTATCTTATCAAATAGAAACTCTAGATACTT
+TACAGGATTCAATCCGTTAAGTTCTGCTGTTTTATATACACTCAGAATGATTCCTGAAGT
+TCGTGCTCCTTCAAGACTTGTGGAATGCAACCAATTTTTCCGTCCTATCACCAGCTCTTT
+GATATTTCGCTCCGCACGATTATTTGTGAGTTCTAAACGACCATCTTCAAAAATAGGTTC
+AAAACCACTTCGTAGTTTACACGCATATTGAACGGCTGCATCCAAC
+>contig00014 len=836 cov=2.5 corr=0 origname=NODE_172_length_836_cov_2.489422_pilon sw=shovill-spades/1.1.0 date=20220302
+GGGGCTACATGCCAACGCTAATTTTAGAATCAGATCATGGTTATCAAGTTTATTTTGTAC
+TAAAGACACCAGGCTATGTCACAAAGAAAAGCAATTTCAAGGTGATCGATGTAGCAAAAA
+AAATTTCAAAAACAATTCGTCTACAGTTGGCTGAAAAATTGTCCGGAGTGGATCTAGGAT
+GTAACCACTTCGGAATTGCTCGATTCCCACAAGAAAATAATATTGTTTTTAAAGAAATGA
+ACTATCAGTATTCTTTTGCTGACTGGATTCAATGGTCGATGAAGCTTGAATCAGATCAAA
+AAACAAAAGAAGATCGAGAACGAAAACTAATTGTCTTTCCTGAGAAAAAAGAAATTCGTC
+AAGTAGATGAACCGTGGTTCGATATGTTACTTCATAAAGCAAACATCGTCGGCGGAGAAG
+GACGTCTTGGTCGAAATAATGTGATTTTCACGCTTTCTTTAGCTTATTACTCTTCAGGTT
+ATGCATTGGATACTTGCGAATACAATATGTTCACATTCAACGAACGGTTACAGGAACCGC
+TATCTGAAGCAGAATTAGTAAAGATTGTACGTAGTGCTTATTCTGGTAATTATCAAGCAG
+CAAGCAGAGAATTCATTATTGAATTGTGCCAGCAATGGGTTTCACCAACCTTAAAAAATA
+ATGATCTGTTCATTCAACGACGTGGCTGGTGGAAATTTAAAAAGCCACGAGATCAAAGAA
+AATATAGTCATAAAAATGAATGGAAAGAAGATCTATTGGCTTATCTAAGCGAAAAAAGTC
+TTGCTAGTGAGCCTTATTTGAACCTGTCAAAAAAAGAATTGGCTTCACAACTAACG
+>contig00015 len=834 cov=2.2 corr=0 origname=NODE_175_length_834_cov_2.244696_pilon sw=shovill-spades/1.1.0 date=20220302
+TAGAAAATGACAATGGTTTAGTGTCTATTAAAGGTACGGGGAAAAGAACTATAGTTGAGG
+TTTCATCTACGTATCCAACTACGATGATTCTATCTTTATTAATTAGTTCAATAACTTTTA
+TATTCTTATTTACACGTTATTTAATAAGATGCTGCGGTGAAATGAAAATAGATTAGATAG
+ATATTATAAATATGTTGATTCTATTTTCATAGCAATGGAGAAAATACATTAGCAATATAT
+AAAAGAAGGTATCAAGAGTCACAGTGAATTTATTCCGAAAAGTGAAAAGAGCAAATATAA
+AATTTAATGAAAATATAGAACTAAATAGGAAAACGTAGACGTAATTTTCTACGTTTTCCT
+TTTCATATATATTAAATATTACGGAAAATTATATAAACTAATTTAGTGTTTTGTTTGTAA
+TTCCTAATTTTGCTCCACTTTTAGATAATTTTTAGGTCTATTTAACTCATCAGACATTCT
+ATGCTCATTTTTCTCCAAATTTGTTTCAACTCTTTCGTACTTAATTTTGCGTATTTGAAA
+ATTCTTCTTTTAGAGTACTTTTATTACGATACTAGTATGATATATATCTATAGCAAACAG
+TTAAAATCTTCCTAAAATAAGCGAATAGCATTCCTAAAACCTATAAAATTTTTAGATGAA
+GCGACAAGTGGACAATTAATAAACTACTTGAACATGAAATTATGGATCACCTTTCAAATT
+TAGAAAATGGAATTCTTATACTTATTGCGCAACATTTATTGATTGCAAAATTATGTGACA
+AAAAAAACTAGTAGAAGAAAGAATAATGGCTTGATAATAAAGTACTACCTATTA
diff -r 000000000000 -r 2b6e795b22a9 test-data/data.fastq.gz
Binary file test-data/data.fastq.gz has changed
diff -r 000000000000 -r 2b6e795b22a9 test-data/plasmidfinder_db.loc
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/plasmidfinder_db.loc	Mon Sep 19 08:47:42 2022 +0000
@@ -0,0 +1,1 @@
+test-plasmindfinder-db	Test Database	${__HERE__}/test-db
diff -r 000000000000 -r 2b6e795b22a9 test-data/test-db/.gitignore
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test-db/.gitignore	Mon Sep 19 08:47:42 2022 +0000
@@ -0,0 +1,2 @@
+*.b
+*.name
diff -r 000000000000 -r 2b6e795b22a9 test-data/test-db/Inc18.comp.b
Binary file test-data/test-db/Inc18.comp.b has changed
diff -r 000000000000 -r 2b6e795b22a9 test-data/test-db/Inc18.fsa
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test-db/Inc18.fsa	Mon Sep 19 08:47:42 2022 +0000
@@ -0,0 +1,2 @@
+>rep2_2_repR(pEF1)_DQ198088
+atgttgagcgaaatttattcagctattcttaaaaacggcttacgtacatacaaatatcgaaacagcaccatgaaacctgcaggtcatattgattccagtaggagtggtgctatctttgcgtaccttagcaagcaattaatgaatgttgggcgtggtatggtcattacttcggaagaagctattttagagaacgaaaagaaactaacgcattggacacctaatacctatcgctttggtacttatgcggatgattatcgaacagtggttaaaggtcattctgagaaaaacttaagtcaaatcaacacatttgtagttgatatcgattcaaaagagaaccatcaaggcgaaattattttagcctgtttagatcaagtgggctacatgccaacgctaattttagaatcagatcatggttatcaagtttattttgtactaaagacaccaggctatgtcacaaagaaaagcaatttcaaggtgatcgatgtagcaaaaaaaatttcaaaaacaattcgtctacagttggctgaaaaattgtccggagtggatctaggatgtaaccacttcggaattgctcgattcccacaagaaaataatattgtttttaaagaaatgaactatcagtattcttttgctgactggattcaatggtcgatgaagcttgaatcagatcaaaaaacaaaagaagatcgagaacgaaaactaattgtctttcctgagaaaaaagaaattcgtcaagtagatgaaccgtggttcgatatgttacttcataaagcaaacatcgtcggcggagaaggacgtcttggtcgaaataatgtgattttcacgctttctttagcttattactcttcaggttatgcattggatacttgcgaatacaatatgttcacattcaacgaacggttacaggaaccgctatctgaagcagaattagtaaagattgtacgtagtgcttattctggtaattatcaagcagcaagcagagaattcattattgaattgtgccagcaatgggtttcaccaaccttaaaaaataatgatctgttcattcaacgacgtggctggtggaaatttaaaaagccacgagatcaaagaaaatatagtcataaaaatgaatggaaagaagatctattggcttatctaagcgaaaaaagtcttgctagtgagccttatttgaacctgtcaaaaaaagaattggcttcacaactaacgatgcccaagcgaacacttgataagatcttaaatgagttacgagaggagaataaagtcttctacaaggtaacacgaggaagaaatggcggaatgatcattgcttcagtcaaaacgttgttcgcgagagttattcaactaagtaaagaaaagagactagattattcaacaaggatcacagaggtatttggactcaacgagagcttagtagaagagacatttagacaattatcaacccccttgaaccctcttaaagaagtgaatctttttgaagtagatacaggttga
diff -r 000000000000 -r 2b6e795b22a9 test-data/test-db/Inc18.length.b
Binary file test-data/test-db/Inc18.length.b has changed
diff -r 000000000000 -r 2b6e795b22a9 test-data/test-db/Inc18.name
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test-db/Inc18.name	Mon Sep 19 08:47:42 2022 +0000
@@ -0,0 +1,3 @@
+rep2_2_repR(pEF1)_DQ198088
+rep11a_1_repA(pB82)_AB178871
+rep14a_2_ORF1(pKQ10)_EFU01917
diff -r 000000000000 -r 2b6e795b22a9 test-data/test-db/Inc18.seq.b
Binary file test-data/test-db/Inc18.seq.b has changed
diff -r 000000000000 -r 2b6e795b22a9 test-data/test-db/Rep3.comp.b
Binary file test-data/test-db/Rep3.comp.b has changed
diff -r 000000000000 -r 2b6e795b22a9 test-data/test-db/Rep3.fsa
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test-db/Rep3.fsa	Mon Sep 19 08:47:42 2022 +0000
@@ -0,0 +1,2 @@
+>rep11a_1_repA(pB82)_AB178871
+atggctaatgagattgtaaaataccaccatgaattaaatacaattcctttaagaaaatttacaccggttgaaatgaatttgtttttttccatcgtgtctagaatgcgtgaaaaaggggataagacagttcgttttacgtttgaccaactaaaagatttaagtaactacaaagcaactgcaaatgtacgatttgtagaagatttaaaagcaacttatgaaaaaatcttatctttacgctttggtcgtagaagtgagtctgggctttcttacgatatgtttgtaatgtttacagaatttaaaatcaacggggacgtagaaaatccttacgtagatatacgaatttacgaaaaagcactgcctttgttaaataatttagacgagtgggtacgctattctttacaacaattcaacgagctacaaagtggctatgcaaagactatgtttcgtctgttaaagcaatacagaaccaaaggtttcgcatatttctccaaagaagactttcttgaattattagatattcctaaaagttataagcaacctgatatagataaacgagttataaaacctatacgtcaagaactaactgcaatcttcaaaggactaacaatcaaaaagaaatacggaaaaggacggggaaaacctgttattggctatcaatttacgttcaaacctgagatcaaaaaagcagacgactttaacaaacatgcaccaaccaaagaagaccaaaataaagcattggctttagctgataaacaaaaagaatacgaagaacccgctacaacaattaacgaaaaaatcaaacagaagaaacgagaacttgaactcctccaacaaatcaaacaactagaaaaagagaaaaaagctcttgaaaaacaaacagagtccgcactttcggaaaaagagaaaaaaagtttattatctgatttagataatttattccagtag
