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Changeset 6:3cb37af59360 (2020-09-05)

Previous changeset 5:a5a3bdd0954b (2019-11-11) Next changeset 7:4e4c6329f6cd (2021-02-19)

Commit message:
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"

modified:
eggnog_macros.xml
eggnog_mapper.xml
test-data/DIA_nlim.emapper.seed_orthologs
test-data/cached_locally/eggnog.db
test-data/cached_locally/eggnog_mapper_db.loc
test-data/cached_locally/eggnog_proteins.dmnd
test-data/make_comp_file.sh
tool-data/eggnog_mapper_db.loc.sample
tool_data_table_conf.xml.sample
tool_data_table_conf.xml.test

added:
test-data/DIA_nlim.emapper.annotations
test-data/DIA_nlim.emapper.annotations_orthologs
test-data/Nmar_0135.fa
test-data/README
test-data/cached_locally/eggnog_proteins.fa
test-data/scoped.emapper.annotations
test-data/scoped.emapper.annotations_orthologs
test-data/scoped.emapper.seed_orthologs

diff -r a5a3bdd0954b -r 3cb37af59360 eggnog_macros.xml
--- a/eggnog_macros.xml Mon Nov 11 11:50:36 2019 -0500
+++ b/eggnog_macros.xml Sat Sep 05 07:21:28 2020 +0000

b'@@ -1,9 +1,11 @@\n <?xml version="1.0"?>\n <macros>\n- <token name="@VERSION@">1.0.3</token>\n+ <token name="@VERSION@">2.0.1</token>\n+ <token name="@EGGNOG_DB_VERSION@">5.0</token>\n <xml name="citations">\n <citations>\n <citation type="doi">10.1093/nar/gkv1248</citation>\n+ <citation type="doi">10.1093/molbev/msx148</citation>\n </citations>\n </xml>\n <xml name="requirements">\n@@ -16,119 +18,7 @@\n </xml>\n <xml name="data_manager_params">\n <param name="test" type="hidden" value="false" />\n- <param name="diamond_database" type="boolean" truevalue="" falsevalue="-D" checked="true" label="Install the diamond database"/>\n- <param argument="dbs" type="select" multiple="true" label="eggNOG HMM databases to download. If none are selected only diamond can be used\'">\n- <option value="arch" selected="true">Archea arch_1 (arch)</option>\n- <option value="bact" selected="true">Bacteria bact_50 (bact)</option>\n- <option value="euk" selected="true">Eukaryote euk_500 (euk)</option>\n- <option value="NOG" selected="true">All organisms (NOG)</option>\n- <option value="aciNOG">Acidobacteria (aciNOG)</option>\n- <option value="acidNOG">Acidobacteriia (acidNOG)</option>\n- <option value="acoNOG">Aconoidasida (acoNOG)</option>\n- <option value="actNOG">Actinobacteria (actNOG)</option>\n- <option value="agaNOG">Agaricales (agaNOG)</option>\n- <option value="agarNOG">Agaricomycetes (agarNOG)</option>\n- <option value="apiNOG">Apicomplexa (apiNOG)</option>\n- <option value="aproNOG">Proteobacteria_alpha (aproNOG)</option>\n- <option value="aquNOG">Aquificae (aquNOG)</option>\n- <option value="arNOG">Archaea (arNOG)</option>\n- <option value="arcNOG">Archaeoglobi (arcNOG)</option>\n- <option value="artNOG">Arthropoda (artNOG)</option>\n- <option value="arthNOG">Arthrodermataceae (arthNOG)</option>\n- <option value="ascNOG">Ascomycota (ascNOG)</option>\n- <option value="aveNOG">Aves (aveNOG)</option>\n- <option value="bacNOG">Bacilli (bacNOG)</option>\n- <option value="bactNOG">Bacteria (bactNOG)</option>\n- <option value="bacteNOG">Bacteroidia (bacteNOG)</option>\n- <option value="basNOG">Basidiomycota (basNOG)</option>\n- <option value="bctoNOG">Bacteroidetes (bctoNOG)</option>\n- <option value="biNOG">Bilateria (biNOG)</option>\n- <option value="bproNOG">Proteobacteria_beta (bproNOG)</option>\n- <option value="braNOG">Brassicales (braNOG)</option>\n- <option value="carNOG">Carnivora (carNOG)</option>\n- <option value="chaNOG">Chaetomiaceae (chaNOG)</option>\n- <option value="chlNOG">Chlorobi (chlNOG)</option>\n- <option value="chlaNOG">Chlamydiae (chlaNOG)</option>\n- <option value="chloNOG">Chloroflexi (chloNOG)</option>\n- <option value="chlorNOG">Chloroflexi (chlorNOG)</option>\n- <option value="chloroNOG">Chlorophyta (chloroNOG)</option>\n- <option value="chorNOG">Chordata (chorNOG)</option>\n- <option value="chrNOG">Chromadorea (chrNOG)</option>\n- <option value="cloNOG">Clostridia (cloNOG)</option>\n- <option value="cocNOG">Coccidia (cocNOG)</option>\n- <option value="creNOG">Crenarchaeota (creNOG)</option>\n- <option value="cryNOG">Cryptosporidiidae (cryNOG)</option>\n- <option value="cyaNOG">Cyanobacteria (cyaNOG)</option>\n- <option value="cytNOG">Cytophagia (cytNOG)</option>\n- <option value="debNOG">Debaryomycetaceae (debNOG)</option>\n- <option value="defNOG">Deferribacteres (defNOG)</option>\n- <option value="dehNOG">Dehalococcoidetes (dehNOG)</option>\n- <option value="deiNOG">Deinococcusthermus (deiNOG)'..b'option value="metNOG">Methanobacteria (metNOG)</option>\n- <option value="methNOG">Methanococci (methNOG)</option>\n- <option value="methaNOG">Methanomicrobia (methaNOG)</option>\n- <option value="necNOG">Nectriaceae (necNOG)</option>\n- <option value="negNOG">Negativicutes (negNOG)</option>\n- <option value="nemNOG">Nematodes (nemNOG)</option>\n- <option value="onyNOG">Onygenales (onyNOG)</option>\n- <option value="opiNOG">Opisthokonts (opiNOG)</option>\n- <option value="perNOG">Peronosporales (perNOG)</option>\n- <option value="plaNOG">Planctomycetes (plaNOG)</option>\n- <option value="pleNOG">Pleosporales (pleNOG)</option>\n- <option value="poaNOG">Poales (poaNOG)</option>\n- <option value="prNOG">Primates (prNOG)</option>\n- <option value="proNOG">Proteobacteria (proNOG)</option>\n- <option value="rhaNOG">Rhabditida (rhaNOG)</option>\n- <option value="roNOG">Rodents (roNOG)</option>\n- <option value="sacNOG">Saccharomycetaceae (sacNOG)</option>\n- <option value="saccNOG">Saccharomycetes (saccNOG)</option>\n- <option value="sorNOG">Sordariales (sorNOG)</option>\n- <option value="sordNOG">Sordariomycetes (sordNOG)</option>\n- <option value="sphNOG">Sphingobacteriia (sphNOG)</option>\n- <option value="spiNOG">Spirochaetes (spiNOG)</option>\n- <option value="spriNOG">Supraprimates (spriNOG)</option>\n- <option value="strNOG">Streptophyta (strNOG)</option>\n- <option value="synNOG">Synergistetes (synNOG)</option>\n- <option value="tenNOG">Tenericutes (tenNOG)</option>\n- <option value="thaNOG">Thaumarchaeota (thaNOG)</option>\n- <option value="theNOG">Thermoplasmata (theNOG)</option>\n- <option value="therNOG">Thermotogae (therNOG)</option>\n- <option value="thermNOG">Thermococci (thermNOG)</option>\n- <option value="treNOG">Tremellales (treNOG)</option>\n- <option value="veNOG">Vertebrates (veNOG)</option>\n- <option value="verNOG">Verrucomicrobia (verNOG)</option>\n- <option value="verrNOG">Verrucomicrobiae (verrNOG)</option>\n- <option value="virNOG">Viridiplantae (virNOG)</option>\n- </param>\n+ <param name="diamond_database" type="boolean" truevalue="" falsevalue="-D" checked="true" label="Install the diamond database" help="Takes ~9Gb, you most probably want it."/>\n </xml>\n <xml name="data_manager_outputs">\n <outputs>\n@@ -141,33 +31,26 @@\n #import os.path\n #set $install_path = $os.path.join($os.path.dirname($__tool_directory__), \'test-data/cached_locally\')\n #end if\n-#if $dbs:\n-#set $eggnogdbs = \' \'.join(str($dbs).split(\',\'))\n-#else\n-#set $eggnogdbs = \'none\'\n-#end if\n mkdir -p \'${install_path}\' &&\n-download_eggnog_data.py \n- $diamond_database -y -q \n+download_eggnog_data.py\n+ $diamond_database -y -q\n #if $test == \'true\'\n -s\n #end if\n- --data_dir \'$install_path\' \n- $eggnogdbs &&\n-python \'${__tool_directory__}/data_manager_eggnog.py\' --config_file \'$out_file\' --install_path \'$install_path\' --dbs \'$dbs\'\n+ --data_dir \'$install_path\' &&\n+python \'${__tool_directory__}/data_manager_eggnog.py\' --config_file \'$out_file\' --install_path \'$install_path\'\n ]]></token>\n <xml name="data_manager_test">\n- \n </xml>\n </macros>\n'

diff -r a5a3bdd0954b -r 3cb37af59360 eggnog_mapper.xml
--- a/eggnog_mapper.xml Mon Nov 11 11:50:36 2019 -0500
+++ b/eggnog_mapper.xml Sat Sep 05 07:21:28 2020 +0000

