Mercurial > repos > iuc > taxpasta
changeset 0:11f0a8f8dfea draft
planemo upload for repository https://github.com/taxprofiler/taxpasta commit 5a6a3c7a86bbf6f9aa8c29dfb70e63425076d488
| author | iuc |
|---|---|
| date | Fri, 07 Jun 2024 14:33:38 +0000 |
| parents | |
| children | 7ffa36716a1e |
| files | taxpasta.xml test-data/2611_se-ERR5766174-db1.kraken2.report.txt test-data/2612_pe-ERR5766176-db1.kraken2.report.txt test-data/ERR7569997.txt test-data/ERR7569998.txt test-data/diamond_valid_1.tsv test-data/ncbi_taxonomy.loc test-data/test-db/names.dmp test-data/test-db/nodes.dmp tool-data/ncbi_taxonomy.loc.sample tool_data_table_conf.xml.sample tool_data_table_conf.xml.test |
| diffstat | 12 files changed, 2610 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/taxpasta.xml Fri Jun 07 14:33:38 2024 +0000 @@ -0,0 +1,238 @@ +<tool id="taxpasta" name="taxpasta" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> + <description>standardise taxonomic profiles</description> + <macros> + <token name="@TOOL_VERSION@">0.6.1</token> + <token name="@VERSION_SUFFIX@">0</token> + <token name="@PROFILE@">22.01</token> + </macros> + <xrefs> + <xref type="bio.tools">taxpasta</xref> + </xrefs> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">taxpasta</requirement> + </requirements> + <command detect_errors="exit_code"><![CDATA[ +taxpasta + $action.action + --profiler $profiler + --taxonomy '$taxonomy.fields.path' +#if $action.action == 'merge' + --output-format '$action.format.output_format' + #if $action.format.output_format == 'TSV' + --output '$tabular_output' + $action.format.wide + #else if $action.format.output_format == 'BIOM' + --output '$biom_output' + #end if +#else + --output-format 'TSV' + --output '$tabular_output' +#end if + $add_name + $add_rank + $add_lineage + $add_id_lineage + $add_rank_lineage +#for $file in $infile + '$file' +#end for + ]]></command> + <inputs> + <conditional name="action"> + <param name="action" type="select" label="Taxpasta action"> + <option value="standardise">Standardise input(s)</option> + <option value="merge">Standardise and combine multiple taxonomic profiles from the same profiler</option> + </param> + <when value="standardise"/> + <when value="merge"> + <conditional name="format"> + <param argument="--output-format" type="select" label="Desired output format"> + <option value="TSV">Tabular</option> + <option value="BIOM">BIOM</option> + </param> + <when value="TSV"> + <param argument="--wide" type="boolean" truevalue="--wide" falsevalue="--long" checked="true" label="Output merged abundance data in either wide or (tidy) long format"/> + </when> + <when value="BIOM"/> + </conditional> + </when> + </conditional> + <param argument="--profiler" type="select" label="What profiling tool created this report?" help="Select one profiler only"> + <option value="bracken">Bracken</option> + <option value="Centrifuge">Centrifuge</option> + <option value="diamond">DIAMOND</option> + <option value="ganon">ganon</option> + <option value="kaiju">Kaiju</option> + <option value="kraken2">Kraken2</option> + <option value="krakenuniq">KrakenUniq</option> + <option value="megan6">MEGAN6/MALT</option> + <option value="metaphlan">MetaPhlAn</option> + <option value="motus">mOTUs</option> + </param> + <param name="infile" type="data" format="tabular" multiple="true" label="Taxonomic report(s) to standardise" help="The reports should be from the same profiling tool" /> + <param argument="--taxonomy" type="select" label="NCBI taxonomy" help="To have actual human-readable taxon names in the standardised output"> + <options from_data_table="ncbi_taxonomy"> + <validator message="No NCBI database is available" type="no_options"/> + </options> + </param> + <param argument="--add-name" type="boolean" truevalue="--add-name" falsevalue="" checked="true" label="Add the taxon name to the output"/> + <param argument="--add-rank" type="boolean" truevalue="--add-rank" falsevalue="" checked="false" label="Add the taxon rank to the output"/> + <param argument="--add-lineage" type="boolean" truevalue="--add-lineage" falsevalue="" checked="false" label="Add the taxon's entire lineage to the output" + help="The taxon names are separated by semi-colons"/> + <param argument="--add-id-lineage" type="boolean" truevalue="--add-id-lineage" falsevalue="" checked="false" label="Add the taxon's entire lineage to the output" + help="The taxon identifiers are separated by semi-colons"/> + <param argument="--add-rank-lineage" type="boolean" truevalue="--add-rank-lineage" falsevalue="" checked="false" label="Add the taxon's entire rank lineage to the output" + help="These are taxon ranks separated by semi-colons"/> + </inputs> + <outputs> + <data name="tabular_output" format="tabular" label="${tool.name} on ${on_string}: Tabular"> + <filter>(action['action'] == 'merge' and action['format']['output_format'] == 'TSV') or action['action'] == 'standardise'</filter> + </data> + <data name="biom_output" format="biom1" label="${tool.name} on ${on_string}: BIOM"> + <filter>(action['action'] == 'merge' and action['format']['output_format'] == 'BIOM')</filter> + </data> + </outputs> + <tests> + <!-- test data from taxpasta https://github.com/taxprofiler/taxpasta/tree/dev/tests/data--> + <test expect_num_outputs="1"> + <conditional name="action"> + <param name="action" value="standardise"/> + </conditional> + <param name="profiler" value="metaphlan"/> + <param name="infile" value="ERR7569997.txt"/> + <param name="taxonomy" value="test-db-tox"/> + <param name="add_name" value="true"/> + <param name="add_rank" value="false" /> + <param name="add_lineage" value="false"/> + <param name="add_id_lineage" value="false"/> + <param name="add_rank_lineage" value="false"/> + <output name="tabular_output" ftype="tabular"> + <assert_contents> + <has_text text="Proteobacteria"/> + <has_n_columns n="3"/> + <has_n_lines n="241"/> + </assert_contents> + </output> + </test> + <!