diff -r 000000000000 -r 2b6e795b22a9 test-data/test-db/Rep3.length.b
Binary file test-data/test-db/Rep3.length.b has changed
diff -r 000000000000 -r 2b6e795b22a9 test-data/test-db/Rep3.name
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test-db/Rep3.name	Mon Sep 19 08:47:42 2022 +0000
@@ -0,0 +1,1 @@
+rep11a_1_repA(pB82)_AB178871
diff -r 000000000000 -r 2b6e795b22a9 test-data/test-db/Rep3.seq.b
Binary file test-data/test-db/Rep3.seq.b has changed
diff -r 000000000000 -r 2b6e795b22a9 test-data/test-db/Rep_trans.comp.b
Binary file test-data/test-db/Rep_trans.comp.b has changed
diff -r 000000000000 -r 2b6e795b22a9 test-data/test-db/Rep_trans.fsa
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test-db/Rep_trans.fsa	Mon Sep 19 08:47:42 2022 +0000
@@ -0,0 +1,2 @@
+>rep14a_2_ORF1(pKQ10)_EFU01917
+gtgcgactgtacaacaaaaagctagagcaggaacgaaaaaaagtaatcgtgccaaaagaaatcgatacgtggtggcggttagaaatgcagctaagacgtggcaaagcaacggattggcatgcgatggttcaggaaagcttagatagttttgcaagcccgcattttttgccgattgatataaaacctattgataaaatagttattgaaggtttgatagctgagccttctaattggtcgataattgctagacatacaaaatataaatatcggaatttgctgaagcaagaaagtcaaaatgatgagttaacgaaccatttacgagagacttttaaggaatctgcagacgaattaaaaaaagaattggatacgtggcttttggggttggatgtgacagagaagtga
diff -r 000000000000 -r 2b6e795b22a9 test-data/test-db/Rep_trans.length.b
Binary file test-data/test-db/Rep_trans.length.b has changed
diff -r 000000000000 -r 2b6e795b22a9 test-data/test-db/Rep_trans.name
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test-db/Rep_trans.name	Mon Sep 19 08:47:42 2022 +0000
@@ -0,0 +1,1 @@
+rep14a_2_ORF1(pKQ10)_EFU01917
diff -r 000000000000 -r 2b6e795b22a9 test-data/test-db/Rep_trans.seq.b
Binary file test-data/test-db/Rep_trans.seq.b has changed
diff -r 000000000000 -r 2b6e795b22a9 test-data/test-db/config
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test-db/config	Mon Sep 19 08:47:42 2022 +0000
@@ -0,0 +1,7 @@
+# Database configuration file - Describes the content of the database
+# Each db consist of 1 file(s) with the following extensions: fsa
+# Other important files are: notes.txt
+#db_prefix	name	description
+Inc18	Gram Positive	Inc18
+Rep3	Gram Positive	Rep3
+Rep_trans	Gram Positive	Rep_trans
diff -r 000000000000 -r 2b6e795b22a9 test-data/test_1/Hit_in_genome_seq_test1.fsa
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_1/Hit_in_genome_seq_test1.fsa	Mon Sep 19 08:47:42 2022 +0000
@@ -0,0 +1,25 @@
+>rep11a:WARNING ID:99.89% COV:100.0% Best_match:contig00003 len=3227 cov=2.2 corr=0 origname=NODE_3_length_3227_cov_2.232903_pilon sw=shovill-spades/1.1.0 date=20220302:308..1252:rep11a_1_repA(pB82)_AB178871:99.894180
+ATGGCTAATGAGATTGTAAAATACCACCATGAGTTAAATACAATTCCTTTAAGAAAATTT
+ACACCGGTTGAAATGAATTTGTTTTTTTCCATCGTGTCTAGAATGCGTGAAAAAGGGGAT
+AAGACAGTTCGTTTTACGTTTGACCAACTAAAAGATTTAAGTAACTACAAAGCAACTGCA
+AATGTACGATTTGTAGAAGATTTAAAAGCAACTTATGAAAAAATCTTATCTTTACGCTTT
+GGTCGTAGAAGTGAGTCTGGGCTTTCTTACGATATGTTTGTAATGTTTACAGAATTTAAA
+ATCAACGGGGACGTAGAAAATCCTTACGTAGATATACGAATTTACGAAAAAGCACTGCCT
+TTGTTAAATAATTTAGACGAGTGGGTACGCTATTCTTTACAACAATTCAACGAGCTACAA
+AGTGGCTATGCAAAGACTATGTTTCGTCTGTTAAAGCAATACAGAACCAAAGGTTTCGCA
+TATTTCTCCAAAGAAGACTTTCTTGAATTATTAGATATTCCTAAAAGTTATAAGCAACCT
+GATATAGATAAACGAGTTATAAAACCTATACGTCAAGAACTAACTGCAATCTTCAAAGGA
+CTAACAATCAAAAAGAAATACGGAAAAGGACGGGGAAAACCTGTTATTGGCTATCAATTT
+ACGTTCAAACCTGAGATCAAAAAAGCAGACGACTTTAACAAACATGCACCAACCAAAGAA
+GACCAAAATAAAGCATTGGCTTTAGCTGATAAACAAAAAGAATACGAAGAACCCGCTACA
+ACAATTAACGAAAAAATCAAACAGAAGAAACGAGAACTTGAACTCCTCCAACAAATCAAA
+CAACTAGAAAAAGAGAAAAAAGCTCTTGAAAAACAAACAGAGTCCGCACTTTCGGAAAAA
+GAGAAAAAAAGTTTATTATCTGATTTAGATAATTTATTCCAGTAG
+>rep14a:WARNING ID:99.5% COV:100.0% Best_match:contig00008 len=2292 cov=2.6 corr=0 origname=NODE_11_length_2292_cov_2.631409_pilon sw=shovill-spades/1.1.0 date=20220302:1703..2104:rep14a_2_ORF1(pKQ10)_EFU01917:99.502488
+GTGCGACTGTACAACAAAAAGCTAGAGCAGGAACGAAAAAAAGTAATCGTGCCAAAAGAA
+ATCGATACGTGGTGGCGGTTAGAAATGCAGCTAAGACGTGGCAAAGCAACGGATTGGCAT
+GCGATGGTTCAGGAAAGCTTAGATAGTTTTGCAAGCCCGCATTTTTTGCCGATTGATATA
+AAACCTATTGATAAAATAGTTATTGATGGTTTGATAGCTGAGCCTTCTAATTGGTCGATA
+ATTGCTAGACATACAAAATATAAATATCGGAATTTGCTGAAGCAAGAAAGTCAAAATGAT
+GAGTTAACGAATCATTTACGAGAGACTTTTAAGGAATCTGCAGACGAATTAAAAAAAGAA
+TTGGATACGTGGCTTTTGGGGTTGGATGTGACAGAGAAGTGA
diff -r 000000000000 -r 2b6e795b22a9 test-data/test_1/Plasmid_seqs_test1.fsa
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_1/Plasmid_seqs_test1.fsa	Mon Sep 19 08:47:42 2022 +0000
@@ -0,0 +1,25 @@
+>contig00003 len=3227 cov=2.2 corr=0 origname=NODE_3_length_3227_cov_2.232903_pilon sw=shovill-spades/1.1.0 date=20220302:308..1252:rep11a_1_repA(pB82)_AB178871:99.894180
+ATGGCTAATGAGATTGTAAAATACCACCATGAATTAAATACAATTCCTTTAAGAAAATTT
+ACACCGGTTGAAATGAATTTGTTTTTTTCCATCGTGTCTAGAATGCGTGAAAAAGGGGAT
+AAGACAGTTCGTTTTACGTTTGACCAACTAAAAGATTTAAGTAACTACAAAGCAACTGCA
+AATGTACGATTTGTAGAAGATTTAAAAGCAACTTATGAAAAAATCTTATCTTTACGCTTT
+GGTCGTAGAAGTGAGTCTGGGCTTTCTTACGATATGTTTGTAATGTTTACAGAATTTAAA
+ATCAACGGGGACGTAGAAAATCCTTACGTAGATATACGAATTTACGAAAAAGCACTGCCT
+TTGTTAAATAATTTAGACGAGTGGGTACGCTATTCTTTACAACAATTCAACGAGCTACAA
+AGTGGCTATGCAAAGACTATGTTTCGTCTGTTAAAGCAATACAGAACCAAAGGTTTCGCA
+TATTTCTCCAAAGAAGACTTTCTTGAATTATTAGATATTCCTAAAAGTTATAAGCAACCT
+GATATAGATAAACGAGTTATAAAACCTATACGTCAAGAACTAACTGCAATCTTCAAAGGA
+CTAACAATCAAAAAGAAATACGGAAAAGGACGGGGAAAACCTGTTATTGGCTATCAATTT
+ACGTTCAAACCTGAGATCAAAAAAGCAGACGACTTTAACAAACATGCACCAACCAAAGAA
+GACCAAAATAAAGCATTGGCTTTAGCTGATAAACAAAAAGAATACGAAGAACCCGCTACA
+ACAATTAACGAAAAAATCAAACAGAAGAAACGAGAACTTGAACTCCTCCAACAAATCAAA
+CAACTAGAAAAAGAGAAAAAAGCTCTTGAAAAACAAACAGAGTCCGCACTTTCGGAAAAA
+GAGAAAAAAAGTTTATTATCTGATTTAGATAATTTATTCCAGTAG
+>contig00008 len=2292 cov=2.6 corr=0 origname=NODE_11_length_2292_cov_2.631409_pilon sw=shovill-spades/1.1.0 date=20220302:1703..2104:rep14a_2_ORF1(pKQ10)_EFU01917:99.502488
+GTGCGACTGTACAACAAAAAGCTAGAGCAGGAACGAAAAAAAGTAATCGTGCCAAAAGAA
+ATCGATACGTGGTGGCGGTTAGAAATGCAGCTAAGACGTGGCAAAGCAACGGATTGGCAT
+GCGATGGTTCAGGAAAGCTTAGATAGTTTTGCAAGCCCGCATTTTTTGCCGATTGATATA
+AAACCTATTGATAAAATAGTTATTGAAGGTTTGATAGCTGAGCCTTCTAATTGGTCGATA
+ATTGCTAGACATACAAAATATAAATATCGGAATTTGCTGAAGCAAGAAAGTCAAAATGAT
+GAGTTAACGAACCATTTACGAGAGACTTTTAAGGAATCTGCAGACGAATTAAAAAAAGAA
+TTGGATACGTGGCTTTTGGGGTTGGATGTGACAGAGAAGTGA
diff -r 000000000000 -r 2b6e795b22a9 test-data/test_1/data_test1.json
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_1/data_test1.json	Mon Sep 19 08:47:42 2022 +0000
@@ -0,0 +1,1 @@