[

b'@@ -1,4 +1,4 @@\n-<tool id="eggnog_mapper" name="eggNOG Mapper" version="@VERSION@.1">\n+<tool id="eggnog_mapper" name="eggNOG Mapper" version="@VERSION@">\n <description>functional sequence annotation by orthology</description>\n <macros>\n <import>eggnog_macros.xml</import>\n@@ -8,28 +8,15 @@\n <command detect_errors="aggressive"><![CDATA[\n emapper.py\n --data_dir \'$eggnog_data.fields.path\'\n- -m $db.mode \n+ -m diamond\n $translate\n- #if ($db.mode == \'hmmer\'):\n- #if $db.database.fields.path:\n- --database=$db.database.fields.path\n- #else\n- --database=$db.database\n- #end if\n- #if $db.hmm_options.hmm_settings == \'specified\':\n- --hmm_maxhits=$db.hmm_options.hmm_maxhits\n- --hmm_evalue=$db.hmm_options.hmm_evalue\n- --hmm_score=$db.hmm_options.hmm_score\n- --hmm_maxseqlen=$db.hmm_options.hmm_maxseqlen\n- #if str($db.hmm_options.hmm_qcov):\n- --hmm_qcov=$db.hmm_options.hmm_qcov\n- #end if\n- --Z=$db.hmm_options.Z\n- #end if\n- #elif ($db.mode == \'diamond\'):\n- --matrix \'$db.matrix_gapcosts.matrix\'\n- $db.matrix_gapcosts.gap_costs\n- #end if\n+\n+ ## Diamond option\n+ --matrix \'$diamond.matrix_gapcosts.matrix\'\n+ $diamond.matrix_gapcosts.gap_costs\n+ --query-cover $diamond.query_cover\n+ --subject-cover $diamond.subject_cover\n+\n #if $annotation_options.tax_scope:\n --tax_scope=$annotation_options.tax_scope\n #end if\n@@ -40,10 +27,10 @@\n --go_evidence=$annotation_options.go_evidence\n #end if\n #if $seed_ortholog_options.seed_ortholog_evalue:\n- --seed_ortholog_evalue=$seed_ortholog_options.seed_ortholog_evalue \n+ --seed_ortholog_evalue=$seed_ortholog_options.seed_ortholog_evalue\n #end if\n #if str($seed_ortholog_options.seed_ortholog_score):\n- --seed_ortholog_score=$seed_ortholog_options.seed_ortholog_score \n+ --seed_ortholog_score=$seed_ortholog_options.seed_ortholog_score\n #end if\n $output_options.no_file_comments\n $output_options.no_annot\n@@ -52,286 +39,149 @@\n -i \'${input}\'\n --cpu "\\${GALAXY_SLOTS:-4}"\n ]]></command>\n- <inputs>\n- <param name="input" type="data" format="fasta" label="Fasta sequences to annotate"/>\n- <param name="eggnog_data" type="select" label="Version of eggNOG Database">\n- <options from_data_table="eggnog_mapper_db"/>\n- </param>\n- <param name="translate" type="boolean" truevalue="--translate" falsevalue="" checked="false"\n- label="Are these coding DNA sequences that need to be translated?"/>\n- <conditional name="db">\n- <param name="mode" type="select" label="Annotation Type">\n- <option value="hmmer">HMM</option>\n- <option value="diamond">DIAMOND</option>\n+ <inputs>\n+ <param name="input" type="data" format="fasta" label="Fasta sequences to annotate"/>\n+ <param name="eggnog_data" type="select" label="Version of eggNOG Database">\n+ <options from_data_table="eggnog_mapper_db"/>\n+ </param>\n+ <param name="translate" type="boolean" truevalue="--translate" falsevalue="" checked="false"\n+ label="Are these coding DNA sequences that need to be translated?"/>\n+\n+ <section name="diamond" expanded="true" title="Diamond Options">\n+ <conditional name="matrix_gapcosts">\n+ <param argument="--matrix" type="select" label="Scoring matrix and gap costs">\n+ <option value="BLOSUM90">BLOSUM90</option>\n+ <option value="BLOSUM80">BLOSUM80</option>\n+ <option value="BLOSUM62" selected="true">B'..b' --------\n \n-``eggnog-mapper`` is a tool for fast functional annotation of novel sequences (genes or proteins) using precomputed eggNOG-based orthology assignments. \n-Obvious examples include the annotation of novel genomes, transcriptomes or even metagenomic gene catalogs. \n-The use of orthology predictions for functional annotation is considered more precise than traditional homology searches, \n+``eggnog-mapper`` is a tool for fast functional annotation of novel sequences (genes or proteins) using precomputed eggNOG-based orthology assignments.\n+Obvious examples include the annotation of novel genomes, transcriptomes or even metagenomic gene catalogs.\n+The use of orthology predictions for functional annotation is considered more precise than traditional homology searches,\n as it avoids transferring annotations from paralogs (duplicate genes with a higher chance of being involved in functional divergence).\n \n EggNOG-mapper is also available as a public online resource: `<http://beta-eggnogdb.embl.de/#/app/emapper>`_.\n \n-Options\n--------\n-\n-``eggnog-mapper`` can use two search algorithms: `HMMER <http://hmmer.org/>`_ and `DIAMOND <https://github.com/bbuchfink/diamond>`_. \n-HMMER is more sensitive, while DIAMOND is faster and useful for larger sets of query sequences. \n-\n-\n Outputs\n -------\n \n-**hmm_hits**\n-\n-For each query sequence, a list of significant \n-hits to eggNOG Orthologous Groups (OGs) is reported. \n-Each line in the file represents a hit, where evalue, bit-score, \n-query-coverage and the sequence coordinates of the match are reported. \n-If multiple hits exist for a given query, results are sorted by e-value.\n-Only returned when using HMMER mode. \n-\n **seed_orthologs**\n \n-each line in the file provides the best match of each query within the best Orthologous Group (OG) \n-reported in the [project].hmm_hits file, obtained running PHMMER against all sequences within the best OG. \n-The seed ortholog is used to fetch fine-grained orthology relationships from eggNOG. \n-If using the diamond search mode, seed orthologs are directly \n+each line in the file provides the best match of each query within the best Orthologous Group (OG)\n+reported in the [project].hmm_hits file, obtained running PHMMER against all sequences within the best OG.\n+The seed ortholog is used to fetch fine-grained orthology relationships from eggNOG.\n+If using the diamond search mode, seed orthologs are directly\n obtained from the best matching sequences by running DIAMOND against the whole eggNOG protein space.\n \n **annotations**\n@@ -463,14 +300,24 @@\n - ``seed_eggNOG_ortholog``: best protein match in eggNOG\n - ``seed_ortholog_evalue``: best protein match (e-value)\n - ``seed_ortholog_score``: best protein match (bit-score)\n-- ``predicted_gene_name``: Predicted gene name for query sequences\n+- ``predicted_taxonomic_group``\n+- ``predicted_protein_name``: Predicted protein name for query sequences\n - ``GO_terms``: Comma delimited list of predicted Gene Ontology terms\n-- ``KEGG_pathways``: Comma delimited list of predicted KEGG pathways\n+- ``EC_number``\n+- ``KEGG_KO``\n+- ``KEGG_Pathway``: Comma delimited list of predicted KEGG pathways\n+- ``KEGG_Module``\n+- ``KEGG_Reaction``\n+- ``KEGG_rclass``\n+- ``BRITE``\n+- ``KEGG_TC``\n+- ``CAZy``\n+- ``BiGG_Reactions``\n - ``Annotation_tax_scope``: The taxonomic scope used to annotate this query sequence\n - ``Matching_OGs``: Comma delimited list of matching eggNOG Orthologous Groups\n-- ``best_OG|evalue|score``: Best matching Orthologous Groups (only in HMM mode)\n-- ``COG functional categories``: COG functional category inferred from best matching OG\n-- ``eggNOG_HMM_model_annotation``: eggNOG functional description inferred from best matching OG\n+- ``best_OG|evalue|score``: Best matching Orthologous Groups (deprecated, use smallest from eggnog OGs)\n+- ``COG_functional_categories``: COG functional category inferred from best matching OG\n+- ``eggNOG_free_text_description``\n \n ]]></help>\n <expand macro="citations"/>\n'

diff -r a5a3bdd0954b -r 3cb37af59360 test-data/DIA_nlim.emapper.annotations
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/DIA_nlim.emapper.annotations Sat Sep 05 07:21:28 2020 +0000

@@ -0,0 +1,1 @@
+Nmar_0135 436308.Nmar_0135 3.8e-149 510.8 Thaumarchaeota Archaea 41T2K@651137,COG1083@1,arCOG04817@2157 NA|NA|NA M Cytidylyltransferase

diff -r a5a3bdd0954b -r 3cb37af59360 test-data/DIA_nlim.emapper.annotations_orthologs
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/DIA_nlim.emapper.annotations_orthologs Sat Sep 05 07:21:28 2020 +0000

@@ -0,0 +1,1 @@
+Nmar_0135

diff -r a5a3bdd0954b -r 3cb37af59360 test-data/DIA_nlim.emapper.seed_orthologs
--- a/test-data/DIA_nlim.emapper.seed_orthologs Mon Nov 11 11:50:36 2019 -0500
+++ b/test-data/DIA_nlim.emapper.seed_orthologs Sat Sep 05 07:21:28 2020 +0000

@@ -1,1 +1,1 @@
-Nlim_1033886738.Nlim_1033Cytidyltransferase-like 886738.Nlim_1033 5.4e-20 78.6
+Nmar_0135 436308.Nmar_0135 3.8e-149 510.8

diff -r a5a3bdd0954b -r 3cb37af59360 test-data/HMM_nlim.emapper.hmm_hits
--- a/test-data/HMM_nlim.emapper.hmm_hits Mon Nov 11 11:50:36 2019 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,1 +0,0 @@
-Nlim_1033886738.Nlim_1033Cytidyltransferase-like ENOG411CB2I 2.3e-16 46.1 39 1 39 1 38 0.948717948718

diff -r a5a3bdd0954b -r 3cb37af59360 test-data/Nmar_0135.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/Nmar_0135.fa Sat Sep 05 07:21:28 2020 +0000

@@ -0,0 +1,6 @@
+>Nmar_0135
+MKFCNVGIIIQARTGSDRFPKKVLASIEKKPMIWHIVNRCKKVKNIDKIILATTTLKEDY
+PLISLAKKNKIEYFRGSKNDVLDRFYQCSTSNNLDIIIRITGDCPLVDPKLIDQFLDFFS
+HKKYDYVSNTINPTYPDGLDIEIFSFKALKKAWNMSKKKSNREHVTTFIKHHPEKFKIKN
+FENNTNLSNYRLTVDHKNDLKLIRKIYKEFRPNIKFSTKSVISLLNKNPELFKINQNISR
+NEGYEKSLLNDN

diff -r a5a3bdd0954b -r 3cb37af59360 test-data/README
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/README Sat Sep 05 07:21:28 2020 +0000

@@ -0,0 +1,1 @@
+cached_locally content is a reduced database, following instructions on https://github.com/galaxyproteomics/egglet

diff -r a5a3bdd0954b -r 3cb37af59360 test-data/cached_locally/OG_fasta/thaNOG/1CB2A.fa
--- a/test-data/cached_locally/OG_fasta/thaNOG/1CB2A.fa Mon Nov 11 11:50:36 2019 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,6 +0,0 @@
->1001994.MY1_1439
-MKIQIYILIGVVVLTLISVGIMTNQDQNTHENKIRVAYFPNISHAIPIVGIEKGFFSNHIGSDIDIQPILFDSGPQVIESIFAGSVDIAYVGPGPAINAFLKSEQHDVKILSGAASGGVSFIVHPKSEIKSVADFAGKRIAAPQIGNTQDISLRTYLSDNGLKPAEKGGSVIILNTGNSDIYILFAKGDIDGAWVPEPTATILVQQLGGTRLFNENELWPENKFATVVLIAKEEYVNSHPEIIQKWLEAHQQTADWINSNKEETKTIFFDFMKNEMGKSLPVELIDESLSNLEITSDPIVSSIDTIAKRADSLGYLGRHGYNLDGLFFDKNSNSQSQEVLVNNDQT
->436308.Nmar_1285
-MKIRSVIAAGIGAIIVFSALGIALSSSDTTYENKIRIAYFPNIGHAIPIVGMEKGFFAEHLGDDVKIETKVFDSGPQAIESLFANSIDIAYVGPGPAINGFLNSNNQNVKILAGAASGGASFIVHPDSEINTADDFAGKKIAAPQIGNTQDVSLRHFLAENQLKPAEKGGNVVVYNIPNPDIYTLFVKGDIDGAWVAEPWATILETELDGKRLFHEEELWPDKEFASVLLIGNVDYIDKNSVVWADYIRAHHETQIWIESNPIETRNVFNDFLDSYLGQSLSDDVVDVALSNIMITADPKPNSVVSFAEKADTLGYLGRNGYDLSGIFYSFDTNSLEEAST
->886738.Nlim_1020
-MKMRSIILAGIASIILILSVGIIVNTDGSTRENKIRVAYFPNITHVVPIIGLERGTFANEIGNTITIQPILFDSGPQVIESIFAGSVNIAYVGPGPAINGFLKSEHHNVKILSGAASGGVSFIVHPDSKINSAEDFIGKRIAAPQIGNSQDISLRTYLSANGLKPAEKGGSVIVLNVPNSDIYTLFAKGDIDAAWVAEPTATLLVQKLNGTRLFDEIDMWPDQKFASVLLIANEDYVNQHPEVIRKWLEAHQQTIDWINSNPEETRIIFNQFLKRELGKSLPDNLIDESLSKLQITSDPIVSSIETFAKRADSLGYLGRHGYSLDGIFFDINSNSQLQEVLIP

diff -r a5a3bdd0954b -r 3cb37af59360 test-data/cached_locally/OG_fasta/thaNOG/1CB2B.fa
--- a/test-data/cached_locally/OG_fasta/thaNOG/1CB2B.fa Mon Nov 11 11:50:36 2019 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,6 +0,0 @@
->1001994.MY1_0167
-MSYDGAIEALSTDALKFVKDDFVIGLGSGRAATAFVKSLSSFIKIKNYNIRGVPTSLQIKLIAEKGGIPLVEAEQVDHIDIVFDGADQIDSQKFVIKGGGGALLRENILFNLAKKVVVMADKSKFVKNFTRSVPVEVHPQARNLVTYEIKKLGGKAELRLIDRGYPFFTENGNIILDCDFGVIKNPKILSQKIKQVAGVIESGIFIRKPDVIYRAKTGGKFDII
->436308.Nmar_0218
-MSYDGAITALSNNALKFVKDDYVVGLGSGRAATVLVKSLGKLIKLKNYNIKGVPTSLQIKLIAEKVGIPLIEADQVEHIDVVFDGADQIDSQKFVIKGGGGALLRENILFSLAKKVVVMADKTKFVKNFTRTVPVEVHPLARNSVSKSMKKLGGKAELRSLDRGYPFFTENGNIILDCDFGTIKNPKALTQKIKATTGVLESGIFLRKPDVIYRAKTGEKFDIL
->886738.Nlim_1248
-MSYDDAIEALSTDALKFVKDGFVIGLGSGRAATSFVKSLSSFIKIKNYSIKAVPTSLQIKLIAEKGGIPLVEADHVEYIDVVFDGADQIDSQKFVIKGGGGALLRENILFNLSKKVVVMADKSKFVKNFTREVPVEVHPLARNSVIDAIRKLGGNAQLRSLDRGYPFFTENGNIILDCNFGTIKNPKSLTQKIKQITGVMESGIFLRKPDVIYKAKTGGKFEII

