changeset 2:a74d61dbd155 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit f431329cd1c7f8a6014207a4ebfd9ffaa67e5497-dirty
author jjohnson
date Mon, 04 Nov 2019 16:38:44 -0500
parents 7de7487a7e8d
children 9d94fe7ce8b9
files data_manager/data_manager_eggnog.py data_manager/data_manager_eggnog.xml data_manager_conf.xml eggnog_mapper.xml test-data/DIA_nlim.emapper.seed_orthologs test-data/HMM_nlim.emapper.hmm_hits test-data/cached_locally/OG_fasta/thaNOG/1CB2A.fa test-data/cached_locally/OG_fasta/thaNOG/1CB2B.fa test-data/cached_locally/OG_fasta/thaNOG/1CB2C.fa test-data/cached_locally/OG_fasta/thaNOG/1CB2D.fa test-data/cached_locally/OG_fasta/thaNOG/1CB2E.fa test-data/cached_locally/OG_fasta/thaNOG/1CB2F.fa test-data/cached_locally/OG_fasta/thaNOG/1CB2G.fa test-data/cached_locally/OG_fasta/thaNOG/1CB2H.fa test-data/cached_locally/OG_fasta/thaNOG/1CB2I.fa test-data/cached_locally/OG_fasta/thaNOG/1CB2J.fa test-data/cached_locally/OG_fasta/thaNOG/1CB2K.fa test-data/cached_locally/OG_fasta/thaNOG/1CB2M.fa test-data/cached_locally/OG_fasta/thaNOG/1CB2N.fa test-data/cached_locally/OG_fasta/thaNOG/1CB2P.fa test-data/cached_locally/OG_fasta/thaNOG/1CB2Q.fa test-data/cached_locally/OG_fasta/thaNOG/1CB2R.fa test-data/cached_locally/OG_fasta/thaNOG/1CB2S.fa test-data/cached_locally/OG_fasta/thaNOG/1CB2T.fa test-data/cached_locally/OG_fasta/thaNOG/1CB2U.fa test-data/cached_locally/OG_fasta/thaNOG/1CB2V.fa test-data/cached_locally/OG_fasta/thaNOG/1CB2W.fa test-data/cached_locally/OG_fasta/thaNOG/1CB2X.fa test-data/cached_locally/OG_fasta/thaNOG/1CB2Y.fa test-data/cached_locally/OG_fasta/thaNOG/1CB2Z.fa test-data/cached_locally/eggnog.db test-data/cached_locally/eggnog_mapper_db.loc test-data/cached_locally/eggnog_mapper_hmm_dbs.loc test-data/cached_locally/eggnog_proteins.dmnd test-data/cached_locally/hmmdb_levels/ENOG411CB2I/ENOG411CB2I test-data/cached_locally/hmmdb_levels/ENOG411CB2I/ENOG411CB2I.h3f test-data/cached_locally/hmmdb_levels/ENOG411CB2I/ENOG411CB2I.h3i test-data/cached_locally/hmmdb_levels/ENOG411CB2I/ENOG411CB2I.h3m test-data/cached_locally/hmmdb_levels/ENOG411CB2I/ENOG411CB2I.h3p test-data/cached_locally/hmmdb_levels/thaNOG/thaNOG test-data/cached_locally/hmmdb_levels/thaNOG/thaNOG.h3f test-data/cached_locally/hmmdb_levels/thaNOG/thaNOG.h3i test-data/cached_locally/hmmdb_levels/thaNOG/thaNOG.h3m test-data/cached_locally/hmmdb_levels/thaNOG/thaNOG.h3p test-data/make_comp_file.sh test-data/nlim_1033.fasta test-data/nlim_fragment.fasta tool-data/eggnog_mapper.loc.sample tool-data/eggnog_mapper_db.loc.sample tool-data/eggnog_mapper_hmm_dbs.loc.sample tool_data_table_conf.xml.sample tool_data_table_conf.xml.test
diffstat 52 files changed, 2038 insertions(+), 201 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/data_manager_eggnog.py	Mon Nov 04 16:38:44 2019 -0500
@@ -0,0 +1,57 @@
+#!/usr/bin/env python
+
+from __future__ import print_function
+
+import argparse
+import json
+import os.path
+import sqlite3
+from sqlite3 import OperationalError
+import sys
+
+def _get_db_version(sqlitedb_path):
+    version = '4.5'
+    try:
+        query = 'select version from version'
+        conn = sqlite3.connect(sqlitedb_path)
+        cur = conn.cursor()
+        cur.execute(query)
+        version = cur.fetchone()[0]
+    except OperationalError as e:
+        print('Assuming eggnog version %s because %s   %s' % (version, sqlitedb_path, e), file=sys.stderr)
+    return version
+
+def main():
+    parser = argparse.ArgumentParser()
+    parser.add_argument( '--config_file' )
+    parser.add_argument( '--install_path' )
+    parser.add_argument( '--dbs', default='')
+    args = parser.parse_args()
+
+    eggnog_db_path = os.path.join(args.install_path,'eggnog.db') 
+    if not os.path.exists(eggnog_db_path):
+        print('Can not open: %s' % eggnog_db_path, file=sys.stderr)
+        exit(1)
+    db_version = _get_db_version(eggnog_db_path)
+
+    params = json.loads( open( args.config_file ).read() )
+    data_manager_dict = {}
+    data_manager_dict['data_tables'] = data_manager_dict.get( 'data_tables', {} )
+    data_table = 'eggnog_mapper_db'
+    data_manager_dict['data_tables'][data_table] = data_manager_dict['data_tables'].get( data_table, [] )
+    data_table_entry = dict(value=db_version, name=db_version, path=eggnog_db_path)
+    data_manager_dict['data_tables'][data_table].append( data_table_entry )
+    data_table = 'eggnog_mapper_hmm_dbs'
+    data_manager_dict['data_tables'][data_table] = data_manager_dict['data_tables'].get( data_table, [] )
+    if args.dbs:
+        dbs = [x.strip() for x in args.dbs.split(',')]
+        for db in dbs:
+            key = '%s_%s' % (db_version, db)
+            data_table_entry = dict(key=key, db_version=db_version, value=db, name=db, path=db)
+            data_manager_dict['data_tables'][data_table].append( data_table_entry )
+
+    # save info to json file
+    open( args.config_file, 'wb' ).write( json.dumps( data_manager_dict ) )
+
+if __name__ == "__main__":
+    main()
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/data_manager_eggnog.xml	Mon Nov 04 16:38:44 2019 -0500
@@ -0,0 +1,165 @@
+<tool id="data_manager_eggnog" name="EggNOG DB Download" version="@VERSION@" tool_type="manage_data">
+    <description>Download a new database</description>
+    <macros>
+        <token name="@VERSION@">4.5.1</token>
+    </macros>
+    <requirements>
+        <requirement type="package" version="@VERSION@">eggnog-mapper</requirement>
+    </requirements>
+    <version_command>emapper.py --version</version_command>
+    <command detect_errors="exit_code"><![CDATA[
+#import json, os
+#set params = json.loads(open(str($out_file)).read())
+#set install_path = $params['output_data'][0]['extra_files_path'].encode('ascii', 'replace')
+#if $dbs:
+#set $eggnogdbs = ' '.join($dbs.split(','))
+#else
+#set $eggnogdbs = 'none'
+#endif
+#if $test == 'false'
+mkdir -p '${target_directory}' &&
+download_eggnog_data.py 
+  $diamond_database -y -q --data_dir $install_path $eggnogdbs
+' '.join(dbs.split(',')) &&
+#end if
+python '${__tool_directory__}/data_manager_eggnog.py --config_file $out_file --install_path $target_directory --dbs '$dbs'
+    ]]></command>
+    <inputs>
+        <param name="test" type="hidden" value="false" />
+        <param name="target_path" type="text" label="Download Destination (full path)" />
+        <param name="diamond_database" type="boolean" truevalue="" falsevalue="-D" checked="true" label="Install the diamond database"/>
+        <param argument="dbs" type="select" multiple="true" label="eggNOG HMM databases to download. If none are selected only diamond can be used'">
+            <option value="arch" selected="true">eggnog_4.5.1 arch</option>
+            <option value="bact" selected="true">eggnog_4.5.1 bact</option>
+            <option value="euk" selected="true">eggnog_4.5.1 euk</option>
+            <option value="NOG" selected="true">All organisms (NOG)</option>
+            <option value="aciNOG">Acidobacteria (aciNOG)</option>
+            <option value="acidNOG">Acidobacteriia (acidNOG)</option>
+            <option value="acoNOG">Aconoidasida (acoNOG)</option>
+            <option value="actNOG">Actinobacteria (actNOG)</option>
+            <option value="agaNOG">Agaricales (agaNOG)</option>
+            <option value="agarNOG">Agaricomycetes (agarNOG)</option>
+            <option value="apiNOG">Apicomplexa (apiNOG)</option>
+            <option value="aproNOG">Proteobacteria_alpha (aproNOG)</option>
+            <option value="aquNOG">Aquificae (aquNOG)</option>
+            <option value="arNOG">Archaea (arNOG)</option>
+            <option value="arcNOG">Archaeoglobi (arcNOG)</option>
+            <option value="artNOG">Arthropoda (artNOG)</option>
+            <option value="arthNOG">Arthrodermataceae (arthNOG)</option>
+            <option value="ascNOG">Ascomycota (ascNOG)</option>
+            <option value="aveNOG">Aves (aveNOG)</option>
+            <option value="bacNOG">Bacilli (bacNOG)</option>
+            <option value="bactNOG">Bacteria (bactNOG)</option>
+            <option value="bacteNOG">Bacteroidia (bacteNOG)</option>
+            <option value="basNOG">Basidiomycota (basNOG)</option>
+            <option value="bctoNOG">Bacteroidetes (bctoNOG)</option>
+            <option value="biNOG">Bilateria (biNOG)</option>
+            <option value="bproNOG">Proteobacteria_beta (bproNOG)</option>
+            <option value="braNOG">Brassicales (braNOG)</option>
+            <option value="carNOG">Carnivora (carNOG)</option>
+            <option value="chaNOG">Chaetomiaceae (chaNOG)</option>
+            <option value="chlNOG">Chlorobi (chlNOG)</option>
+            <option value="chlaNOG">Chlamydiae (chlaNOG)</option>
+            <option value="chloNOG">Chloroflexi (chloNOG)</option>
+            <option value="chlorNOG">Chloroflexi (chlorNOG)</option>
+            <option value="chloroNOG">Chlorophyta (chloroNOG)</option>
+            <option value="chorNOG">Chordata (chorNOG)</option>
+            <option value="chrNOG">Chromadorea (chrNOG)</option>
+            <option value="cloNOG">Clostridia (cloNOG)</option>
+            <option value="cocNOG">Coccidia (cocNOG)</option>
+            <option value="creNOG">Crenarchaeota (creNOG)</option>
+            <option value="cryNOG">Cryptosporidiidae (cryNOG)</option>
+            <option value="cyaNOG">Cyanobacteria (cyaNOG)</option>
+            <option value="cytNOG">Cytophagia (cytNOG)</option>
+            <option value="debNOG">Debaryomycetaceae (debNOG)</option>
+            <option value="defNOG">Deferribacteres (defNOG)</option>
+            <option value="dehNOG">Dehalococcoidetes (dehNOG)</option>
+            <option value="deiNOG">Deinococcusthermus (deiNOG)</option>
+            <option value="delNOG">delta/epsilon (delNOG)</option>
+            <option value="dipNOG">Diptera (dipNOG)</option>
+            <option value="dotNOG">Dothideomycetes (dotNOG)</option>
+            <option value="dproNOG">Proteobacteria_delta (dproNOG)</option>
+            <option value="droNOG">Drosophilidae (droNOG)</option>
+            <option value="eproNOG">Proteobacteria_epsilon (eproNOG)</option>
+            <option value="eryNOG">Erysipelotrichi (eryNOG)</option>
+            <option value="euNOG">Eukaryotes (euNOG)</option>
+            <option value="eurNOG">Euryarchaeota (eurNOG)</option>
+            <option value="euroNOG">Eurotiomycetes (euroNOG)</option>
+            <option value="eurotNOG">Eurotiales (eurotNOG)</option>
+            <option value="fiNOG">Fishes (fiNOG)</option>
+            <option value="firmNOG">Firmicutes (firmNOG)</option>
+            <option value="flaNOG">Flavobacteriia (flaNOG)</option>
+            <option value="fuNOG">Fungi (fuNOG)</option>
+            <option value="fusoNOG">Fusobacteria (fusoNOG)</option>
+            <option value="gproNOG">Proteobacteria_gamma (gproNOG)</option>
+            <option value="haeNOG">Haemosporida (haeNOG)</option>
+            <option value="halNOG">Halobacteria (halNOG)</option>
+            <option value="homNOG">Hominidae (homNOG)</option>
+            <option value="hymNOG">Hymenoptera (hymNOG)</option>
+            <option value="hypNOG">Hypocreales (hypNOG)</option>
+            <option value="inNOG">Insects (inNOG)</option>
+            <option value="kinNOG">Kinetoplastida (kinNOG)</option>
+            <option value="lepNOG">Lepidoptera (lepNOG)</option>
+            <option value="lilNOG">Liliopsida (lilNOG)</option>
+            <option value="maNOG">Mammals (maNOG)</option>
+            <option value="magNOG">Magnaporthales (magNOG)</option>
+            <option value="meNOG">Animals (meNOG)</option>
+            <option value="metNOG">Methanobacteria (metNOG)</option>
+            <option value="methNOG">Methanococci (methNOG)</option>
+            <option value="methaNOG">Methanomicrobia (methaNOG)</option>
+            <option value="necNOG">Nectriaceae (necNOG)</option>
+            <option value="negNOG">Negativicutes (negNOG)</option>
+            <option value="nemNOG">Nematodes (nemNOG)</option>
+            <option value="onyNOG">Onygenales (onyNOG)</option>
+            <option value="opiNOG">Opisthokonts (opiNOG)</option>
+            <option value="perNOG">Peronosporales (perNOG)</option>
+            <option value="plaNOG">Planctomycetes (plaNOG)</option>
+            <option value="pleNOG">Pleosporales (pleNOG)</option>
+            <option value="poaNOG">Poales (poaNOG)</option>
+            <option value="prNOG">Primates (prNOG)</option>
+            <option value="proNOG">Proteobacteria (proNOG)</option>
+            <option value="rhaNOG">Rhabditida (rhaNOG)</option>
+            <option value="roNOG">Rodents (roNOG)</option>
+            <option value="sacNOG">Saccharomycetaceae (sacNOG)</option>
+            <option value="saccNOG">Saccharomycetes (saccNOG)</option>
+            <option value="sorNOG">Sordariales (sorNOG)</option>
+            <option value="sordNOG">Sordariomycetes (sordNOG)</option>
+            <option value="sphNOG">Sphingobacteriia (sphNOG)</option>
+            <option value="spiNOG">Spirochaetes (spiNOG)</option>
+            <option value="spriNOG">Supraprimates (spriNOG)</option>
+            <option value="strNOG">Streptophyta (strNOG)</option>
+            <option value="synNOG">Synergistetes (synNOG)</option>
+            <option value="tenNOG">Tenericutes (tenNOG)</option>
+            <option value="thaNOG">Thaumarchaeota (thaNOG)</option>
+            <option value="theNOG">Thermoplasmata (theNOG)</option>
+            <option value="therNOG">Thermotogae (therNOG)</option>
+            <option value="thermNOG">Thermococci (thermNOG)</option>
+            <option value="treNOG">Tremellales (treNOG)</option>
+            <option value="veNOG">Vertebrates (veNOG)</option>
+            <option value="verNOG">Verrucomicrobia (verNOG)</option>
+            <option value="verrNOG">Verrucomicrobiae (verrNOG)</option>
+            <option value="virNOG">Viridiplantae (virNOG)</option>
+        </param>
+    </inputs>
+    <outputs>
+        <data name="out_file" format="data_manager_json" label="${tool.name}"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="test" value="true"/>
+            <param name="diamond_database" value="false"/>
+            <output name="out_file">
+                <assert_contents>
+                    <has_text text="eggnog_mapper_db" />
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+This tool downloads eggnog data using download_eggnog_data.py 
+and populates the data tables: eggnog_mapper_db and eggnog_mapper_hmm_dbs.