-- test multiple inputs and the merge command--> + <test expect_num_outputs="1"> + <conditional name="action"> + <param name="action" value="merge"/> + <conditional name="format"> + <param name="output_format" value="TSV"/> + <param name="wide" value="true"/> + </conditional> + </conditional> + <param name="profiler" value="metaphlan"/> + <param name="infile" value="ERR7569997.txt,ERR7569998.txt"/> + <param name="taxonomy" value="test-db-tox"/> + <param name="add_name" value="true"/> + <param name="add_rank" value="false" /> + <param name="add_lineage" value="false"/> + <param name="add_id_lineage" value="false"/> + <param name="add_rank_lineage" value="false"/> + <output name="tabular_output" ftype="tabular"> + <assert_contents> + <has_text text="Gammaproteobacteria"/> + <has_n_columns n="4"/> + <has_n_lines n="252"/> + </assert_contents> + </output> + </test> + <!-- testing diamond input--> + <test expect_num_outputs="1"> + <conditional name="action"> + <param name="action" value="standardise"/> + </conditional> + <param name="action" value="standardise"/> + <param name="profiler" value="diamond"/> + <param name="infile" value="diamond_valid_1.tsv"/> + <param name="taxonomy" value="test-db-tox"/> + <param name="add_name" value="true"/> + <param name="add_rank" value="false" /> + <param name="add_lineage" value="false"/> + <param name="add_id_lineage" value="false"/> + <param name="add_rank_lineage" value="false"/> + <output name="tabular_output" ftype="tabular"> + <assert_contents> + <has_text text="1310613"/> + <has_n_columns n="3"/> + <has_n_lines n="4"/> + </assert_contents> + </output> + </test> + <!-- testing kraken input and all boolean--> + <test expect_num_outputs="1"> + <conditional name="action"> + <param name="action" value="standardise"/> + </conditional> + <param name="profiler" value="kraken2"/> + <param name="infile" value="2612_pe-ERR5766176-db1.kraken2.report.txt"/> + <param name="taxonomy" value="test-db-tox"/> + <param name="add_name" value="true"/> + <param name="add_rank" value="true" /> + <param name="add_lineage" value="true"/> + <param name="add_id_lineage" value="true"/> + <param name="add_rank_lineage" value="true"/> + <output name="tabular_output" ftype="tabular"> + <assert_contents> + <has_text text="root"/> + <has_text text="rank_lineage"/> + <has_n_columns n="7"/> + <has_n_lines n="45"/> + </assert_contents> + </output> + </test> + <!-- testing BIOM output--> + <test expect_num_outputs="1"> + <conditional name="action"> + <param name="action" value="merge"/> + <conditional name="format"> + <param name="output_format" value="BIOM"/> + </conditional> + </conditional> + <param name="profiler" value="kraken2"/> + <param name="infile" value="2612_pe-ERR5766176-db1.kraken2.report.txt,2611_se-ERR5766174-db1.kraken2.report.txt"/> + <param name="taxonomy" value="test-db-tox"/> + <param name="add_name" value="true"/> + <param name="add_rank" value="false" /> + <param name="add_lineage" value="false"/> + <param name="add_id_lineage" value="false"/> + <param name="add_rank_lineage" value="false"/> + <output name="biom_output" ftype="biom1"> + <assert_contents> + <has_text text="314146"/> + </assert_contents> + </output> + </test> + </tests> + <help><![CDATA[ + +.. class:: infomark + +**What it does** + +The main purpose of taxpasta is to standardise taxonomic profiles created by a range of bioinformatics tools. +We call those tools taxonomic profilers. They each come with their own particular tabular output format. +Across the profilers, relative abundances can be reported in read counts, fractions, or percentages, as well as +any number of additional columns with extra information. We therefore decided to take the lessons learnt to heart +and provide our own solution to deal with this pasticcio. With taxpasta you can ingest all of those formats and, at a +minimum, output taxonomy identifiers and their integer counts. Taxpasta can not only standardise profiles but also merge +them across samples for the same profiler into a single table. + +**Input(s)** + +* One or many outputs from a particular profiling tool, such as kraken2 or diamond. + +**Output** + +* A reformatted report in tabular format, either for the single input, or for multiple inputs, as long as they are from the same profiling tool. + + +For more information see: https://taxpasta.readthedocs.io/en/latest/ + + ]]></help> + <citations> + <citation type="doi">10.21105/joss.05627</citation> + </citations> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/2611_se-ERR5766174-db1.kraken2.report.txt Fri Jun 07 14:33:38 2024 +0000 @@ -0,0 +1,44 @@ + 99.98 787758 787758 U 0 unclassified + 0.02 119 0 R 1 root + 0.02 119 0 R1 131567 cellular organisms + 0.02 119 0 D 2759 Eukaryota + 0.02 119 0 D1 33154 Opisthokonta + 0.01 96 0 K 4751 Fungi + 0.01 96 0 K1 451864 Dikarya + 0.01 96 0 P 4890 Ascomycota + 0.01 96 0 P1 716545 saccharomyceta + 0.01 96 0 P2 147537 Saccharomycotina + 0.01 96 0 C 4891 Saccharomycetes + 0.01 96 0 O 4892 Saccharomycetales + 0.01 96 0 F 4893 Saccharomycetaceae + 0.01 96 0 G 4930 Saccharomyces + 0.01 96 0 S 4932 Saccharomyces cerevisiae + 0.01 96 96 S1 559292 Saccharomyces cerevisiae S288C + 0.00 23 0 K 33208 Metazoa + 0.00 23 0 K1 6072 Eumetazoa + 0.00 23 0 K2 33213 Bilateria + 0.00 23 0 K3 33511 Deuterostomia + 0.00 23 0 P 7711 Chordata + 0.00 23 0 P1 89593 Craniata + 0.00 23 0 P2 7742 Vertebrata + 0.00 23 0 P3 7776 Gnathostomata + 0.00 23 0 P4 117570 Teleostomi + 0.00 23 0 P5 117571 Euteleostomi + 0.00 23 0 P6 8287 Sarcopterygii + 0.00 23 0 P7 1338369 Dipnotetrapodomorpha + 0.00 23 0 P8 32523 Tetrapoda + 0.00 23 0 P9 32524 Amniota + 0.00 23 0 C 40674 Mammalia + 0.00 23 0 C1 32525 Theria + 0.00 23 0 C2 9347 Eutheria + 0.00 23 0 C3 1437010 Boreoeutheria + 0.00 23 0 C4 314146 Euarchontoglires + 0.00 23 0 O 9443 Primates + 0.00 23 0 O1 376913 Haplorrhini + 0.00 23 0 O2 314293 Simiiformes + 0.00 23 0 O3 9526 Catarrhini + 0.00 23 0 O4 314295 Hominoidea + 0.00 23 0 F 9604 Hominidae + 0.00 23 0 F1 207598 Homininae + 0.00 23 0 G 9605 Homo + 0.00 23 23 S 9606 Homo sapiens