diff -r a5a3bdd0954b -r 3cb37af59360 test-data/cached_locally/OG_fasta/thaNOG/1CB2C.fa
--- a/test-data/cached_locally/OG_fasta/thaNOG/1CB2C.fa Mon Nov 11 11:50:36 2019 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,4 +0,0 @@
->1001994.MY1_1435
-MVQKEPFLTALQNRILLFDGAMGTEIQKYNPKPEDFPNNQDGFNDGLVITHPDWIKKIHKNYLDAGSDCIETNSFGSNKIKLDEYGFGDQTIEFNKKIAQLAVEVCSEYTDKPRYVIGSMGPSGYLPSSNDPDLGQKPLGEIRNAFELQAEGLILGGVDALLIETSQDILEVKLVIEACHNAMKKTGKKVPIIANTTLDQYGKMLLGTNIQAAYTTVSDMGIDVFGLNCSTGPAEMTPSVRWLDEQNEHNLLVVPNAGMPENQGGQAVYKMTPQKMGELLGDFLKQYKKVRIIGGCCGTNPEHIAVLRKVIDEKAYSVKG
->436308.Nmar_1268
-MTEKEPFLDALQNRVLLFDGAMGTEIQKFNPKPEDFPNNQDGFNDGLVVTRPDWIKQIHRHYLDAGADCIETNSFGSNKIKLDEYGFGDQTIEFNKKIAQLASEVCQEYSDRPRYVIGSMGPSGFLPSSNDPDLGQKPLDEIKEAFELQAEGLILGGVDALLIETSQDILEVKLVIEACHQAMEKTGKKIPIIANTTLDQYGKMLLGTNIQAAYTTVSDMGIDVFGMNCSTGPIEMTPSVRWLDEQNEHNILVVPNAGMPENEGGQAVYKMTPEKMGDALGDFLNQYKKVRIIGGCCGTNPEHIKVLRKVIDEKANSVEG

diff -r a5a3bdd0954b -r 3cb37af59360 test-data/cached_locally/OG_fasta/thaNOG/1CB2D.fa
--- a/test-data/cached_locally/OG_fasta/thaNOG/1CB2D.fa Mon Nov 11 11:50:36 2019 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,6 +0,0 @@
->1001994.MY1_0571
-MDKSGVIVGAISGAAIVAIIFAVILAVPPTAVKADVISDNKSIPSATGAILTDYSKKLSLIEIFEKSEPGVVRINVQRAEQSNGTSGVGSGFVFDKQGHIITNAHVVKNVKKVVVTFLDGRSYNAEIVGSDQYTDIGVIKVNADLSLLQPLPLGDSANLKVGEPIAAIGNPFGLSGSMTSGIISQLGRLLPSGAGYSIPDVIQTDAAINPGNSGGPLLNMRGEIVGINTAIQSTTGEFTGVGFAVPSQTLAKIVPKIIVDGKYIHPWIGIAGRDIDPDLAKVLNLNDAVGFLVITVVDDSPAAKAGIHGSNETVEVDGIKYLIGGDIILSVDGNQVRKIDDILIHLQRAKSVGDEMVLEVLRDGRTTNIIITLDERPNGN
->436308.Nmar_0594
-MDKSGVFVGGAIGAVIVVAIFAVLFVSPPESVKPDIVVSNGHGPSTVGEVTPVYSKDLSLIEIFEKSEPGVVRVNVQREEVSDVGGVGSGFVFDKQGHIITNEHVIDDAKKIIITFLDGRSYNAEIIGTDEFTDLAVVKVNADLALLHPLSIGDSSNLKVGEPIAAIGNPFGLSGSMTSGIVSQLGRLLPSGSGYSIPDVIQTDAAINPGNSGGPLLNMRGEIVGINTAIQSATGEFTGVGFAIPSQTVAKIVPTLIEDGDYKHPWIGISGRDIDPDLAKVLELPDAVGFLVVTVIEDSPASKAGLIGSEKTIDVDGVNYPMGGDIILAVDGIEVRKIDDILIHLQRAKSVGDEMVLEVLRDGRTTDISIILQERPNGN
->886738.Nlim_0162
-MSKSEMLVGAAIGASVVAVIFAIILISPAAITKSEINTSDKSIPSVTQTAPAYSTNLSLIDIFEKSEPGVVRVNVQRTDQSNGTSGLGSGFVFDKKGDIITNAHVVKNAKNIVVTFLDGRSYNADLIGSDEFTDIAVIKVNADLTRLHPLSLGDSSSLKVGESIAAIGNPFGLSGSMTSGIVSQLGRLLPSGSGYSIPDVIQTDAAINPGNSGGPLLNMRGEIVGINTAIQSTTGEFTGVGFAVPSQTIVKIVPSLIQDGTYHHPWIGITGRDIEPDLAKVLKLNDAVGFLIVSVIDDSPAAKAGLHGSNETVQVDGLNYQIGGDIILSVDGKQVRKIDDILVHLQRAKSVGDEMVLEILRDGRTTNITINLEERPNGN

diff -r a5a3bdd0954b -r 3cb37af59360 test-data/cached_locally/OG_fasta/thaNOG/1CB2E.fa
--- a/test-data/cached_locally/OG_fasta/thaNOG/1CB2E.fa Mon Nov 11 11:50:36 2019 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,6 +0,0 @@
->1001994.MY1_1525
-MEPSLVTSIGKIQLERPVMLASGILGISLDVFNRLYRSGAGAVVSKSLSTEPWDGYPNPTIFGINGGGWINAVGLSNPGAPNFAKMIEPNKDVPIIISLVGSIPEDFSTMVEQFKNSKVIAYELNLSCPHVAKVGLEVGDDPELVKKIVSTVKNSTNVPVIAKVGLGTTHYLNTVSAAIDSGIDAITAINTIRAIAIDVETQRPILSNKFGGLSGTPIKPIALRCVYEISSKYDIPIIGCGGISTWEDALEFILAGASAIQIGSAIGDNWIHVFNDINKGILQYMKRKGYSKIDEMIGLAKKS
->436308.Nmar_1390
-MEPNLATSIGPIQLDRPVMLASGILGISLDVFSRLYRSGAGAVVTKSLSTEPWEGYPNPTIFSVKGGGWINAVGLSNPGAENFAKMIEPNQDVPIIVSLVGSIPEDFEKMIKQFENCKVTAYELNLSCPHVAKVGLEVGDDPELVKKIVTTVKNSTNVPVIAKVGLGTTHYLNTVGTAIESGIDAITAINTVRSMAIDVETQRPILSNKFGGLSGTPIKPIALRCVYEISSKYDIPIIGCGGISTWEDAVEFFLAGASSVQLGSAIGDNWIDVFNEINTGILQYMEKKNYSKIEEMIGLAKKS
->886738.Nlim_1764
-MEPSLVTSIGKIQLERPVMLASGILGISLDVFNRLYRSGAGAVVTKSLSTEPWDGYPNPTIFSVNGGGWINAVGLSNPGAPNFAKMIESNTTVPIIVSLVGSIAEDFEMMVSQFKNCKVTAYELNLSCPHVAKVGLEVGDDPELVKKIVSTVKNSTAVPVIAKVGLGTTHYLNTVKTAIDSGIDAITAINTVRAMAIDVETQRPILSNKFGGLSGTPIKPIALRCVYEISSKYDIPIIGCGGISTWEDAIEFILGGASAIQLGSAIGDRWLNVFNDINDGIIRYMKRKGYSKLDEMVGLAKKS

diff -r a5a3bdd0954b -r 3cb37af59360 test-data/cached_locally/OG_fasta/thaNOG/1CB2F.fa
--- a/test-data/cached_locally/OG_fasta/thaNOG/1CB2F.fa Mon Nov 11 11:50:36 2019 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,6 +0,0 @@
->1001994.MY1_0238
-MLEISSTPLVIIAILGTVGILLPIISIARKEKGSNSFYAVIAFAALIVSIGYVAYQFVNGNILPSALFSEDVLVDDAFGGFFAIAMLIVAIFTTVGSFNYMRKKNYPAVYYSLILLSTIGMVLVAYSTDLVMLFVAWELMSIPTYVLAGFMKKNPSSNEAALKYFLFGALSSAIIVYGISLSYGLTGSTNIGEVIQGYATLDPSLLPLALLSVGMFIAGFGFKMGLVPFHQWLPDTYEGAPPTITTLLAAGTKKAGFAATIRIVVLGMVVLNLDWTLALGVIAVMTMTIGNIAAIMQKNLARMLAYSSIAHAGYILIGLAVSPYSSLGLQGSLYHILNHAVMKGMAFIAVTGIITTLAVTHIDKLKGLGRRMPITALGLIISLFALAGVPPLAGFWSKLVLFGGALDAGTSIWWAPWLAIAGVLNSALSLAYYGWITRKMYFEGENEKRVSEPKSIIAIMIFSIVFLVGFGIYPDPIIKFVEFAAPTFSLGVMP
->436308.Nmar_0286
-MLEITSTPLILIAILGTVGVILPIISIARKEKGSNSFYAVIAFAALIVSMAYVGYEFINENVAASALFSDDVIVDDAFGGFFAIAMLIVALFTTVGSFNYMRKHNSPAVYYSLILLATIGMILVAYSTDLVMLFVAWELMSIPTYILVGYMKKNPSSNEAALKYFLFGALSSAIIVYGIAISYGLTGSTNIGEVIEGYSTLDPSLLPLALLSVGMFIAGFGFKMGLVPFHQWLPDTYEGAPSPVTALLAAATKKAGFAAAIRIIVLGMMALNLDWTLALGIIAVMTMTIGNVAAIMQKNLSRMLAYSSIAHAGYILIGLAVAPYSSLGLQGSLYQIFNHAVMKGAAFIAIAGIVTTLAVTHIDKLKGLGRRMPITALGMVISLFALAGVPPLSGFWSKLMLFGSALDASTALWWAPWLAIAGVLNSALSLAYYGWITRKMYFEGETEKRVSEPKSIVAVMIFSIIFLVGFGVYPEPLLKFVEFATPVVSLGLMP
->886738.Nlim_1181
-MLEITSTPLVIIAILGTVGVLLPIISIARKEKGSNSFYAIIAFAALIVSIGYVAYQFINDNVLPSALFSEDVLVDDAFGGFFAIAMLIVAIFTTIGSFNYMRKKNYPAVYYSLILLSTIGMVLVAYSTDLVMLFVAWELMSIPTYVLVGFMKKNPSSNEAALKYFLFGALSSAIIVYGISLSYGLTGSTNIGEVIQGYATLDASLLPLALLSVGMFIAGFGFKMGLVPFHQWLPDTYEGAPPTITTLLAAGTKKAGFAATIRIVVLGMVVLNLDWTLALGVIAVMTMTIGNIAAIMQKNLARMLAYSSIAHAGYILIGLAVSPYSSLGLQGSLYQILNHAVMKGMAFIAVTGIVTTLAVTHIDKLKGLGRRMPITAFGLVISLFALAGVPPLAGFWSKLMLFGGALDAGSTIWWAPWLAIAGVLNSALSLAYYGWITRKMYFEGETEKRVREPKSIIAIMVFSIIFLVGFGVYPDPIIKFVEFAAPTFSLGIMP

diff -r a5a3bdd0954b -r 3cb37af59360 test-data/cached_locally/OG_fasta/thaNOG/1CB2G.fa
--- a/test-data/cached_locally/OG_fasta/thaNOG/1CB2G.fa Mon Nov 11 11:50:36 2019 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,6 +0,0 @@
->1001994.MY1_1852
-MISLNRFVIILIVGIFVSGILTISFISNSYVDANSTKKINFTKTIISSQDPGQGHENHQLSLILSPNEGTLYDGSMTFTSNEPVDVVVLHEITGNDVKGQPTWTIDGKTIYAMSLIDLKSKSDSFEFTGAALALHSSNSKEFTATVSVDGWIRGQPTEVIMQKIQVEKDPSLMLSRANVEATMPMHEGLYKGNSIFYIITDTSREEYSKKITEKQDWKVQTSTLIEKMPEEILQKIFIFNNGVRGQGIYGHQKEIFSSTPVQESKYSALNSVIEVSWKKGQNAKVLESFEDVIDAEKNGRIEFTKTGVVINSPQIIWPNGQMLVRNDTKITDDLTFSGGQITKINKDEMTVTFVAHRMWGPDGKTIYAIVTDATPSNPSEIMGIPFSPVYDNLITNSSAADLFQFQNGIKGSGSLGYQPGITSVNSDQENYSPIWRIYNVEWHNPKDAKILQTMSDIDSFKAKDLISVSLARPMNSHHIINGPLIDPFQ
->436308.Nmar_1753
-MLRKLIAILIIGIFATSIITASSLSDQFADAGSRKKIHFTQTFTSSQDPGQGHENHQLSLILSPNQGTIYDGSMTFTSSEPVQIVVLHEINSDDAKGQPTWSIDGNTVYGLSLIDLQEKSGSFEFTGAALGLHSPNSKQFTSTVSVDGWIRGQPTEVIMQKIELEKEEPMSLLSRANVPATIPIHEGIYGGEKVLYIITDGSDEEYARELSEKQEWNVELAPVLADVPEDALQKIFVFKNGVKGEGLYGFQNEIFSSTPQQESEYSALSSVIEVTWKTGQKEIVFESANDVIAAEENGRIEFDETGVVLNTPHIVWPGGQMQVRADQEIADDMPYGGGQITEINEEEMTVTFVAHRGWGPDGRTIYYIVTDATPFGPAEMMGVTSSPTSANLIAHSGAVDLFQFKNGIKGTGPLGFQAGIAAASLGDENYSPMWRIYLIEWNDSENAKILETKSDIDSFRADDLITVSITRPTNSDHIVNCPFIDPFQ
->886738.Nlim_1479
-MNRFTIILIVGIFIIGALTVSFVSDNYVNANSTKKINFTKTITSSQDPGQGHENHQLALILSPNQGTLYVGSMTFTSSEPVEIVVLHEINNDDVKGQSTWTIDGKTVYAISLIELKAKSGSLEFTGAALALHSTNSKEFTATVSIDGWIRGQPTEVTMQKIQVQQNPPLELSRANIAASIPMHEGFYDGKSVFYIITDSSQKEYAEMITKKQNWKVEVAPEIKKISENTLQTIFIFKNGVNGDGIYGRQKEVFSSTPSQVQKYSALNSVIEVTWKKGQNASTLESYEDIINAEKNGRIEFSKTGIVINTPQIIWPDGQMLVRNNKEITNNLKFDGGQITEINKDEMTVTFVAHRGWGPDGKTIYYIITDTTPSGPAKIMGIPFSPVSEHLITNSSKSDLYQFKNGIKSSGSLGYQAEIISVMPGDDSYSPIWRVYNIEWNNPENASILETISDITSSKIKDLILVSLARSMNNQYVINGPIIDPFQ