+    ]]></help>
+    <citations>
+        <citation type="doi">10.1093/nar/gkv1248</citation>
+    </citations>
+</tool>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager_conf.xml	Mon Nov 04 16:38:44 2019 -0500
@@ -0,0 +1,27 @@
+<?xml version="1.0"?>
+<data_managers>
+  <data_manager tool_file="data_manager/data_manager_eggnog.xml" id="data_manager_eggnog" >
+    <data_table name="eggnog_mapper_db">  <!-- Defines a Data Table to be modified. -->
+      <output> <!-- Handle the output of the Data Manager Tool -->
+        <column name="value" /> <!-- columns that are going to be specified by the Data Manager Tool -->
+        <column name="name" />  <!-- columns that are going to be specified by the Data Manager Tool -->
+        <column name="path" output_ref="out_file" >
+          <move type="directory" relativize_symlinks="True">
+            <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">${value}</target>
+          </move>
+          <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/${value}</value_translation>
+          <value_translation type="function">abspath</value_translation>
+        </column>
+      </output>
+    </data_table>
+    <data_table name="eggnog_mapper_hmm_dbs">  <!-- Defines a Data Table to be modified. -->
+      <output> <!-- Handle the output of the Data Manager Tool -->
+        <column name="key" /> <!-- columns that are going to be specified by the Data Manager Tool -->
+        <column name="db_version" /> <!-- columns that are going to be specified by the Data Manager Tool -->
+        <column name="value" /> <!-- columns that are going to be specified by the Data Manager Tool -->
+        <column name="name" />  <!-- columns that are going to be specified by the Data Manager Tool -->
+        <column name="path" /> <!-- columns that are going to be specified by the Data Manager Tool -->
+      </output>
+    </data_table>
+  </data_manager>
+</data_managers>
--- a/eggnog_mapper.xml	Tue Aug 08 12:40:56 2017 -0400
+++ b/eggnog_mapper.xml	Mon Nov 04 16:38:44 2019 -0500
@@ -1,24 +1,23 @@
-<tool id="eggnog_mapper" name="eggNOG Mapper" version="0.1.0">
+<tool id="eggnog_mapper" name="eggNOG Mapper" version="@VERSION@.1">
     <description>functional sequence annotation by orthology</description>
+    <macros>
+        <token name="@VERSION@">1.0.3</token>
+    </macros>
     <requirements>
-        <requirement type="package" version="0.99.2">eggnog-mapper</requirement>
+        <requirement type="package" version="@VERSION@">eggnog-mapper</requirement>
     </requirements>
-    <stdio>
-        <exit_code range="1:" />
-    </stdio>
-    <version_command>python emapper.py --version</version_command>
-    <command><![CDATA[
-        ### Load on demand - with changes to download_eggnog_data.py
-        ## #if $db.mode == 'hmmer':
-        ##     download_eggnog_data.py -y -q --data_dir ~/src/eggnog-mapper/data $db.database && 
-        ## #else
-        ##     download_eggnog_data.py -y -q --data_dir ~/src/eggnog-mapper/data $db.database && 
-        ## #end if
-        emapper.py  
-        --data_dir '$eggnog_data.fields.data_dir'
-        -m $db.mode $translate
-        #if $db.mode == 'hmmer':
-            --database=$db.database
+    <version_command>emapper.py --version</version_command>
+    <command detect_errors="aggressive"><![CDATA[
+        emapper.py
+        --data_dir '$eggnog_data.fields.path'
+        -m $db.mode 
+        $translate
+        #if ($db.mode == 'hmmer'):
+            #if $db.database.fields.path:
+                --database=$db.database.fields.path
+            #else
+                --database=$db.database
+            #end if
             #if $db.hmm_options.hmm_settings == 'specified':
                 --hmm_maxhits=$db.hmm_options.hmm_maxhits
                 --hmm_evalue=$db.hmm_options.hmm_evalue
@@ -29,13 +28,9 @@
                 #end if
                 --Z=$db.hmm_options.Z
             #end if
-        #elif $db.mode == 'diamond':
-            ## $db.sensitive
-            ## $db.more_sensitive
-            --matrix '$db.matrix'
-            --gapopen '$db.gapopen'
-            --gapextend '$db.gapextend'
-            ## --seg '$db.seg'
+        #elif ($db.mode == 'diamond'):
+            --matrix '$db.matrix_gapcosts.matrix'
+            $db.matrix_gapcosts.gap_costs
         #end if
         #if $annotation_options.tax_scope:
             --tax_scope=$annotation_options.tax_scope
@@ -49,75 +44,186 @@
         #if $seed_ortholog_options.seed_ortholog_evalue:
             --seed_ortholog_evalue=$seed_ortholog_options.seed_ortholog_evalue 
         #end if
-        #if $seed_ortholog_options.seed_ortholog_score:
+        #if str($seed_ortholog_options.seed_ortholog_score):
             --seed_ortholog_score=$seed_ortholog_options.seed_ortholog_score 
         #end if
-        $output_options.file_comments
+        $output_options.no_file_comments
         $output_options.no_annot
         $output_options.report_orthologs
         --output='results'
         -i '${input}'
+        --cpu "\${GALAXY_SLOTS:-4}"
     ]]></command>
-    <inputs>
-        <param name="input" type="data" format="fasta" label="Fasta sequences to annotate"/>
-        <param name="translate" type="boolean" truevalue="--translate" falsevalue="" checked="false" 
-            label="Are these CDS sequences that need to be translated"/>
-        <param name="eggnog_data" type="select" label="Eggnog Data">
-            <options from_data_table="eggnog_mapper" >
-                <filter type="static_value" name="type" value="data" column="2"/>
-                <validator type="no_options" message="No cached eggnog data is available" />
-            </options>
-        </param>
-        <conditional name="db">
-            <param name="mode" type="select" label="Annotation Type">
-                <option value="hmmer">HMM</option>
-                <option value="diamond">DIAMOND</option>
+        <inputs>
+            <param name="input" type="data" format="fasta" label="Fasta sequences to annotate"/>
+            <param name="eggnog_data" type="select" label="Version of eggNOG Database">
+                <options from_data_table="eggnog_mapper_db"/>
             </param>
-            <when value="hmmer">
-                <param name="database" type="select" multiple="true" min="1" label="HMM target database">
-                    <options from_data_table="eggnog_mapper" >
-                        <!--
-                        -->
-                        <filter type="param_value" ref="eggnog_data" column="3" />
-                        <filter type="static_value" name="type" value="hmmer" column="2"/>
-                        <validator type="no_options" message="No HMM DBs are available, request from your galaxy admin" />
-                    </options>
+            <param name="translate" type="boolean" truevalue="--translate" falsevalue="" checked="false"
+                label="Are these coding DNA sequences that need to be translated?"/>
+            <conditional name="db">
+                <param name="mode" type="select" label="Annotation Type">
+                    <option value="hmmer">HMM</option>
+                    <option value="diamond">DIAMOND</option>
                 </param>
-                <conditional name="hmm_options">
-                    <param name="hmm_settings" type="select" label="HMM Search Options">
-                         <option value="default">Use defaults</option>
-                         <option value="specified">Set HMM Search Options</option>
+                <when value="hmmer">
+                    <param name="database" type="select" label="HMM target database" help="Choose either the full eggNOG database or a subset of it. Contact your Galaxy admin to have additional HMM databases installed.">
+                        <options from_data_table="eggnog_mapper_hmm_dbs">
+                            <!--
+                            <filter type="param_value" ref="eggnog_data" column="1" />
+                            <filter type="unique_value" column="3" />
+                            <validator type="no_options" message="No HMM databases are available; request installation from your Galaxy admin." />
+                            -->
+                        </options>
                     </param>
-                    <when value="default"/>
-                    <when value="specified">
-                        <param name="hmm_maxhits" type="integer" value="1" label="Max number of hits to report. Default=1" />
-                        <param name="hmm_evalue" type="float" value="0.001" label="E-value threshold. Default=0.001" />
-                        <param name="hmm_score" type="integer" value="20" label="Bit score threshold. Default=20" />
-                        <param name="hmm_maxseqlen" type="integer" value="5000" label="Ignore query sequences larger than `maxseqlen`.  Default=5000" />
-                        <param name="hmm_qcov" type="float" value="" min="0." max="1." optional="true" label="min query coverage (from 0 to 1). Default=(disabled)" />
-                        <param name="Z" type="integer" value="" label="Fixed database size used in phmmer/hmmscan (allows comparing e-values among databases).  Default=40,000,000" />
-                    </when>
-                </conditional>
-            </when>
-            <when value="diamond">
-                <param name="database" type="hidden" value="diamond"/>
-                <param argument="--sensitive" type="boolean" truevalue="--sensitive" falsevalue="" checked="false" label="Trigger the sensitive alignment mode with a 16x9 seed shape configuration?" help=""/>
-                <param name="more_sensitive" argument="--more-sensitive" type="boolean" truevalue="--more-sensitive" falsevalue="" checked="false" label="Trigger the more sensitive mode?" help="This mode provides some additional sensitivity compared to the sensitive mode."/>
-                <param argument="--seg" type="boolean" truevalue="yes" falsevalue="no" checked="true" label="Enable SEG masking of low complexity segments in the query?" help=""/>
-                <param argument="--matrix" type="select" label="Scoring matrix" help="In brackets are the supported values for (gap open)/(gap extend)">
-                    <option value="BLOSUM45">BLOSUM45 ((10-13)/3; (12-16)/2; (16-19)/1)</option>
-                    <option value="BLOSUM50">BLOSUM50 ((9-13)/3; (12-16)/2; (15-19)/1)</option>
-                    <option value="BLOSUM62" selected="True">BLOSUM62 ((6-11)/2; (9-13)/1)</option>
-                    <option value="BLOSUM80">BLOSUM80 ((6-9)/2; 13/2; 25/2; (9-11)/1)</option>
-                    <option value="BLOSUM90">BLOSUM90 ((6-9)/2; (9-11)/1)</option>
-                    <option value="PAM250">PAM250 ((11-15)/3; (13-17)/2; (17-21)/1)</option>
-                    <option value="PAM70">PAM70 ((6-8)/2; (9-11)/1)</option>
-                    <option value="PAM30">PAM30 ((5-7)/2; (8-10)/1)</option>
-                </param>
-                <param argument="--gapopen" type="integer" value="11" label="Gap open penalty" help="" />
-                <param argument="--gapextend" type="integer" value="1" label="Gap extension penalty" help="" />
-            </when>
-        </conditional>
+                    <conditional name="hmm_options">
+                        <param name="hmm_settings" type="select" label="HMM Search Options">
+                            <option value="default">Use defaults</option>
+                            <option value="specified">Set HMM Search Options</option>
+                        </param>
+                        <when value="default"/>
+                        <when value="specified">
+                            <param name="hmm_maxhits" type="integer" value="1" label="Max number of hits to report per query sequence"/>
+                            <param name="hmm_evalue" type="float" min="0" value="0.001" label="E-value threshold" />
+                            <param name="hmm_score" type="integer" min="0" value="20" label="Bit score threshold" />
+                            <param name="hmm_maxseqlen" type="integer" value="5000" label="Ignore query sequences larger than `maxseqlen`.  Default=5000" />
+                            <param name="hmm_qcov" type="float" value="" min="0." max="1." optional="true" label="min query coverage (from 0 to 1). Default=(disabled)" />
+                            <param name="Z" type="integer" value="40000000" min="0" label="Fixed database size used in phmmer/hmmscan (allows comparing e-values among databases).  Default=40,000,000" />
+                        </when>
+                    </conditional>
+                </when>
+                <when value="diamond">
+                    <!-- db.database is used in diamond mode only to name outputs -->
+                    <param name="database" type="hidden" value="diamond"/>
+                    <conditional name="matrix_gapcosts">
+                        <param argument="--matrix" type="select" label="Scoring matrix and gap costs">
+                            <option value="BLOSUM90">BLOSUM90</option>
+                            <option value="BLOSUM80">BLOSUM80</option>
+                            <option value="BLOSUM62" selected="true">BLOSUM62</option>
+                            <option value="BLOSUM50">BLOSUM50</option>
+                            <option value="BLOSUM45">BLOSUM45</option>
+                            <option value="PAM250">PAM250</option>
+                            <option value="PAM70">PAM70</option>
+                            <option value="PAM30">PAM30</option>
+                        </param>
+                        <when value="BLOSUM90">
+                            <param name="gap_costs" type="select" label="Gap Costs">
+                                <option value="--gapopen 9 --gapextend 2">Existence: 9  Extension: 2</option>
+                                <option value="--gapopen 8 --gapextend 2">Existence: 8  Extension: 2</option>
+                                <option value="--gapopen 7 --gapextend 2">Existence: 7  Extension: 2</option>
+                                <option value="--gapopen 6 --gapextend 2">Existence: 6  Extension: 2</option>
+                                <option value="--gapopen 11 --gapextend 1">Existence: 11  Extension: 1</option>
+                                <option value="--gapopen 10 --gapextend 1" selected="true">Existence: 10  Extension: 1</option>
+                                <option value="--gapopen 9 --gapextend 1">Existence: 9  Extension: 1</option>
+                            </param>
+                        </when>
+                        <when value="BLOSUM80">
+                            <param name="gap_costs" type="select" label="Gap Costs">
+                                <option value="--gapopen 8 --gapextend 2">Existence: 8  Extension: 2</option>
+                                <option value="--gapopen 7 --gapextend 2">Existence: 7  Extension: 2</option>
+                                <option value="--gapopen 6 --gapextend 2">Existence: 6  Extension: 2</option>
+                                <option value="--gapopen 11 --gapextend 1">Existence: 11  Extension: 1</option>
+                                <option value="--gapopen 10 --gapextend 1" selected="true">Existence: 10  Extension: 1</option>
+                                <option value="--gapopen 9 --gapextend 1">Existence: 9  Extension: 1</option>
+                            </param>
+                        </when>
+                        <when value="BLOSUM62">
+                            <param name="gap_costs" type="select" label="Gap Costs">
+                                <option value="--gapopen 11 --gapextend 2">Existence: 11  Extension: 2</option>
+                                <option value="--gapopen 10 --gapextend 2">Existence: 10  Extension: 2</option>
+                                <option value="--gapopen 9 --gapextend 2">Existence: 9  Extension: 2</option>
+                                <option value="--gapopen 8 --gapextend 2">Existence: 8  Extension: 2</option>
+                                <option value="--gapopen 7 --gapextend 2">Existence: 7  Extension: 2</option>
+                                <option value="--gapopen 6 --gapextend 2">Existence: 6  Extension: 2</option>
+                                <option value="--gapopen 13 --gapextend 1">Existence: 13  Extension: 1</option>
+                                <option value="--gapopen 12 --gapextend 1">Existence: 12  Extension: 1</option>
+                                <option value="--gapopen 11 --gapextend 1" selected="true">Existence: 11  Extension: 1</option>
+                                <option value="--gapopen 10 --gapextend 1">Existence: 10  Extension: 1</option>
+                                <option value="--gapopen 9 --gapextend 1">Existence: 9  Extension: 1</option>
+                            </param>
+                        </when>
+                        <when value="BLOSUM50">
+                            <param name="gap_costs" type="select" label="Gap Costs">
+                                <option value="--gapopen 13 --gapextend 3">Existence: 13  Extension: 3</option>
+                                <option value="--gapopen 12 --gapextend 3">Existence: 12  Extension: 3</option>
+                                <option value="--gapopen 11 --gapextend 3">Existence: 11  Extension: 3</option>
+                                <option value="--gapopen 10 --gapextend 3">Existence: 10  Extension: 3</option>
+                                <option value="--gapopen 9 --gapextend 3">Existence: 9  Extension: 3</option>
+                                <option value="--gapopen 16 --gapextend 2">Existence: 16  Extension: 2</option>
+                                <option value="--gapopen 15 --gapextend 2">Existence: 15  Extension: 2</option>
+                                <option value="--gapopen 14 --gapextend 2">Existence: 14  Extension: 2</option>
+                                <option value="--gapopen 13 --gapextend 2" selected="true">Existence: 13  Extension: 2</option>
+                                <option value="--gapopen 12 --gapextend 2">Existence: 12  Extension: 2</option>
+                                <option value="--gapopen 19 --gapextend 1">Existence: 19  Extension: 1</option>
+                                <option value="--gapopen 18 --gapextend 1">Existence: 18  Extension: 1</option>
+                                <option value="--gapopen 17 --gapextend 1">Existence: 17  Extension: 1</option>
+                                <option value="--gapopen 16 --gapextend 1">Existence: 16  Extension: 1</option>
+                                <option value="--gapopen 15 --gapextend 1">Existence: 15  Extension: 1</option>
+                            </param>
+                        </when>
+                        <when value="BLOSUM45">
+                            <param name="gap_costs" type="select" label="Gap Costs">
+                                <option value="--gapopen 13 --gapextend 3">Existence: 13  Extension: 3</option>
+                                <option value="--gapopen 12 --gapextend 3">Existence: 12  Extension: 3</option>
+                                <option value="--gapopen 11 --gapextend 3">Existence: 11  Extension: 3</option>
+                                <option value="--gapopen 10 --gapextend 3">Existence: 10  Extension: 3</option>
+                                <option value="--gapopen 15 --gapextend 2" selected="true">Existence: 15  Extension: 2</option>
+                                <option value="--gapopen 14 --gapextend 2">Existence: 14  Extension: 2</option>
+                                <option value="--gapopen 13 --gapextend 2">Existence: 13  Extension: 2</option>
+                                <option value="--gapopen 12 --gapextend 2">Existence: 12  Extension: 2</option>
+                                <option value="--gapopen 19 --gapextend 1">Existence: 19  Extension: 1</option>
+                                <option value="--gapopen 18 --gapextend 1">Existence: 18  Extension: 1</option>
+                                <option value="--gapopen 17 --gapextend 1">Existence: 17  Extension: 1</option>
+                                <option value="--gapopen 16 --gapextend 1">Existence: 16  Extension: 1</option>
+                            </param>
+                        </when>
+                        <when value="PAM250">
+                            <param name="gap_costs" type="select" label="Gap Costs">
+                                <option value="--gapopen 15 --gapextend 3">Existence: 15  Extension: 3</option>
+                                <option value="--gapopen 14 --gapextend 3">Existence: 14  Extension: 3</option>
+                                <option value="--gapopen 13 --gapextend 3">Existence: 13  Extension: 3</option>
+                                <option value="--gapopen 12 --gapextend 3">Existence: 12  Extension: 3</option>
+                                <option value="--gapopen 17 --gapextend 2">Existence: 17  Extension: 2</option>
+                                <option value="--gapopen 16 --gapextend 2">Existence: 16  Extension: 2</option>
+                                <option value="--gapopen 15 --gapextend 2">Existence: 15  Extension: 2</option>
+                                <option value="--gapopen 14 --gapextend 2" selected="true">Existence: 14  Extension: 2</option>
+                                <option value="--gapopen 13 --gapextend 2">Existence: 13  Extension: 2</option>
+                                <option value="--gapopen 21 --gapextend 1">Existence: 21  Extension: 1</option>
+                                <option value="--gapopen 20 --gapextend 1">Existence: 20  Extension: 1</option>
+                                <option value="--gapopen 19 --gapextend 1">Existence: 19  Extension: 1</option>
+                                <option value="--gapopen 18 --gapextend 1">Existence: 18  Extension: 1</option>
+                                <option value="--gapopen 17 --gapextend 1">Existence: 17  Extension: 1</option>
+                            </param>
+                        </when>
+                        <when value="PAM70">
+                            <param name="gap_costs" type="select" label="Gap Costs">
+                                <option value="--gapopen 12 --gapextend 3">Existence: 12 Extension: 3</option>
+                                <option value="--gapopen 11 --gapextend 2">Existence: 11 Extension: 2</option>
+                                <option value="--gapopen 8 --gapextend 2">Existence: 8  Extension: 2</option>
+                                <option value="--gapopen 7 --gapextend 2">Existence: 7  Extension: 2</option>
+                                <option value="--gapopen 6 --gapextend 2">Existence: 6  Extension: 2</option>
+                                <option value="--gapopen 11 --gapextend 1">Existence: 11  Extension: 1</option>
+                                <option value="--gapopen 10 --gapextend 1" selected="true">Existence: 10  Extension: 1</option>
+                                <option value="--gapopen 9 --gapextend 1">Existence: 9  Extension: 1</option>
+                            </param>
+                        </when>
+                        <when value="PAM30">
+                            <param name="gap_costs" type="select" label="Gap Costs">
+                                <option value="--gapopen 15 --gapextend 3">Existence: 15 Extension: 3</option>
+                                <option value="--gapopen 13 --gapextend 3">Existence: 13 Extension: 3</option>
+                                <option value="--gapopen 14 --gapextend 2">Existence: 14 Extension: 2</option>
+                                <option value="--gapopen 7 --gapextend 2">Existence: 7  Extension: 2</option>
+                                <option value="--gapopen 6 --gapextend 2">Existence: 6  Extension: 2</option>
+                                <option value="--gapopen 5 --gapextend 2">Existence: 5  Extension: 2</option>
+                                <option value="--gapopen 14 --gapextend 1">Existence: 14 Extension: 1</option>
+                                <option value="--gapopen 10 --gapextend 1">Existence: 10  Extension: 1</option>
+                                <option value="--gapopen 9 --gapextend 1" selected="true">Existence: 9  Extension: 1</option>
+                                <option value="--gapopen 8 --gapextend 1">Existence: 8  Extension: 1</option>
+                            </param>
+                        </when>
+                    </conditional>
+                </when>
+            </conditional>
         <section name="annotation_options" expanded="false" title="Annotation Options">
             <param name="tax_scope" type="select" optional="true" label="Set taxonomic scope">
                 <option value="NOG">All organisms  (NOG)</option>
@@ -228,38 +334,39 @@
                 <option value="verrNOG">Verrucomicrobiae  (verrNOG)</option>
                 <option value="virNOG">Viridiplantae  (virNOG)</option>
             </param>
-            <param name="target_orthologs" type="select" optional="true" label="target orthologs for functional transfer">
+            <param name="target_orthologs" type="select" label="target orthologs for functional transfer">
                 <option value="one2one">one2one</option>
                 <option value="many2one">many2one</option>
                 <option value="one2many">one2many</option>
                 <option value="many2many">many2many</option>
-                <option value="all">all</option>
+                <option value="all" selected="true">all</option>
             </param>
-            <param name="go_evidence" type="select" optional="true" label="Type of GO terms should be used for annotation">
+            <param name="go_evidence" type="select"
+                    label="Select the set of GO terms that should be used for annotation">
                 <option value="experimental">experimental = Use only terms inferred from experimental evidence</option>
-                <option value="non-electronic">non-electronic = Use only non-electronically curated terms</option>
+                <option value="non-electronic" selected="true">non-electronic = Use only non-electronically curated terms</option>
             </param>
         </section>
         <section name="seed_ortholog_options" expanded="false" title="Seed Ortholog Search Options">
-            <param name="seed_ortholog_evalue" type="float" value="0.001" optional="true" label="Min E-value threshold. Default=0.001">
+            <param name="seed_ortholog_evalue" type="float" value="0.001" min="0" label="Min E-value threshold">
                 <help>
                 Min E-value expected when searching for seed eggNOG ortholog. Applies to phmmer/diamond searches. 