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/2612_pe-ERR5766176-db1.kraken2.report.txt Fri Jun 07 14:33:38 2024 +0000 @@ -0,0 +1,44 @@ + 99.97 627680 627680 U 0 unclassified + 0.03 168 0 R 1 root + 0.03 168 0 R1 131567 cellular organisms + 0.03 168 0 D 2759 Eukaryota + 0.03 168 0 D1 33154 Opisthokonta + 0.02 152 0 K 33208 Metazoa + 0.02 152 0 K1 6072 Eumetazoa + 0.02 152 0 K2 33213 Bilateria + 0.02 152 0 K3 33511 Deuterostomia + 0.02 152 0 P 7711 Chordata + 0.02 152 0 P1 89593 Craniata + 0.02 152 0 P2 7742 Vertebrata + 0.02 152 0 P3 7776 Gnathostomata + 0.02 152 0 P4 117570 Teleostomi + 0.02 152 0 P5 117571 Euteleostomi + 0.02 152 0 P6 8287 Sarcopterygii + 0.02 152 0 P7 1338369 Dipnotetrapodomorpha + 0.02 152 0 P8 32523 Tetrapoda + 0.02 152 0 P9 32524 Amniota + 0.02 152 0 C 40674 Mammalia + 0.02 152 0 C1 32525 Theria + 0.02 152 0 C2 9347 Eutheria + 0.02 152 0 C3 1437010 Boreoeutheria + 0.02 152 0 C4 314146 Euarchontoglires + 0.02 152 0 O 9443 Primates + 0.02 152 0 O1 376913 Haplorrhini + 0.02 152 0 O2 314293 Simiiformes + 0.02 152 0 O3 9526 Catarrhini + 0.02 152 0 O4 314295 Hominoidea + 0.02 152 0 F 9604 Hominidae + 0.02 152 0 F1 207598 Homininae + 0.02 152 0 G 9605 Homo + 0.02 152 152 S 9606 Homo sapiens + 0.00 16 0 K 4751 Fungi + 0.00 16 0 K1 451864 Dikarya + 0.00 16 0 P 4890 Ascomycota + 0.00 16 0 P1 716545 saccharomyceta + 0.00 16 0 P2 147537 Saccharomycotina + 0.00 16 0 C 4891 Saccharomycetes + 0.00 16 0 O 4892 Saccharomycetales + 0.00 16 0 F 4893 Saccharomycetaceae + 0.00 16 0 G 4930 Saccharomyces + 0.00 16 0 S 4932 Saccharomyces cerevisiae + 0.00 16 16 S1 559292 Saccharomyces cerevisiae S288C
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ERR7569997.txt Fri Jun 07 14:33:38 2024 +0000 @@ -0,0 +1,1116 @@ +#mpa_vOct22_CHOCOPhlAnSGB_202212 +#/home/geoadmin/.mambaforge/envs/metaphlan/bin/metaphlan trimmed/ERR7569997_1.fastq.gz,trimmed/ERR7569997_2.fastq.gz --force --offline --bowtie2db /home/geoadmin/geonomecontainer/METAPHLAN --bowtie2out metaphlan/ERR7569997.bowtie2.bz2 --input_type fastq -o metaphlan/ERR7569997.txt --sample_id_key ERR7569997 --nproc 16 +#211037392 reads processed +#ERR7569997 Metaphlan_Analysis +#clade_name NCBI_tax_id relative_abundance additional_species +k__Bacteria 2 85.33321 +k__Archaea 2157 14.66679 +k__Bacteria|p__Proteobacteria 2|1224 44.71121 +k__Bacteria|p__Bacteroidetes 2|976 16.25495 +k__Archaea|p__Euryarchaeota 2157|28890 14.66679 +k__Bacteria|p__Candidatus_Cloacimonetes 2|456828 7.60322 +k__Bacteria|p__Chloroflexi 2|200795 3.34155 +k__Bacteria|p__Thermotogae 2|200918 2.1851 +k__Bacteria|p__Verrucomicrobia 2|74201 2.09846 +k__Bacteria|p__Candidatus_Aminicenantes 2|67817 2.06248 +k__Bacteria|p__Firmicutes 2|1239 1.60042 +k__Bacteria|p__Tenericutes 2|544448 1.21018 +k__Bacteria|p__Spirochaetes 2|203691 1.09337 +k__Bacteria|p__Actinobacteria 2|201174 0.74631 +k__Bacteria|p__Ignavibacteriae 2|1134404 0.57853 +k__Bacteria|p__Bacteria_unclassified 2| 0.56978 +k__Bacteria|p__Planctomycetes 2|203682 0.43633 +k__Bacteria|p__Candidatus_Saccharibacteria 2|95818 0.19863 +k__Bacteria|p__Synergistetes 2|508458 0.18079 +k__Bacteria|p__Candidatus_Hydrogenedentes 2|142187 0.15657 +k__Bacteria|p__Calditrichaeota 2|1930617 0.11307 +k__Bacteria|p__Atribacterota 2|67818 0.08197 +k__Bacteria|p__Acidobacteria 2|57723 0.02352 +k__Bacteria|p__Deferribacteres 2|200930 0.02267 +k__Bacteria|p__Candidatus_Parcubacteria 2|221216 0.02178 +k__Bacteria|p__Kiritimatiellaeota 2|134625 0.01581 +k__Bacteria|p__Gemmatimonadetes 2|142182 0.01398 +k__Bacteria|p__Candidatus_Cryosericota 2|2498705 0.01071 +k__Bacteria|p__Candidatus_Bipolaricaulota 2|67810 0.00113 +k__Bacteria|p__Candidatus_Roizmanbacteria 2|1752723 0.00067 +k__Bacteria|p__Proteobacteria|c__CFGB8514 2|1224| 24.16898 +k__Bacteria|p__Proteobacteria|c__CFGB43452 2|1224| 13.53671 +k__Archaea|p__Euryarchaeota|c__CFGB27277 2157|28890| 9.34522 +k__Bacteria|p__Candidatus_Cloacimonetes|c__Candidatus_Cloacimonetes_unclassified 2|456828| 7.39933 +k__Archaea|p__Euryarchaeota|c__Methanomicrobia 2157|28890|224756 4.92916 +k__Bacteria|p__Bacteroidetes|c__CFGB42019 2|976| 3.86428 +k__Bacteria|p__Bacteroidetes|c__CFGB7465 2|976| 3.06969 +k__Bacteria|p__Bacteroidetes|c__CFGB7739 2|976| 2.64288 +k__Bacteria|p__Proteobacteria|c__CFGB41806 2|1224| 2.57413 +k__Bacteria|p__Chloroflexi|c__CFGB39849 2|200795| 2.47611 +k__Bacteria|p__Candidatus_Aminicenantes|c__CFGB10837 2|67817| 2.06248 +k__Bacteria|p__Bacteroidetes|c__CFGB24658 2|976| 2.04086 +k__Bacteria|p__Thermotogae|c__CFGB73272 2|200918| 1.88954 +k__Bacteria|p__Proteobacteria|c__Betaproteobacteria 2|1224|28216 1.41908 +k__Bacteria|p__Bacteroidetes|c__CFGB7726 2|976| 1.38206 +k__Bacteria|p__Proteobacteria|c__CFGB8676 2|1224| 1.33492 +k__Bacteria|p__Verrucomicrobia|c__CFGB38799 2|74201| 1.31767 +k__Bacteria|p__Bacteroidetes|c__CFGB7461 2|976| 1.26491 +k__Bacteria|p__Firmicutes|c__CFGB4798 2|1239| 1.07694 +k__Bacteria|p__Tenericutes|c__CFGB26653 2|544448| 0.97538 +k__Bacteria|p__Spirochaetes|c__CFGB42821 2|203691| 0.95774 +k__Bacteria|p__Bacteroidetes|c__CFGB36012 2|976| 0.84596 +k__Bacteria|p__Verrucomicrobia|c__CFGB45184 2|74201| 0.78079 +k__Bacteria|p__Chloroflexi|c__CFGB24537 2|200795| 0.73809 +k__Bacteria|p__Proteobacteria|c__CFGB8946 2|1224| 0.57702 +k__Bacteria|p__Ignavibacteriae|c__CFGB41734 2|1134404| 0.57069 +k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria 2|1224|1236 0.42359 +k__Bacteria|p__Proteobacteria|c__CFGB20881 2|1224| 0.38004 +k__Bacteria|p__Bacteria_unclassified|c__CFGB7371 2|| 0.35445 +k__Bacteria|p__Planctomycetes|c__CFGB26100 2|203682| 0.35189 +k__Bacteria|p__Bacteroidetes|c__CFGB24578 2|976| 0.34293 +k__Archaea|p__Euryarchaeota|c__CFGB9262 2157|28890| 0.31924 +k__Bacteria|p__Actinobacteria|c__Acidimicrobiia 2|201174|84992 0.30161 +k__Bacteria|p__Thermotogae|c__Thermotogae 2|200918|188708 0.29556 +k__Bacteria|p__Bacteroidetes|c__CFGB7503 2|976| 0.26888 +k__Bacteria|p__Tenericutes|c__CFGB9180 2|544448| 0.23479 +k__Bacteria|p__Candidatus_Cloacimonetes|c__CFGB7869 2|456828| 0.20389 +k__Bacteria|p__Firmicutes|c__CFGB25401 2|1239| 0.20368 +k__Bacteria|p__Bacteria_unclassified|c__Bacteria_unclassified 2|| 0.17372 +k__Bacteria|p__Synergistetes|c__CFGB7945 2|508458| 0.16979 +k__Bacteria|p__Actinobacteria|c__Actinomycetia 2|201174|1760 0.16001 +k__Bacteria|p__Candidatus_Hydrogenedentes|c__CFGB8426 2|142187| 0.15657 +k__Bacteria|p__Actinobacteria|c__CFGB76414 2|201174| 0.14962 +k__Bacteria|p__Bacteroidetes|c__CFGB72604 2|976| 0.14037 +k__Bacteria|p__Firmicutes|c__Clostridia 2|1239|186801 0.13525 +k__Bacteria|p__Candidatus_Saccharibacteria|c__CFGB7348 2|95818| 0.12773 +k__Bacteria|p__Calditrichaeota|c__CFGB23645 2|1930617| 0.11307 +k__Bacteria|p__Proteobacteria|c__CFGB3362 2|1224| 0.10024 +k__Bacteria|p__Bacteroidetes|c__CFGB42009 2|976| 0.08997 +k__Bacteria|p__Chloroflexi|c__Anaerolineae 2|200795|292625 0.08915 +k__Bacteria|p__Actinobacteria|c__CFGB76411 2|201174| 0.08895 +k__Bacteria|p__Planctomycetes|c__CFGB45746 2|203682| 0.08444 +k__Bacteria|p__Firmicutes|c__CFGB39919 2|1239| 0.07662 +k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria 2|1224|28211 0.07367 +k__Bacteria|p__Spirochaetes|c__CFGB41075 2|203691| 0.0674 +k__Archaea|p__Euryarchaeota|c__Methanobacteria 2157|28890|183925 0.06613 +k__Bacteria|p__Atribacterota|c__Atribacteria 2|67818|2847774 0.06061 +k__Bacteria|p__Spirochaetes|c__Spirochaetia 2|203691|203692 0.05561 +k__Bacteria|p__Candidatus_Saccharibacteria|c__CFGB3614 2|95818| 0.05236 +k__Bacteria|p__Bacteroidetes|c__CFGB23790 2|976| 0.05144 +k__Bacteria|p__Proteobacteria|c__CFGB11081 2|1224| 0.05025 +k__Bacteria|p__Bacteroidetes|c__Bacteroidia 2|976|200643 0.04953 +k__Bacteria|p__Actinobacteria|c__CFGB76413 2|201174| 0.04612 +k__Bacteria|p__Bacteroidetes|c__CFGB42248 2|976| 0.04549 +k__Bacteria|p__Bacteria_unclassified|c__CFGB76099 2|| 0.03658 +k__Bacteria|p__Chloroflexi|c__Chloroflexi_unclassified 2|200795| 0.03294 +k__Bacteria|p__Bacteroidetes|c__CFGB43468 2|976| 0.03133 +k__Bacteria|p__Bacteroidetes|c__CFGB24417 2|976| 0.02624 +k__Bacteria|p__Bacteroidetes|c__CFGB46194 2|976| 0.02446 +k__Bacteria|p__Bacteroidetes|c__CFGB76562 2|976| 0.02445 +k__Bacteria|p__Acidobacteria|c__CFGB32401 2|57723| 0.02337 +k__Bacteria|p__Deferribacteres|c__CFGB25719 2|200930| 0.02267 +k__Bacteria|p__Atribacterota|c__CFGB8897 2|67818| 0.02135 +k__Bacteria|p__Proteobacteria|c__CFGB75967 2|1224| 0.02107 +k__Bacteria|p__Firmicutes|c__Bacilli 2|1239|91061 0.01767 +k__Bacteria|p__Candidatus_Saccharibacteria|c__CFGB47556 2|95818| 0.01667 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0.95295 +k__Bacteria|p__Spirochaetes|c__CFGB42821|o__OFGB42821|f__FGB42821|g__GGB42821|s__GGB42821_SGB60031|t__SGB60031 2|203691|||||| 0.84555 +k__Bacteria|p__Bacteroidetes|c__CFGB36012|o__OFGB36012|f__FGB36012|g__GGB35206|s__GGB35206_SGB49924|t__SGB49924 2|976|||||| 0.84484 +k__Bacteria|p__Verrucomicrobia|c__CFGB45184|o__OFGB45184|f__FGB45184|g__GGB61845|s__GGB61845_SGB83974|t__SGB83974 2|74201|||||| 0.78079 +k__Bacteria|p__Chloroflexi|c__CFGB24537|o__OFGB24537|f__FGB24537|g__GGB41833|s__GGB41833_SGB58930|t__SGB58930 2|200795|||||| 0.73809 +k__Bacteria|p__Proteobacteria|c__CFGB8946|o__OFGB8946|f__FGB8946|g__GGB26731|s__GGB26731_SGB83492|t__SGB83492 2|1224|||||| 0.57702 +k__Bacteria|p__Ignavibacteriae|c__CFGB41734|o__OFGB41734|f__FGB41734|g__GGB45669|s__GGB45669_SGB63385|t__SGB63385 2|1134404|||||| 0.57069 +k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Gammaproteobacteria_unclassified|f__Candidatus_Competibacteraceae|g__GGB38705|s__GGB38705_SGB102987|t__SGB102987 2|1224|1236||1400857||| 0.38884 +k__Bacteria|p__Candidatus_Cloacimonetes|c__Candidatus_Cloacimonetes_unclassified|o__Candidatus_Cloacimonetes_unclassified|f__Candidatus_Cloacimonetes_unclassified|g__Candidatus_Syntrophosphaera|s__Candidatus_Syntrophosphaera_thermopropionivorans|t__SGB28408 2|456828||||2593013|2593015| 0.38557 +k__Bacteria|p__Proteobacteria|c__CFGB20881|o__OFGB20881|f__FGB20881|g__GGB58408|s__GGB58408_SGB80063|t__SGB80063 2|1224|||||| 0.38004 +k__Bacteria|p__Bacteria_unclassified|c__CFGB7371|o__OFGB7371|f__FGB7371|g__GGB54287|s__GGB54287_SGB75505|t__SGB75505 2||||||| 0.35445 +k__Bacteria|p__Planctomycetes|c__CFGB26100|o__OFGB26100|f__FGB26100|g__GGB45184|s__GGB45184_SGB62700|t__SGB62700 2|203682|||||| 0.35189 +k__Bacteria|p__Bacteroidetes|c__CFGB24578|o__OFGB24578|f__FGB24578|g__GGB45701|s__GGB45701_SGB63418|t__SGB63418 2|976|||||| 0.34293 +k__Archaea|p__Euryarchaeota|c__CFGB9262|o__OFGB9262|f__FGB9262|g__GGB27278|s__GGB27278_SGB39510|t__SGB39510 2157|28890|||||| 0.31924 +k__Archaea|p__Euryarchaeota|c__Methanomicrobia|o__Methanomicrobiales|f__Methanospirillaceae|g__Methanospirillum|s__Methanospirillum_hungatei|t__SGB145 2157|28890|224756|2191|196137|2202|2203| 0.28017 +k__Bacteria|p__Bacteroidetes|c__CFGB7503|o__OFGB7503|f__FGB7503|g__GGB23904|s__GGB23904_SGB35645|t__SGB35645 2|976|||||| 0.26888 +k__Bacteria|p__Actinobacteria|c__Acidimicrobiia|o__Acidimicrobiales|f__Microthrixaceae|g__Candidatus_Microthrix|s__Candidatus_Microthrix_SGB36776|t__SGB36776 