diff -r a5a3bdd0954b -r 3cb37af59360 test-data/cached_locally/OG_fasta/thaNOG/1CB2H.fa
--- a/test-data/cached_locally/OG_fasta/thaNOG/1CB2H.fa Mon Nov 11 11:50:36 2019 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,4 +0,0 @@
->436308.Nmar_0483
-MTALATKSENIEKQIISDPSDTIDSEKYKMIAENVTISYDGIQAVKNITMKFKEKSVTALIGPSGCGKTTFLRCLNRMHDMTKNAKVDGKVMIDNIDLYDQSIDPIYHRRKVGMVFQKPNPFPTMSIYDNVTAGLKLNGVKDKRILDEIVEDSLKMAYLWDEVKGDLKKSAIELSGGQQQRLCIARALAIQPEVLLMDEPASALDPIATQKIEETITELKKEYTIIIVTHNMQQAVRVSDYTGFMYLGDLVEFRETKKLFTDPKNELTAKYVQGQFG
->886738.Nlim_0922
-MTAMTTKPTHAETSFTSKSQPTLDSDKYKMIAENITVSYGGVDAVKNVTMKFKEKSVTALIGPSGCGKTTFLRCLNRMHDMTKNAKVTGKVMIDNIDLYAKDIDPIYHRRKVGMVFQKPNPFPTMSVYDNVTAGLRLNGVRDKRILDEIVEDSLKMAYLWDEVKNDLKKSAIELSGGQQQRLCIARALAIQPEVLLMDEPASALDPIATQKIEETIIELKKDYTIIIVTHNMQQAIRVSDYTGFMYLGDLIEFRETKKLFTDPKDDLTAKYVQGHFG

diff -r a5a3bdd0954b -r 3cb37af59360 test-data/cached_locally/OG_fasta/thaNOG/1CB2I.fa
--- a/test-data/cached_locally/OG_fasta/thaNOG/1CB2I.fa Mon Nov 11 11:50:36 2019 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,6 +0,0 @@
->1001994.MY1_1452
-MELIEKIILTQIYLSGITGKSYKDNLKTKKGFTENIINSKIDELVKNKLITEDKSALTELGRSSLRVVLAGGVFDIIHPGHIHTLNAAKILGDVLVVVVATDNTAIKMKKRQPLHSKEQRQELVNSLSMVDLCLIGQEDDIFKTVNLVKPQIIALGYDQVHQEKFIIEGCKKINLDAKVARLQSPIPESSSSKIQKEYGESIHGI
->436308.Nmar_1298
-MLEQSQRTILSTIYVCQIEGTNPIEKIKRKTAFSDDQINSKIEELIKKQLVNEDKKTLTESGRDSLKVVLAGGVFDIIHPGHIHTLNAAKELGDALVVVVATDNTAVKMKKRRPLHSQEQRQELVNSLSMVDLCLIGQEDDIFKTVNNVRPQIIALGYDQAHQEKFITEGCKKINLDAKVARLQSPIPDSSSSKIEKEYGESIHGI
->886738.Nlim_1033
-MELIKKSILTELYLSGITGKSHIDNLTKKGFTQKLIDLEIDELIKNKLVKEDRAILTELGRSSLRVVLAGGVFDIIHPGHIYTLNAAKSLGDVLIVVVATDNTALKMKKRQPLHSKEQRQELVNSLIMVDLCLIGQEDDIFKTVNLVKPQIIALGYDQVHQEKFIIDGCKKIQLDAKVARLQSPIPESSSSKIQKEYGESIHGI

diff -r a5a3bdd0954b -r 3cb37af59360 test-data/cached_locally/OG_fasta/thaNOG/1CB2J.fa
--- a/test-data/cached_locally/OG_fasta/thaNOG/1CB2J.fa Mon Nov 11 11:50:36 2019 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,6 +0,0 @@
->1001994.MY1_1646
-MSCSGEIVDEEKLIQIKPGILQQLKKAKYGVADHSTVELCHWTKKSFKHEGSCYKHKFYGISTHRCMEFSPAGMHCENRCVYCWRPMEFYDSLKMEPEKVSEPKEILTKLMEERKKLIMGYYGDSRNDKQRLDESLLPSHYAISLSGEPTMYPKLPELIKYLKSLEATKSIFLVTNGQEPDMIQRLQDKDALPTQLYLSTNAADYDSFLKINRPKYDDSWQRWNRTLEMLKHLDTRTVLRITLIRNYNDQKEMIPAFAAMLKQASPHFIEIKSYMHIGRSTNRLEHSNMLEMEEVRRFSEEVAKHSEIFSIMDESLVSRIVILQNNQRSINRWISAYSNTN
->436308.Nmar_1529
-MSCSGEVVEEEQLIQIKPAISEQLKKAKYGVSDHSTVELCHWTKKSFKHEGSCYKHKFYGISTHRCMEFSPAGMHCENRCVYCWRPMEFYDSLEMKPEQVAEPEEILTKLMAERKKLINGYYGDSRNDKQRLDESLLPSHYAISLSGEPTMYPKLPELIKYLNSLEATKSIFLVTNGQEPDMIQKLQDEDALPTQLYLSTNAADYESFLKINKPKYDDSWERWNRTLGMLKHLNTRTVLRITLIRNYNDQKSMIPAFAKMFKEASPHFIEIKSYMHIGRSTNRLEHSNMLEMEEVKRFSEQIAKQSQIFSVMDESFVSRISILQNNERFIDRWIPAYVNTN
->886738.Nlim_1932
-MSCSGEIVDEERLIQIKPGISQQLKKAKYGVADHSTVELCHWTKKSFKHEGSCYKHKFYGISTHRCMEFSPAGMHCENRCVYCWRPMEFYDSLKMDPEKVAEPKEILTKLMAERKKLINGYYGDSRNDKQRLDESLLPSHYAISLSGEPTMYPKLPELIKYLKSLEETKSIFLVTNGQEPDMIQRLQDEDALPTQLYLSTNAADYESFLKINKPKYDDSWQRWNRTLEMLKKLDTRTVLRITLIRNYNDQEEMIPAFAAMLKQASPHFIEIKSYMHIGRSTNRLEHSNMLEMEEVRKFSESVAEHSQIFSVMDESLVSRIVILQNNQRTIDRWIPAYANTN

diff -r a5a3bdd0954b -r 3cb37af59360 test-data/cached_locally/OG_fasta/thaNOG/1CB2K.fa
--- a/test-data/cached_locally/OG_fasta/thaNOG/1CB2K.fa Mon Nov 11 11:50:36 2019 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,4 +0,0 @@
->436308.Nmar_0061
-MPNFDKTWARQETQSVTGKLREAVKPQGALKPRIQTAVNKLQVQISKMDSMLGKLHERDAQLFQRVVTAMQQHDTSTSRVLSNELAEIRKVTKMLGNARMSLEQVQLRLTTIHDLGDAMVAIGPAMSTMKGLKSSLGRFMPEADSELNTMTQTLNGLMMDSLAGDSFNMESDVSSEETEKILQEASAVAEQQIGDKFPSVPSSTGLSSGTSTSTFE
->886738.Nlim_1611
-MPNFDKTWARQETPGVTEKLRETIKPQGALKPRIQTAVNKLQVQISKMDSMLGKLHERDAQLFQRVVTAMQQHDTSTSRVLSNELAEIRKVTKMLGNARMSLEQVQLRLTTIHDLGDAMVAIGPAMSTMKGLKSSLGRFMPEADSELNSMTQTLNGLMMDSLAGDSFSMETGASSEETERILQEASAVAEQQIGDKFPSVPTSTGLSQSSQSTY

diff -r a5a3bdd0954b -r 3cb37af59360 test-data/cached_locally/OG_fasta/thaNOG/1CB2M.fa
--- a/test-data/cached_locally/OG_fasta/thaNOG/1CB2M.fa Mon Nov 11 11:50:36 2019 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,6 +0,0 @@
->1001994.MY1_0188
-MLSTGMWVEKYRPSKLSEIVNQKEIIGSLEALIKDPTDMPHLMFSGSAGVGKTTTALCISRQILGEYAKDYTLELNASDERGIGMVREKVKKFSRFAGMVDVPFKIIILDEADEMTSDAQTALRRIIEDTAKYCRFILIANNISKIIDPIQSRCATFKFTSIPEEDVINHLENIAKKEKVKSDKKGLKAIYDYSEGDLRHAINLMQATASIGEISEENVKSSAGLTKTSDVDIVLKMALSGKIVDAREKMIELTKVYGMSESDFLKYLNSAVFKIKHDNISDILEVIAKYDYRILVGANPEIQLTAMLAELGKLEK
->436308.Nmar_0240
-MAATGMWVEKYRPMKLSEVVNQTEIIGSLEALIKDPTDMPHLLFSGSAGVGKTTTALCISRQILGDYAKDYTLELNASDERGIGMVREKVKKFSRYAGMADVPFKIIILDEADEMTSDAQTALRRIIEDTAKICRFILIANNISKIIDPIQSRCATFKFTAVPEEDVIKRLEEIAKKEKVKADKKGLKAIYDYSEGDLRHAINLMQATASLGSISEDNVKASAGLTKTTDVDEVLKIALSGKVPEAREKMIELIKVYGMSESDFLKYLNSAVFKSKHDKLSDILEIIAKYDYRILVGSNSEIQLSAMLAELAKVEN
->886738.Nlim_1226
-MLSTGMWVEKYRPTKLSEIVNQTEIIGSLEALIKDPTDMPHLMFSGSAGVGKTTTALCIARQILGEYAKDYTLELNASDERGIGMVREKVKKFSRFAGMAEVPFKIIILDEADEMTADAQTALRRIIEDTAKYCRFILIANNISKIIDPIQSRCATFKFTSIPQEDVINHLESISKKEKIKSDKKGLKAIYDYSEGDLRHAINLLQATASLGEVTEENVKASAGLTKTSDVDEVLKMALAGKVLEAREKMIELIKVYGMSESDFLKYINSAVFKTKHEKLSDILQVIAKYDFRILSGANSEIQLSALLAELSTLK

diff -r a5a3bdd0954b -r 3cb37af59360 test-data/cached_locally/OG_fasta/thaNOG/1CB2N.fa
--- a/test-data/cached_locally/OG_fasta/thaNOG/1CB2N.fa Mon Nov 11 11:50:36 2019 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,6 +0,0 @@
->1001994.MY1_0435
-MNKVNLNIKQRKIISDKIFKIGVTTAGAYVLIVVVLIAFQLVSESYPVWEEEGLSFITKTDWNAVEGRESFGALPYILGTLTTSAIAMMIGVPLSIGIAMFISDAPPKIGAPLGFLVELLAAVPSVIYGLWGLYVFRIYFRDWFETPLHDAFGDNIWLFSGNPYGLDILTASVILAIMIIPTVSAVSREIMKAVPQQQKEAAYMLGATKWEMFKLAIFPYSKTGLIGASILGLGRAVGETMAVTMLIGNATGLGAIPSSLFGPSQTMSSIIANEFVEASPASIHMPALIGIGLILLLIAIVINVVAHLLVTRMLKIKEGAINN
->436308.Nmar_0481
-MGRPKLNPPKVGRRPISDKIFKVGATVAGVYVLVVIVLLAFQLISESAPIWDEYGLSFIVKSEWNAIDDRQDFGVLPYIFGTLVTSALAMVIGVPLSIGIAMFISDAPSKIGGPLGFLVELLAAVPSVIYGLWGLFVFRVYFVDWVEKPLHNTFGDSIWLFSGTPFGLDILTASVILAIMIIPTVSAVSREVMKAVPQQQKEAAYMLGATKWEMFKLAVFPYSKTGLIGASILGLGRAVGETMAVTMLIGNATGPNAFADSLFDPSQTMSSIIANEFNEASLGTLHLPALIGVAVVLLLIAIAINVVAHILVTRMLKVKEGAINN
->886738.Nlim_0924
-MISDKVFKIGATVAGTYVLVVVVLIAFQLISESYPIWEKEGLSFITSTDWNAVEGRESFGALPYIIGTLTTSAIAMAIGVPLSIGIAMFISDAPAKIGGPLGFLVELLAAVPSVIYGLWGLFVFRIYFRDWIETPLHNAFGDNIWLFSGNPYGLDIITASVILAIMIIPTVSAVSREIMKAVPQQQKEAAYMLGATKWEMFKLAVFPYSKTGLIGASILGLGRAVGETMAVTMLIGNATGIGAIPSSLFGPSQTMSSIIANEFVEASPASVHMPALIGIGLILLLIAIVINVIAHLLVTKMLKIKEGAINN