-                Queries not having a significant seed orthologs will not be annotated.
+                Queries not having a significant seed orthologs (E-value less than threshold) will not be annotated.
                 </help>
             </param>
-            <param name="seed_ortholog_score" type="integer" value="60" optional="true" label="Bit score threshold. Default=60">
+            <param name="seed_ortholog_score" type="integer" value="60" min="0" label="Minimum bit score threshold">
                 <help>
-                Min bit score expected when searching for seed eggNOG ortholog.  Applies to phmmer/diamond searches.
-                Queries not having a significant seed orthologs will not be annotated. Default=60
+                Min bit score expected when searching for seed eggNOG ortholog. 
+                Queries not having a significant seed orthologs will not be annotated.
                 </help>
             </param>
         </section>
         <section name="output_options" expanded="false" title="Output Options">
-            <param name="file_comments" type="boolean" truevalue="--no_file_comments" falsevalue="" checked="false" 
+            <param name="no_file_comments" type="boolean" truevalue="--no_file_comments" falsevalue="" checked="true"
                 label="Exclude header lines and stats from output files"/>
-            <param name="no_annot" type="boolean" truevalue="--no_annot" falsevalue="" checked="false" 
+            <param name="no_annot" type="boolean" truevalue="--no_annot" falsevalue="" checked="false"
                 label="Skip functional annotation, reporting only hits"/>
-            <param name="report_orthologs" type="boolean" truevalue="--report_orthologs" falsevalue="" checked="false" 
+            <param name="report_orthologs" type="boolean" truevalue="--report_orthologs" falsevalue="" checked="false"
                 label="Output a file with the list of orthologs for each hits"/>
         </section>
     </inputs>
@@ -272,7 +379,7 @@
         <data name="annotations" format="tabular" label="${tool.name} on ${on_string}: ${db.database}.annotations" from_work_dir="results.emapper.annotations">
             <filter>not output_options['no_annot']</filter>
             <actions>
-                <action name="column_names" type="metadata" default="query_name,seed_eggNOG_ortholog,seed_ortholog_evalue,seed_ortholog_score,predicted_gene_name,GO_terms,KEGG_pathways,Annotation_tax_scope,Matching_OGs,best_OG|evalue|score,COG,functional,categories,eggNOG_HMM_model_annotation"/>
+                <action name="column_names" type="metadata" default="query_name,seed_eggNOG_ortholog,seed_ortholog_evalue,seed_ortholog_score,predicted_gene_name,GO_terms,KEGG_KO,BiGG_Reactions,Annotation_tax_scope,Matching_OGs,best_OG|evalue|score,COG_functional_categories,eggNOG_HMM_model_annotation"/>
             </actions>
         </data>
         <data name="hmm_hits" format="tabular" label="${tool.name} on ${on_string}: ${db.database}.hmm_hits"  from_work_dir="results.emapper.hmm_hits">
@@ -288,98 +395,84 @@
             </actions>
         </data>
     </outputs>
+    <tests>
+        <test>
+            <param name="input" value="nlim_fragment.fasta" ftype="fasta"/>
+            <param name="database" value="ENOG411CB2I"/>
+            <param name="mode" value="hmmer"/>
+            <!--
+            <param name="test" value="true"/>
+            -->
+            <param name="eggnog_data" value="4.5"/>
+            <param name="no_annot" value="true"/>
+            <param name="no_file_comments" value="true"/>
+            <output name="hmm_hits" file="HMM_nlim.emapper.hmm_hits" ftype="tabular"/>
+        </test>
+        <test>
+            <param name="input" value="nlim_fragment.fasta" ftype="fasta"/>
+            <param name="eggnog_data" value="4.5"/> <!-- not passed in test, but required for test to work -->
+            <param name="no_annot" value="true"/>
+            <param name="mode" value="diamond"/>
+            <output name="seed_orthologs" file="DIA_nlim.emapper.seed_orthologs" ftype="tabular"/>
+        </test>
+    </tests>
     <help><![CDATA[
 
 eggnog-mapper
-
-optional arguments:
-  -h, --help            show this help message and exit
-  --version
+=============
+Overview
+--------
 
-Target HMM Database Options:
-  --guessdb             guess eggnog db based on the provided taxid
-  --database , -d       specify the target database for sequence searches.
-                        Choose among: euk,bact,arch, host:port, or a local
-                        hmmpressed database
-  --dbtype {hmmdb,seqdb}
-  --qtype {hmm,seq}
+``eggnog-mapper`` is a tool for fast functional annotation of novel sequences (genes or proteins) using precomputed eggNOG-based orthology assignments. 
+Obvious examples include the annotation of novel genomes, transcriptomes or even metagenomic gene catalogs. 
+The use of orthology predictions for functional annotation is considered more precise than traditional homology searches, 
+as it avoids transferring annotations from paralogs (duplicate genes with a higher chance of being involved in functional divergence).
+
+EggNOG-mapper is also available as a public online resource:  `<http://beta-eggnogdb.embl.de/#/app/emapper>`_.
 
-Annotation Options:
-  --tax_scope           Fix the taxonomic scope used for annotation, so only
-                        orthologs from a particular clade are used for
-                        functional transfer. By default, this is automatically
-                        adjusted for every query sequence.
-  --target_orthologs {one2one,many2one,one2many,many2many,all}
-                        defines what type of orthologs should be used for
-                        functional transfer
-  --excluded_taxa       (for debugging and benchmark purposes)
-  --go_evidence {experimental,non-electronic}
-                        Defines what type of GO terms should be used for
-                        annotation:experimental = Use only terms inferred from
-                        experimental evidencenon-electronic = Use only non-
-                        electronically curated terms
+Options
+-------
+
+``eggnog-mapper`` can use two search algorithms: `HMMER <http://hmmer.org/>`_ and `DIAMOND <https://github.com/bbuchfink/diamond>`_. 
+HMMER is more sensitive, while DIAMOND is faster and useful for larger sets of query sequences. 
 
-HMM search_options:
-  --hmm_maxhits         Max number of hits to report. Default=1
-  --hmm_evalue          E-value threshold. Default=0.001
-  --hmm_score           Bit score threshold. Default=20
-  --hmm_maxseqlen       Ignore query sequences larger than `maxseqlen`.
-                        Default=5000
-  --hmm_qcov            min query coverage (from 0 to 1). Default=(disabled)
-  --Z                   Fixed database size used in phmmer/hmmscan (allows
-                        comparing e-values among databases).
-                        Default=40,000,000
+
+Outputs
+-------
+
+**hmm_hits**
 
-Seed ortholog search option:
-  --seed_ortholog_evalue 
-                        Min E-value expected when searching for seed eggNOG
-                        ortholog. Applies to phmmer/diamond searches. Queries
-                        not having a significant seed orthologs will not be
-                        annotated. Default=0.001
-  --seed_ortholog_score 
-                        Min bit score expected when searching for seed eggNOG
-                        ortholog. Applies to phmmer/diamond searches. Queries
-                        not having a significant seed orthologs will not be
-                        annotated. Default=60
+For each query sequence, a list of significant 
+hits to eggNOG Orthologous Groups (OGs) is reported. 
+Each line in the file represents a hit, where evalue, bit-score, 
+query-coverage and the sequence coordinates of the match are reported. 
+If multiple hits exist for a given query, results are sorted by e-value.
+Only returned when using HMMER mode. 
+
+**seed_orthologs**
+
+each line in the file provides the best match of each query within the best Orthologous Group (OG) 
+reported in the [project].hmm_hits file, obtained running PHMMER against all sequences within the best OG. 
+The seed ortholog is used to fetch fine-grained orthology relationships from eggNOG. 
+If using the diamond search mode, seed orthologs are directly 
+obtained from the best matching sequences by running DIAMOND against the whole eggNOG protein space.
 
-Output options:
-  --output , -o         base name for output files
-  --resume              Resumes a previous execution skipping reported hits in
-                        the output file.
-  --override            Overwrites output files if they exist.
-  --no_refine           Skip hit refinement, reporting only HMM hits.
-  --no_annot            Skip functional annotation, reporting only hits
-  --no_search           Skip HMM search mapping. Use existing hits file
-  --report_orthologs    The list of orthologs used for functional transferred
-                        are dumped into a separate file
-  --scratch_dir         Write output files in a temporary scratch dir, move
-                        them to final the final output dir when finished.
-                        Speed up large computations using network file
-                        systems.
-  --output_dir          Where output files should be written
-  --temp_dir            Where temporary files are created. Better if this is a
-                        local disk.
-  --no_file_comments    No header lines nor stats are included in the output
-                        files
-  --keep_mapping_files  Do not delete temporary mapping files used for
-                        annotation (i.e. HMMER and DIAMOND search outputs)
+**annotations**
+
+This file provides final annotations of each query. Tab-delimited columns in the file are:
 
-Execution options:
-  -m {hmmer,diamond}    Default:hmmer
-  -i                    Computes annotations for the provided FASTA file
-  --translate           Assume sequences are genes instead of proteins
-  --servermode          Loads target database in memory and keeps running in
-                        server mode, so another instance of eggnog-mapper can
-                        connect to this sever. Auto turns on the --usemem flag
-  --usemem              If a local hmmpressed database is provided as target
-                        using --db, this flag will allocate the whole database
-                        in memory using hmmpgmd. Database will be unloaded
-                        after execution.
-  --cpu 
-  --annotate_hits_table 
-                        Annotatate TSV formatted table of query->hits. 4
-                        fields required: query, hit, evalue, score. Implies
-                        --no_search and --no_refine.
+- ``query_name``: query sequence name
+- ``seed_eggNOG_ortholog``: best protein match in eggNOG
+- ``seed_ortholog_evalue``: best protein match (e-value)
+- ``seed_ortholog_score``: best protein match (bit-score)
+- ``predicted_gene_name``: Predicted gene name for query sequences
+- ``GO_terms``: Comma delimited list of predicted Gene Ontology terms
+- ``KEGG_pathways``: Comma delimited list of predicted KEGG pathways
+- ``Annotation_tax_scope``: The taxonomic scope used to annotate this query sequence
+- ``Matching_OGs``: Comma delimited list of matching eggNOG Orthologous Groups
+- ``best_OG|evalue|score``: Best matching Orthologous Groups (only in HMM mode)
+- ``COG functional categories``: COG functional category inferred from best matching OG
+- ``eggNOG_HMM_model_annotation``: eggNOG functional description inferred from best matching OG
 
     ]]></help>
     <citations>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/DIA_nlim.emapper.seed_orthologs	Mon Nov 04 16:38:44 2019 -0500
@@ -0,0 +1,1 @@
+Nlim_1033886738.Nlim_1033Cytidyltransferase-like	886738.Nlim_1033	5.4e-20	78.6
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/HMM_nlim.emapper.hmm_hits	Mon Nov 04 16:38:44 2019 -0500
@@ -0,0 +1,1 @@
+Nlim_1033886738.Nlim_1033Cytidyltransferase-like	ENOG411CB2I	2.3e-16	46.1	39	1	39	1	38	0.948717948718