+{"plasmidfinder": {"user_input": {"filename(s)": ["/tmp/tmpj3aqa6lu/files/9/6/4/dataset_9649367d-27ab-42b3-8f51-56f81f942d9c.dat"], "method": "blast", "file_format": "fasta"}, "run_info": {"date": "09.09.2022", "time": "08:52:55"}, "results": {"Gram Positive": {"Inc18": "No hit found", "Rep3": {"contig00003 len=3227 cov=2.2 corr=0 origname=NODE_3_length_3227_cov_2.232903_pilon sw=shovill-spades/1.1.0 date=20220302:308..1252:rep11a_1_repA(pB82)_AB178871:99.894180": {"plasmid": "rep11a", "identity": 99.89, "HSP_length": 945, "template_length": 945, "position_in_ref": "1..945", "contig_name": "contig00003 len=3227 cov=2.2 corr=0 origname=NODE_3_length_3227_cov_2.232903_pilon sw=shovill-spades/1.1.0 date=20220302", "positions_in_contig": "308..1252", "note": "repA(pB82)", "accession": "AB178871", "coverage": 100.0, "hit_id": "contig00003 len=3227 cov=2.2 corr=0 origname=NODE_3_length_3227_cov_2.232903_pilon sw=shovill-spades/1.1.0 date=20220302:308..1252:rep11a_1_repA(pB82)_AB178871:99.894180"}}, "Rep_trans": {"contig00008 len=2292 cov=2.6 corr=0 origname=NODE_11_length_2292_cov_2.631409_pilon sw=shovill-spades/1.1.0 date=20220302:1703..2104:rep14a_2_ORF1(pKQ10)_EFU01917:99.502488": {"plasmid": "rep14a", "identity": 99.5, "HSP_length": 402, "template_length": 402, "position_in_ref": "1..402", "contig_name": "contig00008 len=2292 cov=2.6 corr=0 origname=NODE_11_length_2292_cov_2.631409_pilon sw=shovill-spades/1.1.0 date=20220302", "positions_in_contig": "1703..2104", "note": "ORF1(pKQ10)", "accession": "EFU01917", "coverage": 100.0, "hit_id": "contig00008 len=2292 cov=2.6 corr=0 origname=NODE_11_length_2292_cov_2.631409_pilon sw=shovill-spades/1.1.0 date=20220302:1703..2104:rep14a_2_ORF1(pKQ10)_EFU01917:99.502488"}}}}}}
\ No newline at end of file
diff -r 000000000000 -r 2b6e795b22a9 test-data/test_1/logfile_test1.log
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_1/logfile_test1.log	Mon Sep 19 08:47:42 2022 +0000
@@ -0,0 +1,57 @@
+Found: rep2_2_repR(pEF1)_DQ198088
+Saving: contig00014 len=836 cov=2.5 corr=0 origname=NODE_172_length_836_cov_2.489422_pilon sw=shovill-spades/1.1.0 date=20220302:2..836:rep2_2_repR(pEF1)_DQ198088:55.890228
+Found: rep11a_1_repA(pB82)_AB178871
+Saving: contig00003 len=3227 cov=2.2 corr=0 origname=NODE_3_length_3227_cov_2.232903_pilon sw=shovill-spades/1.1.0 date=20220302:308..1252:rep11a_1_repA(pB82)_AB178871:99.894180
+Found: rep14a_2_ORF1(pKQ10)_EFU01917
+Saving: contig00008 len=2292 cov=2.6 corr=0 origname=NODE_11_length_2292_cov_2.631409_pilon sw=shovill-spades/1.1.0 date=20220302:1703..2104:rep14a_2_ORF1(pKQ10)_EFU01917:99.502488
+{'plasmidfinder': {'results': {'Gram Positive': {'Inc18': 'No hit found',
+                                                 'Rep3': {'contig00003 len=3227 cov=2.2 corr=0 origname=NODE_3_length_3227_cov_2.232903_pilon sw=shovill-spades/1.1.0 date=20220302:308..1252:rep11a_1_repA(pB82)_AB178871:99.894180': {'HSP_length': 945,
+                                                                                                                                                                                                                                        'accession': 'AB178871',
+                                                                                                                                                                                                                                        'contig_name': 'contig00003 '
+                                                                                                                                                                                                                                                       'len=3227 '
+                                                                                                                                                                                                                                                       'cov=2.2 '
+                                                                                                                                                                                                                                                       'corr=0 '
+                                                                                                                                                                                                                                                       'origname=NODE_3_length_3227_cov_2.232903_pilon '
+                                                                                                                                                                                                                                                       'sw=shovill-spades/1.1.0 '
+                                                                                                                                                                                                                                                       'date=20220302',
+                                                                                                                                                                                                                                        'coverage': 100.0,
+                                                                                                                                                                                                                                        'hit_id': 'contig00003 '
+                                                                                                                                                                                                                                                  'len=3227 '
+                                                                                                                                                                                                                                                  'cov=2.2 '
+                                                                                                                                                                                                                                                  'corr=0 '