diff -r a5a3bdd0954b -r 3cb37af59360 test-data/cached_locally/OG_fasta/thaNOG/1CB2P.fa
--- a/test-data/cached_locally/OG_fasta/thaNOG/1CB2P.fa Mon Nov 11 11:50:36 2019 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,4 +0,0 @@
->1001994.MY1_1290
-MTPSELNEEKLVEIPAEHTFSELYDDVKYDPDIRPGRELQERDSLHEVLLKRRLRQKLVELNPGNPDIVYDIAVQKIELISEPTLIETNRAFHQMLLSGIKVAYQEDNQTKYSVMKLIDFDNPEKNDFIAVRQFLLVQHEERRLDHVIFVNGIPLIILEYKSMADKNATIVDAFHQLGKTKYQRDIPIIFRYNAFLVISDRLNAKYGTINAPFERFSDWNDLTQPDKKVANRLEILQKLLLNKTTILDVIKNFIEYESDGKNLIKKICQQHQYHAVNTIVKKTSDVYSQQGENRIGVVWHTTGSGKSLTMIYYVNSLSQIEKFENPTFIIITDRRDLDEQLNHFFRIAGFPYPKPETAILEADSILDLREKLQVPSGKIIFTTIQKFQTTEEEREGKVKYPKISDRRNIIIIADEAHRSQYKKMAQNLQTALPNALRIGFTGTPIELEDRSTTQVFGDIISSYKIPEAVRDGATVQISCETHPVTLLLLNKFIGKDFEEITQGLDEENVTTLARRGAEFTKLVEDPDRIKTIANDIVSHFNKKQKIFKGKAMIATSTKLAAARFADYISSLKVAPECTCIVSGATSQKPESTPEKRTREAIIQKHYKDKLTIENILTRFKDENDPLSLLIVCDMYLTGFDAPLIHTMYIDKPLRDHNLIQAISRVNRVWKNKPGGAIIDYIGIADDLDRAFSAYAQDDVKGAMIPTAEIIEIMKKKHSDLINFFDPKISNRQGLDESQELQLIYDAIDEIVYDDIVKREFIKIVTELTKAYAVCTPHPSCLDVEDDLRFFQKLRKILLKATSNVPVDLTEMESAISDLVEQGIGADQVVKGFKISFDPKKQDISKEYLNDIKKLKQKNLKAELAYKLLDDAIQAKFKRNLVKRKSFQDRIEEALSKYHARFWDNDDTIQKLEEVGKEITNESSREQELGLNDEEIAFYDVVSLGKDYVKSDAVIKQISLDLTKYLKGNIRIDWINQENIKAEIRMGVRKILLRADFPTDKIEEIVPKIMDQAETNYG
->436308.Nmar_0608
-MNFRIEDNEEGRQVELPALELITALGYTYIPNYELNIPKERPDHRQVLLYPRLRAAIKRLNDFDDDGIEQAIAQIHEDNFPIGMPMIDANEKIRIKLTGRAGENAIAQPITIKQYGKKGIEYPTVKFFDFDPKKIGTKEDKNEYLVTNQFKHLGNRTEIECDIVIFVNGIPLVLIECKKPTTIDLMKTVWKENLEKYQRDGSHSLGHEKLFFFNHVIMATSAIQARYGTLKALPNKYAKWTSLTNITTKELEKLVGRKPTPQDIMLAGMIKKETLLDMLKNFVLYEIEEHKKIKKVAKHQQYRVVTKSVDRISHHKKVEDKGGVIWHTQGSGKSLSMVWFATQLYYKFSRPTIMVITDRRQLNKQIFDTFRNCGFPEPEKPRNRSQLAKTLQYSKGKTIMVNLQKFDKPEKFVETKEKIYVLVDEAHRSQYKWTAGYMRKAMPNAVFFAFTGTPLDRENKNTYRRFGPLIDKYSFTESKEDGATVKVEHMGLLPEIEIEGGNSLNNIFDNLFGHLPKAQQAEIRRKYATKKKIASSPARIRKICEKIVDHYTKKILPNGYKAMIVAPTRAAAVTYKRELEDLTKLPARIIMDSKKDEVGPDEFSWADYYLPQNEALKKAEEFTNPDDPTKFLIVVDMLLVGYDAPIVQVMYLDRPLREHALLQAIARVNRIYDEHKDRGFIIDFWGVTRDLQNALKMFEEQDVQGALDNVDDDLLELDVRHKDFMEKIQGIDSKDHNEIAKRFEDEDEQEEFEYAFKRFAKALEAVLPDKEAVPYEKDLKKGYEIRGKIRAWFYGDRADLSEYGKKVQKIIDKHIRAIGISEISGSKEITYDNFLGFIAKFKGDNRAKAALIKKRATLVIREMSPDNPAFYQKLKERLEKLIQDEKERRVDDAQYFEGIRDIFEEALSGPEKLQKQTGIKDRFQLAIYMLLEEKHSDLKQNKKYSEEIFKKVKKAASVKDWRDKEPQENEIELAVIDTLDKKIFDEKTRDKLASEVYKMAVNNNEW

diff -r a5a3bdd0954b -r 3cb37af59360 test-data/cached_locally/OG_fasta/thaNOG/1CB2Q.fa
--- a/test-data/cached_locally/OG_fasta/thaNOG/1CB2Q.fa Mon Nov 11 11:50:36 2019 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,6 +0,0 @@
->1001994.MY1_1750
-MDRKILGISGGIAVIIAIVAVMLLTPNLESTPIQKHNEKIGLVINAPHSAISLQDLNQIYAEASSTGIGRSNVYMFWNIVEPVRGEYDWKQSDVLMSFNKNNNLKVTLFFSVINGETLGPFPNWIGKPSLNAIGEDRLVNVLDAILSRYDIIDTVVIAGETESQFRYHEQNIPVYKELFNGVYAKLKEKHPDVQIGNGFALHNVLNKNLEHIVSDLAIGDFVAFSYFPVDTLNDIVKTPEEAKADLQKTFEIIPDKKIGLFEVSWSTSDFVGGNETSQQIFLEKSFEFYTENESKIEFFTWYRQYDRPDGTCVIDKPEIANQTLTVGGGSGLGSSEYIMERLSHYICNSGLLDVDGTPKSSWNEFKNQIELIN
->436308.Nmar_1626
-MDKKILGVGIGVAVVIAIIAGVLSIPSDSNPEVTPVKTNEKIGLVINSPNQSVTLQELDEIYSTASESGIGRSNVYLFWNLIEPEHREYNWQYSDALMSFNQKNDLKVTLYFSIINGETLGPFPDWIGKPPIQSLNEDRVVSVLDAILSRYHIVDTVILAGETESQFRYYEQNIPPYKELFVGVYDKIKEKHPDVKIGNAFALHQVLNKDLQNIVTDLDVGDFVAFSYSPVDTVGDMVKTPQQAKEDLEQIIDLAGDRNAAIFEISWSTSDFVGGSEESQTEFLEKSFEFYAENESELEFFTWYRQNDKPEGTCAFEVQEVGEDKLTVGGSGFGSSEHVIERLDHYVCNAGLFDENGNPKSGWNEFKNQIQMLN
->886738.Nlim_1388
-MDKKILSIGIGIAIVIALVLVVIGFQSAEIITNQKQDEKIGLVINTPNPSISLKELHKIYADASSTGIGRSNVYIFWNVVEPVKGEFDWTQSDVLMSYNKNNDLKVTLYFSVINGETLGPFPNWIGKPSLNAIGEDRVVSVLDAILSRYDIIDTVVIAGETESQFRYYEQNIPVYKELFTGVYDKIKEKHPTVKIGNAFALHNVLNKNLEYIVTDLSLGDFVAFSYSPVDTLNEIVKTPQEAKEDLQKIFEIVPDKKIGLFEISWSTSDFVGGNSTSQQEFLEKSFEFYKENKSKIEFFTWYRQYDKPDGTCVIEKPEIGNKTLSVGGGSGLGSSEYVIERLSHYVCSVGLLDADGTPKPSWNEFKNQIELINQ

diff -r a5a3bdd0954b -r 3cb37af59360 test-data/cached_locally/OG_fasta/thaNOG/1CB2R.fa
--- a/test-data/cached_locally/OG_fasta/thaNOG/1CB2R.fa Mon Nov 11 11:50:36 2019 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,4 +0,0 @@
->1001994.MY1_0222
-MWSEKYRPQNISDMIGNEESRSSIIEWFTKWKKGTKPLLLVGPPGIGKTTIAYLTAKQFQYDMVGLNASDVRSKSRINEILSPVLGNVSILGLPMIFIDEVDGIHGRGDYGGAEALIEILKEPTIPIILAANSDTSDKMKSIKKVVKTISFKPIPPRLLKIYLENILKKENVTLSPGSIIKVIDRSRGDVRSMINLTQSLVTGFNPQTEKSFESINVEDGINAFFKANSFDEARGVLYSMQIDPRLKIDAFYSSIVTSNLDNQTLAKLLEIISEADILYGKIMKTQNWRLLRYLNEILIRLYLNDERIRYSQYNLSWPLLNRIRWDGKKIKSLSSVMAKTLHLSSSAFVTICLPYILFCIKNKKLSLDLEETFGDVIEKEIELIK
->436308.Nmar_0270
-MWSEKYRPQIISDMVGNEESRAAIMEWFAKWKKGTKPLLLAGPPGIGKTTMAFLVAKQFGYDMIGLNASDVRSKSRINEILTPVLGNVSVLGTPMIFVDEVDGIHGRGDYGGVAALVDILKEPTVPIILAANDDTSDKMKNIKKVVKTISFKKIPPRLLRVYLENILKKESAKLSPGSLIKVIDKSRGDIRSMINLTQSMVTGFNPQTETTFENIDVEDGVNAFFKSKSVDEARGVLYSMQIDPREKINAFYSSIVMSSLDPETLAKYLEIISEADMLYGKIVRTQNWRLLRYLNDILIKLYHDDDRVRYAQYNLSWPLLNRIRWDGSKIKSLSSVMAKKLHLSSSAFVTFGLPFVLFCIKNNALELELEETFGDIIEKEIELIQ

diff -r a5a3bdd0954b -r 3cb37af59360 test-data/cached_locally/OG_fasta/thaNOG/1CB2S.fa
--- a/test-data/cached_locally/OG_fasta/thaNOG/1CB2S.fa Mon Nov 11 11:50:36 2019 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,4 +0,0 @@
->1001994.MY1_0691
-MSFKSLIDEIENNLHKILEDMSIYDISFTVEPAKPGFGDASSNISFLLAKSLKKSPKEIANLMSEKYRQSQNILVLKVEPHQTGYLNFFADWEKLNQLILSESNLNEFGFIDLGHNSEIVVEHTSVNPNKALHIGHIRNIVLGDTVARILKKSNYKVNVLNYVDDSGLQVADIIVGFKHLGFAQQSPTGKKFDHYCGDDVYVKTTEKYEQDPNFEEIRKNTLKELEDGASETAKFADTITRRVLENQLETCWNLGVYYDCLNFESQIIRSGLWSKIFEKLKEMNLVEFENDGKNAGCWIIRGENNEEDKVIVRSNGTATYIAKDIPYAAWKLGLIEDPFSYKKYEKTQPGNKILWQTTLTATNEPKQNFTGNKVITVIDSRQARLQKIITGLMSKFKSTNDAYVHLGYESVTLSSDTAQTLGLDTDGKQAQMSGRKGLYVDADSVYDLLKNKTIEETKKRHPEMSDSEIEQIAHYVSVGTLRYEMIKQDLDKMITFDLTKSLSLEGDTAPYIQYTHARASRIIEKSARNPSIDVDFSLLNDASELSLIKIIGLFEIYVLDAAKNLSPKVIARYCHNLAVAFNSFYEHVKVLELGDEKLENSRLCLVNSFKITLEKALELLGITAPEKM
->436308.Nmar_0686
-MTFKSILDEIENNLNKILDDLSISDVKFSVEPAKPGFGDVSSNVSFLLAKQLKKSPKEISEMLSEKYSQCVSTLVSKSESHPSGYLNFYADWPKLNQLILSESNLPEFGDVDIGKNSTIVVEHTSVNPNKALHIGHIRNIIIGDTISRILQKANYKVNVLNYVDDSGLQVADIIVGFKHFGYPIEPPQGKKFDHYCGDDVYVKTTEKYEQDSSLEEIRKNVLKELEDGTSETAQFADKITRRVLSNQLETCWNLAVSYDCLNFESQIIRSGLWDGIFEKLKEMNLVEFENDGKNAGCWVIRGEGKEEDKVIVRSNGTATYIAKDIPYAAWKLGLLDDPFHYEKYEKEQPNSRVLWQTILNDGASESQNFSGDKVITVIDSRQARLQKIITSLMGKFKSIPDAYVHLGYESVTLSSDTAKILGLETDGKQAQMSGRKGLYVNADSVYDLLKEKTTEETKKRHPEMDDSEIEKISHSVSVATLRYEMIKQDLDKIIAFDLTKSLSLEGDTAPYIQYTHARASRILEKSGRTPSIDVDFSLLKEQSEIDLVKMIGLFNLQVRDAANNLSPKVISRYCHDLAVTFNSFYEKSKVLDLGDEKLENSRLCLVNSFKITIEKALNLLGISAPDKM