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cached_locally/OG_fasta/thaNOG/1CB2A.fa	Mon Nov 04 16:38:44 2019 -0500
@@ -0,0 +1,6 @@
+>1001994.MY1_1439
+MKIQIYILIGVVVLTLISVGIMTNQDQNTHENKIRVAYFPNISHAIPIVGIEKGFFSNHIGSDIDIQPILFDSGPQVIESIFAGSVDIAYVGPGPAINAFLKSEQHDVKILSGAASGGVSFIVHPKSEIKSVADFAGKRIAAPQIGNTQDISLRTYLSDNGLKPAEKGGSVIILNTGNSDIYILFAKGDIDGAWVPEPTATILVQQLGGTRLFNENELWPENKFATVVLIAKEEYVNSHPEIIQKWLEAHQQTADWINSNKEETKTIFFDFMKNEMGKSLPVELIDESLSNLEITSDPIVSSIDTIAKRADSLGYLGRHGYNLDGLFFDKNSNSQSQEVLVNNDQT
+>436308.Nmar_1285
+MKIRSVIAAGIGAIIVFSALGIALSSSDTTYENKIRIAYFPNIGHAIPIVGMEKGFFAEHLGDDVKIETKVFDSGPQAIESLFANSIDIAYVGPGPAINGFLNSNNQNVKILAGAASGGASFIVHPDSEINTADDFAGKKIAAPQIGNTQDVSLRHFLAENQLKPAEKGGNVVVYNIPNPDIYTLFVKGDIDGAWVAEPWATILETELDGKRLFHEEELWPDKEFASVLLIGNVDYIDKNSVVWADYIRAHHETQIWIESNPIETRNVFNDFLDSYLGQSLSDDVVDVALSNIMITADPKPNSVVSFAEKADTLGYLGRNGYDLSGIFYSFDTNSLEEAST
+>886738.Nlim_1020
+MKMRSIILAGIASIILILSVGIIVNTDGSTRENKIRVAYFPNITHVVPIIGLERGTFANEIGNTITIQPILFDSGPQVIESIFAGSVNIAYVGPGPAINGFLKSEHHNVKILSGAASGGVSFIVHPDSKINSAEDFIGKRIAAPQIGNSQDISLRTYLSANGLKPAEKGGSVIVLNVPNSDIYTLFAKGDIDAAWVAEPTATLLVQKLNGTRLFDEIDMWPDQKFASVLLIANEDYVNQHPEVIRKWLEAHQQTIDWINSNPEETRIIFNQFLKRELGKSLPDNLIDESLSKLQITSDPIVSSIETFAKRADSLGYLGRHGYSLDGIFFDINSNSQLQEVLIP
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cached_locally/OG_fasta/thaNOG/1CB2B.fa	Mon Nov 04 16:38:44 2019 -0500
@@ -0,0 +1,6 @@
+>1001994.MY1_0167
+MSYDGAIEALSTDALKFVKDDFVIGLGSGRAATAFVKSLSSFIKIKNYNIRGVPTSLQIKLIAEKGGIPLVEAEQVDHIDIVFDGADQIDSQKFVIKGGGGALLRENILFNLAKKVVVMADKSKFVKNFTRSVPVEVHPQARNLVTYEIKKLGGKAELRLIDRGYPFFTENGNIILDCDFGVIKNPKILSQKIKQVAGVIESGIFIRKPDVIYRAKTGGKFDII
+>436308.Nmar_0218
+MSYDGAITALSNNALKFVKDDYVVGLGSGRAATVLVKSLGKLIKLKNYNIKGVPTSLQIKLIAEKVGIPLIEADQVEHIDVVFDGADQIDSQKFVIKGGGGALLRENILFSLAKKVVVMADKTKFVKNFTRTVPVEVHPLARNSVSKSMKKLGGKAELRSLDRGYPFFTENGNIILDCDFGTIKNPKALTQKIKATTGVLESGIFLRKPDVIYRAKTGEKFDIL
+>886738.Nlim_1248
+MSYDDAIEALSTDALKFVKDGFVIGLGSGRAATSFVKSLSSFIKIKNYSIKAVPTSLQIKLIAEKGGIPLVEADHVEYIDVVFDGADQIDSQKFVIKGGGGALLRENILFNLSKKVVVMADKSKFVKNFTREVPVEVHPLARNSVIDAIRKLGGNAQLRSLDRGYPFFTENGNIILDCNFGTIKNPKSLTQKIKQITGVMESGIFLRKPDVIYKAKTGGKFEII
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cached_locally/OG_fasta/thaNOG/1CB2C.fa	Mon Nov 04 16:38:44 2019 -0500
@@ -0,0 +1,4 @@
+>1001994.MY1_1435
+MVQKEPFLTALQNRILLFDGAMGTEIQKYNPKPEDFPNNQDGFNDGLVITHPDWIKKIHKNYLDAGSDCIETNSFGSNKIKLDEYGFGDQTIEFNKKIAQLAVEVCSEYTDKPRYVIGSMGPSGYLPSSNDPDLGQKPLGEIRNAFELQAEGLILGGVDALLIETSQDILEVKLVIEACHNAMKKTGKKVPIIANTTLDQYGKMLLGTNIQAAYTTVSDMGIDVFGLNCSTGPAEMTPSVRWLDEQNEHNLLVVPNAGMPENQGGQAVYKMTPQKMGELLGDFLKQYKKVRIIGGCCGTNPEHIAVLRKVIDEKAYSVKG
+>436308.Nmar_1268
+MTEKEPFLDALQNRVLLFDGAMGTEIQKFNPKPEDFPNNQDGFNDGLVVTRPDWIKQIHRHYLDAGADCIETNSFGSNKIKLDEYGFGDQTIEFNKKIAQLASEVCQEYSDRPRYVIGSMGPSGFLPSSNDPDLGQKPLDEIKEAFELQAEGLILGGVDALLIETSQDILEVKLVIEACHQAMEKTGKKIPIIANTTLDQYGKMLLGTNIQAAYTTVSDMGIDVFGMNCSTGPIEMTPSVRWLDEQNEHNILVVPNAGMPENEGGQAVYKMTPEKMGDALGDFLNQYKKVRIIGGCCGTNPEHIKVLRKVIDEKANSVEG
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cached_locally/OG_fasta/thaNOG/1CB2D.fa	Mon Nov 04 16:38:44 2019 -0500
@@ -0,0 +1,6 @@
+>1001994.MY1_0571
+MDKSGVIVGAISGAAIVAIIFAVILAVPPTAVKADVISDNKSIPSATGAILTDYSKKLSLIEIFEKSEPGVVRINVQRAEQSNGTSGVGSGFVFDKQGHIITNAHVVKNVKKVVVTFLDGRSYNAEIVGSDQYTDIGVIKVNADLSLLQPLPLGDSANLKVGEPIAAIGNPFGLSGSMTSGIISQLGRLLPSGAGYSIPDVIQTDAAINPGNSGGPLLNMRGEIVGINTAIQSTTGEFTGVGFAVPSQTLAKIVPKIIVDGKYIHPWIGIAGRDIDPDLAKVLNLNDAVGFLVITVVDDSPAAKAGIHGSNETVEVDGIKYLIGGDIILSVDGNQVRKIDDILIHLQRAKSVGDEMVLEVLRDGRTTNIIITLDERPNGN
+>436308.Nmar_0594
+MDKSGVFVGGAIGAVIVVAIFAVLFVSPPESVKPDIVVSNGHGPSTVGEVTPVYSKDLSLIEIFEKSEPGVVRVNVQREEVSDVGGVGSGFVFDKQGHIITNEHVIDDAKKIIITFLDGRSYNAEIIGTDEFTDLAVVKVNADLALLHPLSIGDSSNLKVGEPIAAIGNPFGLSGSMTSGIVSQLGRLLPSGSGYSIPDVIQTDAAINPGNSGGPLLNMRGEIVGINTAIQSATGEFTGVGFAIPSQTVAKIVPTLIEDGDYKHPWIGISGRDIDPDLAKVLELPDAVGFLVVTVIEDSPASKAGLIGSEKTIDVDGVNYPMGGDIILAVDGIEVRKIDDILIHLQRAKSVGDEMVLEVLRDGRTTDISIILQERPNGN
+>886738.Nlim_0162
+MSKSEMLVGAAIGASVVAVIFAIILISPAAITKSEINTSDKSIPSVTQTAPAYSTNLSLIDIFEKSEPGVVRVNVQRTDQSNGTSGLGSGFVFDKKGDIITNAHVVKNAKNIVVTFLDGRSYNADLIGSDEFTDIAVIKVNADLTRLHPLSLGDSSSLKVGESIAAIGNPFGLSGSMTSGIVSQLGRLLPSGSGYSIPDVIQTDAAINPGNSGGPLLNMRGEIVGINTAIQSTTGEFTGVGFAVPSQTIVKIVPSLIQDGTYHHPWIGITGRDIEPDLAKVLKLNDAVGFLIVSVIDDSPAAKAGLHGSNETVQVDGLNYQIGGDIILSVDGKQVRKIDDILVHLQRAKSVGDEMVLEILRDGRTTNITINLEERPNGN
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cached_locally/OG_fasta/thaNOG/1CB2E.fa	Mon Nov 04 16:38:44 2019 -0500
@@ -0,0 +1,6 @@
+>1001994.MY1_1525
+MEPSLVTSIGKIQLERPVMLASGILGISLDVFNRLYRSGAGAVVSKSLSTEPWDGYPNPTIFGINGGGWINAVGLSNPGAPNFAKMIEPNKDVPIIISLVGSIPEDFSTMVEQFKNSKVIAYELNLSCPHVAKVGLEVGDDPELVKKIVSTVKNSTNVPVIAKVGLGTTHYLNTVSAAIDSGIDAITAINTIRAIAIDVETQRPILSNKFGGLSGTPIKPIALRCVYEISSKYDIPIIGCGGISTWEDALEFILAGASAIQIGSAIGDNWIHVFNDINKGILQYMKRKGYSKIDEMIGLAKKS
+>436308.Nmar_1390
+MEPNLATSIGPIQLDRPVMLASGILGISLDVFSRLYRSGAGAVVTKSLSTEPWEGYPNPTIFSVKGGGWINAVGLSNPGAENFAKMIEPNQDVPIIVSLVGSIPEDFEKMIKQFENCKVTAYELNLSCPHVAKVGLEVGDDPELVKKIVTTVKNSTNVPVIAKVGLGTTHYLNTVGTAIESGIDAITAINTVRSMAIDVETQRPILSNKFGGLSGTPIKPIALRCVYEISSKYDIPIIGCGGISTWEDAVEFFLAGASSVQLGSAIGDNWIDVFNEINTGILQYMEKKNYSKIEEMIGLAKKS
+>886738.Nlim_1764
+MEPSLVTSIGKIQLERPVMLASGILGISLDVFNRLYRSGAGAVVTKSLSTEPWDGYPNPTIFSVNGGGWINAVGLSNPGAPNFAKMIESNTTVPIIVSLVGSIAEDFEMMVSQFKNCKVTAYELNLSCPHVAKVGLEVGDDPELVKKIVSTVKNSTAVPVIAKVGLGTTHYLNTVKTAIDSGIDAITAINTVRAMAIDVETQRPILSNKFGGLSGTPIKPIALRCVYEISSKYDIPIIGCGGISTWEDAIEFILGGASAIQLGSAIGDRWLNVFNDINDGIIRYMKRKGYSKLDEMVGLAKKS
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cached_locally/OG_fasta/thaNOG/1CB2F.fa	Mon Nov 04 16:38:44 2019 -0500
@@ -0,0 +1,6 @@
+>1001994.MY1_0238
+MLEISSTPLVIIAILGTVGILLPIISIARKEKGSNSFYAVIAFAALIVSIGYVAYQFVNGNILPSALFSEDVLVDDAFGGFFAIAMLIVAIFTTVGSFNYMRKKNYPAVYYSLILLSTIGMVLVAYSTDLVMLFVAWELMSIPTYVLAGFMKKNPSSNEAALKYFLFGALSSAIIVYGISLSYGLTGSTNIGEVIQGYATLDPSLLPLALLSVGMFIAGFGFKMGLVPFHQWLPDTYEGAPPTITTLLAAGTKKAGFAATIRIVVLGMVVLNLDWTLALGVIAVMTMTIGNIAAIMQKNLARMLAYSSIAHAGYILIGLAVSPYSSLGLQGSLYHILNHAVMKGMAFIAVTGIITTLAVTHIDKLKGLGRRMPITALGLIISLFALAGVPPLAGFWSKLVLFGGALDAGTSIWWAPWLAIAGVLNSALSLAYYGWITRKMYFEGENEKRVSEPKSIIAIMIFSIVFLVGFGIYPDPIIKFVEFAAPTFSLGVMP
+>436308.Nmar_0286
+MLEITSTPLILIAILGTVGVILPIISIARKEKGSNSFYAVIAFAALIVSMAYVGYEFINENVAASALFSDDVIVDDAFGGFFAIAMLIVALFTTVGSFNYMRKHNSPAVYYSLILLATIGMILVAYSTDLVMLFVAWELMSIPTYILVGYMKKNPSSNEAALKYFLFGALSSAIIVYGIAISYGLTGSTNIGEVIEGYSTLDPSLLPLALLSVGMFIAGFGFKMGLVPFHQWLPDTYEGAPSPVTALLAAATKKAGFAAAIRIIVLGMMALNLDWTLALGIIAVMTMTIGNVAAIMQKNLSRMLAYSSIAHAGYILIGLAVAPYSSLGLQGSLYQIFNHAVMKGAAFIAIAGIVTTLAVTHIDKLKGLGRRMPITALGMVISLFALAGVPPLSGFWSKLMLFGSALDASTALWWAPWLAIAGVLNSALSLAYYGWITRKMYFEGETEKRVSEPKSIVAVMIFSIIFLVGFGVYPEPLLKFVEFATPVVSLGLMP
+>886738.Nlim_1181
+MLEITSTPLVIIAILGTVGVLLPIISIARKEKGSNSFYAIIAFAALIVSIGYVAYQFINDNVLPSALFSEDVLVDDAFGGFFAIAMLIVAIFTTIGSFNYMRKKNYPAVYYSLILLSTIGMVLVAYSTDLVMLFVAWELMSIPTYVLVGFMKKNPSSNEAALKYFLFGALSSAIIVYGISLSYGLTGSTNIGEVIQGYATLDASLLPLALLSVGMFIAGFGFKMGLVPFHQWLPDTYEGAPPTITTLLAAGTKKAGFAATIRIVVLGMVVLNLDWTLALGVIAVMTMTIGNIAAIMQKNLARMLAYSSIAHAGYILIGLAVSPYSSLGLQGSLYQILNHAVMKGMAFIAVTGIVTTLAVTHIDKLKGLGRRMPITAFGLVISLFALAGVPPLAGFWSKLMLFGGALDAGSTIWWAPWLAIAGVLNSALSLAYYGWITRKMYFEGETEKRVREPKSIIAIMVFSIIFLVGFGVYPDPIIKFVEFAAPTFSLGIMP
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cached_locally/OG_fasta/thaNOG/1CB2G.fa	Mon Nov 04 16:38:44 2019 -0500
@@ -0,0 +1,6 @@
+>1001994.MY1_1852
+MISLNRFVIILIVGIFVSGILTISFISNSYVDANSTKKINFTKTIISSQDPGQGHENHQLSLILSPNEGTLYDGSMTFTSNEPVDVVVLHEITGNDVKGQPTWTIDGKTIYAMSLIDLKSKSDSFEFTGAALALHSSNSKEFTATVSVDGWIRGQPTEVIMQKIQVEKDPSLMLSRANVEATMPMHEGLYKGNSIFYIITDTSREEYSKKITEKQDWKVQTSTLIEKMPEEILQKIFIFNNGVRGQGIYGHQKEIFSSTPVQESKYSALNSVIEVSWKKGQNAKVLESFEDVIDAEKNGRIEFTKTGVVINSPQIIWPNGQMLVRNDTKITDDLTFSGGQITKINKDEMTVTFVAHRMWGPDGKTIYAIVTDATPSNPSEIMGIPFSPVYDNLITNSSAADLFQFQNGIKGSGSLGYQPGITSVNSDQENYSPIWRIYNVEWHNPKDAKILQTMSDIDSFKAKDLISVSLARPMNSHHIINGPLIDPFQ
+>436308.Nmar_1753
+MLRKLIAILIIGIFATSIITASSLSDQFADAGSRKKIHFTQTFTSSQDPGQGHENHQLSLILSPNQGTIYDGSMTFTSSEPVQIVVLHEINSDDAKGQPTWSIDGNTVYGLSLIDLQEKSGSFEFTGAALGLHSPNSKQFTSTVSVDGWIRGQPTEVIMQKIELEKEEPMSLLSRANVPATIPIHEGIYGGEKVLYIITDGSDEEYARELSEKQEWNVELAPVLADVPEDALQKIFVFKNGVKGEGLYGFQNEIFSSTPQQESEYSALSSVIEVTWKTGQKEIVFESANDVIAAEENGRIEFDETGVVLNTPHIVWPGGQMQVRADQEIADDMPYGGGQITEINEEEMTVTFVAHRGWGPDGRTIYYIVTDATPFGPAEMMGVTSSPTSANLIAHSGAVDLFQFKNGIKGTGPLGFQAGIAAASLGDENYSPMWRIYLIEWNDSENAKILETKSDIDSFRADDLITVSITRPTNSDHIVNCPFIDPFQ
+>886738.Nlim_1479
+MNRFTIILIVGIFIIGALTVSFVSDNYVNANSTKKINFTKTITSSQDPGQGHENHQLALILSPNQGTLYVGSMTFTSSEPVEIVVLHEINNDDVKGQSTWTIDGKTVYAISLIELKAKSGSLEFTGAALALHSTNSKEFTATVSIDGWIRGQPTEVTMQKIQVQQNPPLELSRANIAASIPMHEGFYDGKSVFYIITDSSQKEYAEMITKKQNWKVEVAPEIKKISENTLQTIFIFKNGVNGDGIYGRQKEVFSSTPSQVQKYSALNSVIEVTWKKGQNASTLESYEDIINAEKNGRIEFSKTGIVINTPQIIWPDGQMLVRNNKEITNNLKFDGGQITEINKDEMTVTFVAHRGWGPDGKTIYYIITDTTPSGPAKIMGIPFSPVSEHLITNSSKSDLYQFKNGIKSSGSLGYQAEIISVMPGDDSYSPIWRVYNIEWNNPENASILETISDITSSKIKDLILVSLARSMNNQYVINGPIIDPFQ
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cached_locally/OG_fasta/thaNOG/1CB2H.fa	Mon Nov 04 16:38:44 2019 -0500
@@ -0,0 +1,4 @@
+>436308.Nmar_0483
+MTALATKSENIEKQIISDPSDTIDSEKYKMIAENVTISYDGIQAVKNITMKFKEKSVTALIGPSGCGKTTFLRCLNRMHDMTKNAKVDGKVMIDNIDLYDQSIDPIYHRRKVGMVFQKPNPFPTMSIYDNVTAGLKLNGVKDKRILDEIVEDSLKMAYLWDEVKGDLKKSAIELSGGQQQRLCIARALAIQPEVLLMDEPASALDPIATQKIEETITELKKEYTIIIVTHNMQQAVRVSDYTGFMYLGDLVEFRETKKLFTDPKNELTAKYVQGQFG
+>886738.Nlim_0922
+MTAMTTKPTHAETSFTSKSQPTLDSDKYKMIAENITVSYGGVDAVKNVTMKFKEKSVTALIGPSGCGKTTFLRCLNRMHDMTKNAKVTGKVMIDNIDLYAKDIDPIYHRRKVGMVFQKPNPFPTMSVYDNVTAGLRLNGVRDKRILDEIVEDSLKMAYLWDEVKNDLKKSAIELSGGQQQRLCIARALAIQPEVLLMDEPASALDPIATQKIEETIIELKKDYTIIIVTHNMQQAIRVSDYTGFMYLGDLIEFRETKKLFTDPKDDLTAKYVQGHFG
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cached_locally/OG_fasta/thaNOG/1CB2I.fa	Mon Nov 04 16:38:44 2019 -0500
@@ -0,0 +1,6 @@
+>1001994.MY1_1452
+MELIEKIILTQIYLSGITGKSYKDNLKTKKGFTENIINSKIDELVKNKLITEDKSALTELGRSSLRVVLAGGVFDIIHPGHIHTLNAAKILGDVLVVVVATDNTAIKMKKRQPLHSKEQRQELVNSLSMVDLCLIGQEDDIFKTVNLVKPQIIALGYDQVHQEKFIIEGCKKINLDAKVARLQSPIPESSSSKIQKEYGESIHGI
+>436308.Nmar_1298
+MLEQSQRTILSTIYVCQIEGTNPIEKIKRKTAFSDDQINSKIEELIKKQLVNEDKKTLTESGRDSLKVVLAGGVFDIIHPGHIHTLNAAKELGDALVVVVATDNTAVKMKKRRPLHSQEQRQELVNSLSMVDLCLIGQEDDIFKTVNNVRPQIIALGYDQAHQEKFITEGCKKINLDAKVARLQSPIPDSSSSKIEKEYGESIHGI
+>886738.Nlim_1033
+MELIKKSILTELYLSGITGKSHIDNLTKKGFTQKLIDLEIDELIKNKLVKEDRAILTELGRSSLRVVLAGGVFDIIHPGHIYTLNAAKSLGDVLIVVVATDNTALKMKKRQPLHSKEQRQELVNSLIMVDLCLIGQEDDIFKTVNLVKPQIIALGYDQVHQEKFIIDGCKKIQLDAKVARLQSPIPESSSSKIQKEYGESIHGI
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cached_locally/OG_fasta/thaNOG/1CB2J.fa	Mon Nov 04 16:38:44 2019 -0500
@@ -0,0 +1,6 @@
+>1001994.MY1_1646
+MSCSGEIVDEEKLIQIKPGILQQLKKAKYGVADHSTVELCHWTKKSFKHEGSCYKHKFYGISTHRCMEFSPAGMHCENRCVYCWRPMEFYDSLKMEPEKVSEPKEILTKLMEERKKLIMGYYGDSRNDKQRLDESLLPSHYAISLSGEPTMYPKLPELIKYLKSLEATKSIFLVTNGQEPDMIQRLQDKDALPTQLYLSTNAADYDSFLKINRPKYDDSWQRWNRTLEMLKHLDTRTVLRITLIRNYNDQKEMIPAFAAMLKQASPHFIEIKSYMHIGRSTNRLEHSNMLEMEEVRRFSEEVAKHSEIFSIMDESLVSRIVILQNNQRSINRWISAYSNTN
+>436308.Nmar_1529
+MSCSGEVVEEEQLIQIKPAISEQLKKAKYGVSDHSTVELCHWTKKSFKHEGSCYKHKFYGISTHRCMEFSPAGMHCENRCVYCWRPMEFYDSLEMKPEQVAEPEEILTKLMAERKKLINGYYGDSRNDKQRLDESLLPSHYAISLSGEPTMYPKLPELIKYLNSLEATKSIFLVTNGQEPDMIQKLQDEDALPTQLYLSTNAADYESFLKINKPKYDDSWERWNRTLGMLKHLNTRTVLRITLIRNYNDQKSMIPAFAKMFKEASPHFIEIKSYMHIGRSTNRLEHSNMLEMEEVKRFSEQIAKQSQIFSVMDESFVSRISILQNNERFIDRWIPAYVNTN
+>886738.Nlim_1932
+MSCSGEIVDEERLIQIKPGISQQLKKAKYGVADHSTVELCHWTKKSFKHEGSCYKHKFYGISTHRCMEFSPAGMHCENRCVYCWRPMEFYDSLKMDPEKVAEPKEILTKLMAERKKLINGYYGDSRNDKQRLDESLLPSHYAISLSGEPTMYPKLPELIKYLKSLEETKSIFLVTNGQEPDMIQRLQDEDALPTQLYLSTNAADYESFLKINKPKYDDSWQRWNRTLEMLKKLDTRTVLRITLIRNYNDQEEMIPAFAAMLKQASPHFIEIKSYMHIGRSTNRLEHSNMLEMEEVRKFSESVAEHSQIFSVMDESLVSRIVILQNNQRTIDRWIPAYANTN
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cached_locally/OG_fasta/thaNOG/1CB2K.fa	Mon Nov 04 16:38:44 2019 -0500
@@ -0,0 +1,4 @@
+>436308.Nmar_0061
+MPNFDKTWARQETQSVTGKLREAVKPQGALKPRIQTAVNKLQVQISKMDSMLGKLHERDAQLFQRVVTAMQQHDTSTSRVLSNELAEIRKVTKMLGNARMSLEQVQLRLTTIHDLGDAMVAIGPAMSTMKGLKSSLGRFMPEADSELNTMTQTLNGLMMDSLAGDSFNMESDVSSEETEKILQEASAVAEQQIGDKFPSVPSSTGLSSGTSTSTFE
+>886738.Nlim_1611
+MPNFDKTWARQETPGVTEKLRETIKPQGALKPRIQTAVNKLQVQISKMDSMLGKLHERDAQLFQRVVTAMQQHDTSTSRVLSNELAEIRKVTKMLGNARMSLEQVQLRLTTIHDLGDAMVAIGPAMSTMKGLKSSLGRFMPEADSELNSMTQTLNGLMMDSLAGDSFSMETGASSEETERILQEASAVAEQQIGDKFPSVPTSTGLSQSSQSTY
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cached_locally/OG_fasta/thaNOG/1CB2M.fa	Mon Nov 04 16:38:44 2019 -0500