2|201174|84992|84993|1798913|41949|| 0.26055 +k__Bacteria|p__Thermotogae|c__Thermotogae|o__Kosmotogales|f__Kosmotogaceae|g__GGB24759|s__GGB24759_SGB36651|t__SGB36651 2|200918|188708|1643946|1643948||| 0.25642 +k__Bacteria|p__Tenericutes|c__CFGB9180|o__OFGB9180|f__FGB9180|g__GGB73886|s__GGB73886_SGB39359|t__SGB39359 2|544448|||||| 0.23479 +k__Bacteria|p__Firmicutes|c__CFGB25401|o__OFGB25401|f__FGB25401|g__GGB45485|s__GGB45485_SGB79908|t__SGB79908 2|1239|||||| 0.19728 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2|203691|203692|136|2791015||| 0.05485 +k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Acidovorax|s__Acidovorax_sp_BoFeN1|t__SGB22471 2|1224|28216|80840|80864|12916|1231053| 0.05437 k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Acidovorax|s__Acidovorax_sp_JHL_3 +k__Bacteria|p__Candidatus_Saccharibacteria|c__CFGB3614|o__OFGB3614|f__FGB3614|g__GGB54796|s__GGB54796_SGB76023|t__SGB76023 2|95818|||||| 0.05236 +k__Bacteria|p__Bacteroidetes|c__CFGB23790|o__OFGB23790|f__FGB23790|g__GGB46018|s__GGB46018_SGB63757|t__SGB63757 2|976|||||| 0.05144 +k__Bacteria|p__Proteobacteria|c__CFGB11081|o__OFGB11081|f__FGB11081|g__GGB46283|s__GGB46283_SGB64057|t__SGB64057 2|1224|||||| 0.05025 +k__Bacteria|p__Actinobacteria|c__CFGB76413|o__OFGB76413|f__FGB76413|g__GGB44055|s__GGB44055_SGB61432|t__SGB61432 2|201174|||||| 0.04612 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2|1224|28216|32003|206379||| 0.03106 +k__Bacteria|p__Actinobacteria|c__CFGB76414|o__OFGB76414|f__FGB76414|g__GGB44034|s__GGB44034_SGB61410|t__SGB61410 2|201174|||||| 0.03089 +k__Bacteria|p__Bacteroidetes|c__CFGB42248|o__OFGB42248|f__FGB42248|g__GGB46504|s__GGB46504_SGB91066|t__SGB91066 2|976|||||| 0.02921 +k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__GGB44435|s__GGB44435_SGB61857|t__SGB61857 2|1224|28216|80840|80864||| 0.02846 +k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Macellibacteroides|s__Macellibacteroides_fermentans|t__SGB1927 2|976|200643|171549|171551|1159323|879969| 0.02639 k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides_chartae,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Macellibacteroides|s__Macellibacteroides_sp_HH_ZS 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2|1224|28216|80840|80864|201096|| 0.00747 +k__Bacteria|p__Bacteroidetes|c__CFGB46549|o__OFGB46549|f__FGB46549|g__GGB75170|s__GGB75170_SGB103651|t__SGB103651 2|976|||||| 0.00733 +k__Bacteria|p__Bacteroidetes|c__CFGB76561|o__OFGB76561|f__FGB76561|g__GGB46503|s__GGB46503_SGB91068|t__SGB91068 2|976|||||| 0.00715 +k__Bacteria|p__Actinobacteria|c__CFGB76414|o__OFGB76414|f__FGB76414|g__GGB44031|s__GGB44031_SGB61405|t__SGB61405 2|201174|||||| 0.00712 +k__Bacteria|p__Proteobacteria|c__CFGB26025|o__OFGB26025|f__FGB26025|g__GGB43049|s__GGB43049_SGB60289|t__SGB60289 2|1224|||||| 0.00697 +k__Bacteria|p__Proteobacteria|c__CFGB76416|o__OFGB76416|f__FGB76416|g__GGB44369|s__GGB44369_SGB61784|t__SGB61784 2|1224|||||| 0.00661 +k__Bacteria|p__Firmicutes|c__CFGB25401|o__OFGB25401|f__FGB25401|g__GGB45481|s__GGB45481_SGB63153|t__SGB63153 2|1239|||||| 0.0064 +k__Bacteria|p__Ignavibacteriae|c__CFGB24766|o__OFGB24766|f__FGB24766|g__GGB75380|s__GGB75380_SGB103363|t__SGB103363 2|1134404|||||| 0.00613 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2157|28890|183925|2158|2159||| 0.00503 +k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium_SGB6179|t__SGB6179 2|1239|186801|186802|31979|1485|| 0.00482 +k__Bacteria|p__Bacteria_unclassified|c__CFGB76452|o__OFGB76452|f__FGB76452|g__GGB42785|s__GGB42785_SGB59992|t__SGB59992 2||||||| 0.0046 +k__Bacteria|p__Spirochaetes|c__CFGB13404|o__OFGB13404|f__FGB13404|g__GGB73569|s__GGB73569_SGB52454|t__SGB52454 2|203691|||||| 0.00451 +k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Streptomycetales|f__Streptomycetaceae|g__GGB44047|s__GGB44047_SGB61423|t__SGB61423 2|201174|1760|85011|2062||| 0.00417 +k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter_johnsonii|t__SGB10398 2|1224|1236|2887326|468|469|40214| 0.00416 k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter_sp_8I_beige,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter_sp_SwsAc2,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter_sp_NEB_394,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter_sp_MF4640,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter_sp_BMW17,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter_sp_MF4642 +k__Bacteria|p__Firmicutes|c__CFGB27080|o__OFGB27080|f__FGB27080|g__GGB27082|s__GGB27082_SGB39291|t__SGB39291 2|1239|||||| 0.00386 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k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter_sp_CS_2,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter_sp_YH16039,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter_sp_YH12201,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter_sp_YH01022,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter_sp_SA01,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter_sp_YH01016 +k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae|g__GGB4456|s__GGB4456_SGB6141|t__SGB6141 2|1239|186801|186802|186804||| 0.0031 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k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Comamonadaceae_unclassified|s__Comamonadaceae_bacterium_CCH4_C5,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Acidovorax|s__Acidovorax_sp_IB03,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Comamonadaceae_unclassified|s__Comamonadaceae_bacterium_CCH12_A10 +k__Bacteria|p__Firmicutes|c__CFGB8207|o__OFGB8207|f__FGB8207|g__GGB25206|s__GGB25206_SGB41973|t__SGB41973 2|1239|||||| 0.00022 +k__Bacteria|p__Bacteroidetes|c__CFGB24433|o__OFGB24433|f__FGB24433|g__GGB46510|s__GGB46510_SGB64371|t__SGB64371 