diff -r a5a3bdd0954b -r 3cb37af59360 test-data/cached_locally/OG_fasta/thaNOG/1CB2T.fa
--- a/test-data/cached_locally/OG_fasta/thaNOG/1CB2T.fa Mon Nov 11 11:50:36 2019 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,6 +0,0 @@
->1001994.MY1_0879
-MSTEQIEKFQEVVDIPAGVKVTLKKNMMHFEGPLGKTHKNFRNIPVNIEIKEGKVILKSQGYRKRDYSILHTARSVIRNLCEGLVVGYTIKMKIAFAHFPITVKVQDRTVLIENFQGERSSRITKIIGNTKVVPKGEDVILTGEVWNHITQTAANIELRSKVKDKDHRVFLDGVYVYEKKKGIEK
->436308.Nmar_0794
-MSTSQLEKMQDQVEIPEGVTVTQNKNMLLFEGPLGKTHKNFRNIPVKIEIADGKVNLKTIGERKRDYAILHTARSIIRNICEGLVEGYTIKMKVVFAHFPITVKVEGKKILIENFQGERAPRSTHIMGNTKVIPKGEDVLLTGEVWTDITQTAANIELTTKVKNKDHRVFLDGIYVYEKKKGIEK
->886738.Nlim_0395
-MSTEQIEKFQEVVEIPKGVTVTLKKHMLHFQGPLGKTHKNFRNIPVNIEVKDGKVILKSQGYRKRDYSILHTARSIIRNICEGLITGYTIKMKIVFAHFPITVKVQDKTVLIENFQGERSARVTRIIGNTKVVPKGEDVILTGEVWNDITQTAANIELRSKVKDKDHRVFLDGVYSYEKKKGIDK

diff -r a5a3bdd0954b -r 3cb37af59360 test-data/cached_locally/OG_fasta/thaNOG/1CB2U.fa
--- a/test-data/cached_locally/OG_fasta/thaNOG/1CB2U.fa Mon Nov 11 11:50:36 2019 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,6 +0,0 @@
->1001994.MY1_1727
-MVIEVVRIGQRLVRDDRVTTHVALVARAFGCSKIFMTEVNPEIKDTLEKINNTWGGDFVVEFIDNWKSIVKMKKKDSKIVHLTMYGESINEVDMQLRKEENLLIVVGAEKVPREIYELADYNVGIGNQPHSEISALAIILDRIQKGEQFKNSFPGAKRKIIPTRNGKNVLVRGTRD
->436308.Nmar_1606
-MVIEVVRIGQRLVRDDRVTTHVALVSRAFGAERIFMTEINPEIKDTLGKINDTWGGNFEIEFIDSWKPIVKKKKEEGFKIVHLSMYGEKINDAQEEIRKEENLLIVVGAEKVPREIYELADFNVGVGSQPHSEISALAILLDRIQGGQQFEKEFPNAKRKIIPTKTGKNVQVKETRD
->886738.Nlim_1365
-MVLEVVRIGQRLVRDDRVTTHVALVARAFGCTKIFMTEVNPEIKDTVEKINKTWGGDFVVEFIDNWKSIVKKKKEEYKIVHLTMYGESIDDVDEQLRKEKNLLIVVGAEKVPREIYELADYNISIGNQPHSEISALAITLDRIQKGKQFKNSFSGAKRKIIPTKKGKNVFVSGTRD

diff -r a5a3bdd0954b -r 3cb37af59360 test-data/cached_locally/OG_fasta/thaNOG/1CB2V.fa
--- a/test-data/cached_locally/OG_fasta/thaNOG/1CB2V.fa Mon Nov 11 11:50:36 2019 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,6 +0,0 @@
->1001994.MY1_1241
-MKIRIFDTTLRDGEQTIGVSLSPDQKLAIAKKLDELGVDAIEAGFPVISAGEFKAVKMIAAAGLSCEIAGLTRTIKNDIDAAVDAGLNYIHTFIATSDIHLQYKLKMTREQALEKAIEAVEYGKSRGLQVEFSAEDATRTDREFLKKVFGDVAKAGADRVNIPDTVGYSTPEYMAVLTKDTVEVTKLPVSVHCHNDFGLAVANSLAGIHAGASCAHVTINGIGERAGNASLEEFSMALKCLPFEKKYETNIKSELIYDTSRFISKTVGIIVQPNKAIVGTNAFGHESGIHTHGVLSNPLTYEPISPELVGRKRWLQVGKHAGIHGMNAMLAEYGVKPTEEQSKQILDKVKTLGDAGKQITDVELLSIASDVLGEKELKRIVQLTGFSVSTGIGTMPYAFVKLNIDGQDHIGTDYGVGPVDAALNAIQKITGKISEIRIKDYGLASISGGSSALCEVTVKVEDAFGNKVSAKSVGEDIVTTSVKAVIDAINRIMLKKMLQEKQVR
->436308.Nmar_1070
-MTNVRIFDTTLRDGEQTLGVSLSPDQKLAIAKKLDELGVDAIEAGFPVISEGELQAVKMITAAGLSSEICGLTRTIKKDIDAAIDAGLNYVHTFIATSDIHLEHKLQMTREQALEKAIEAVEYGKSHGLQVEFSAEDASRTDREFLKKVFSEVAKAGADRVNIPDTVGYSTPEYMAQITKDTIEATNLPVSVHCHNDFGLAVANALAGIHVGAACAHVTINGIGERAGNASLEELSMALKCLPYEQKYETNIKSELIYDVSRFISKTVGIIVQPNKAIVGANAFGHESGIHTHGVLNNPLTYEPISPELVGRKRWLKVGKHAGVHGMNAMLEEYGVKPTEDQAKQILEKVKVLGDQGKQITDVELLSMASEVLGKKDLKRIVQLTGFSVSTGIGTMPYAFVKLNVDGQDHIGTDYGVGPVDAALNAIQKITGKISEIRIKDYGLASISGGSGALCEVTVKVEDPLGNKVSAKSVGEDIVTTSVKAVIDAINRIMLKKMLQEKQVS
->886738.Nlim_0759
-MKVRIFDTTLRDGEQTIGVSLSPDQKLAIAKKLDELGVDAIEAGFPVISSGEFKAVKMIASEGLSCEIAGLTRTIKNDVDAAVNAGLNYIHTFIATSDIHLQYKLKMTREQALEKAIEAVEYGKSRGLQVEFSAEDATRTDREFLKKVFGDVAKAGADRVNIPDTVGYSTPEYMAELTRDTVEATHLPVSVHCHNDFGLAVANSLAGIHAGASCAHVTINGIGERAGNASLEEFSMALKCLPFEQKYETNIKSELIYETSRFISKTVGIIVQPNKAIVGTNAFGHESGIHTHGVLSNPLTYEPISPELVGRKRWLQVGKHAGIHGMNAMLAEYGVKPTEEQSKQILDKVKTLGDAGKQITDVELLSIASDVLGEKELKRIVQLTGFSVSTGIGTMPYAFVKLNIDGQDHIGTDYGVGPVDAALNAIQKITGKISEIRIKDYGLASISGGSSALCEVTVKVEDALGNKVSAKSVGEDIVTTSVKAVIDAINRIMLKKMLQEKQVR

diff -r a5a3bdd0954b -r 3cb37af59360 test-data/cached_locally/OG_fasta/thaNOG/1CB2W.fa
--- a/test-data/cached_locally/OG_fasta/thaNOG/1CB2W.fa Mon Nov 11 11:50:36 2019 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,6 +0,0 @@
->1001994.MY1_1343
-MQNQKSEWATNESPRIMSYTLANFRQLPQIQKLGEEKQFEMEVVGNVLPFKTNNYVVEQLIDWNNIPDDPMFVLTFPQRGMLIPEHYAKMEAALKKGDKKEIQNTANEIRLQLNPHPAGQMELNVPTLKDGTKLYGMQHKYKETCLFFPSQSQTCHAYCSFCFRWPQFVGMDELKFAMKEGEQLVQYLQEHPEISDVLFTGGDPMIMKARIFSTYINPLLEANLPNLRTIRIGTKALSYWPYKFLTDDDAEEMLDIFKRVVDKGIHLALMGHFNHTVELKTDAVKEAIKKVRATGAQIRTQSPILRHINDDSEMWAEMWKTQVQLGCIPYYMFVVRDTGAQHYFGIPLIEAQRIFRDAYKKVTGLARTVRGPSMSATPGKVQILGIAEYGGEKLMVLRFLQGRNPDWVQIPFLAKYDEKAIWLDDLKPATGDKFFFEDELNEKMKVIKNQDYPES
->436308.Nmar_1772
-MTYQESVWDDSPSLKSYTLSNFRDLPQIQNISEEKQFEMEVVGNVLPFKANNYVVEQLINWNDIPNDPMYVLTFPQRGMLKPEHYAKMENTLKNTSDKKEIANVANEIRLQLNPHPAGQMELNVPTLKDGTKLYGMQHKYKETCLFFPSQSQTCHAYCSFCFRWPQFVGMDEMKFAMQEGEQLVQYVSEHPEISDVLFTGGDPMIMKAKMFSKYVDALIEAKLPNLKTIRIGTKALSYWPYKFLTDSDSQEMLQVFQKITDSGLHLAFMAHFNHLNELSTNAVKSAIKEVRKTGAQIRTQSPLLAHINDDAEMWANMWTKQVQLGCIPYYMFVVRDTGAQHYFGVPLVKAYEIFSQAYSTVSGLGRTVRGPSMSATPGKVQVVGTTQINGEKLLILRFLQGRNPNWIKEPFFAKYDENAIWLDDLKPAFGDKFFFEDELDAIKASKTS
->886738.Nlim_0892
-MQRQDSAWGVKESPRLKSYTLANFRELPQIQKMGAKKQFEMEVVGNVLPFKTNNYVIEQLIDWNNIPNDPMFVLTFPQRGMLIPEHYSKMESALKKGDKKEIQNTANEIRLQLNPHPAGQMELNVPTLKDGTKLYGMQHKYKETCLFFPSQSQTCHAYCSFCFRWPQFVGMDELKFAMREGEQLVQYLREHPEISDVLFTGGDPMIMKAKIFSTYINPLLEANLPNLRTIRIGTKALSYWPYKFLTEDDAEEMLDIFKRVVDKGIHLAVMGHFNHLVELKTDAVKEAIKKIRATGAQIRTQSPLLRHINDDADMWAEMWKVQVQLGCIPYYMFVVRDTGAQHYFGISLIDAQRIFRDAYKKVTGLARTVRGPSMSATPGKVQILGITEVNDEKFMVLRFLQGRNPDWVQIPFLAKYDEKAIWLDDLKPATGDKFFFENELKEMMMTIKNEDYPES

diff -r a5a3bdd0954b -r 3cb37af59360 test-data/cached_locally/OG_fasta/thaNOG/1CB2X.fa
--- a/test-data/cached_locally/OG_fasta/thaNOG/1CB2X.fa Mon Nov 11 11:50:36 2019 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,6 +0,0 @@
->1001994.MY1_1050
-MKFLIIDNYDSFVYNIAQYLGELGVDCDVIRNDKITLEKIKQNNYDAVIISPGPGTPTDRKYFGICSDVIKDMGSTTPILGVCLGHQGIIHAFGGKVTNAGCVRHGKTSPVDHTNSDLFKDVKNPFRATRYHSLVGDKTIIPDVLEVTAVAADDGEVMAVRHKEYLIEGVQFHPESIMTEDGKKILANFIKQVKDRK
->436308.Nmar_0912
-MKFLIIDNYDSFVYNIAQYLGELGVDCDVIRNDKITLNEIQEKKYDAIIISPGPGTPEDKKYFGVCSEVIKDMGSSTPILGVCLGHQGIIDAFGGKVTNAGCVRHGKTSPVNHEDSKLFKDVKNPFRATRYHSLVGDKTIIPEVLKVTATASDDGEVMAIEHKDYLIQGVQFHPESIMTEDGKKILSNFIQQVKEKQK
->886738.Nlim_0576
-MKFLIIDNYDSFVYNIAQYLGELGVDSDVIRNDKITVEQIKQNKYDAIIISPGPGTPSDRKYFGVCGDVIKDIGPITPILGVCLGHQGIIEAFGGKVTNARCVRHGKTSPVDHTNSELFKDVKNPFRATRYHSLVGDKTIIPDALEITAIAADDGEVMAVRHKKYLIEGVQFHPESIMTEDGKKILANFIKQVKSKK