@@ -0,0 +1,6 @@
+>1001994.MY1_0188
+MLSTGMWVEKYRPSKLSEIVNQKEIIGSLEALIKDPTDMPHLMFSGSAGVGKTTTALCISRQILGEYAKDYTLELNASDERGIGMVREKVKKFSRFAGMVDVPFKIIILDEADEMTSDAQTALRRIIEDTAKYCRFILIANNISKIIDPIQSRCATFKFTSIPEEDVINHLENIAKKEKVKSDKKGLKAIYDYSEGDLRHAINLMQATASIGEISEENVKSSAGLTKTSDVDIVLKMALSGKIVDAREKMIELTKVYGMSESDFLKYLNSAVFKIKHDNISDILEVIAKYDYRILVGANPEIQLTAMLAELGKLEK
+>436308.Nmar_0240
+MAATGMWVEKYRPMKLSEVVNQTEIIGSLEALIKDPTDMPHLLFSGSAGVGKTTTALCISRQILGDYAKDYTLELNASDERGIGMVREKVKKFSRYAGMADVPFKIIILDEADEMTSDAQTALRRIIEDTAKICRFILIANNISKIIDPIQSRCATFKFTAVPEEDVIKRLEEIAKKEKVKADKKGLKAIYDYSEGDLRHAINLMQATASLGSISEDNVKASAGLTKTTDVDEVLKIALSGKVPEAREKMIELIKVYGMSESDFLKYLNSAVFKSKHDKLSDILEIIAKYDYRILVGSNSEIQLSAMLAELAKVEN
+>886738.Nlim_1226
+MLSTGMWVEKYRPTKLSEIVNQTEIIGSLEALIKDPTDMPHLMFSGSAGVGKTTTALCIARQILGEYAKDYTLELNASDERGIGMVREKVKKFSRFAGMAEVPFKIIILDEADEMTADAQTALRRIIEDTAKYCRFILIANNISKIIDPIQSRCATFKFTSIPQEDVINHLESISKKEKIKSDKKGLKAIYDYSEGDLRHAINLLQATASLGEVTEENVKASAGLTKTSDVDEVLKMALAGKVLEAREKMIELIKVYGMSESDFLKYINSAVFKTKHEKLSDILQVIAKYDFRILSGANSEIQLSALLAELSTLK
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cached_locally/OG_fasta/thaNOG/1CB2N.fa	Mon Nov 04 16:38:44 2019 -0500
@@ -0,0 +1,6 @@
+>1001994.MY1_0435
+MNKVNLNIKQRKIISDKIFKIGVTTAGAYVLIVVVLIAFQLVSESYPVWEEEGLSFITKTDWNAVEGRESFGALPYILGTLTTSAIAMMIGVPLSIGIAMFISDAPPKIGAPLGFLVELLAAVPSVIYGLWGLYVFRIYFRDWFETPLHDAFGDNIWLFSGNPYGLDILTASVILAIMIIPTVSAVSREIMKAVPQQQKEAAYMLGATKWEMFKLAIFPYSKTGLIGASILGLGRAVGETMAVTMLIGNATGLGAIPSSLFGPSQTMSSIIANEFVEASPASIHMPALIGIGLILLLIAIVINVVAHLLVTRMLKIKEGAINN
+>436308.Nmar_0481
+MGRPKLNPPKVGRRPISDKIFKVGATVAGVYVLVVIVLLAFQLISESAPIWDEYGLSFIVKSEWNAIDDRQDFGVLPYIFGTLVTSALAMVIGVPLSIGIAMFISDAPSKIGGPLGFLVELLAAVPSVIYGLWGLFVFRVYFVDWVEKPLHNTFGDSIWLFSGTPFGLDILTASVILAIMIIPTVSAVSREVMKAVPQQQKEAAYMLGATKWEMFKLAVFPYSKTGLIGASILGLGRAVGETMAVTMLIGNATGPNAFADSLFDPSQTMSSIIANEFNEASLGTLHLPALIGVAVVLLLIAIAINVVAHILVTRMLKVKEGAINN
+>886738.Nlim_0924
+MISDKVFKIGATVAGTYVLVVVVLIAFQLISESYPIWEKEGLSFITSTDWNAVEGRESFGALPYIIGTLTTSAIAMAIGVPLSIGIAMFISDAPAKIGGPLGFLVELLAAVPSVIYGLWGLFVFRIYFRDWIETPLHNAFGDNIWLFSGNPYGLDIITASVILAIMIIPTVSAVSREIMKAVPQQQKEAAYMLGATKWEMFKLAVFPYSKTGLIGASILGLGRAVGETMAVTMLIGNATGIGAIPSSLFGPSQTMSSIIANEFVEASPASVHMPALIGIGLILLLIAIVINVIAHLLVTKMLKIKEGAINN
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cached_locally/OG_fasta/thaNOG/1CB2P.fa	Mon Nov 04 16:38:44 2019 -0500
@@ -0,0 +1,4 @@
+>1001994.MY1_1290
+MTPSELNEEKLVEIPAEHTFSELYDDVKYDPDIRPGRELQERDSLHEVLLKRRLRQKLVELNPGNPDIVYDIAVQKIELISEPTLIETNRAFHQMLLSGIKVAYQEDNQTKYSVMKLIDFDNPEKNDFIAVRQFLLVQHEERRLDHVIFVNGIPLIILEYKSMADKNATIVDAFHQLGKTKYQRDIPIIFRYNAFLVISDRLNAKYGTINAPFERFSDWNDLTQPDKKVANRLEILQKLLLNKTTILDVIKNFIEYESDGKNLIKKICQQHQYHAVNTIVKKTSDVYSQQGENRIGVVWHTTGSGKSLTMIYYVNSLSQIEKFENPTFIIITDRRDLDEQLNHFFRIAGFPYPKPETAILEADSILDLREKLQVPSGKIIFTTIQKFQTTEEEREGKVKYPKISDRRNIIIIADEAHRSQYKKMAQNLQTALPNALRIGFTGTPIELEDRSTTQVFGDIISSYKIPEAVRDGATVQISCETHPVTLLLLNKFIGKDFEEITQGLDEENVTTLARRGAEFTKLVEDPDRIKTIANDIVSHFNKKQKIFKGKAMIATSTKLAAARFADYISSLKVAPECTCIVSGATSQKPESTPEKRTREAIIQKHYKDKLTIENILTRFKDENDPLSLLIVCDMYLTGFDAPLIHTMYIDKPLRDHNLIQAISRVNRVWKNKPGGAIIDYIGIADDLDRAFSAYAQDDVKGAMIPTAEIIEIMKKKHSDLINFFDPKISNRQGLDESQELQLIYDAIDEIVYDDIVKREFIKIVTELTKAYAVCTPHPSCLDVEDDLRFFQKLRKILLKATSNVPVDLTEMESAISDLVEQGIGADQVVKGFKISFDPKKQDISKEYLNDIKKLKQKNLKAELAYKLLDDAIQAKFKRNLVKRKSFQDRIEEALSKYHARFWDNDDTIQKLEEVGKEITNESSREQELGLNDEEIAFYDVVSLGKDYVKSDAVIKQISLDLTKYLKGNIRIDWINQENIKAEIRMGVRKILLRADFPTDKIEEIVPKIMDQAETNYG
+>436308.Nmar_0608
+MNFRIEDNEEGRQVELPALELITALGYTYIPNYELNIPKERPDHRQVLLYPRLRAAIKRLNDFDDDGIEQAIAQIHEDNFPIGMPMIDANEKIRIKLTGRAGENAIAQPITIKQYGKKGIEYPTVKFFDFDPKKIGTKEDKNEYLVTNQFKHLGNRTEIECDIVIFVNGIPLVLIECKKPTTIDLMKTVWKENLEKYQRDGSHSLGHEKLFFFNHVIMATSAIQARYGTLKALPNKYAKWTSLTNITTKELEKLVGRKPTPQDIMLAGMIKKETLLDMLKNFVLYEIEEHKKIKKVAKHQQYRVVTKSVDRISHHKKVEDKGGVIWHTQGSGKSLSMVWFATQLYYKFSRPTIMVITDRRQLNKQIFDTFRNCGFPEPEKPRNRSQLAKTLQYSKGKTIMVNLQKFDKPEKFVETKEKIYVLVDEAHRSQYKWTAGYMRKAMPNAVFFAFTGTPLDRENKNTYRRFGPLIDKYSFTESKEDGATVKVEHMGLLPEIEIEGGNSLNNIFDNLFGHLPKAQQAEIRRKYATKKKIASSPARIRKICEKIVDHYTKKILPNGYKAMIVAPTRAAAVTYKRELEDLTKLPARIIMDSKKDEVGPDEFSWADYYLPQNEALKKAEEFTNPDDPTKFLIVVDMLLVGYDAPIVQVMYLDRPLREHALLQAIARVNRIYDEHKDRGFIIDFWGVTRDLQNALKMFEEQDVQGALDNVDDDLLELDVRHKDFMEKIQGIDSKDHNEIAKRFEDEDEQEEFEYAFKRFAKALEAVLPDKEAVPYEKDLKKGYEIRGKIRAWFYGDRADLSEYGKKVQKIIDKHIRAIGISEISGSKEITYDNFLGFIAKFKGDNRAKAALIKKRATLVIREMSPDNPAFYQKLKERLEKLIQDEKERRVDDAQYFEGIRDIFEEALSGPEKLQKQTGIKDRFQLAIYMLLEEKHSDLKQNKKYSEEIFKKVKKAASVKDWRDKEPQENEIELAVIDTLDKKIFDEKTRDKLASEVYKMAVNNNEW
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cached_locally/OG_fasta/thaNOG/1CB2Q.fa	Mon Nov 04 16:38:44 2019 -0500
@@ -0,0 +1,6 @@
+>1001994.MY1_1750
+MDRKILGISGGIAVIIAIVAVMLLTPNLESTPIQKHNEKIGLVINAPHSAISLQDLNQIYAEASSTGIGRSNVYMFWNIVEPVRGEYDWKQSDVLMSFNKNNNLKVTLFFSVINGETLGPFPNWIGKPSLNAIGEDRLVNVLDAILSRYDIIDTVVIAGETESQFRYHEQNIPVYKELFNGVYAKLKEKHPDVQIGNGFALHNVLNKNLEHIVSDLAIGDFVAFSYFPVDTLNDIVKTPEEAKADLQKTFEIIPDKKIGLFEVSWSTSDFVGGNETSQQIFLEKSFEFYTENESKIEFFTWYRQYDRPDGTCVIDKPEIANQTLTVGGGSGLGSSEYIMERLSHYICNSGLLDVDGTPKSSWNEFKNQIELIN
+>436308.Nmar_1626
+MDKKILGVGIGVAVVIAIIAGVLSIPSDSNPEVTPVKTNEKIGLVINSPNQSVTLQELDEIYSTASESGIGRSNVYLFWNLIEPEHREYNWQYSDALMSFNQKNDLKVTLYFSIINGETLGPFPDWIGKPPIQSLNEDRVVSVLDAILSRYHIVDTVILAGETESQFRYYEQNIPPYKELFVGVYDKIKEKHPDVKIGNAFALHQVLNKDLQNIVTDLDVGDFVAFSYSPVDTVGDMVKTPQQAKEDLEQIIDLAGDRNAAIFEISWSTSDFVGGSEESQTEFLEKSFEFYAENESELEFFTWYRQNDKPEGTCAFEVQEVGEDKLTVGGSGFGSSEHVIERLDHYVCNAGLFDENGNPKSGWNEFKNQIQMLN
+>886738.Nlim_1388
+MDKKILSIGIGIAIVIALVLVVIGFQSAEIITNQKQDEKIGLVINTPNPSISLKELHKIYADASSTGIGRSNVYIFWNVVEPVKGEFDWTQSDVLMSYNKNNDLKVTLYFSVINGETLGPFPNWIGKPSLNAIGEDRVVSVLDAILSRYDIIDTVVIAGETESQFRYYEQNIPVYKELFTGVYDKIKEKHPTVKIGNAFALHNVLNKNLEYIVTDLSLGDFVAFSYSPVDTLNEIVKTPQEAKEDLQKIFEIVPDKKIGLFEISWSTSDFVGGNSTSQQEFLEKSFEFYKENKSKIEFFTWYRQYDKPDGTCVIEKPEIGNKTLSVGGGSGLGSSEYVIERLSHYVCSVGLLDADGTPKPSWNEFKNQIELINQ
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cached_locally/OG_fasta/thaNOG/1CB2R.fa	Mon Nov 04 16:38:44 2019 -0500
@@ -0,0 +1,4 @@
+>1001994.MY1_0222
+MWSEKYRPQNISDMIGNEESRSSIIEWFTKWKKGTKPLLLVGPPGIGKTTIAYLTAKQFQYDMVGLNASDVRSKSRINEILSPVLGNVSILGLPMIFIDEVDGIHGRGDYGGAEALIEILKEPTIPIILAANSDTSDKMKSIKKVVKTISFKPIPPRLLKIYLENILKKENVTLSPGSIIKVIDRSRGDVRSMINLTQSLVTGFNPQTEKSFESINVEDGINAFFKANSFDEARGVLYSMQIDPRLKIDAFYSSIVTSNLDNQTLAKLLEIISEADILYGKIMKTQNWRLLRYLNEILIRLYLNDERIRYSQYNLSWPLLNRIRWDGKKIKSLSSVMAKTLHLSSSAFVTICLPYILFCIKNKKLSLDLEETFGDVIEKEIELIK
+>436308.Nmar_0270
+MWSEKYRPQIISDMVGNEESRAAIMEWFAKWKKGTKPLLLAGPPGIGKTTMAFLVAKQFGYDMIGLNASDVRSKSRINEILTPVLGNVSVLGTPMIFVDEVDGIHGRGDYGGVAALVDILKEPTVPIILAANDDTSDKMKNIKKVVKTISFKKIPPRLLRVYLENILKKESAKLSPGSLIKVIDKSRGDIRSMINLTQSMVTGFNPQTETTFENIDVEDGVNAFFKSKSVDEARGVLYSMQIDPREKINAFYSSIVMSSLDPETLAKYLEIISEADMLYGKIVRTQNWRLLRYLNDILIKLYHDDDRVRYAQYNLSWPLLNRIRWDGSKIKSLSSVMAKKLHLSSSAFVTFGLPFVLFCIKNNALELELEETFGDIIEKEIELIQ
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cached_locally/OG_fasta/thaNOG/1CB2S.fa	Mon Nov 04 16:38:44 2019 -0500
@@ -0,0 +1,4 @@
+>1001994.MY1_0691
+MSFKSLIDEIENNLHKILEDMSIYDISFTVEPAKPGFGDASSNISFLLAKSLKKSPKEIANLMSEKYRQSQNILVLKVEPHQTGYLNFFADWEKLNQLILSESNLNEFGFIDLGHNSEIVVEHTSVNPNKALHIGHIRNIVLGDTVARILKKSNYKVNVLNYVDDSGLQVADIIVGFKHLGFAQQSPTGKKFDHYCGDDVYVKTTEKYEQDPNFEEIRKNTLKELEDGASETAKFADTITRRVLENQLETCWNLGVYYDCLNFESQIIRSGLWSKIFEKLKEMNLVEFENDGKNAGCWIIRGENNEEDKVIVRSNGTATYIAKDIPYAAWKLGLIEDPFSYKKYEKTQPGNKILWQTTLTATNEPKQNFTGNKVITVIDSRQARLQKIITGLMSKFKSTNDAYVHLGYESVTLSSDTAQTLGLDTDGKQAQMSGRKGLYVDADSVYDLLKNKTIEETKKRHPEMSDSEIEQIAHYVSVGTLRYEMIKQDLDKMITFDLTKSLSLEGDTAPYIQYTHARASRIIEKSARNPSIDVDFSLLNDASELSLIKIIGLFEIYVLDAAKNLSPKVIARYCHNLAVAFNSFYEHVKVLELGDEKLENSRLCLVNSFKITLEKALELLGITAPEKM
+>436308.Nmar_0686
+MTFKSILDEIENNLNKILDDLSISDVKFSVEPAKPGFGDVSSNVSFLLAKQLKKSPKEISEMLSEKYSQCVSTLVSKSESHPSGYLNFYADWPKLNQLILSESNLPEFGDVDIGKNSTIVVEHTSVNPNKALHIGHIRNIIIGDTISRILQKANYKVNVLNYVDDSGLQVADIIVGFKHFGYPIEPPQGKKFDHYCGDDVYVKTTEKYEQDSSLEEIRKNVLKELEDGTSETAQFADKITRRVLSNQLETCWNLAVSYDCLNFESQIIRSGLWDGIFEKLKEMNLVEFENDGKNAGCWVIRGEGKEEDKVIVRSNGTATYIAKDIPYAAWKLGLLDDPFHYEKYEKEQPNSRVLWQTILNDGASESQNFSGDKVITVIDSRQARLQKIITSLMGKFKSIPDAYVHLGYESVTLSSDTAKILGLETDGKQAQMSGRKGLYVNADSVYDLLKEKTTEETKKRHPEMDDSEIEKISHSVSVATLRYEMIKQDLDKIIAFDLTKSLSLEGDTAPYIQYTHARASRILEKSGRTPSIDVDFSLLKEQSEIDLVKMIGLFNLQVRDAANNLSPKVISRYCHDLAVTFNSFYEKSKVLDLGDEKLENSRLCLVNSFKITIEKALNLLGISAPDKM
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cached_locally/OG_fasta/thaNOG/1CB2T.fa	Mon Nov 04 16:38:44 2019 -0500
@@ -0,0 +1,6 @@
+>1001994.MY1_0879
+MSTEQIEKFQEVVDIPAGVKVTLKKNMMHFEGPLGKTHKNFRNIPVNIEIKEGKVILKSQGYRKRDYSILHTARSVIRNLCEGLVVGYTIKMKIAFAHFPITVKVQDRTVLIENFQGERSSRITKIIGNTKVVPKGEDVILTGEVWNHITQTAANIELRSKVKDKDHRVFLDGVYVYEKKKGIEK
+>436308.Nmar_0794
+MSTSQLEKMQDQVEIPEGVTVTQNKNMLLFEGPLGKTHKNFRNIPVKIEIADGKVNLKTIGERKRDYAILHTARSIIRNICEGLVEGYTIKMKVVFAHFPITVKVEGKKILIENFQGERAPRSTHIMGNTKVIPKGEDVLLTGEVWTDITQTAANIELTTKVKNKDHRVFLDGIYVYEKKKGIEK
+>886738.Nlim_0395
+MSTEQIEKFQEVVEIPKGVTVTLKKHMLHFQGPLGKTHKNFRNIPVNIEVKDGKVILKSQGYRKRDYSILHTARSIIRNICEGLITGYTIKMKIVFAHFPITVKVQDKTVLIENFQGERSARVTRIIGNTKVVPKGEDVILTGEVWNDITQTAANIELRSKVKDKDHRVFLDGVYSYEKKKGIDK
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cached_locally/OG_fasta/thaNOG/1CB2U.fa	Mon Nov 04 16:38:44 2019 -0500
@@ -0,0 +1,6 @@
+>1001994.MY1_1727
+MVIEVVRIGQRLVRDDRVTTHVALVARAFGCSKIFMTEVNPEIKDTLEKINNTWGGDFVVEFIDNWKSIVKMKKKDSKIVHLTMYGESINEVDMQLRKEENLLIVVGAEKVPREIYELADYNVGIGNQPHSEISALAIILDRIQKGEQFKNSFPGAKRKIIPTRNGKNVLVRGTRD
+>436308.Nmar_1606
+MVIEVVRIGQRLVRDDRVTTHVALVSRAFGAERIFMTEINPEIKDTLGKINDTWGGNFEIEFIDSWKPIVKKKKEEGFKIVHLSMYGEKINDAQEEIRKEENLLIVVGAEKVPREIYELADFNVGVGSQPHSEISALAILLDRIQGGQQFEKEFPNAKRKIIPTKTGKNVQVKETRD
+>886738.Nlim_1365
+MVLEVVRIGQRLVRDDRVTTHVALVARAFGCTKIFMTEVNPEIKDTVEKINKTWGGDFVVEFIDNWKSIVKKKKEEYKIVHLTMYGESIDDVDEQLRKEKNLLIVVGAEKVPREIYELADYNISIGNQPHSEISALAITLDRIQKGKQFKNSFSGAKRKIIPTKKGKNVFVSGTRD
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cached_locally/OG_fasta/thaNOG/1CB2V.fa	Mon Nov 04 16:38:44 2019 -0500
@@ -0,0 +1,6 @@
+>1001994.MY1_1241
+MKIRIFDTTLRDGEQTIGVSLSPDQKLAIAKKLDELGVDAIEAGFPVISAGEFKAVKMIAAAGLSCEIAGLTRTIKNDIDAAVDAGLNYIHTFIATSDIHLQYKLKMTREQALEKAIEAVEYGKSRGLQVEFSAEDATRTDREFLKKVFGDVAKAGADRVNIPDTVGYSTPEYMAVLTKDTVEVTKLPVSVHCHNDFGLAVANSLAGIHAGASCAHVTINGIGERAGNASLEEFSMALKCLPFEKKYETNIKSELIYDTSRFISKTVGIIVQPNKAIVGTNAFGHESGIHTHGVLSNPLTYEPISPELVGRKRWLQVGKHAGIHGMNAMLAEYGVKPTEEQSKQILDKVKTLGDAGKQITDVELLSIASDVLGEKELKRIVQLTGFSVSTGIGTMPYAFVKLNIDGQDHIGTDYGVGPVDAALNAIQKITGKISEIRIKDYGLASISGGSSALCEVTVKVEDAFGNKVSAKSVGEDIVTTSVKAVIDAINRIMLKKMLQEKQVR
+>436308.Nmar_1070
+MTNVRIFDTTLRDGEQTLGVSLSPDQKLAIAKKLDELGVDAIEAGFPVISEGELQAVKMITAAGLSSEICGLTRTIKKDIDAAIDAGLNYVHTFIATSDIHLEHKLQMTREQALEKAIEAVEYGKSHGLQVEFSAEDASRTDREFLKKVFSEVAKAGADRVNIPDTVGYSTPEYMAQITKDTIEATNLPVSVHCHNDFGLAVANALAGIHVGAACAHVTINGIGERAGNASLEELSMALKCLPYEQKYETNIKSELIYDVSRFISKTVGIIVQPNKAIVGANAFGHESGIHTHGVLNNPLTYEPISPELVGRKRWLKVGKHAGVHGMNAMLEEYGVKPTEDQAKQILEKVKVLGDQGKQITDVELLSMASEVLGKKDLKRIVQLTGFSVSTGIGTMPYAFVKLNVDGQDHIGTDYGVGPVDAALNAIQKITGKISEIRIKDYGLASISGGSGALCEVTVKVEDPLGNKVSAKSVGEDIVTTSVKAVIDAINRIMLKKMLQEKQVS
+>886738.Nlim_0759
+MKVRIFDTTLRDGEQTIGVSLSPDQKLAIAKKLDELGVDAIEAGFPVISSGEFKAVKMIASEGLSCEIAGLTRTIKNDVDAAVNAGLNYIHTFIATSDIHLQYKLKMTREQALEKAIEAVEYGKSRGLQVEFSAEDATRTDREFLKKVFGDVAKAGADRVNIPDTVGYSTPEYMAELTRDTVEATHLPVSVHCHNDFGLAVANSLAGIHAGASCAHVTINGIGERAGNASLEEFSMALKCLPFEQKYETNIKSELIYETSRFISKTVGIIVQPNKAIVGTNAFGHESGIHTHGVLSNPLTYEPISPELVGRKRWLQVGKHAGIHGMNAMLAEYGVKPTEEQSKQILDKVKTLGDAGKQITDVELLSIASDVLGEKELKRIVQLTGFSVSTGIGTMPYAFVKLNIDGQDHIGTDYGVGPVDAALNAIQKITGKISEIRIKDYGLASISGGSSALCEVTVKVEDALGNKVSAKSVGEDIVTTSVKAVIDAINRIMLKKMLQEKQVR
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cached_locally/OG_fasta/thaNOG/1CB2W.fa	Mon Nov 04 16:38:44 2019 -0500
@@ -0,0 +1,6 @@
+>1001994.MY1_1343
+MQNQKSEWATNESPRIMSYTLANFRQLPQIQKLGEEKQFEMEVVGNVLPFKTNNYVVEQLIDWNNIPDDPMFVLTFPQRGMLIPEHYAKMEAALKKGDKKEIQNTANEIRLQLNPHPAGQMELNVPTLKDGTKLYGMQHKYKETCLFFPSQSQTCHAYCSFCFRWPQFVGMDELKFAMKEGEQLVQYLQEHPEISDVLFTGGDPMIMKARIFSTYINPLLEANLPNLRTIRIGTKALSYWPYKFLTDDDAEEMLDIFKRVVDKGIHLALMGHFNHTVELKTDAVKEAIKKVRATGAQIRTQSPILRHINDDSEMWAEMWKTQVQLGCIPYYMFVVRDTGAQHYFGIPLIEAQRIFRDAYKKVTGLARTVRGPSMSATPGKVQILGIAEYGGEKLMVLRFLQGRNPDWVQIPFLAKYDEKAIWLDDLKPATGDKFFFEDELNEKMKVIKNQDYPES
+>436308.Nmar_1772
+MTYQESVWDDSPSLKSYTLSNFRDLPQIQNISEEKQFEMEVVGNVLPFKANNYVVEQLINWNDIPNDPMYVLTFPQRGMLKPEHYAKMENTLKNTSDKKEIANVANEIRLQLNPHPAGQMELNVPTLKDGTKLYGMQHKYKETCLFFPSQSQTCHAYCSFCFRWPQFVGMDEMKFAMQEGEQLVQYVSEHPEISDVLFTGGDPMIMKAKMFSKYVDALIEAKLPNLKTIRIGTKALSYWPYKFLTDSDSQEMLQVFQKITDSGLHLAFMAHFNHLNELSTNAVKSAIKEVRKTGAQIRTQSPLLAHINDDAEMWANMWTKQVQLGCIPYYMFVVRDTGAQHYFGVPLVKAYEIFSQAYSTVSGLGRTVRGPSMSATPGKVQVVGTTQINGEKLLILRFLQGRNPNWIKEPFFAKYDENAIWLDDLKPAFGDKFFFEDELDAIKASKTS