+                                                                                                                                                                                                                                                  'origname=NODE_3_length_3227_cov_2.232903_pilon '
+                                                                                                                                                                                                                                                  'sw=shovill-spades/1.1.0 '
+                                                                                                                                                                                                                                                  'date=20220302:308..1252:rep11a_1_repA(pB82)_AB178871:99.894180',
+                                                                                                                                                                                                                                        'identity': 99.89,
+                                                                                                                                                                                                                                        'note': 'repA(pB82)',
+                                                                                                                                                                                                                                        'plasmid': 'rep11a',
+                                                                                                                                                                                                                                        'position_in_ref': '1..945',
+                                                                                                                                                                                                                                        'positions_in_contig': '308..1252',
+                                                                                                                                                                                                                                        'template_length': 945}},
+                                                 'Rep_trans': {'contig00008 len=2292 cov=2.6 corr=0 origname=NODE_11_length_2292_cov_2.631409_pilon sw=shovill-spades/1.1.0 date=20220302:1703..2104:rep14a_2_ORF1(pKQ10)_EFU01917:99.502488': {'HSP_length': 402,
+                                                                                                                                                                                                                                                'accession': 'EFU01917',
+                                                                                                                                                                                                                                                'contig_name': 'contig00008 '
+                                                                                                                                                                                                                                                               'len=2292 '
+                                                                                                                                                                                                                                                               'cov=2.6 '
+                                                                                                                                                                                                                                                               'corr=0 '
+                                                                                                                                                                                                                                                               'origname=NODE_11_length_2292_cov_2.631409_pilon '
+                                                                                                                                                                                                                                                               'sw=shovill-spades/1.1.0 '
+                                                                                                                                                                                                                                                               'date=20220302',
+                                                                                                                                                                                                                                                'coverage': 100.0,
+                                                                                                                                                                                                                                                'hit_id': 'contig00008 '
+                                                                                                                                                                                                                                                          'len=2292 '
+                                                                                                                                                                                                                                                          'cov=2.6 '
+                                                                                                                                                                                                                                                          'corr=0 '
+                                                                                                                                                                                                                                                          'origname=NODE_11_length_2292_cov_2.631409_pilon '