diff -r a5a3bdd0954b -r 3cb37af59360 test-data/cached_locally/OG_fasta/thaNOG/1CB2Y.fa
--- a/test-data/cached_locally/OG_fasta/thaNOG/1CB2Y.fa Mon Nov 11 11:50:36 2019 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,6 +0,0 @@
->1001994.MY1_1793
-MMGDRDYRSIIKNAVDSIGRELEIEIDAKDIKTIHLKEVVQCLRRSYYDRIEPKEVERRGFNDLLSGLLRKLQYGSDPKEFSIEDIKLRGHADMIADNSIILFRPTNASLESPLANDLLYLNACMWIYDKTDGVIIYITGDREEIMFSLTRDKKMFEEIIRRVRVLNDLLKEQKTPILEPSSDCMECQYYQRCFITKKNTKQVSLAEMLGLGKD
->436308.Nmar_1701
-MMGDRDFRTTIQNAIKSIGNELEIDIDSKDFETIHLQEVVRCMRRSYYDRVEPLEIERRGFNELLSGLLRKLEYGSNPKDFDINEIKLRGQADMMVDDAILLFRSATEELENPHASDVLYLNACMWIYDKEDGMIVYITGDRKESTFSLTRNKKMFEDTIRRVRVLNNLLKEQKTPILEPSAECTECQYYERCFTKRKNTKQTSLAEMLGLGKQD
->886738.Nlim_1425
-MMGDRDFRSIVKNAVDTIGRELEIQIDAKNIKTIHLKEVVQCLRRSYYDRIDPKEVERRGFNDLLSGLLRKLHYGSDPKEFSIDEIKLRGQADMIADDSIVLFRPSKTVIEAPVANDLLYLNACMWIYDKTDGIIVYITGDREEIMFSLTRDKKMFEEIIRRVRVLNDLLKEQKTPILEPSNDCAECQYYQRCFTTKKNTKQVSLAEMIGLGKD

diff -r a5a3bdd0954b -r 3cb37af59360 test-data/cached_locally/OG_fasta/thaNOG/1CB2Z.fa
--- a/test-data/cached_locally/OG_fasta/thaNOG/1CB2Z.fa Mon Nov 11 11:50:36 2019 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,6 +0,0 @@
->1001994.MY1_1440
-MAEKGILAFSGGLDTSVVIKYLQEEYNMDVITVTVDVGQGDDQKKIEAKAKKLGVIKHYNIDARKEFVENFIFPSIKANALYQKKYCLATALARPLIAEKVLEIAKKEKVTSLAHGCSGKGNDQVRFDITLRSGSDLPIIAPIRDKNLDRVTELEFAKKHGIEIDSVAKRFSIDQNLWGRAIEGGVLEDPYNEPPEDAFIWVKTKNLPDKPTYLEIKFEKGIPVSVDGKILEPIKLIEYVNKKAGDAGVGIVDHIEDRVVGIKSREVYETPGALCLIEAHSDLEKMVHTKHENKFKSIIDDEWAYLAYSGLWQDPLKQDLDAFIQASQKPVSGTVKLKLFKGSIRVVGRKSDYSLYNHKIATYGTESTFDQRLAKGFVELWGIQSTEANKLQKKRSTKT
->436308.Nmar_1286
-MTQKGILAFSGGLDTSVVVKYLQDEHDMDVITVTVDVGQGDDNKKIAAKAKKLGVKKHYNIDARKEFVKDYIFPSIKANALYQKKYCLATALARPLIAEKVLEIAKKEKVTSLAHGCSGKGNDQVRFDITLRSGSNLPIIAPIRDKNLDRVTELKFAKKHGIEIDTVAKKFSIDQNLWGRAIEGGVLEDPYNEPPDDAFIWVKTKNLPDKPTYLEIKFEKGIPVGVDGKTMDGQKLIEYINKKAGDAGVGIVDHIEDRVVGIKSREVYETPAATCLIEAHSDLEKMVHTKHENKFKSIIDDEWAYLAYSGLWQDPLKSDLDGFIEASQKPVTGTVKLKLYKGSLRVVGRKSKNSLYSHEIATYGTESTFDQRLAKGFVELWGMQSTEANKLQKKRSTKI
->886738.Nlim_1021
-MTEKGILAFSGGLDTSVVVKYLQEEYDMDVITVTVDVGQGDDQRKIEAKAKKLGVKKHYNIDARKEFVEKFIFPSIKANALYQKKYCLATALARPLIAEKVLEIAKKEKVTSLAHGCSGKGNDQVRFDITLRSGSDLPIIAPIRDKNLDRVTELAFAKKHGIEIDSVAKRFSIDQNLWGRAIEGGVLEDPYSEPPDDAFIWVKTKNLPDKPTYIEIKFEKGIPVAVDGKILEPIKLIEYVNKKAGDAGVGIVDHIEDRVVGIKSREVYETPGALCLIEAHSDLEKMVHTKHENKFKSIIDDEWAYLAYSGLWQDPLKQDLDSFIETSQKPVTGTVKIKLFKGSMRVVGRKSDYSLYSHKIATYGSESTFDQKMAKGFVELWGIQSTEANKLQKKRSTKI

diff -r a5a3bdd0954b -r 3cb37af59360 test-data/cached_locally/eggnog.db

Binary file test-data/cached_locally/eggnog.db has changed

diff -r a5a3bdd0954b -r 3cb37af59360 test-data/cached_locally/eggnog_mapper_db.loc
--- a/test-data/cached_locally/eggnog_mapper_db.loc Mon Nov 11 11:50:36 2019 -0500
+++ b/test-data/cached_locally/eggnog_mapper_db.loc Sat Sep 05 07:21:28 2020 +0000

@@ -1,2 +1,2 @@
#value name path
-4.5 eggNOG_4.5 ${__HERE__}
+5.0 eggNOG_5.0 ${__HERE__}

diff -r a5a3bdd0954b -r 3cb37af59360 test-data/cached_locally/eggnog_mapper_hmm_dbs.loc
--- a/test-data/cached_locally/eggnog_mapper_hmm_dbs.loc Mon Nov 11 11:50:36 2019 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,2 +0,0 @@
-#key db_version value name path
-4.5_ENOG411CB2I 4.5 ENOG411CB2I ENOG411CB2I ${__HERE__}/hmmdb_levels/ENOG411CB2I/ENOG411CB2I

diff -r a5a3bdd0954b -r 3cb37af59360 test-data/cached_locally/eggnog_proteins.dmnd

Binary file test-data/cached_locally/eggnog_proteins.dmnd has changed

diff -r a5a3bdd0954b -r 3cb37af59360 test-data/cached_locally/eggnog_proteins.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cached_locally/eggnog_proteins.fa Sat Sep 05 07:21:28 2020 +0000

@@ -0,0 +1,8 @@
+>1001994.MY1_1452
+MELIEKIILTQIYLSGITGKSYKDNLKTKKGFTENIINSKIDELVKNKLITEDKSALTELGRSSLRVVLAGGVFDIIHPGHIHTLNAAKILGDVLVVVVATDNTAIKMKKRQPLHSKEQRQELVNSLSMVDLCLIGQEDDIFKTVNLVKPQIIALGYDQVHQEKFIIEGCKKINLDAKVARLQSPIPESSSSKIQKEYGESIHGI
+>436308.Nmar_1298
+MLEQSQRTILSTIYVCQIEGTNPIEKIKRKTAFSDDQINSKIEELIKKQLVNEDKKTLTESGRDSLKVVLAGGVFDIIHPGHIHTLNAAKELGDALVVVVATDNTAVKMKKRRPLHSQEQRQELVNSLSMVDLCLIGQEDDIFKTVNNVRPQIIALGYDQAHQEKFITEGCKKINLDAKVARLQSPIPDSSSSKIEKEYGESIHGI
+>886738.Nlim_1033
+MELIKKSILTELYLSGITGKSHIDNLTKKGFTQKLIDLEIDELIKNKLVKEDRAILTELGRSSLRVVLAGGVFDIIHPGHIYTLNAAKSLGDVLIVVVATDNTALKMKKRQPLHSKEQRQELVNSLIMVDLCLIGQEDDIFKTVNLVKPQIIALGYDQVHQEKFIIDGCKKIQLDAKVARLQSPIPESSSSKIQKEYGESIHGI
+>436308.Nmar_0135
+MKFCNVGIIIQARTGSDRFPKKVLASIEKKPMIWHIVNRCKKVKNIDKIILATTTLKEDYPLISLAKKNKIEYFRGSKNDVLDRFYQCSTSNNLDIIIRITGDCPLVDPKLIDQFLDFFSHKKYDYVSNTINPTYPDGLDIEIFSFKALKKAWNMSKKKSNREHVTTFIKHHPEKFKIKNFENNTNLSNYRLTVDHKNDLKLIRKIYKEFRPNIKFSTKSVISLLNKNPELFKINQNISRNEGYEKSLLNDN

diff -r a5a3bdd0954b -r 3cb37af59360 test-data/cached_locally/hmmdb_levels/ENOG411CB2I/ENOG411CB2I
--- a/test-data/cached_locally/hmmdb_levels/ENOG411CB2I/ENOG411CB2I Mon Nov 11 11:50:36 2019 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

b'@@ -1,637 +0,0 @@\n-HMMER3/f [3.1b1 | May 2013]\n-NAME ENOG411CB2I\n-LENG 205\n-ALPH amino\n-RF no\n-MM no\n-CONS yes\n-CS no\n-MAP yes\n-DATE Thu Apr 16 06:29:18 2015\n-NSEQ 3\n-EFFN 0.454102\n-CKSUM 2514733105\n-STATS LOCAL MSV -10.6020 0.70508\n-STATS LOCAL VITERBI -11.4006 0.70508\n-STATS LOCAL FORWARD -4.9608 0.70508\n-HMM A C D E F G H I K L M N P Q R S T V W Y \n- m->m m->i m->d i->m i->i d->m d->d\n- 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\n- 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\n- 0.17176 1.91497 4.55917 0.35031 1.21898 0.00000 *\n- 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 - - -\n- 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\n- 0.03256 3.83682 4.55917 0.61958 0.77255 0.48576 0.95510\n- 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 - - -\n- 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\n- 0.03256 3.83682 4.55917 0.61958 0.77255 0.48576 0.95510\n- 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 - - -\n- 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\n- 0.03256 3.83682 4.55917 0.61958 0.77255 0.48576 0.95510\n- 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 - - -\n- 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\n- 0.03256 3.83682 4.55917 0.61958 0.77255 0.48576 0.95510\n- 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 - - -\n- 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\n- 0.03256 3.83682 4.55917 0.61958 0.77255 0.48576 0.95510\n- 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 - - -\n- 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\n- 0.03256 3.83682 4.55917 0.61958 0.77255 0.48576 0.95510\n- 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.'..b'.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\n- 0.03256 3.83682 4.55917 0.61958 0.77255 0.48576 0.95510\n- 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 - - -\n- 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\n- 0.03256 3.83682 4.55917 0.61958 0.77255 0.48576 0.95510\n- 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 - - -\n- 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\n- 0.03256 3.83682 4.55917 0.61958 0.77255 0.48576 0.95510\n- 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 - - -\n- 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\n- 0.03256 3.83682 4.55917 0.61958 0.77255 0.48576 0.95510\n- 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 - - -\n- 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\n- 0.03256 3.83682 4.55917 0.61958 0.77255 0.48576 0.95510\n- 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 - - -\n- 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\n- 0.03256 3.83682 4.55917 0.61958 0.77255 0.48576 0.95510\n- 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 - - -\n- 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\n- 0.03256 3.83682 4.55917 0.61958 0.77255 0.48576 0.95510\n- 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 - - -\n- 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\n- 0.03256 3.83682 4.55917 0.61958 0.77255 0.48576 0.95510\n- 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 - - -\n- 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\n- 0.02203 3.82629 * 0.61958 0.77255 0.00000 *\n-//\n'

diff -r a5a3bdd0954b -r 3cb37af59360 test-data/cached_locally/hmmdb_levels/ENOG411CB2I/ENOG411CB2I.h3f

Binary file test-data/cached_locally/hmmdb_levels/ENOG411CB2I/ENOG411CB2I.h3f has changed

diff -r a5a3bdd0954b -r 3cb37af59360 test-data/cached_locally/hmmdb_levels/ENOG411CB2I/ENOG411CB2I.h3i

Binary file test-data/cached_locally/hmmdb_levels/ENOG411CB2I/ENOG411CB2I.h3i has changed

diff -r a5a3bdd0954b -r 3cb37af59360 test-data/cached_locally/hmmdb_levels/ENOG411CB2I/ENOG411CB2I.h3m

Binary file test-data/cached_locally/hmmdb_levels/ENOG411CB2I/ENOG411CB2I.h3m has changed

diff -r a5a3bdd0954b -r 3cb37af59360 test-data/cached_locally/hmmdb_levels/ENOG411CB2I/ENOG411CB2I.h3p