+>886738.Nlim_0892
+MQRQDSAWGVKESPRLKSYTLANFRELPQIQKMGAKKQFEMEVVGNVLPFKTNNYVIEQLIDWNNIPNDPMFVLTFPQRGMLIPEHYSKMESALKKGDKKEIQNTANEIRLQLNPHPAGQMELNVPTLKDGTKLYGMQHKYKETCLFFPSQSQTCHAYCSFCFRWPQFVGMDELKFAMREGEQLVQYLREHPEISDVLFTGGDPMIMKAKIFSTYINPLLEANLPNLRTIRIGTKALSYWPYKFLTEDDAEEMLDIFKRVVDKGIHLAVMGHFNHLVELKTDAVKEAIKKIRATGAQIRTQSPLLRHINDDADMWAEMWKVQVQLGCIPYYMFVVRDTGAQHYFGISLIDAQRIFRDAYKKVTGLARTVRGPSMSATPGKVQILGITEVNDEKFMVLRFLQGRNPDWVQIPFLAKYDEKAIWLDDLKPATGDKFFFENELKEMMMTIKNEDYPES
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cached_locally/OG_fasta/thaNOG/1CB2X.fa	Mon Nov 04 16:38:44 2019 -0500
@@ -0,0 +1,6 @@
+>1001994.MY1_1050
+MKFLIIDNYDSFVYNIAQYLGELGVDCDVIRNDKITLEKIKQNNYDAVIISPGPGTPTDRKYFGICSDVIKDMGSTTPILGVCLGHQGIIHAFGGKVTNAGCVRHGKTSPVDHTNSDLFKDVKNPFRATRYHSLVGDKTIIPDVLEVTAVAADDGEVMAVRHKEYLIEGVQFHPESIMTEDGKKILANFIKQVKDRK
+>436308.Nmar_0912
+MKFLIIDNYDSFVYNIAQYLGELGVDCDVIRNDKITLNEIQEKKYDAIIISPGPGTPEDKKYFGVCSEVIKDMGSSTPILGVCLGHQGIIDAFGGKVTNAGCVRHGKTSPVNHEDSKLFKDVKNPFRATRYHSLVGDKTIIPEVLKVTATASDDGEVMAIEHKDYLIQGVQFHPESIMTEDGKKILSNFIQQVKEKQK
+>886738.Nlim_0576
+MKFLIIDNYDSFVYNIAQYLGELGVDSDVIRNDKITVEQIKQNKYDAIIISPGPGTPSDRKYFGVCGDVIKDIGPITPILGVCLGHQGIIEAFGGKVTNARCVRHGKTSPVDHTNSELFKDVKNPFRATRYHSLVGDKTIIPDALEITAIAADDGEVMAVRHKKYLIEGVQFHPESIMTEDGKKILANFIKQVKSKK
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cached_locally/OG_fasta/thaNOG/1CB2Y.fa	Mon Nov 04 16:38:44 2019 -0500
@@ -0,0 +1,6 @@
+>1001994.MY1_1793
+MMGDRDYRSIIKNAVDSIGRELEIEIDAKDIKTIHLKEVVQCLRRSYYDRIEPKEVERRGFNDLLSGLLRKLQYGSDPKEFSIEDIKLRGHADMIADNSIILFRPTNASLESPLANDLLYLNACMWIYDKTDGVIIYITGDREEIMFSLTRDKKMFEEIIRRVRVLNDLLKEQKTPILEPSSDCMECQYYQRCFITKKNTKQVSLAEMLGLGKD
+>436308.Nmar_1701
+MMGDRDFRTTIQNAIKSIGNELEIDIDSKDFETIHLQEVVRCMRRSYYDRVEPLEIERRGFNELLSGLLRKLEYGSNPKDFDINEIKLRGQADMMVDDAILLFRSATEELENPHASDVLYLNACMWIYDKEDGMIVYITGDRKESTFSLTRNKKMFEDTIRRVRVLNNLLKEQKTPILEPSAECTECQYYERCFTKRKNTKQTSLAEMLGLGKQD
+>886738.Nlim_1425
+MMGDRDFRSIVKNAVDTIGRELEIQIDAKNIKTIHLKEVVQCLRRSYYDRIDPKEVERRGFNDLLSGLLRKLHYGSDPKEFSIDEIKLRGQADMIADDSIVLFRPSKTVIEAPVANDLLYLNACMWIYDKTDGIIVYITGDREEIMFSLTRDKKMFEEIIRRVRVLNDLLKEQKTPILEPSNDCAECQYYQRCFTTKKNTKQVSLAEMIGLGKD
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cached_locally/OG_fasta/thaNOG/1CB2Z.fa	Mon Nov 04 16:38:44 2019 -0500
@@ -0,0 +1,6 @@
+>1001994.MY1_1440
+MAEKGILAFSGGLDTSVVIKYLQEEYNMDVITVTVDVGQGDDQKKIEAKAKKLGVIKHYNIDARKEFVENFIFPSIKANALYQKKYCLATALARPLIAEKVLEIAKKEKVTSLAHGCSGKGNDQVRFDITLRSGSDLPIIAPIRDKNLDRVTELEFAKKHGIEIDSVAKRFSIDQNLWGRAIEGGVLEDPYNEPPEDAFIWVKTKNLPDKPTYLEIKFEKGIPVSVDGKILEPIKLIEYVNKKAGDAGVGIVDHIEDRVVGIKSREVYETPGALCLIEAHSDLEKMVHTKHENKFKSIIDDEWAYLAYSGLWQDPLKQDLDAFIQASQKPVSGTVKLKLFKGSIRVVGRKSDYSLYNHKIATYGTESTFDQRLAKGFVELWGIQSTEANKLQKKRSTKT
+>436308.Nmar_1286
+MTQKGILAFSGGLDTSVVVKYLQDEHDMDVITVTVDVGQGDDNKKIAAKAKKLGVKKHYNIDARKEFVKDYIFPSIKANALYQKKYCLATALARPLIAEKVLEIAKKEKVTSLAHGCSGKGNDQVRFDITLRSGSNLPIIAPIRDKNLDRVTELKFAKKHGIEIDTVAKKFSIDQNLWGRAIEGGVLEDPYNEPPDDAFIWVKTKNLPDKPTYLEIKFEKGIPVGVDGKTMDGQKLIEYINKKAGDAGVGIVDHIEDRVVGIKSREVYETPAATCLIEAHSDLEKMVHTKHENKFKSIIDDEWAYLAYSGLWQDPLKSDLDGFIEASQKPVTGTVKLKLYKGSLRVVGRKSKNSLYSHEIATYGTESTFDQRLAKGFVELWGMQSTEANKLQKKRSTKI
+>886738.Nlim_1021
+MTEKGILAFSGGLDTSVVVKYLQEEYDMDVITVTVDVGQGDDQRKIEAKAKKLGVKKHYNIDARKEFVEKFIFPSIKANALYQKKYCLATALARPLIAEKVLEIAKKEKVTSLAHGCSGKGNDQVRFDITLRSGSDLPIIAPIRDKNLDRVTELAFAKKHGIEIDSVAKRFSIDQNLWGRAIEGGVLEDPYSEPPDDAFIWVKTKNLPDKPTYIEIKFEKGIPVAVDGKILEPIKLIEYVNKKAGDAGVGIVDHIEDRVVGIKSREVYETPGALCLIEAHSDLEKMVHTKHENKFKSIIDDEWAYLAYSGLWQDPLKQDLDSFIETSQKPVTGTVKIKLFKGSMRVVGRKSDYSLYSHKIATYGSESTFDQKMAKGFVELWGIQSTEANKLQKKRSTKI
Binary file test-data/cached_locally/eggnog.db has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cached_locally/eggnog_mapper_db.loc	Mon Nov 04 16:38:44 2019 -0500
@@ -0,0 +1,2 @@
+#value	name	path
+4.5	eggNOG_4.5	${__HERE__}
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cached_locally/eggnog_mapper_hmm_dbs.loc	Mon Nov 04 16:38:44 2019 -0500
@@ -0,0 +1,2 @@
+#key	db_version	value	name	path
+4.5_ENOG411CB2I	4.5	ENOG411CB2I	ENOG411CB2I	${__HERE__}/hmmdb_levels/ENOG411CB2I/ENOG411CB2I
Binary file test-data/cached_locally/eggnog_proteins.dmnd has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cached_locally/hmmdb_levels/ENOG411CB2I/ENOG411CB2I	Mon Nov 04 16:38:44 2019 -0500
@@ -0,0 +1,637 @@
+HMMER3/f [3.1b1 | May 2013]
+NAME  ENOG411CB2I
+LENG  205
+ALPH  amino
+RF    no
+MM    no
+CONS  yes
+CS    no
+MAP   yes
+DATE  Thu Apr 16 06:29:18 2015
+NSEQ  3
+EFFN  0.454102
+CKSUM 2514733105
+STATS LOCAL MSV      -10.6020  0.70508
+STATS LOCAL VITERBI  -11.4006  0.70508
+STATS LOCAL FORWARD   -4.9608  0.70508
+HMM          A        C        D        E        F        G        H        I        K        L        M        N        P        Q        R        S        T        V        W        Y   
+            m->m     m->i     m->d     i->m     i->i     d->m     d->d
+  COMPO   2.60488  4.26537  2.86806  2.68812  3.48541  2.84597  3.68190  2.58658  2.57105  2.36046  3.71753  3.12796  3.51194  3.07828  3.00549  2.67857  2.91482  2.52396  5.16454  3.68907
+          2.68619  4.42226  2.77521  2.73125  3.46355  2.40514  3.72496  3.29355  2.67742  2.69356  4.24578  2.90348  2.73741  3.18148  2.89802  2.37888  2.77521  2.98520  4.58478  3.61505
+          0.17176  1.91497  4.55917  0.35031  1.21898  0.00000        *
+      1   3.06761  4.52439  4.31327  3.78099  3.05250  4.16350  4.46561  2.17607  3.57234  1.30879  1.91901  4.09154  4.45690  3.86045  3.77957  3.51234  3.30962  2.23580  5.01687  3.83610      2 l - - -
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.03256  3.83682  4.55917  0.61958  0.77255  0.48576  0.95510
+      2   2.92273  5.02492  2.47434  1.07719  4.36685  3.25185  3.83632  3.81369  2.71243  3.43683  4.41304  2.91439  3.85493  3.05312  3.11711  2.90913  3.22689  3.50145  5.54519  4.26810      3 e - - -
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.03256  3.83682  4.55917  0.61958  0.77255  0.48576  0.95510
+      3   2.78351  4.58087  3.32911  2.88754  3.40933  3.59103  3.84122  2.81006  2.61259  1.66760  3.45029  3.30455  4.01739  2.39416  2.89621  2.95209  3.03282  2.70991  4.99124  3.67436      4 l - - -
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.03256  3.83682  4.55917  0.61958  0.77255  0.48576  0.95510
+      4   2.53418  4.23705  3.59368  3.16853  3.49025  3.42404  4.06074  1.74993  3.06664  2.43412  3.49971  3.45907  3.96332  3.42386  3.35145  2.21772  2.86823  2.25074  5.06222  3.78462      5 i - - -
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.03256  3.83682  4.55917  0.61958  0.77255  0.48576  0.95510
+      5   2.78589  5.09914  2.65704  2.00312  4.42838  3.36184  3.58271  3.84850  1.89046  3.35615  4.18804  2.85104  3.82604  2.22691  2.52714  2.75121  3.01078  3.49213  5.49453  4.17260      6 k - - -
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.03256  3.83682  4.55917  0.61958  0.77255  0.48576  0.95510
+      6   2.93327  5.02405  3.29627  2.69847  4.43219  3.55593  3.56756  3.79912  1.41937  3.28272  4.16078  3.11215  3.94769  2.71245  1.76026  2.94298  3.11879  3.48852  5.35872  4.16856      7 k - - -
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.03256  3.83682  4.55917  0.61958  0.77255  0.48576  0.95510
+      7   2.42315  4.21787  3.44026  2.97006  3.62502  3.28653  3.93296  2.25259  2.89478  2.62127  3.57447  3.29089  3.83488  3.23909  3.22031  2.19519  2.23227  2.47087  5.09408  3.85175      8 s - - -
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.03256  3.83682  4.55917  0.61958  0.77255  0.48576  0.95510
+      8   3.00341  4.43279  4.28393  3.89883  3.35077  4.02713  4.63395  1.12320  3.72623  1.94475  3.29234  4.14920  4.46227  4.07854  3.92692  3.51945  3.30343  1.84653  5.23382  3.96866      9 i - - -
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.03256  3.83682  4.55917  0.61958  0.77255  0.48576  0.95510
+      9   3.11581  4.58898  4.13200  3.77226  3.12310  3.93638  4.43920  2.32589  3.54034  0.92039  3.15824  4.05113  4.37826  3.91722  3.72201  3.50392  3.41191  2.35386  4.98887  3.70377     10 l - - -
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.03256  3.83682  4.55917  0.61958  0.77255  0.48576  0.95510
+     10   2.21970  4.14708  3.27216  2.97236  4.05658  2.94753  4.04583  3.36566  2.97325  3.13664  4.01775  3.19548  3.65760  3.31810  3.28297  1.86435  1.69294  2.93575  5.43271  4.18954     11 t - - -
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.03256  3.83682  4.55917  0.61958  0.77255  0.48576  0.95510
+     11   2.67125  4.89170  2.63995  2.01286  4.19991  3.30620  3.62584  3.60098  2.37369  3.19109  4.03621  2.84971  3.79086  2.33541  2.77812  2.67728  2.37271  3.26758  5.41474  4.07676     12 e - - -
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.03256  3.83682  4.55917  0.61958  0.77255  0.48576  0.95510
+     12   3.08388  4.45892  4.50779  3.99931  3.20318  4.29602  4.67441  1.39467  3.81924  1.46323  3.07061  4.27722  4.58606  4.09884  4.01845  3.66823  3.33503  1.84767  5.18001  3.96570     13 i - - -
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.03256  3.83682  4.55917  0.61958  0.77255  0.48576  0.95510
+     13   3.19664  4.70006  3.78606  3.50925  2.29569  3.78896  3.60349  3.21093  3.36780  2.67393  3.88982  3.68029  4.26389  3.68239  3.55861  3.33670  3.48329  3.07987  3.93791  1.02720     14 y - - -
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.03256  3.83682  4.55917  0.61958  0.77255  0.48576  0.95510
+     14   2.98251  4.43779  4.31388  3.82115  3.20877  4.08952  4.54007  2.00695  3.64555  1.30599  3.09552  4.09798  4.45211  3.94746  3.86362  3.46665  3.25564  1.64211  5.13725  3.91385     15 l - - -
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.03256  3.83682  4.55917  0.61958  0.77255  0.48576  0.95510
+     15   2.15254  2.45969  3.69479  3.31339  3.86059  2.92557  4.16344  3.17236  3.21287  2.97886  3.87676  3.36254  3.65358  3.52003  3.46091  1.53946  2.62341  2.77195  5.29578  4.07476     16 s - - -
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.03256  3.83682  4.55917  0.61958  0.77255  0.48576  0.95510
+     16   2.59251  4.66552  2.70968  2.48311  4.18488  1.89749  3.77255  3.67484  2.56229  3.27203  4.14808  2.94825  3.77150  2.19715  2.92693  2.65455  2.93244  3.29447  5.43421  4.12493     17 g - - -
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.03256  3.83682  4.55917  0.61958  0.77255  0.48576  0.95510
+     17   3.00341  4.43279  4.28393  3.89883  3.35077  4.02713  4.63395  1.12320  3.72623  1.94475  3.29234  4.14920  4.46227  4.07854  3.92692  3.51945  3.30343  1.84653  5.23382  3.96866     18 i - - -
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.03256  3.83682  4.55917  0.61958  0.77255  0.48576  0.95510
+     18   2.60329  4.67395  2.70600  2.00150  4.09633  3.24110  3.74529  3.37050  2.56262  3.09514  3.99481  2.93437  3.79294  2.94110  2.95657  2.66876  1.95122  3.05941  5.40020  4.08679     19 t - - -
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.03256  3.83682  4.55917  0.61958  0.77255  0.48576  0.95510
+     19   2.62209  4.40041  3.28850  3.18371  4.32546  0.78630  4.30564  3.91689  3.36007  3.57539  4.55128  3.45295  3.79040  3.68714  3.59951  2.79308  3.10058  3.45214  5.42949  4.42634     20 g - - -
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.03256  3.83682  4.55917  0.61958  0.77255  0.48576  0.95510
+     20   2.65547  4.70380  3.01820  2.59794  4.14489  3.34071  3.68321  3.44079  1.66289  3.10417  3.99661  3.03826  3.83752  2.85967  2.55384  2.72496  2.29676  3.12897  5.34446  4.08131     21 k - - -
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.03256  3.83682  4.55917  0.61958  0.77255  0.48576  0.95510
+     21   2.41051  4.45743  2.76314  2.55610  4.16025  3.04300  3.85109  3.67733  2.73646  3.31958  4.16963  2.20738  3.70062  3.07277  3.12216  1.67816  2.81237  3.22852  5.47353  4.13338     22 s - - -
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.03256  3.83682  4.55917  0.61958  0.77255  0.48576  0.95510
+     22   2.65353  4.59175  3.08992  2.62618  3.21831  3.45751  2.78699  3.20248  2.55484  2.81536  3.72079  3.07821  2.83953  2.94374  2.92698  2.74675  2.89512  2.94118  4.70593  2.60361     23 k - - -