2|976|||||| 0.00022 +k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Propionibacteriales|f__Propionibacteriaceae|g__Propioniciclava|s__Propioniciclava_sp_MC1595|t__SGB87720 2|201174|1760|85009|31957|1085622|2760308| 0.00016 k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Propionibacteriales|f__Propionibacteriaceae|g__Propioniciclava|s__Propioniciclava_sp_MC1683 +k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Propionibacteriales|f__Nocardioidaceae|g__Micropruina|s__Micropruina_glycogenica|t__SGB23995 2|201174|1760|85009|85015|116071|75385| 0.00015 +k__Bacteria|p__Acidobacteria|c__CFGB24388|o__OFGB24388|f__FGB24388|g__GGB27044|s__GGB27044_SGB39251|t__SGB39251 2|57723|||||| 0.00015 +k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Brachymonas|s__Brachymonas_chironomi|t__SGB32580 2|1224|28216|80840|80864|28219|491919| 0.00013 +k__Bacteria|p__Proteobacteria|c__CFGB43452|o__OFGB43452|f__FGB43452|g__GGB25803|s__GGB25803_SGB37788|t__SGB37788 2|1224|||||| 0.00013 +k__Bacteria|p__Firmicutes|c__CFGB40121|o__OFGB40121|f__FGB40121|g__GGB42288|s__GGB42288_SGB59452|t__SGB59452 2|1239|||||| 0.00013 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ERR7569998.txt Fri Jun 07 14:33:38 2024 +0000 @@ -0,0 +1,1036 @@ +#mpa_vOct22_CHOCOPhlAnSGB_202212 +#/home/geoadmin/.mambaforge/envs/metaphlan/bin/metaphlan trimmed/ERR7569998_1.fastq.gz,trimmed/ERR7569998_2.fastq.gz --force --offline --bowtie2db /home/geoadmin/geonomecontainer/METAPHLAN --bowtie2out metaphlan/ERR7569998.bowtie2.bz2 --input_type fastq -o metaphlan/ERR7569998.txt --sample_id_key ERR7569998 --nproc 16 +#159082552 reads processed +#ERR7569998 Metaphlan_Analysis +#clade_name NCBI_tax_id relative_abundance additional_species +k__Bacteria 2 88.425 +k__Archaea 2157 11.575 +k__Bacteria|p__Proteobacteria 2|1224 42.17746 +k__Bacteria|p__Bacteroidetes 2|976 19.8537 +k__Archaea|p__Euryarchaeota 2157|28890 11.575 +k__Bacteria|p__Candidatus_Cloacimonetes 2|456828 8.3344 +k__Bacteria|p__Chloroflexi 2|200795 4.94902 +k__Bacteria|p__Thermotogae 2|200918 2.27536 +k__Bacteria|p__Verrucomicrobia 2|74201 2.18525 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0.06089 +k__Bacteria|p__Bacteroidetes|c__CFGB24417|o__OFGB24417|f__FGB24417|g__GGB75161|s__GGB75161_SGB103627|t__SGB103627 2|976|||||| 0.05933 +k__Bacteria|p__Atribacterota|c__Atribacteria|o__Atribacterales|f__Atribacteraceae|g__Atribacter|s__Atribacter_laminatus|t__SGB94678 2|67818|2847774|2847775|2847776|2847777|2847778| 0.0575 +k__Bacteria|p__Candidatus_Saccharibacteria|c__CFGB3614|o__OFGB3614|f__FGB3614|g__GGB54796|s__GGB54796_SGB76023|t__SGB76023 2|95818|||||| 0.05575 +k__Bacteria|p__Proteobacteria|c__CFGB11081|o__OFGB11081|f__FGB11081|g__GGB46283|s__GGB46283_SGB64057|t__SGB64057 2|1224|||||| 0.05085 +k__Archaea|p__Euryarchaeota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter|s__Methanobrevibacter_smithii|t__SGB714 2157|28890|183925|2158|2159|2172|2173| 0.04904 k__Archaea|p__Euryarchaeota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter|s__Methanobrevibacter_sp_A54 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2|201174|1760|2037|2049|2529408|2758572| 0.02095 +k__Bacteria|p__Synergistetes|c__CFGB7945|o__OFGB7945|f__FGB7945|g__GGB24768|s__GGB24768_SGB36660|t__SGB36660 2|508458|||||| 0.0201 +k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Simplicispira|s__Simplicispira_suum|t__SGB22488 2|1224|28216|80840|80864|352450|2109915| 0.01995 +k__Bacteria|p__Gemmatimonadetes|c__CFGB73260|o__OFGB73260|f__FGB73260|g__GGB80069|s__GGB80069_SGB62355|t__SGB62355 2|142182|||||| 0.0197 +k__Archaea|p__Euryarchaeota|c__CFGB38|o__OFGB38|f__FGB38|g__GGB50|s__GGB50_SGB67|t__SGB67 2157|28890|||||| 0.01911 +k__Bacteria|p__Bacteroidetes|c__CFGB9571|o__OFGB9571|f__FGB9571|g__GGB45918|s__GGB45918_SGB63647|t__SGB63647 2|976|||||| 0.01905 +k__Bacteria|p__Bacteroidetes|c__CFGB7709|o__OFGB7709|f__FGB7709|g__GGB46555|s__GGB46555_SGB64420|t__SGB64420 2|976|||||| 0.01898 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k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus_sp_AM28_29LB,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus_sp_TF12_19AC,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus_sp_AF37_3AC,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus_sp_AF43_11,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus_sp_AM34_10LB,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus_sp_AF16_40,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus_sp_AF17_11,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus_sp_AM31_32,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus_sp_AF42_10,k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus_sp_AM36_18 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2157|28890|183925|2158|2159||| 0.00175 +k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Peptostreptococcaceae|g__Intestinibacter|s__Intestinibacter_bartlettii|t__SGB6140 2|1239|186801|186802|186804|1505657|261299| 0.00173 +k__Archaea|p__Euryarchaeota|c__Methanomicrobia|o__Methanosarcinales|f__Methanosarcinaceae|g__Methanomethylovorans|s__Methanomethylovorans_hollandica|t__SGB611 2157|28890|224756|94695|2206|101191|101192| 0.00168 +k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter_sp_ANC_4218|t__SGB10391 2|1224|1236|2887326|468|469|1977880| 0.00145 k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter_sp_CS_2,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter_sp_YH16039,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter_sp_YH12201,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter_sp_YH01022,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter_sp_SA01,k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter_sp_YH01016 +k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Aminicella|s__Aminicella_lysinilytica|t__SGB28980 2|1239|186801|186802|186806|1637744|433323| 0.00143 +k__Bacteria|p__Proteobacteria|c__CFGB8704|o__OFGB8704|f__FGB8704|g__GGB26186|s__GGB26186_SGB38199|t__SGB38199 2|1224|||||| 0.00137 +k__Bacteria|p__Candidatus_Roizmanbacteria|c__CFGB7841|o__OFGB7841|f__FGB7841|g__GGB31872|s__GGB31872_SGB65430|t__SGB65430 2|1752723|||||| 0.00137 +k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Nakamurellales|f__Nakamurellaceae|g__Nakamurella|s__Nakamurella_multipartita|t__SGB15953 2|201174|1760|1643684|85031|53460|53461| 0.00112 +k__Archaea|p__Euryarchaeota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter|s__Methanobrevibacter_thaueri|t__SGB25645 2157|28890|183925|2158|2159|2172|190975| 0.00108 +k__Bacteria|p__Proteobacteria|c__CFGB8157|o__OFGB8157|f__FGB8157|g__GGB15004|s__GGB15004_SGB62020|t__SGB62020 2|1224|||||| 0.00106 +k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas_loveana|t__SGB21591 2|976|200643|171549|171551|836|1884669| 0.00103 +k__Archaea|p__Euryarchaeota|c__CFGB38|o__OFGB38|f__FGB38|g__GGB52|s__GGB52_SGB75109|t__SGB75109 2157|28890|||||| 0.0009 +k__Bacteria|p__Proteobacteria|c__CFGB41332|o__OFGB41332|f__FGB41332|g__GGB44374|s__GGB44374_SGB61789|t__SGB61789 2|1224|||||| 0.00066 +k__Bacteria|p__Bacteroidetes|c__CFGB24433|o__OFGB24433|f__FGB24433|g__GGB46510|s__GGB46510_SGB64371|t__SGB64371 2|976|||||| 0.00061 +k__Bacteria|p__Bacteroidetes|c__CFGB42240|o__OFGB42240|f__FGB42240|g__GGB75191|s__GGB75191_SGB103428|t__SGB103428 2|976|||||| 0.00059 +k__Bacteria|p__Spirochaetes|c__CFGB41322|o__OFGB41322|f__FGB41322|g__GGB25659|s__GGB25659_SGB37630|t__SGB37630 2|203691|||||| 0.00044 +k__Bacteria|p__Firmicutes|c__CFGB8389|o__OFGB8389|f__FGB8389|g__GGB25664|s__GGB25664_SGB37636|t__SGB37636 2|1239|||||| 0.00043 +k__Bacteria|p__Nitrospirae|c__Nitrospira|o__Nitrospirales|f__Nitrospiraceae|g__Nitrospira|s__Candidatus_Nitrospira_nitrosa|t__SGB9022 2|40117|203693|189778|189779|1234|1742972| 0.00043 +k__Archaea|p__Euryarchaeota|c__Methanomicrobia|o__Methanomicrobiales|f__Methanomicrobiaceae|g__Methanoculleus|s__Methanoculleus_SGB45879|t__SGB45879 2157|28890|224756|2191|2194|45989|| 0.00038 +k__Bacteria|p__Bacteroidetes|c__CFGB46194|o__OFGB46194|f__FGB46194|g__GGB46194|s__GGB46194_SGB63962|t__SGB63962 2|976|||||| 0.00037 +k__Bacteria|p__Bacteroidetes|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Cloacibacterium|s__Cloacibacterium_caeni|t__SGB2534 2|976|117743|200644|2762318|501783|2004710| 0.00036 k__Bacteria|p__Bacteroidetes|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Cloacibacterium|s__Cloacibacterium_normanense +k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Syntrophomonadaceae|g__Syntrophomonas|s__Syntrophomonas_wolfei|t__SGB3855 2|1239|186801|186802|68298|862|863| 0.00035 +k__Bacteria|p__Proteobacteria|c__CFGB8510|o__OFGB8510|f__FGB8510|g__GGB63136|s__GGB63136_SGB85401|t__SGB85401 2|1224|||||| 0.00032 +k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Xanthomonadales|f__Xanthomonadaceae|g__Pseudoxanthomonas|s__Pseudoxanthomonas_mexicana|t__SGB88901 2|1224|1236|135614|32033|83618|128785| 0.00026 +k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium_sp_1001270J_160509_D11|t__SGB6139 2|1239|186801|186802|31979|1485|2787103| 0.00021 +k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Comamonas|s__Comamonas_denitrificans|t__SGB61890 2|1224|28216|80840|80864|283|117506| 0.00021 +k__Bacteria|p__Bacteria_unclassified|c__CFGB76452|o__OFGB76452|f__FGB76452|g__GGB42786|s__GGB42786_SGB59995|t__SGB59995 2||||||| 0.00018 +k__Archaea|p__Euryarchaeota|c__CFGB76181|o__OFGB76181|f__FGB76181|g__GGB27196|s__GGB27196_SGB39419|t__SGB39419 2157|28890|||||| 0.00018 +k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Microbacteriaceae|g__Microbacterium|s__Microbacterium_mitrae|t__SGB87762 2|201174|1760|85006|85023|33882|664640| 0.0001 +k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Rhodocyclales|f__Zoogloeaceae|g__Thauera|s__Thauera_aminoaromatica|t__SGB12599 2|1224|28216|206389|2008794|33057|164330| 9e-05 k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Rhodocyclales|f__Zoogloeaceae|g__Thauera|s__Thauera_sp_MZ1T,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Rhodocyclales|f__Zoogloeaceae|g__Thauera|s__Thauera_sp_DNT_1,k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Rhodocyclales|f__Zoogloeaceae|g__Thauera|s__Thauera_sp_SWB20 +k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Microbacteriaceae|g__Microbacterium|s__Microbacterium_paulum|t__SGB93166 2|201174|1760|85006|85023|33882|2707006| 9e-05 +k__Bacteria|p__Acidobacteria|c__CFGB41084|o__OFGB41084|f__FGB41084|g__GGB75354|s__GGB75354_SGB102763|t__SGB102763 2|57723|||||| 5e-05
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/diamond_valid_1.tsv Fri Jun 07 14:33:38 2024 +0000 @@ -0,0 +1,30 @@ +shigella_dysenteriae_958/1 511145 2.46e-08 +shigella_dysenteriae_1069/1 511145 2.37e-07 +escherichia_coli_308/1 511145 1.55e-12 +shigella_dysenteriae_1418/1 1310613 7.75e-10 +escherichia_coli_962/1 1310613 7.02e-06 +shigella_dysenteriae_520/1 1310613 5.46e-12 +shigella_dysenteriae_242/1 1310613 2.91e-12 +escherichia_coli_1146/1 1310613 2.61e-11 +escherichia_coli_551/1 1310613 1.94e-14 +shigella_dysenteriae_1094/1 1310613 1.74e-13 +shigella_dysenteriae_999/1 0 0 +shigella_dysenteriae_998/1 0 0 +shigella_dysenteriae_997/1 0 0 +shigella_dysenteriae_996/1 0 0 +shigella_dysenteriae_995/1 0 0 +shigella_dysenteriae_994/1 0 0 +shigella_dysenteriae_993/1 0 0 +shigella_dysenteriae_992/1 0 0 +shigella_dysenteriae_991/1 0 0 +shigella_dysenteriae_990/1 0 0 +shigella_dysenteriae_99/1 0 0 +shigella_dysenteriae_989/1 0 0 +shigella_dysenteriae_988/1 0 0 +shigella_dysenteriae_987/1 0 0 +shigella_dysenteriae_986/1 0 0 +shigella_dysenteriae_985/1 0 0 +shigella_dysenteriae_984/1 0 0 +shigella_dysenteriae_983/1 0 0 +shigella_dysenteriae_982/1 0 0 +shigella_dysenteriae_981/1 0 0