+                                                                                                                                                                                                                                                          'sw=shovill-spades/1.1.0 '
+                                                                                                                                                                                                                                                          'date=20220302:1703..2104:rep14a_2_ORF1(pKQ10)_EFU01917:99.502488',
+                                                                                                                                                                                                                                                'identity': 99.5,
+                                                                                                                                                                                                                                                'note': 'ORF1(pKQ10)',
+                                                                                                                                                                                                                                                'plasmid': 'rep14a',
+                                                                                                                                                                                                                                                'position_in_ref': '1..402',
+                                                                                                                                                                                                                                                'positions_in_contig': '1703..2104',
+                                                                                                                                                                                                                                                'template_length': 402}}}},
+                   'run_info': {'date': '09.09.2022', 'time': '08:52:55'},
+                   'user_input': {'file_format': 'fasta',
+                                  'filename(s)': ['/tmp/tmpj3aqa6lu/files/9/6/4/dataset_9649367d-27ab-42b3-8f51-56f81f942d9c.dat'],
+                                  'method': 'blast'}}}
diff -r 000000000000 -r 2b6e795b22a9 test-data/test_1/results_tab_test1.tsv
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_1/results_tab_test1.tsv	Mon Sep 19 08:47:42 2022 +0000
@@ -0,0 +1,3 @@
+Database	Plasmid	Identity	Query / Template length	Contig	Position in contig	Note	Accession number
+Rep3	rep11a	99.89	945 / 945	contig00003 len=3227 cov=2.2 corr=0 origname=NODE_3_length_3227_cov_2.232903_pilon sw=shovill-spades/1.1.0 date=20220302	308..1252	repA(pB82)	AB178871
+Rep_trans	rep14a	99.5	402 / 402	contig00008 len=2292 cov=2.6 corr=0 origname=NODE_11_length_2292_cov_2.631409_pilon sw=shovill-spades/1.1.0 date=20220302	1703..2104	ORF1(pKQ10)	EFU01917
diff -r 000000000000 -r 2b6e795b22a9 test-data/test_1/results_test1.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_1/results_test1.txt	Mon Sep 19 08:47:42 2022 +0000
@@ -0,0 +1,127 @@
+plasmidfinder Results
+
+Organism(s): Gram Positive
+
+****************************************************************************************
+Inc18
+****************************************************************************************************************
+Plasmid    Identity    Query / Template length    Contig        Position in contig    Note    Accession number
+****************************************************************************************************************
+-          -           -                          No hit found  -                     -       -
+================================================================================================================
+
+****************************************************************************************
+Rep3
+********************************************************************************************************************************************************************************************************************************
+Plasmid      Identity  Query / Template length    Contig                                                                                                                    Position in contig    Note        Accession number
+********************************************************************************************************************************************************************************************************************************
+rep11a          99.89  945 / 945                  contig00003 len=3227 cov=2.2 corr=0 origname=NODE_3_length_3227_cov_2.232903_pilon sw=shovill-spades/1.1.0 date=20220302  308..1252             repA(pB82)  AB178871
+================================================================================================================================================================================================================================
+
+****************************************************************************************
+Rep_trans
+**********************************************************************************************************************************************************************************************************************************
+Plasmid      Identity  Query / Template length    Contig                                                                                                                     Position in contig    Note         Accession number
+**********************************************************************************************************************************************************************************************************************************
+rep14a           99.5  402 / 402                  contig00008 len=2292 cov=2.6 corr=0 origname=NODE_11_length_2292_cov_2.631409_pilon sw=shovill-spades/1.1.0 date=20220302  1703..2104            ORF1(pKQ10)  EFU01917
+==================================================================================================================================================================================================================================