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.03256  3.83682  4.55917  0.61958  0.77255  0.48576  0.95510
+     23   2.72437  4.43914  3.47351  2.98245  3.55531  3.61673  3.90477  1.80448  2.22279  2.42136  3.50035  3.37449  4.03540  3.18688  2.94028  2.95940  2.97488  2.33967  5.07615  3.82063     24 i - - -
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.03256  3.83682  4.55917  0.61958  0.77255  0.48576  0.95510
+     24   2.86943  5.37025  1.48720  1.68161  4.65650  3.15841  3.70427  4.15303  2.71392  3.68857  4.55432  2.63699  3.77801  2.87679  3.29068  2.76612  3.15953  3.74941  5.84870  4.37021     25 d - - -
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.03256  3.83682  4.55917  0.61958  0.77255  0.48576  0.95510
+     25   2.75188  4.95425  2.64292  2.37822  4.30694  3.30335  3.64804  3.77364  1.89460  3.33558  4.19487  1.92755  3.82286  2.81601  2.63305  2.75003  3.01785  3.41959  5.46070  4.12901     26 k - - -
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
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+          0.03256  3.83682  4.55917  0.61958  0.77255  0.48576  0.95510
+    182   3.11581  4.58898  4.13200  3.77226  3.12310  3.93638  4.43920  2.32589  3.54034  0.92039  3.15824  4.05113  4.37826  3.91722  3.72201  3.50392  3.41191  2.35386  4.98887  3.70377    183 l - - -
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+          0.03256  3.83682  4.55917  0.61958  0.77255  0.48576  0.95510
+    183   2.85365  4.83720  2.88061  2.63544  4.00086  3.34314  3.79321  3.62673  2.45886  3.13257  4.16207  3.09462  3.89649  1.29884  2.74347  2.90320  3.15094  3.35882  5.27952  3.97110    184 q - - -
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.03256  3.83682  4.55917  0.61958  0.77255  0.48576  0.95510
+    184   2.29842  4.21804  3.17637  2.99106  4.04109  2.94862  4.10162  3.55914  3.06240  3.28234  4.21181  3.22118  3.68461  3.41464  3.34915  1.14610  2.77598  3.10206  5.41656  4.12456    185 s - - -
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+          0.03256  3.83682  4.55917  0.61958  0.77255  0.48576  0.95510
+    185   2.70596  4.46862  3.30939  3.14372  4.14097  3.15818  4.22369  3.67772  3.19807  3.30824  4.35696  3.45374  0.89665  3.58796  3.44718  2.87246  3.14485  3.32711  5.33681  4.26134    186 p - - -
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+          0.03256  3.83682  4.55917  0.61958  0.77255  0.48576  0.95510
+    186   3.00341  4.43279  4.28393  3.89883  3.35077  4.02713  4.63395  1.12320  3.72623  1.94475  3.29234  4.14920  4.46227  4.07854  3.92692  3.51945  3.30343  1.84653  5.23382  3.96866    187 i - - -
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.03256  3.83682  4.55917  0.61958  0.77255  0.48576  0.95510
+    187   2.70596  4.46862  3.30939  3.14372  4.14097  3.15818  4.22369  3.67772  3.19807  3.30824  4.35696  3.45374  0.89665  3.58796  3.44718  2.87246  3.14485  3.32711  5.33681  4.26134    188 p - - -
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+          0.03256  3.83682  4.55917  0.61958  0.77255  0.48576  0.95510
+    188   2.85405  5.34323  1.74169  1.47720  4.63099  3.16711  3.69593  4.12227  2.68527  3.65888  4.51884  2.64677  3.77697  2.86564  3.24995  2.75659  3.14022  3.72146  5.82005  4.35065    189 e - - -
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+          0.03256  3.83682  4.55917  0.61958  0.77255  0.48576  0.95510
+    189   2.29842  4.21804  3.17637  2.99106  4.04109  2.94862  4.10162  3.55914  3.06240  3.28234  4.21181  3.22118  3.68461  3.41464  3.34915  1.14610  2.77598  3.10206  5.41656  4.12456    190 s - - -
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+          0.03256  3.83682  4.55917  0.61958  0.77255  0.48576  0.95510
+    190   2.29842  4.21804  3.17637  2.99106  4.04109  2.94862  4.10162  3.55914  3.06240  3.28234  4.21181  3.22118  3.68461  3.41464  3.34915  1.14610  2.77598  3.10206  5.41656  4.12456    191 s - - -
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+          0.03256  3.83682  4.55917  0.61958  0.77255  0.48576  0.95510
+    191   2.29842  4.21804  3.17637  2.99106  4.04109  2.94862  4.10162  3.55914  3.06240  3.28234  4.21181  3.22118  3.68461  3.41464  3.34915  1.14610  2.77598  3.10206  5.41656  4.12456    192 s - - -
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.03256  3.83682  4.55917  0.61958  0.77255  0.48576  0.95510
+    192   2.29842  4.21804  3.17637  2.99106  4.04109  2.94862  4.10162  3.55914  3.06240  3.28234  4.21181  3.22118  3.68461  3.41464  3.34915  1.14610  2.77598  3.10206  5.41656  4.12456    193 s - - -
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.03256  3.83682  4.55917  0.61958  0.77255  0.48576  0.95510
+    193   2.94036  4.90159  3.11392  2.74278  4.27986  3.43307  3.74090  3.70703  1.08817  3.28019  4.24408  3.16863  3.93637  2.93480  2.42690  2.98500  3.19656  3.41702  5.34960  4.15744    194 k - - -
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+          0.03256  3.83682  4.55917  0.61958  0.77255  0.48576  0.95510
+    194   3.00341  4.43279  4.28393  3.89883  3.35077  4.02713  4.63395  1.12320  3.72623  1.94475  3.29234  4.14920  4.46227  4.07854  3.92692  3.51945  3.30343  1.84653  5.23382  3.96866    195 i - - -
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.03256  3.83682  4.55917  0.61958  0.77255  0.48576  0.95510
+    195   2.79709  5.08659  2.49459  1.88859  4.36827  3.29795  3.63911  3.82257  2.35064  3.35770  4.22674  2.81254  3.81850  1.90750  2.73001  2.76234  3.04847  3.47891  5.52674  4.17093    196 e - - -
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+          0.03256  3.83682  4.55917  0.61958  0.77255  0.48576  0.95510
+    196   2.94036  4.90159  3.11392  2.74278  4.27986  3.43307  3.74090  3.70703  1.08817  3.28019  4.24408  3.16863  3.93637  2.93480  2.42690  2.98500  3.19656  3.41702  5.34960  4.15744    197 k - - -
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.03256  3.83682  4.55917  0.61958  0.77255  0.48576  0.95510
+    197   2.92273  5.02492  2.47434  1.07719  4.36685  3.25185  3.83632  3.81369  2.71243  3.43683  4.41304  2.91439  3.85493  3.05312  3.11711  2.90913  3.22689  3.50145  5.54519  4.26810    198 e - - -
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.03256  3.83682  4.55917  0.61958  0.77255  0.48576  0.95510
+    198   3.19664  4.70006  3.78606  3.50925  2.29569  3.78896  3.60349  3.21093  3.36780  2.67393  3.88982  3.68029  4.26389  3.68239  3.55861  3.33670  3.48329  3.07987  3.93791  1.02720    199 y - - -
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.03256  3.83682  4.55917  0.61958  0.77255  0.48576  0.95510
+    199   2.62209  4.40041  3.28850  3.18371  4.32546  0.78630  4.30564  3.91689  3.36007  3.57539  4.55128  3.45295  3.79040  3.68714  3.59951  2.79308  3.10058  3.45214  5.42949  4.42634    200 g - - -
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.03256  3.83682  4.55917  0.61958  0.77255  0.48576  0.95510
+    200   2.92273  5.02492  2.47434  1.07719  4.36685  3.25185  3.83632  3.81369  2.71243  3.43683  4.41304  2.91439  3.85493  3.05312  3.11711  2.90913  3.22689  3.50145  5.54519  4.26810    201 e - - -
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.03256  3.83682  4.55917  0.61958  0.77255  0.48576  0.95510
+    201   2.29842  4.21804  3.17637  2.99106  4.04109  2.94862  4.10162  3.55914  3.06240  3.28234  4.21181  3.22118  3.68461  3.41464  3.34915  1.14610  2.77598  3.10206  5.41656  4.12456    202 s - - -
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+          0.03256  3.83682  4.55917  0.61958  0.77255  0.48576  0.95510
+    202   3.00341  4.43279  4.28393  3.89883  3.35077  4.02713  4.63395  1.12320  3.72623  1.94475  3.29234  4.14920  4.46227  4.07854  3.92692  3.51945  3.30343  1.84653  5.23382  3.96866    203 i - - -
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.03256  3.83682  4.55917  0.61958  0.77255  0.48576  0.95510
+    203   2.95756  4.78041  3.09252  2.84941  3.26099  3.41845  1.21998  3.65490  2.69349  3.15313  4.19373  3.25996  3.96930  3.21533  2.96107  3.02872  3.25993  3.39076  4.72643  3.21297    204 h - - -
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.03256  3.83682  4.55917  0.61958  0.77255  0.48576  0.95510
+    204   2.62209  4.40041  3.28850  3.18371  4.32546  0.78630  4.30564  3.91689  3.36007  3.57539  4.55128  3.45295  3.79040  3.68714  3.59951  2.79308  3.10058  3.45214  5.42949  4.42634    205 g - - -
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.03256  3.83682  4.55917  0.61958  0.77255  0.48576  0.95510
+    205   3.00341  4.43279  4.28393  3.89883  3.35077  4.02713  4.63395  1.12320  3.72623  1.94475  3.29234  4.14920  4.46227  4.07854  3.92692  3.51945  3.30343  1.84653  5.23382  3.96866    206 i - - -
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.02203  3.82629        *  0.61958  0.77255  0.00000        *
+//
Binary file test-data/cached_locally/hmmdb_levels/ENOG411CB2I/ENOG411CB2I.h3f has changed
Binary file test-data/cached_locally/hmmdb_levels/ENOG411CB2I/ENOG411CB2I.h3i has changed
Binary file test-data/cached_locally/hmmdb_levels/ENOG411CB2I/ENOG411CB2I.h3m has changed
Binary file test-data/cached_locally/hmmdb_levels/ENOG411CB2I/ENOG411CB2I.h3p has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cached_locally/hmmdb_levels/thaNOG/thaNOG	Mon Nov 04 16:38:44 2019 -0500
@@ -0,0 +1,637 @@
+HMMER3/f [3.1b1 | May 2013]
+NAME  thaNOG
+LENG  205
+ALPH  amino
+RF    no
+MM    no
+CONS  yes
+CS    no
+MAP   yes
+DATE  Thu Apr 16 06:29:18 2015
+NSEQ  3
+EFFN  0.454102
+CKSUM 2514733105
+STATS LOCAL MSV      -10.6020  0.70508
+STATS LOCAL VITERBI  -11.4006  0.70508
+STATS LOCAL FORWARD   -4.9608  0.70508
+HMM          A        C        D        E        F        G        H        I        K        L        M        N        P        Q        R        S        T        V        W        Y   
+            m->m     m->i     m->d     i->m     i->i     d->m     d->d
+  COMPO   2.60488  4.26537  2.86806  2.68812  3.48541  2.84597  3.68190  2.58658  2.57105  2.36046  3.71753  3.12796  3.51194  3.07828  3.00549  2.67857  2.91482  2.52396  5.16454  3.68907
+          2.68619  4.42226  2.77521  2.73125  3.46355  2.40514  3.72496  3.29355  2.67742  2.69356  4.24578  2.90348  2.73741  3.18148  2.89802  2.37888  2.77521  2.98520  4.58478  3.61505
+          0.17176  1.91497  4.55917  0.35031  1.21898  0.00000        *
+      1   3.06761  4.52439  4.31327  3.78099  3.05250  4.16350  4.46561  2.17607  3.57234  1.30879  1.91901  4.09154  4.45690  3.86045  3.77957  3.51234  3.30962  2.23580  5.01687  3.83610      2 l - - -
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.03256  3.83682  4.55917  0.61958  0.77255  0.48576  0.95510
+      2   2.92273  5.02492  2.47434  1.07719  4.36685  3.25185  3.83632  3.81369  2.71243  3.43683  4.41304  2.91439  3.85493  3.05312  3.11711  2.90913  3.22689  3.50145  5.54519  4.26810      3 e - - -
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.03256  3.83682  4.55917  0.61958  0.77255  0.48576  0.95510
+      3   2.78351  4.58087  3.32911  2.88754  3.40933  3.59103  3.84122  2.81006  2.61259  1.66760  3.45029  3.30455  4.01739  2.39416  2.89621  2.95209  3.03282  2.70991  4.99124  3.67436      4 l - - -
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.03256  3.83682  4.55917  0.61958  0.77255  0.48576  0.95510
+      4   2.53418  4.23705  3.59368  3.16853  3.49025  3.42404  4.06074  1.74993  3.06664  2.43412  3.49971  3.45907  3.96332  3.42386  3.35145  2.21772  2.86823  2.25074  5.06222  3.78462      5 i - - -
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+          0.03256  3.83682  4.55917  0.61958  0.77255  0.48576  0.95510
+    190   2.29842  4.21804  3.17637  2.99106  4.04109  2.94862  4.10162  3.55914  3.06240  3.28234  4.21181  3.22118  3.68461  3.41464  3.34915  1.14610  2.77598  3.10206  5.41656  4.12456    191 s - - -
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.03256  3.83682  4.55917  0.61958  0.77255  0.48576  0.95510
+    191   2.29842  4.21804  3.17637  2.99106  4.04109  2.94862  4.10162  3.55914  3.06240  3.28234  4.21181  3.22118  3.68461  3.41464  3.34915  1.14610  2.77598  3.10206  5.41656  4.12456    192 s - - -