Binary file test-data/cached_locally/hmmdb_levels/ENOG411CB2I/ENOG411CB2I.h3p has changed

diff -r a5a3bdd0954b -r 3cb37af59360 test-data/cached_locally/hmmdb_levels/thaNOG/thaNOG
--- a/test-data/cached_locally/hmmdb_levels/thaNOG/thaNOG Mon Nov 11 11:50:36 2019 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

b'@@ -1,637 +0,0 @@\n-HMMER3/f [3.1b1 | May 2013]\n-NAME thaNOG\n-LENG 205\n-ALPH amino\n-RF no\n-MM no\n-CONS yes\n-CS no\n-MAP yes\n-DATE Thu Apr 16 06:29:18 2015\n-NSEQ 3\n-EFFN 0.454102\n-CKSUM 2514733105\n-STATS LOCAL MSV -10.6020 0.70508\n-STATS LOCAL VITERBI -11.4006 0.70508\n-STATS LOCAL FORWARD -4.9608 0.70508\n-HMM A C D E F G H I K L M N P Q R S T V W Y \n- m->m m->i m->d i->m i->i d->m d->d\n- 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\n- 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\n- 0.17176 1.91497 4.55917 0.35031 1.21898 0.00000 *\n- 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 - - -\n- 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\n- 0.03256 3.83682 4.55917 0.61958 0.77255 0.48576 0.95510\n- 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 - - -\n- 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\n- 0.03256 3.83682 4.55917 0.61958 0.77255 0.48576 0.95510\n- 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 - - -\n- 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\n- 0.03256 3.83682 4.55917 0.61958 0.77255 0.48576 0.95510\n- 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 - - -\n- 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\n- 0.03256 3.83682 4.55917 0.61958 0.77255 0.48576 0.95510\n- 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 - - -\n- 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\n- 0.03256 3.83682 4.55917 0.61958 0.77255 0.48576 0.95510\n- 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 - - -\n- 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\n- 0.03256 3.83682 4.55917 0.61958 0.77255 0.48576 0.95510\n- 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'..b'.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\n- 0.03256 3.83682 4.55917 0.61958 0.77255 0.48576 0.95510\n- 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 - - -\n- 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\n- 0.03256 3.83682 4.55917 0.61958 0.77255 0.48576 0.95510\n- 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 - - -\n- 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\n- 0.03256 3.83682 4.55917 0.61958 0.77255 0.48576 0.95510\n- 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 - - -\n- 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\n- 0.03256 3.83682 4.55917 0.61958 0.77255 0.48576 0.95510\n- 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 - - -\n- 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\n- 0.03256 3.83682 4.55917 0.61958 0.77255 0.48576 0.95510\n- 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 - - -\n- 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\n- 0.03256 3.83682 4.55917 0.61958 0.77255 0.48576 0.95510\n- 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 - - -\n- 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\n- 0.03256 3.83682 4.55917 0.61958 0.77255 0.48576 0.95510\n- 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 - - -\n- 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\n- 0.03256 3.83682 4.55917 0.61958 0.77255 0.48576 0.95510\n- 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 - - -\n- 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\n- 0.02203 3.82629 * 0.61958 0.77255 0.00000 *\n-//\n'

diff -r a5a3bdd0954b -r 3cb37af59360 test-data/cached_locally/hmmdb_levels/thaNOG/thaNOG.h3f

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diff -r a5a3bdd0954b -r 3cb37af59360 test-data/cached_locally/hmmdb_levels/thaNOG/thaNOG.h3m

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diff -r a5a3bdd0954b -r 3cb37af59360 test-data/cached_locally/hmmdb_levels/thaNOG/thaNOG.h3p

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diff -r a5a3bdd0954b -r 3cb37af59360 test-data/cached_locally/hmmdb_levels/thaNOG_hmm/thaNOG_hmm.all_hmm.h3f

Binary file test-data/cached_locally/hmmdb_levels/thaNOG_hmm/thaNOG_hmm.all_hmm.h3f has changed

diff -r a5a3bdd0954b -r 3cb37af59360 test-data/cached_locally/hmmdb_levels/thaNOG_hmm/thaNOG_hmm.all_hmm.h3i

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diff -r a5a3bdd0954b -r 3cb37af59360 test-data/cached_locally/hmmdb_levels/thaNOG_hmm/thaNOG_hmm.all_hmm.h3m

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diff -r a5a3bdd0954b -r 3cb37af59360 test-data/cached_locally/hmmdb_levels/thaNOG_hmm/thaNOG_hmm.all_hmm.h3p

Binary file test-data/cached_locally/hmmdb_levels/thaNOG_hmm/thaNOG_hmm.all_hmm.h3p has changed

diff -r a5a3bdd0954b -r 3cb37af59360 test-data/cached_locally/hmmdb_levels/thaNOG_hmm/thaNOG_hmm.all_hmm.idmap
--- a/test-data/cached_locally/hmmdb_levels/thaNOG_hmm/thaNOG_hmm.all_hmm.idmap Mon Nov 11 11:50:36 2019 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

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thaNOG.ENOG411CBBZ.meta_raw\n-1399 thaNOG.ENOG411CBM5.meta_raw\n-1400 thaNOG.ENOG411CB4R.meta_raw\n-1401 thaNOG.ENOG411CBH9.meta_raw\n-1402 thaNOG.ENOG411CBU4.meta_raw\n-1403 thaNOG.ENOG411CBQ4.meta_raw\n-1404 thaNOG.ENOG411CB37.meta_raw\n-1405 thaNOG.ENOG411CC1T.meta_raw\n-1406 thaNOG.ENOG411CC96.meta_raw\n-1407 thaNOG.ENOG411CB8X.meta_raw\n-1408 thaNOG.ENOG411CBRX.meta_raw\n-1409 thaNOG.ENOG411CBC5.meta_raw\n-1410 thaNOG.ENOG411CBQ7.meta_raw\n-1411 thaNOG.ENOG411CBVK.meta_raw\n-1412 thaNOG.ENOG411CBQJ.meta_raw\n-1413 thaNOG.ENOG411CBSI.meta_raw\n-1414 thaNOG.ENOG411CBD1.meta_raw\n-1415 thaNOG.ENOG411CC24.meta_raw\n-1416 thaNOG.ENOG411CCA4.meta_raw\n-1417 thaNOG.ENOG411CC72.meta_raw\n-1418 thaNOG.ENOG411CBQ2.meta_raw\n-1419 thaNOG.ENOG411CB5Q.meta_raw\n-1420 thaNOG.ENOG411CBA0.meta_raw\n-1421 thaNOG.ENOG411CC6G.meta_raw\n-1422 thaNOG.ENOG411CBQ1.meta_raw\n-1423 thaNOG.ENOG411CCAE.meta_raw\n-1424 thaNOG.ENOG411CCA3.meta_raw\n-1425 thaNOG.ENOG411CBNM.meta_raw\n-1426 thaNOG.ENOG411CBZ5.meta_raw\n-1427 thaNOG.ENOG411CC9J.meta_raw\n-1428 thaNOG.ENOG411CBRH.meta_raw\n-1429 thaNOG.ENOG411CBFC.meta_raw\n-1430 thaNOG.ENOG411CBJV.meta_raw\n-1431 thaNOG.ENOG411CBJS.meta_raw\n-1432 thaNOG.ENOG411CBZW.meta_raw\n-1433 thaNOG.ENOG411CBQQ.meta_raw\n-1434 thaNOG.ENOG411CBQA.meta_raw\n-1435 thaNOG.ENOG411CBG7.meta_raw\n-1436 thaNOG.ENOG411CBGD.meta_raw\n-1437 thaNOG.ENOG411CB9Y.meta_raw\n-1438 thaNOG.ENOG411CB2R.meta_raw\n-1439 thaNOG.ENOG411CB9U.meta_raw\n-1440 thaNOG.ENOG411CBWS.meta_raw\n-1441 thaNOG.ENOG411CBWQ.meta_raw\n-1442 thaNOG.ENOG411CB7Q.meta_raw\n-1443 thaNOG.ENOG411CBMM.meta_raw\n-1444 thaNOG.ENOG411CBRG.meta_raw\n-1445 thaNOG.ENOG411CBG1.meta_raw\n-1446 thaNOG.ENOG411CC8W.meta_raw\n-1447 thaNOG.ENOG411CBBG.meta_raw\n-1448 thaNOG.ENOG411CB8S.meta_raw\n-1449 thaNOG.ENOG411CC5F.meta_raw\n-1450 thaNOG.ENOG411CBC9.meta_raw\n-1451 thaNOG.ENOG411CBHE.meta_raw\n-1452 thaNOG.ENOG411CBPR.meta_raw\n-1453 thaNOG.ENOG411CB88.meta_raw\n-1454 thaNOG.ENOG411CBV1.meta_raw\n-1455 thaNOG.ENOG411CC9N.meta_raw\n-1456 thaNOG.ENOG411CBK9.meta_raw\n-1457 thaNOG.ENOG411CB8F.meta_raw\n-1458 thaNOG.ENOG411CBVZ.meta_raw\n-1459 thaNOG.ENOG411CC5S.meta_raw\n-1460 thaNOG.ENOG411CBXJ.meta_raw\n-1461 thaNOG.ENOG411CC0E.meta_raw\n-1462 thaNOG.ENOG411CBHU.meta_raw\n-1463 thaNOG.ENOG411CBHT.meta_raw\n-1464 thaNOG.ENOG411CB87.meta_raw\n'

diff -r a5a3bdd0954b -r 3cb37af59360 test-data/make_comp_file.sh
--- a/test-data/make_comp_file.sh Mon Nov 11 11:50:36 2019 -0500
+++ b/test-data/make_comp_file.sh Sat Sep 05 07:21:28 2020 +0000

@@ -4,17 +4,6 @@

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 \

diff -r a5a3bdd0954b -r 3cb37af59360 test-data/scoped.emapper.annotations
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/scoped.emapper.annotations Sat Sep 05 07:21:28 2020 +0000

@@ -0,0 +1,1 @@
+Nmar_0135 436308.Nmar_0135 3.8e-149 510.8 Thaumarchaeota ko:K07257 ko00000 Thaumarchaeota 41T2K@651137,COG1083@1,arCOG04817@2157 NA|NA|NA M Cytidylyltransferase

diff -r a5a3bdd0954b -r 3cb37af59360 test-data/scoped.emapper.annotations_orthologs
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/scoped.emapper.annotations_orthologs Sat Sep 05 07:21:28 2020 +0000

@@ -0,0 +1,1 @@
+Nmar_0135 1131266.ARWQ01000003_gene1537,436308.Nmar_0135

diff -r a5a3bdd0954b -r 3cb37af59360 test-data/scoped.emapper.seed_orthologs
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/scoped.emapper.seed_orthologs Sat Sep 05 07:21:28 2020 +0000

@@ -0,0 +1,1 @@
+Nmar_0135 436308.Nmar_0135 3.8e-149 510.8

diff -r a5a3bdd0954b -r 3cb37af59360 tool-data/eggnog_mapper_db.loc.sample
--- a/tool-data/eggnog_mapper_db.loc.sample Mon Nov 11 11:50:36 2019 -0500
+++ b/tool-data/eggnog_mapper_db.loc.sample Sat Sep 05 07:21:28 2020 +0000

@@ -1,25 +1,22 @@
#This is a sample file distributed with Galaxy that enables tools
-#to use a directory of eggnog_mapper data files.
+#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/
+#  http://eggnog5.embl.de/download/emapperdb-5.0.0/eggnog.db.gz
# A complete diamond database is available from:
-#  http://eggnogdb.embl.de/download/eggnog_4.5/eggnog-mapper-data/eggnog_proteins.dmnd.gz
+#  http://eggnog5.embl.de/download/emapperdb-5.0.0/eggnog_proteins.dmnd.gz
#
-# The python script download_eggnog_data.py,
+# 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.
+# 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,
+# 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
+#db_version name path
+#5.0 eggnog_5.0 /path/to/directory/that/contains/eggnog.db

diff -r a5a3bdd0954b -r 3cb37af59360 tool-data/eggnog_mapper_hmm_dbs.loc.sample
--- a/tool-data/eggnog_mapper_hmm_dbs.loc.sample Mon Nov 11 11:50:36 2019 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,28 +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
-#
-# 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

diff -r a5a3bdd0954b -r 3cb37af59360 tool_data_table_conf.xml.sample
--- a/tool_data_table_conf.xml.sample Mon Nov 11 11:50:36 2019 -0500
+++ b/tool_data_table_conf.xml.sample Sat Sep 05 07:21:28 2020 +0000

@@ -4,8 +4,4 @@
         <columns>value,name,path</columns>
         <file path="tool-data/eggnog_mapper_db.loc" />
     </table>
-    <table name="eggnog_mapper_hmm_dbs" comment_char="#" allow_duplicate_entries="False">
-        <columns>key,db_version,value,name,path</columns>
-        <file path="tool-data/eggnog_mapper_hmm_dbs.loc" />
-    </table>
</tables>

diff -r a5a3bdd0954b -r 3cb37af59360 tool_data_table_conf.xml.test
--- a/tool_data_table_conf.xml.test Mon Nov 11 11:50:36 2019 -0500
+++ b/tool_data_table_conf.xml.test Sat Sep 05 07:21:28 2020 +0000

@@ -4,8 +4,4 @@
         <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>