+
+
+
+
+Extended Output:
+
+# rep11a_AB178871
+template: 	ATGGCTAATGAGATTGTAAAATACCACCATGAATTAAATACAATTCCTTTAAGAAAATTT
+          	|||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||
+query:    	ATGGCTAATGAGATTGTAAAATACCACCATGAGTTAAATACAATTCCTTTAAGAAAATTT
+
+template: 	ACACCGGTTGAAATGAATTTGTTTTTTTCCATCGTGTCTAGAATGCGTGAAAAAGGGGAT
+          	||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
+query:    	ACACCGGTTGAAATGAATTTGTTTTTTTCCATCGTGTCTAGAATGCGTGAAAAAGGGGAT
+
+template: 	AAGACAGTTCGTTTTACGTTTGACCAACTAAAAGATTTAAGTAACTACAAAGCAACTGCA
+          	||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
+query:    	AAGACAGTTCGTTTTACGTTTGACCAACTAAAAGATTTAAGTAACTACAAAGCAACTGCA
+
+template: 	AATGTACGATTTGTAGAAGATTTAAAAGCAACTTATGAAAAAATCTTATCTTTACGCTTT
+          	||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
+query:    	AATGTACGATTTGTAGAAGATTTAAAAGCAACTTATGAAAAAATCTTATCTTTACGCTTT
+
+template: 	GGTCGTAGAAGTGAGTCTGGGCTTTCTTACGATATGTTTGTAATGTTTACAGAATTTAAA
+          	||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
+query:    	GGTCGTAGAAGTGAGTCTGGGCTTTCTTACGATATGTTTGTAATGTTTACAGAATTTAAA
+
+template: 	ATCAACGGGGACGTAGAAAATCCTTACGTAGATATACGAATTTACGAAAAAGCACTGCCT
+          	||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
+query:    	ATCAACGGGGACGTAGAAAATCCTTACGTAGATATACGAATTTACGAAAAAGCACTGCCT
+
+template: 	TTGTTAAATAATTTAGACGAGTGGGTACGCTATTCTTTACAACAATTCAACGAGCTACAA
+          	||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
+query:    	TTGTTAAATAATTTAGACGAGTGGGTACGCTATTCTTTACAACAATTCAACGAGCTACAA
+
+template: 	AGTGGCTATGCAAAGACTATGTTTCGTCTGTTAAAGCAATACAGAACCAAAGGTTTCGCA
+          	||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
+query:    	AGTGGCTATGCAAAGACTATGTTTCGTCTGTTAAAGCAATACAGAACCAAAGGTTTCGCA
+
+template: 	TATTTCTCCAAAGAAGACTTTCTTGAATTATTAGATATTCCTAAAAGTTATAAGCAACCT
+          	||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
+query:    	TATTTCTCCAAAGAAGACTTTCTTGAATTATTAGATATTCCTAAAAGTTATAAGCAACCT
+
+template: 	GATATAGATAAACGAGTTATAAAACCTATACGTCAAGAACTAACTGCAATCTTCAAAGGA
+          	||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
+query:    	GATATAGATAAACGAGTTATAAAACCTATACGTCAAGAACTAACTGCAATCTTCAAAGGA
+
+template: 	CTAACAATCAAAAAGAAATACGGAAAAGGACGGGGAAAACCTGTTATTGGCTATCAATTT
+          	||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
+query:    	CTAACAATCAAAAAGAAATACGGAAAAGGACGGGGAAAACCTGTTATTGGCTATCAATTT
+
+template: 	ACGTTCAAACCTGAGATCAAAAAAGCAGACGACTTTAACAAACATGCACCAACCAAAGAA
+          	||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
+query:    	ACGTTCAAACCTGAGATCAAAAAAGCAGACGACTTTAACAAACATGCACCAACCAAAGAA
+
+template: 	GACCAAAATAAAGCATTGGCTTTAGCTGATAAACAAAAAGAATACGAAGAACCCGCTACA
+          	||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
+query:    	GACCAAAATAAAGCATTGGCTTTAGCTGATAAACAAAAAGAATACGAAGAACCCGCTACA
+
+template: 	ACAATTAACGAAAAAATCAAACAGAAGAAACGAGAACTTGAACTCCTCCAACAAATCAAA
+          	||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
+query:    	ACAATTAACGAAAAAATCAAACAGAAGAAACGAGAACTTGAACTCCTCCAACAAATCAAA
+
+template: 	CAACTAGAAAAAGAGAAAAAAGCTCTTGAAAAACAAACAGAGTCCGCACTTTCGGAAAAA
+          	||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
+query:    	CAACTAGAAAAAGAGAAAAAAGCTCTTGAAAAACAAACAGAGTCCGCACTTTCGGAAAAA
+
+template: 	GAGAAAAAAAGTTTATTATCTGATTTAGATAATTTATTCCAGTAG
+          	|||||||||||||||||||||||||||||||||||||||||||||
+query:    	GAGAAAAAAAGTTTATTATCTGATTTAGATAATTTATTCCAGTAG
+
+# rep14a_EFU01917
+template: 	GTGCGACTGTACAACAAAAAGCTAGAGCAGGAACGAAAAAAAGTAATCGTGCCAAAAGAA
+          	||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
+query:    	GTGCGACTGTACAACAAAAAGCTAGAGCAGGAACGAAAAAAAGTAATCGTGCCAAAAGAA
+
+template: 	ATCGATACGTGGTGGCGGTTAGAAATGCAGCTAAGACGTGGCAAAGCAACGGATTGGCAT
+          	||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
+query:    	ATCGATACGTGGTGGCGGTTAGAAATGCAGCTAAGACGTGGCAAAGCAACGGATTGGCAT
+
+template: 	GCGATGGTTCAGGAAAGCTTAGATAGTTTTGCAAGCCCGCATTTTTTGCCGATTGATATA
+          	||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
+query:    	GCGATGGTTCAGGAAAGCTTAGATAGTTTTGCAAGCCCGCATTTTTTGCCGATTGATATA
+
+template: 	AAACCTATTGATAAAATAGTTATTGAAGGTTTGATAGCTGAGCCTTCTAATTGGTCGATA
+          	|||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||
+query:    	AAACCTATTGATAAAATAGTTATTGATGGTTTGATAGCTGAGCCTTCTAATTGGTCGATA
+
+template: 	ATTGCTAGACATACAAAATATAAATATCGGAATTTGCTGAAGCAAGAAAGTCAAAATGAT
+          	||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
+query:    	ATTGCTAGACATACAAAATATAAATATCGGAATTTGCTGAAGCAAGAAAGTCAAAATGAT
+
+template: 	GAGTTAACGAACCATTTACGAGAGACTTTTAAGGAATCTGCAGACGAATTAAAAAAAGAA
+          	||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||
+query:    	GAGTTAACGAATCATTTACGAGAGACTTTTAAGGAATCTGCAGACGAATTAAAAAAAGAA
+
+template: 	TTGGATACGTGGCTTTTGGGGTTGGATGTGACAGAGAAGTGA
+          	||||||||||||||||||||||||||||||||||||||||||
+query:    	TTGGATACGTGGCTTTTGGGGTTGGATGTGACAGAGAAGTGA
+
diff -r 000000000000 -r 2b6e795b22a9 test-data/test_2/data_test2.json
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_2/data_test2.json	Mon Sep 19 08:47:42 2022 +0000
@@ -0,0 +1,1 @@
+{"plasmidfinder": {"user_input": {"filename(s)": ["/tmp/tmpj3aqa6lu/files/3/2/3/dataset_32342c91-595d-40c3-b39a-60aa67724edc.dat"], "method": "kma", "file_format": "fastq"}, "run_info": {"date": "09.09.2022", "time": "08:53:07"}, "results": {"Gram Positive": {"Inc18": "No hit found", "Rep3": "No hit found", "Rep_trans": "No hit found"}}}}
\ No newline at end of file
diff -r 000000000000 -r 2b6e795b22a9 test-data/test_2/logfile_test2.log
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_2/logfile_test2.log	Mon Sep 19 08:47:42 2022 +0000
@@ -0,0 +1,7 @@
+{'plasmidfinder': {'results': {'Gram Positive': {'Inc18': 'No hit found',
+                                                 'Rep3': 'No hit found',
+                                                 'Rep_trans': 'No hit found'}},
+                   'run_info': {'date': '09.09.2022', 'time': '08:53:07'},
+                   'user_input': {'file_format': 'fastq',
+                                  'filename(s)': ['/tmp/tmpj3aqa6lu/files/3/2/3/dataset_32342c91-595d-40c3-b39a-60aa67724edc.dat'],
+                                  'method': 'kma'}}}
diff -r 000000000000 -r 2b6e795b22a9 test-data/test_2/results_tab_test2.tsv