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.03256  3.83682  4.55917  0.61958  0.77255  0.48576  0.95510
+    192   2.29842  4.21804  3.17637  2.99106  4.04109  2.94862  4.10162  3.55914  3.06240  3.28234  4.21181  3.22118  3.68461  3.41464  3.34915  1.14610  2.77598  3.10206  5.41656  4.12456    193 s - - -
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.03256  3.83682  4.55917  0.61958  0.77255  0.48576  0.95510
+    193   2.94036  4.90159  3.11392  2.74278  4.27986  3.43307  3.74090  3.70703  1.08817  3.28019  4.24408  3.16863  3.93637  2.93480  2.42690  2.98500  3.19656  3.41702  5.34960  4.15744    194 k - - -
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.03256  3.83682  4.55917  0.61958  0.77255  0.48576  0.95510
+    194   3.00341  4.43279  4.28393  3.89883  3.35077  4.02713  4.63395  1.12320  3.72623  1.94475  3.29234  4.14920  4.46227  4.07854  3.92692  3.51945  3.30343  1.84653  5.23382  3.96866    195 i - - -
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.03256  3.83682  4.55917  0.61958  0.77255  0.48576  0.95510
+    195   2.79709  5.08659  2.49459  1.88859  4.36827  3.29795  3.63911  3.82257  2.35064  3.35770  4.22674  2.81254  3.81850  1.90750  2.73001  2.76234  3.04847  3.47891  5.52674  4.17093    196 e - - -
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.03256  3.83682  4.55917  0.61958  0.77255  0.48576  0.95510
+    196   2.94036  4.90159  3.11392  2.74278  4.27986  3.43307  3.74090  3.70703  1.08817  3.28019  4.24408  3.16863  3.93637  2.93480  2.42690  2.98500  3.19656  3.41702  5.34960  4.15744    197 k - - -
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.03256  3.83682  4.55917  0.61958  0.77255  0.48576  0.95510
+    197   2.92273  5.02492  2.47434  1.07719  4.36685  3.25185  3.83632  3.81369  2.71243  3.43683  4.41304  2.91439  3.85493  3.05312  3.11711  2.90913  3.22689  3.50145  5.54519  4.26810    198 e - - -
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.03256  3.83682  4.55917  0.61958  0.77255  0.48576  0.95510
+    198   3.19664  4.70006  3.78606  3.50925  2.29569  3.78896  3.60349  3.21093  3.36780  2.67393  3.88982  3.68029  4.26389  3.68239  3.55861  3.33670  3.48329  3.07987  3.93791  1.02720    199 y - - -
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.03256  3.83682  4.55917  0.61958  0.77255  0.48576  0.95510
+    199   2.62209  4.40041  3.28850  3.18371  4.32546  0.78630  4.30564  3.91689  3.36007  3.57539  4.55128  3.45295  3.79040  3.68714  3.59951  2.79308  3.10058  3.45214  5.42949  4.42634    200 g - - -
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.03256  3.83682  4.55917  0.61958  0.77255  0.48576  0.95510
+    200   2.92273  5.02492  2.47434  1.07719  4.36685  3.25185  3.83632  3.81369  2.71243  3.43683  4.41304  2.91439  3.85493  3.05312  3.11711  2.90913  3.22689  3.50145  5.54519  4.26810    201 e - - -
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.03256  3.83682  4.55917  0.61958  0.77255  0.48576  0.95510
+    201   2.29842  4.21804  3.17637  2.99106  4.04109  2.94862  4.10162  3.55914  3.06240  3.28234  4.21181  3.22118  3.68461  3.41464  3.34915  1.14610  2.77598  3.10206  5.41656  4.12456    202 s - - -
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.03256  3.83682  4.55917  0.61958  0.77255  0.48576  0.95510
+    202   3.00341  4.43279  4.28393  3.89883  3.35077  4.02713  4.63395  1.12320  3.72623  1.94475  3.29234  4.14920  4.46227  4.07854  3.92692  3.51945  3.30343  1.84653  5.23382  3.96866    203 i - - -
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.03256  3.83682  4.55917  0.61958  0.77255  0.48576  0.95510
+    203   2.95756  4.78041  3.09252  2.84941  3.26099  3.41845  1.21998  3.65490  2.69349  3.15313  4.19373  3.25996  3.96930  3.21533  2.96107  3.02872  3.25993  3.39076  4.72643  3.21297    204 h - - -
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.03256  3.83682  4.55917  0.61958  0.77255  0.48576  0.95510
+    204   2.62209  4.40041  3.28850  3.18371  4.32546  0.78630  4.30564  3.91689  3.36007  3.57539  4.55128  3.45295  3.79040  3.68714  3.59951  2.79308  3.10058  3.45214  5.42949  4.42634    205 g - - -
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.03256  3.83682  4.55917  0.61958  0.77255  0.48576  0.95510
+    205   3.00341  4.43279  4.28393  3.89883  3.35077  4.02713  4.63395  1.12320  3.72623  1.94475  3.29234  4.14920  4.46227  4.07854  3.92692  3.51945  3.30343  1.84653  5.23382  3.96866    206 i - - -
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.02203  3.82629        *  0.61958  0.77255  0.00000        *
+//
Binary file test-data/cached_locally/hmmdb_levels/thaNOG/thaNOG.h3f has changed
Binary file test-data/cached_locally/hmmdb_levels/thaNOG/thaNOG.h3i has changed
Binary file test-data/cached_locally/hmmdb_levels/thaNOG/thaNOG.h3m has changed
Binary file test-data/cached_locally/hmmdb_levels/thaNOG/thaNOG.h3p has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/make_comp_file.sh	Mon Nov 04 16:38:44 2019 -0500
@@ -0,0 +1,24 @@
+#!/bin/bash
+
+base_path=$1
+
+emapper.py \
+    -i $base_path/test-data/nlim_fragment.fasta \
+    --output HMM_nlim \
+    --output_dir $base_path/test-data \
+    --override \
+    --database $base_path/test-data/cached_locally/hmmdb_levels/ENOG411CB2I/ENOG411CB2I \
+    --data_dir $base_path/test-data/cached_locally \
+    --no_refine\
+    --no_annot \
+    --no_file_comments
+
+emapper.py \
+    -i $base_path/test-data/nlim_fragment.fasta \
+    --output DIA_nlim \
+    --output_dir $base_path/test-data \
+    --override \
+    -m diamond \
+    --data_dir $base_path/test-data/cached_locally \
+    --no_file_comments \
+    --no_annot
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/nlim_1033.fasta	Mon Nov 04 16:38:44 2019 -0500
@@ -0,0 +1,7 @@
+>Nlim_1033886738.Nlim_1033Cytidyltransferase-like protein 
+MELIKKSILTELYLSGITGKSHIDNLTKKGFTQKLIDLE
+IDELIKNKLVKEDRAILTELGRSSLRVVLAGGVFDIIHP
+GHIYTLNAAKSLGDVLIVVVATDNTALKMKKRQPLHSKE
+QRQELVNSLIMVDLCLIGQEDDIFKTVNLVKPQIIALGY
+DQVHQEKFIIDGCKKIQLDAKVARLQSPIPESSSSKIQK
+EYGESIHGI
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/nlim_fragment.fasta	Mon Nov 04 16:38:44 2019 -0500
@@ -0,0 +1,2 @@
+>Nlim_1033886738.Nlim_1033Cytidyltransferase-like protein 
+MELIKKSILTELYLSGITGKSHIDNLTKKGFTQKLIDLE
--- a/tool-data/eggnog_mapper.loc.sample	Tue Aug 08 12:40:56 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,18 +0,0 @@
-#This is a sample file distributed with Galaxy that enables tools
-#to use a directory of eggnog_mapper data files. 
-#
-# eggnog-mapper requires the following files to be installed in the data directory:
-#  https://github.com/jhcepas/eggnog-mapper/blob/master/data/og2level.tsv.gz
-#  http://eggnogdb.embl.de/download/eggnog_4.5/eggnog-mapper-data/eggnog.db.gz
-#  http://eggnogdb.embl.de/download/eggnog_4.5/eggnog-mapper-data/OG_fasta.tar.gz
-# In addition individual HMM DBs can be installed from:
-#  http://eggnogdb.embl.de/download/eggnog_4.5/eggnog-mapper-data/hmmdb_levels/
-# A complete diamond database is available from:
-#  http://eggnogdb.embl.de/download/eggnog_4.5/eggnog-mapper-data/eggnog_proteins.dmnd.gz
-#
-# 
-#name	value	type	data_dir	
-#eggnog_4.5	eggnog_4.5 data	/depot/data2/galaxy/eggnog/eggnog_4.5/data
-#eggnog_4.5arcNOG	arcNOG	hmmer	eggnog_4.5
-#eggnog_4.5euk	euk	hmmer	eggnog_4.5
-#eggnog_4.5dmnd	eggnog_proteins.dmnd	diamond	eggnog_4.5
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/eggnog_mapper_db.loc.sample	Mon Nov 04 16:38:44 2019 -0500
@@ -0,0 +1,25 @@
+#This is a sample file distributed with Galaxy that enables tools
+#to use a directory of eggnog_mapper data files. 
+#
+# eggnog-mapper requires the following files to be installed in the data directory:
+#  https://github.com/jhcepas/eggnog-mapper/blob/master/data/og2level.tsv.gz
+#  http://eggnogdb.embl.de/download/eggnog_4.5/eggnog-mapper-data/eggnog.db.gz
+#  http://eggnogdb.embl.de/download/eggnog_4.5/eggnog-mapper-data/OG_fasta.tar.gz
+# In addition individual HMM DBs can be installed from:
+#  http://eggnogdb.embl.de/download/eggnog_4.5/eggnog-mapper-data/hmmdb_levels/
+# A complete diamond database is available from:
+#  http://eggnogdb.embl.de/download/eggnog_4.5/eggnog-mapper-data/eggnog_proteins.dmnd.gz
+#
+# The python script download_eggnog_data.py, 
+# included with eggnog_mapper, can be used to download the files to the correct directory
+#
+# The near-equivalence of columns "value" and "db" is needed for the tests to work,
+# and for the setting of --data_dir to the parent directory of eggnog.db
+# The complicated eggNOG database structure makes passing custom HMM databases somewhat tricky. 
+# See test-data/cached_locally/eggnog_mapper.loc for how this was done with the included test databases
+# In all other cases, when the appropriate HMM database (for example, "thaNOG") was downloaded from eggnogdb.embl.de, 
+# value and db should be the same (in the example, both should be "thaNOG")
+#
+#
+#db_version	name	path	
+#4.5.1	eggnog_4.5.1	/path/to/directory/that/contains/eggnog.db
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/eggnog_mapper_hmm_dbs.loc.sample	Mon Nov 04 16:38:44 2019 -0500
@@ -0,0 +1,28 @@
+#This is a sample file distributed with Galaxy that enables tools
+#to use a directory of eggnog_mapper data files. 
+#
+# eggnog-mapper requires the following files to be installed in the data directory:
+#  https://github.com/jhcepas/eggnog-mapper/blob/master/data/og2level.tsv.gz
+#  http://eggnogdb.embl.de/download/eggnog_4.5/eggnog-mapper-data/eggnog.db.gz
+#  http://eggnogdb.embl.de/download/eggnog_4.5/eggnog-mapper-data/OG_fasta.tar.gz
+# In addition individual HMM DBs can be installed from:
+#  http://eggnogdb.embl.de/download/eggnog_4.5/eggnog-mapper-data/hmmdb_levels/
+# A complete diamond database is available from:
+#  http://eggnogdb.embl.de/download/eggnog_4.5/eggnog-mapper-data/eggnog_proteins.dmnd.gz
+#
+# The python script download_eggnog_data.py, 
+# included with eggnog_mapper, can be used to download the files to the correct directory
+#
+# The near-equivalence of columns "value" and "db" is needed for the tests to work,
+# and for the setting of --data_dir to the parent directory of eggnog.db
+# The complicated eggNOG database structure makes passing custom HMM databases somewhat tricky. 
+# See test-data/cached_locally/eggnog_mapper.loc for how this was done with the included test databases
+# In all other cases, when the appropriate HMM database (for example, "thaNOG") was downloaded from eggnogdb.embl.de, 
+# value and db should be the same (in the example, both should be "thaNOG")
+#
+#
+#key	db_version	value	name	path
+#4.5.1_NOG	4.5.1	NOG	Full eggNOG database (NOG)	
+#4.5.1_euk	4.5.1	euk	Eukaryotes (euk)	
+#4.5.1_aproNOG	4.5.1	aproNOG	Proteobacteria_alpha (aproNOG)	
+#4.5.1_aproNOG	4.5.1	ENOG411CB2I	ENOG411CB2I (custom)	/path/to/custom/hmmdb/ENOG411CB2I
--- a/tool_data_table_conf.xml.sample	Tue Aug 08 12:40:56 2017 -0400
+++ b/tool_data_table_conf.xml.sample	Mon Nov 04 16:38:44 2019 -0500
@@ -1,7 +1,11 @@
 <tables>
     <!-- Locations of all eggnog_mapper data -->
-    <table name="eggnog_mapper" comment_char="#">
-        <columns>name,value,type,data_dir</columns>
-        <file path="tool-data/eggnog_mapper.loc" />
+    <table name="eggnog_mapper_db" comment_char="#">
+        <columns>value,name,path</columns>
+        <file path="tool-data/eggnog_mapper_db.loc" />
+    </table>
+    <table name="eggnog_mapper_hmm_dbs" comment_char="#">
+        <columns>key,db_version,value,name,path</columns>
+        <file path="tool-data/eggnog_mapper_hmm_dbs.loc" />
     </table>
 </tables>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.test	Mon Nov 04 16:38:44 2019 -0500
@@ -0,0 +1,11 @@
+<tables>
+    <!-- Locations of all eggnog_mapper data -->
+    <table name="eggnog_mapper_db" comment_char="#">
+        <columns>value,name,path</columns>
+        <file path="${__HERE__}/test-data/cached_locally/eggnog_mapper_db.loc" />
+    </table>
+    <table name="eggnog_mapper_hmm_dbs" comment_char="#">
+        <columns>key,db_version,value,name,path</columns>
+        <file path="${__HERE__}/test-data/cached_locally/eggnog_mapper_hmm_dbs.loc" />
+    </table>
+</tables>