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ncbi_taxonomy.loc Fri Jun 07 14:33:38 2024 +0000 @@ -0,0 +1,1 @@ +test-db-tox Test Database ${__HERE__}/test-db \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test-db/names.dmp Fri Jun 07 14:33:38 2024 +0000 @@ -0,0 +1,74 @@ +83333 | Escherichia coli K-12 | | scientific name | +83333 | Escherichia coli K12 | | equivalent name | +562 | "Bacillus coli" Migula 1895 | | authority | +562 | "Bacterium coli commune" Escherich 1885 | | authority | +562 | "Bacterium coli" (Migula 1895) Lehmann and Neumann 1896 | | authority | +562 | ATCC 11775 | | type material | +562 | Bacillus coli | | synonym | +562 | Bacterium coli | | synonym | +562 | Bacterium coli commune | | synonym | +562 | CCUG 24 | | type material | +562 | CCUG 29300 | | type material | +562 | CIP 54.8 | | type material | +562 | DSM 30083 | | type material | +562 | Enterococcus coli | | synonym | +562 | Escherchia coli | | misspelling | +562 | Escherichia coli | | scientific name | +562 | Escherichia coli (Migula 1895) Castellani and Chalmers 1919 | | authority | +562 | Escherichia sp. MAR | | includes | +562 | Escherichia/Shigella coli | | equivalent name | +562 | Eschericia coli | | misspelling | +562 | JCM 1649 | | type material | +562 | LMG 2092 | | type material | +562 | NBRC 102203 | | type material | +562 | NCCB 54008 | | type material | +562 | NCTC 9001 | | type material | +562 | bacterium 10a | | includes | +562 | bacterium E3 | | includes | +561 | Escherchia | | misspelling | +561 | Escherichia | | scientific name | +561 | Escherichia Castellani and Chalmers 1919 | | authority | +543 | Enterobacteraceae | | synonym | +543 | Enterobacteraceae (ex Lapage 1979) Lapage 1982, fam. nov., nom. rev. | | synonym | +543 | Enterobacteriaceae | | scientific name | +543 | Enterobacteriaceae (ex Rahn 1937) Ewing et al. 1980, fam. nov., nom. rev. | | synonym | +543 | Enterobacteriaceae Rahn 1937 | | synonym | +543 | gamma-3 proteobacteria | gamma-3 proteobacteria <#1> | in-part | +91347 | 'Enterobacteriales' | | synonym | +91347 | Enterobacteriaceae and related endosymbionts | | synonym | +91347 | Enterobacteriaceae group | | synonym | +91347 | Enterobacteriales | | scientific name | +91347 | enterobacteria | enterobacteria<blast91347> | blast name | +91347 | gamma-3 proteobacteria | gamma-3 proteobacteria <#5> | in-part | +1236 | Gammaproteobacteria | | scientific name | +1236 | Gammaproteobacteria Garrity et al. 2005 | | synonym | +1236 | Proteobacteria gamma subdivision | | synonym | +1236 | Purple bacteria, gamma subdivision | | synonym | +1236 | g-proteobacteria | gamma proteos<blast1236> | blast name | +1236 | gamma proteobacteria | | synonym | +1236 | gamma subdivision | | synonym | +1236 | gamma subgroup | | synonym | +1224 | Proteobacteria | | scientific name | +1224 | Proteobacteria Garrity et al. 2005 | | authority | +1224 | Proteobacteria [class] Stackebrandt et al. 1988 | | authority | +1224 | not Proteobacteria Cavalier-Smith 2002 | | authority | +1224 | proteobacteria | proteobacteria<blast1224> | blast name | +1224 | purple bacteria | | common name | +1224 | purple bacteria and relatives | | common name | +1224 | purple non-sulfur bacteria | | common name | +1224 | purple photosynthetic bacteria | | common name | +1224 | purple photosynthetic bacteria and relatives | | common name | +2 | Bacteria | Bacteria <prokaryote> | scientific name | +2 | Monera | Monera <Bacteria> | in-part | +2 | Procaryotae | Procaryotae <Bacteria> | in-part | +2 | Prokaryota | Prokaryota <Bacteria> | in-part | +2 | Prokaryotae | Prokaryotae <Bacteria> | in-part | +2 | bacteria | bacteria <blast2> | blast name | +2 | eubacteria | | genbank common name | +2 | not Bacteria Haeckel 1894 | | synonym | +2 | prokaryote | prokaryote <Bacteria> | in-part | +2 | prokaryotes | prokaryotes <Bacteria> | in-part | +1 | all | | synonym | +1 | root | | scientific name | +131567 | biota | | synonym | +131567 | cellular organisms | | scientific name |
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test-db/nodes.dmp Fri Jun 07 14:33:38 2024 +0000 @@ -0,0 +1,10 @@ +83333 | 562 | no rank | | 0 | 1 | 11 | 1 | 0 | 1 | 1 | 0 | | +562 | 561 | species | EC | 0 | 1 | 11 | 1 | 0 | 1 | 1 | 0 | | +561 | 543 | genus | | 0 | 1 | 11 | 1 | 0 | 1 | 0 | 0 | | +543 | 91347 | family | | 0 | 1 | 11 | 1 | 0 | 1 | 0 | 0 | | +91347 | 1236 | order | | 0 | 1 | 11 | 1 | 0 | 1 | 0 | 0 | | +1236 | 1224 | class | | 0 | 1 | 11 | 1 | 0 | 1 | 0 | 0 | | +1224 | 2 | phylum | | 0 | 1 | 11 | 1 | 0 | 1 | 0 | 0 | | +2 | 131567 | superkingdom | | 0 | 0 | 11 | 0 | 0 | 0 | 0 | 0 | | +131567 | 1 | no rank | | 8 | 1 | 1 | 1 | 0 | 1 | 1 | 0 | | +1 | 1 | no rank | | 8 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | |
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/ncbi_taxonomy.loc.sample Fri Jun 07 14:33:38 2024 +0000 @@ -0,0 +1,1 @@ +#value name path \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Fri Jun 07 14:33:38 2024 +0000 @@ -0,0 +1,8 @@ +<?xml version="1.0"?> +<tables> + <!-- Locations of taxonomy data downloaded from NCBI --> + <table name="ncbi_taxonomy" comment_char="#"> + <columns>value, name, path</columns> + <file path="${__HERE__}/test-data/ncbi_taxonomy.loc" /> + </table> +</tables>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.test Fri Jun 07 14:33:38 2024 +0000 @@ -0,0 +1,8 @@ +<?xml version="1.0"?> +<tables> + <!-- Locations of taxonomy data downloaded from NCBI --> + <table name="ncbi_taxonomy" comment_char="#"> + <columns>value, name, path</columns> + <file path="${__HERE__}/test-data/ncbi_taxonomy.loc" /> + </table> +</tables>