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_2/results_tab_test2.tsv	Mon Sep 19 08:47:42 2022 +0000
@@ -0,0 +1,1 @@
+Database	Plasmid	Identity	Query / Template length	Contig	Position in contig	Note	Accession number
diff -r 000000000000 -r 2b6e795b22a9 test-data/test_2/results_test2.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_2/results_test2.txt	Mon Sep 19 08:47:42 2022 +0000
@@ -0,0 +1,33 @@
+plasmidfinder Results
+
+Organism(s): Gram Positive
+
+****************************************************************************************
+Inc18
+****************************************************************************************************************
+Plasmid    Identity    Query / Template length    Contig        Position in contig    Note    Accession number
+****************************************************************************************************************
+-          -           -                          No hit found  -                     -       -
+================================================================================================================
+
+****************************************************************************************
+Rep3
+****************************************************************************************************************
+Plasmid    Identity    Query / Template length    Contig        Position in contig    Note    Accession number
+****************************************************************************************************************
+-          -           -                          No hit found  -                     -       -
+================================================================================================================
+
+****************************************************************************************
+Rep_trans
+****************************************************************************************************************
+Plasmid    Identity    Query / Template length    Contig        Position in contig    Note    Accession number
+****************************************************************************************************************
+-          -           -                          No hit found  -                     -       -
+================================================================================================================
+
+
+
+
+Extended Output:
+
diff -r 000000000000 -r 2b6e795b22a9 test-data/test_3/Hit_in_genome_seq_test3.fsa
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_3/Hit_in_genome_seq_test3.fsa	Mon Sep 19 08:47:42 2022 +0000
@@ -0,0 +1,59 @@
+>rep2:WARNING ID:100.0% COV:55.89% Best_match:contig00014 len=836 cov=2.5 corr=0 origname=NODE_172_length_836_cov_2.489422_pilon sw=shovill-spades/1.1.0 date=20220302:2..836:rep2_2_repR(pEF1)_DQ198088:55.890228
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+--------------GGGCTACATGCCAACGCTAATTTTAGAATCAGATCATGGTTATCAA
+GTTTATTTTGTACTAAAGACACCAGGCTATGTCACAAAGAAAAGCAATTTCAAGGTGATC
+GATGTAGCAAAAAAAATTTCAAAAACAATTCGTCTACAGTTGGCTGAAAAATTGTCCGGA
+GTGGATCTAGGATGTAACCACTTCGGAATTGCTCGATTCCCACAAGAAAATAATATTGTT
+TTTAAAGAAATGAACTATCAGTATTCTTTTGCTGACTGGATTCAATGGTCGATGAAGCTT
+GAATCAGATCAAAAAACAAAAGAAGATCGAGAACGAAAACTAATTGTCTTTCCTGAGAAA
+AAAGAAATTCGTCAAGTAGATGAACCGTGGTTCGATATGTTACTTCATAAAGCAAACATC
+GTCGGCGGAGAAGGACGTCTTGGTCGAAATAATGTGATTTTCACGCTTTCTTTAGCTTAT
+TACTCTTCAGGTTATGCATTGGATACTTGCGAATACAATATGTTCACATTCAACGAACGG
+TTACAGGAACCGCTATCTGAAGCAGAATTAGTAAAGATTGTACGTAGTGCTTATTCTGGT
+AATTATCAAGCAGCAAGCAGAGAATTCATTATTGAATTGTGCCAGCAATGGGTTTCACCA
+ACCTTAAAAAATAATGATCTGTTCATTCAACGACGTGGCTGGTGGAAATTTAAAAAGCCA
+CGAGATCAAAGAAAATATAGTCATAAAAATGAATGGAAAGAAGATCTATTGGCTTATCTA
+AGCGAAAAAAGTCTTGCTAGTGAGCCTTATTTGAACCTGTCAAAAAAAGAATTGGCTTCA
+CAACTAACG---------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------
+>rep11a:WARNING ID:99.89% COV:100.0% Best_match:contig00003 len=3227 cov=2.2 corr=0 origname=NODE_3_length_3227_cov_2.232903_pilon sw=shovill-spades/1.1.0 date=20220302:308..1252:rep11a_1_repA(pB82)_AB178871:99.894180
+ATGGCTAATGAGATTGTAAAATACCACCATGAGTTAAATACAATTCCTTTAAGAAAATTT
+ACACCGGTTGAAATGAATTTGTTTTTTTCCATCGTGTCTAGAATGCGTGAAAAAGGGGAT
+AAGACAGTTCGTTTTACGTTTGACCAACTAAAAGATTTAAGTAACTACAAAGCAACTGCA
+AATGTACGATTTGTAGAAGATTTAAAAGCAACTTATGAAAAAATCTTATCTTTACGCTTT
+GGTCGTAGAAGTGAGTCTGGGCTTTCTTACGATATGTTTGTAATGTTTACAGAATTTAAA
+ATCAACGGGGACGTAGAAAATCCTTACGTAGATATACGAATTTACGAAAAAGCACTGCCT
+TTGTTAAATAATTTAGACGAGTGGGTACGCTATTCTTTACAACAATTCAACGAGCTACAA
+AGTGGCTATGCAAAGACTATGTTTCGTCTGTTAAAGCAATACAGAACCAAAGGTTTCGCA
+TATTTCTCCAAAGAAGACTTTCTTGAATTATTAGATATTCCTAAAAGTTATAAGCAACCT
+GATATAGATAAACGAGTTATAAAACCTATACGTCAAGAACTAACTGCAATCTTCAAAGGA
+CTAACAATCAAAAAGAAATACGGAAAAGGACGGGGAAAACCTGTTATTGGCTATCAATTT
+ACGTTCAAACCTGAGATCAAAAAAGCAGACGACTTTAACAAACATGCACCAACCAAAGAA
+GACCAAAATAAAGCATTGGCTTTAGCTGATAAACAAAAAGAATACGAAGAACCCGCTACA
+ACAATTAACGAAAAAATCAAACAGAAGAAACGAGAACTTGAACTCCTCCAACAAATCAAA
+CAACTAGAAAAAGAGAAAAAAGCTCTTGAAAAACAAACAGAGTCCGCACTTTCGGAAAAA
+GAGAAAAAAAGTTTATTATCTGATTTAGATAATTTATTCCAGTAG
+>rep14a:WARNING ID:99.5% COV:100.0% Best_match:contig00008 len=2292 cov=2.6 corr=0 origname=NODE_11_length_2292_cov_2.631409_pilon sw=shovill-spades/1.1.0 date=20220302:1703..2104:rep14a_2_ORF1(pKQ10)_EFU01917:99.502488
+GTGCGACTGTACAACAAAAAGCTAGAGCAGGAACGAAAAAAAGTAATCGTGCCAAAAGAA
+ATCGATACGTGGTGGCGGTTAGAAATGCAGCTAAGACGTGGCAAAGCAACGGATTGGCAT
+GCGATGGTTCAGGAAAGCTTAGATAGTTTTGCAAGCCCGCATTTTTTGCCGATTGATATA
+AAACCTATTGATAAAATAGTTATTGATGGTTTGATAGCTGAGCCTTCTAATTGGTCGATA
+ATTGCTAGACATACAAAATATAAATATCGGAATTTGCTGAAGCAAGAAAGTCAAAATGAT
+GAGTTAACGAATCATTTACGAGAGACTTTTAAGGAATCTGCAGACGAATTAAAAAAAGAA
+TTGGATACGTGGCTTTTGGGGTTGGATGTGACAGAGAAGTGA
+>rep14a:WARNING ID:78.5% COV:97.01% Best_match:contig00009 len=2060 cov=9.4 corr=0 origname=NODE_14_length_2060_cov_9.400414_pilon sw=shovill-spades/1.1.0 date=20220302:1478..1872:rep14a_2_ORF1(pKQ10)_EFU01917:76.156716
+ATTCGGATGTATAATAAAAAACTGGAACAAGAGAA-GAAAAGAAA-AATTGTGCCAAAAG
+AAATCGTGAGTTGGTGGCGGTTAGAAATGCAGCTAAGACGTGGCAAAGCAACAGATTGGC
+ATGCGATGGTTCGGGAAAGTTTAGATAGCTTTGCAAGTCCTCATTACTTGCCTGGA-GAT
+GTAAAACCTGTTGATAGAATTATGATAAAAGGGCTGA-ATCAAGATCATTCAGAGTGGGC
+GTATATTAGC-AGAAATTTGAAATATAGATTGCGCAAATTGTTGAAAGAAGAAAGCCAAA
+ATGATGAATTGACGAATCATTTGCGAGAAACCTTTGCAGAATCGGCAGACGATTTAAAAA
+AAGAATTAGACACATGGCTTCTAGGGCTAGACGTAACAGAGGAGTGA
diff -r 000000000000 -r 2b6e795b22a9 test-data/test_3/Plasmid_seqs_test3.fsa
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_3/Plasmid_seqs_test3.fsa	Mon Sep 19 08:47:42 2022 +0000
@@ -0,0 +1,59 @@
+>contig00014 len=836 cov=2.5 corr=0 origname=NODE_172_length_836_cov_2.489422_pilon sw=shovill-spades/1.1.0 date=20220302:2..836:rep2_2_repR(pEF1)_DQ198088:55.890228
+atgttgagcgaaatttattcagctattcttaaaaacggcttacgtacatacaaatatcga
+aacagcaccatgaaacctgcaggtcatattgattccagtaggagtggtgctatctttgcg
+taccttagcaagcaattaatgaatgttgggcgtggtatggtcattacttcggaagaagct
+attttagagaacgaaaagaaactaacgcattggacacctaatacctatcgctttggtact
+tatgcggatgattatcgaacagtggttaaaggtcattctgagaaaaacttaagtcaaatc
+aacacatttgtagttgatatcgattcaaaagagaaccatcaaggcgaaattattttagcc
+tgtttagatcaagtGGGCTACATGCCAACGCTAATTTTAGAATCAGATCATGGTTATCAA
+GTTTATTTTGTACTAAAGACACCAGGCTATGTCACAAAGAAAAGCAATTTCAAGGTGATC
+GATGTAGCAAAAAAAATTTCAAAAACAATTCGTCTACAGTTGGCTGAAAAATTGTCCGGA
+GTGGATCTAGGATGTAACCACTTCGGAATTGCTCGATTCCCACAAGAAAATAATATTGTT
+TTTAAAGAAATGAACTATCAGTATTCTTTTGCTGACTGGATTCAATGGTCGATGAAGCTT
+GAATCAGATCAAAAAACAAAAGAAGATCGAGAACGAAAACTAATTGTCTTTCCTGAGAAA
+AAAGAAATTCGTCAAGTAGATGAACCGTGGTTCGATATGTTACTTCATAAAGCAAACATC
+GTCGGCGGAGAAGGACGTCTTGGTCGAAATAATGTGATTTTCACGCTTTCTTTAGCTTAT
+TACTCTTCAGGTTATGCATTGGATACTTGCGAATACAATATGTTCACATTCAACGAACGG
+TTACAGGAACCGCTATCTGAAGCAGAATTAGTAAAGATTGTACGTAGTGCTTATTCTGGT
+AATTATCAAGCAGCAAGCAGAGAATTCATTATTGAATTGTGCCAGCAATGGGTTTCACCA
+ACCTTAAAAAATAATGATCTGTTCATTCAACGACGTGGCTGGTGGAAATTTAAAAAGCCA
+CGAGATCAAAGAAAATATAGTCATAAAAATGAATGGAAAGAAGATCTATTGGCTTATCTA
+AGCGAAAAAAGTCTTGCTAGTGAGCCTTATTTGAACCTGTCAAAAAAAGAATTGGCTTCA
+CAACTAACGatgcccaagcgaacacttgataagatcttaaatgagttacgagaggagaat
+aaagtcttctacaaggtaacacgaggaagaaatggcggaatgatcattgcttcagtcaaa
+acgttgttcgcgagagttattcaactaagtaaagaaaagagactagattattcaacaagg
+atcacagaggtatttggactcaacgagagcttagtagaagagacatttagacaattatca
+acccccttgaaccctcttaaagaagtgaatctttttgaagtagatacaggttga
+>contig00003 len=3227 cov=2.2 corr=0 origname=NODE_3_length_3227_cov_2.232903_pilon sw=shovill-spades/1.1.0 date=20220302:308..1252:rep11a_1_repA(pB82)_AB178871:99.894180
+ATGGCTAATGAGATTGTAAAATACCACCATGAATTAAATACAATTCCTTTAAGAAAATTT
+ACACCGGTTGAAATGAATTTGTTTTTTTCCATCGTGTCTAGAATGCGTGAAAAAGGGGAT
+AAGACAGTTCGTTTTACGTTTGACCAACTAAAAGATTTAAGTAACTACAAAGCAACTGCA
+AATGTACGATTTGTAGAAGATTTAAAAGCAACTTATGAAAAAATCTTATCTTTACGCTTT
+GGTCGTAGAAGTGAGTCTGGGCTTTCTTACGATATGTTTGTAATGTTTACAGAATTTAAA
+ATCAACGGGGACGTAGAAAATCCTTACGTAGATATACGAATTTACGAAAAAGCACTGCCT
+TTGTTAAATAATTTAGACGAGTGGGTACGCTATTCTTTACAACAATTCAACGAGCTACAA
+AGTGGCTATGCAAAGACTATGTTTCGTCTGTTAAAGCAATACAGAACCAAAGGTTTCGCA
+TATTTCTCCAAAGAAGACTTTCTTGAATTATTAGATATTCCTAAAAGTTATAAGCAACCT
+GATATAGATAAACGAGTTATAAAACCTATACGTCAAGAACTAACTGCAATCTTCAAAGGA
+CTAACAATCAAAAAGAAATACGGAAAAGGACGGGGAAAACCTGTTATTGGCTATCAATTT
+ACGTTCAAACCTGAGATCAAAAAAGCAGACGACTTTAACAAACATGCACCAACCAAAGAA
+GACCAAAATAAAGCATTGGCTTTAGCTGATAAACAAAAAGAATACGAAGAACCCGCTACA
+ACAATTAACGAAAAAATCAAACAGAAGAAACGAGAACTTGAACTCCTCCAACAAATCAAA
+CAACTAGAAAAAGAGAAAAAAGCTCTTGAAAAACAAACAGAGTCCGCACTTTCGGAAAAA
+GAGAAAAAAAGTTTATTATCTGATTTAGATAATTTATTCCAGTAG
+>contig00008 len=2292 cov=2.6 corr=0 origname=NODE_11_length_2292_cov_2.631409_pilon sw=shovill-spades/1.1.0 date=20220302:1703..2104:rep14a_2_ORF1(pKQ10)_EFU01917:99.502488
+GTGCGACTGTACAACAAAAAGCTAGAGCAGGAACGAAAAAAAGTAATCGTGCCAAAAGAA
+ATCGATACGTGGTGGCGGTTAGAAATGCAGCTAAGACGTGGCAAAGCAACGGATTGGCAT
+GCGATGGTTCAGGAAAGCTTAGATAGTTTTGCAAGCCCGCATTTTTTGCCGATTGATATA
+AAACCTATTGATAAAATAGTTATTGAAGGTTTGATAGCTGAGCCTTCTAATTGGTCGATA
+ATTGCTAGACATACAAAATATAAATATCGGAATTTGCTGAAGCAAGAAAGTCAAAATGAT
+GAGTTAACGAACCATTTACGAGAGACTTTTAAGGAATCTGCAGACGAATTAAAAAAAGAA
+TTGGATACGTGGCTTTTGGGGTTGGATGTGACAGAGAAGTGA
+>contig00009 len=2060 cov=9.4 corr=0 origname=NODE_14_length_2060_cov_9.400414_pilon sw=shovill-spades/1.1.0 date=20220302:1478..1872:rep14a_2_ORF1(pKQ10)_EFU01917:76.156716
+gtgcgacTGTACAACAAAAAGCTAGAGCA-G-GAACGAAAAAAAGTAATCGTGCCAAAAG
+AAATCGATACGTGGTGGCGGTTAGAAATGCAGCTAAGACGTGGCAAAGCAACGGATTGGC
+ATGCGATGGTTCAGGAAAGCTTAGATAGTTTTGCAAGCCCGCATTTTTTGCC-GATTGAT
+ATAAAACCTATTGATAAAATAGTTATTGAAGGTTTGATAGCT-GAGCCTTCTAATTGGTC
+G-ATAATTGCTAGACATACAAAATATAAATATCGGAATTTGCTGAAGCAAGAAAGTCAAA
+ATGATGAGTTAACGAACCATTTACGAGAGACTTTTAAGGAATCTGCAGACGAATTAAAAA
+AAGAATTGGATACGTGGCTTTTGGGGTTGGATGTGACAGAGAAGTGA
diff -r 000000000000 -r 2b6e795b22a9 test-data/test_3/results_tab_test3.tsv
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_3/results_tab_test3.tsv	Mon Sep 19 08:47:42 2022 +0000
@@ -0,0 +1,5 @@
+Database	Plasmid	Identity	Query / Template length	Contig	Position in contig	Note	Accession number
+Inc18	rep2	100.0	835 / 1494	contig00014 len=836 cov=2.5 corr=0 origname=NODE_172_length_836_cov_2.489422_pilon sw=shovill-spades/1.1.0 date=20220302	2..836	repR(pEF1)	DQ198088
+Rep3	rep11a	99.89	945 / 945	contig00003 len=3227 cov=2.2 corr=0 origname=NODE_3_length_3227_cov_2.232903_pilon sw=shovill-spades/1.1.0 date=20220302	308..1252	repA(pB82)	AB178871
+Rep_trans	rep14a	99.5	402 / 402	contig00008 len=2292 cov=2.6 corr=0 origname=NODE_11_length_2292_cov_2.631409_pilon sw=shovill-spades/1.1.0 date=20220302	1703..2104	ORF1(pKQ10)	EFU01917
+Rep_trans	rep14a	78.5	400 / 402	contig00009 len=2060 cov=9.4 corr=0 origname=NODE_14_length_2060_cov_9.400414_pilon sw=shovill-spades/1.1.0 date=20220302	1478..1872	ORF1(pKQ10)	EFU01917
diff -r 000000000000 -r 2b6e795b22a9 tool-data/plasmidfinder.loc.sample
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/plasmidfinder.loc.sample	Mon Sep 19 08:47:42 2022 +0000
@@ -0,0 +1,2 @@
+#value	name	path
+test-db-2022	"Test Database"  ${__HERE__}/test-db
diff -r 000000000000 -r 2b6e795b22a9 tool_data_table_conf.xml.sample
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample	Mon Sep 19 08:47:42 2022 +0000
@@ -0,0 +1,8 @@
+<?xml version="1.0"?>
+<tables>
+        <!-- Locations of plasmid database to plasmidfinder -->
+    <table name="plasmidfinder_db" comment_char="#">
+        <columns>value, name, path</columns>
+        <file path="${__HERE__}/test-data/plasmidfinder_db.loc" />
+    </table>
+</tables>
diff -r 000000000000 -r 2b6e795b22a9 tool_data_table_conf.xml.test
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.test	Mon Sep 19 08:47:42 2022 +0000
@@ -0,0 +1,8 @@
+<?xml version="1.0"?>
+<tables>
+        <!-- Locations of plasmid database to plasmidfinder -->
+    <table name="plasmidfinder_db" comment_char="#">
+        <columns>value, name, path</columns>
+        <file path="${__HERE__}/test-data/plasmidfinder_db.loc" />
+    </table>
+</tables>