# Why are some HUMAnN features in \[name\]\_pathabundance.tsv missing taxonomy? **URL:** \ **Category:** HUMAnN\ **Created:** [October 13, 2023, 12:47am UTC](https://forum.biobakery.org/t/why-are-some-humann-features-in-name-pathabundance-tsv-missing-taxonomy/6057 "2023-10-13T00:47:56Z")\ **Posts on this page:** 2\ **Page:** 1
**Author:** ![jolespin](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/jolespin/32/1838_2.png) [@jolespin](https://forum.biobakery.org/u/jolespin)\ **Post date:** [October 13, 2023, 12:47am UTC](https://forum.biobakery.org/t/why-are-some-humann-features-in-name-pathabundance-tsv-missing-taxonomy/6057/1 "2023-10-13T00:47:56Z")
I’m using HUMAnN 3.8 I made a custom HUMAnN protein database using UniRef50 mappings. My command was the following: ```auto INPUT=veba_output/preprocess/S4/output/joined.fastq.gz OUTPUT=test_output DMND_DB_DIR=veba_output/misc/diamond_database/ NUM_THREADS=1 humann --input ${INPUT} --output ${OUTPUT} --protein-database ${DMND_DB_DIR} --threads ${NUM_THREADS} --bypass-nucleotide-search --input-format fastq.gz --translated-identity-threshold 50 --translated-query-coverage-threshold 80 --search-mode uniref50 --id-mapping veba_output/misc/humann_uniref_annotations.tsv ``` Everything ran as expected however, I’m not sure why the output is missing taxonomy when each protein contains the taxonomy info. ```auto (base) [jespinoz@login02 TestVEBA]$ head veba_output/misc/humann_uniref_annotations.tsv S1__NODE_166_length_33212_cov_10.244534_32964:33209(+) UniRef50_Q41093 82 c__Bacillariophyceae;o __Naviculales;f__ Phaeodactylaceae;g __Phaeodactylum;s__ Phaeodactylum tricornutum [CCAP 1055/1];t __S1__ METABAT2 __E.1__ bin.1 S1__NODE_229_length_28347_cov_10.467447_5060:5751(-) UniRef50_Q41093 196 c__Bacillariophyceae;o __Naviculales;f__ Phaeodactylaceae;g __Phaeodactylum;s__ Phaeodactylum tricornutum [CCAP 1055/1];t __S1__ METABAT2 __E.1__ bin.1 S1__NODE_298_length_24477_cov_10.374539_11070:11663(+) UniRef50_Q41093 198 c__Bacillariophyceae;o __Naviculales;f__ Phaeodactylaceae;g __Phaeodactylum;s__ Phaeodactylum tricornutum [CCAP 1055/1];t __S1__ METABAT2 __E.1__ bin.1 S1__NODE_56_length_52126_cov_10.433043_49957:50562(+) UniRef50_Q41093 202 c__Bacillariophyceae;o __Naviculales;f__ Phaeodactylaceae;g __Phaeodactylum;s__ Phaeodactylum tricornutum [CCAP 1055/1];t __S1__ METABAT2 __E.1__ bin.1 S1__NODE_56_length_52126_cov_10.433043_50725:52123(-) UniRef50_Q41093 338 c__Bacillariophyceae;o __Naviculales;f__ Phaeodactylaceae;g __Phaeodactylum;s__ Phaeodactylum tricornutum [CCAP 1055/1];t __S1__ METABAT2 __E.1__ bin.1 S1__NODE_743_length_9370_cov_9.617391_5:550(+) UniRef50_Q41093 182 c__Bacillariophyceae;o __Naviculales;f__ Phaeodactylaceae;g __Phaeodactylum;s__ Phaeodactylum tricornutum [CCAP 1055/1];t __S1__ METABAT2 __E.1__ bin.1 S1__NODE_14_length_79184_cov_10.324875_17207:17686(+) UniRef50_A0A1Z5JXG7 160 c__Bacillariophyceae;o __Naviculales;f__ Phaeodactylaceae;g __Phaeodactylum;s__ Phaeodactylum tricornutum [CCAP 1055/1];t __S1__ METABAT2 __E.1__ bin.1 S1__NODE_646_length_11435_cov_10.486731_5428:5952(-) UniRef50_A0A1Z5JXG7 175 c__Bacillariophyceae;o __Naviculales;f__ Phaeodactylaceae;g __Phaeodactylum;s__ Phaeodactylum tricornutum [CCAP 1055/1];t __S1__ METABAT2 __E.1__ bin.1 S1__NODE_674_length_10805_cov_9.362977_3661:4200(-) UniRef50_A0A1Z5JXG7 180 c__Bacillariophyceae;o __Naviculales;f__ Phaeodactylaceae;g __Phaeodactylum;s__ Phaeodactylum tricornutum [CCAP 1055/1];t __S1__ METABAT2 __E.1__ bin.1 S1__NODE_8_length_86326_cov_10.138192_57293:57772(+) UniRef50_A0A1Z5JXG7 160 c__Bacillariophyceae;o __Naviculales;f__ Phaeodactylaceae;g __Phaeodactylum;s__ Phaeodactylum tricornutum [CCAP 1055/1];t __S1__ METABAT2 __E.1__ bin.1 ``` Check it out: ```auto (base) [jespinoz@login02 TestVEBA]$ head -n 20 test_output/joined_pathabundance.tsv # Pathway joined_Abundance UNMAPPED 280562.1981557097 UNINTEGRATED 503525.8301515482 UNINTEGRATED|c __Bacillariophyceae;o__ Bacillariales;f __Bacillariaceae;g__ ;s __;t__ S4 __METABAT2__ E.1__bin.2 557698.9739954222 UNINTEGRATED|c __Bacillariophyceae;o__ Naviculales;f __Phaeodactylaceae;g__ Phaeodactylum;s__Phaeodactylum tricornutum [CCAP 1055/1];t__S1 __METABAT2__ E.1__bin.1 22571.9607414017 UNINTEGRATED|c __Bacillariophyceae;o__ Naviculales;f __Phaeodactylaceae;g__ Phaeodactylum;s__Phaeodactylum tricornutum [CCAP 1055/1];t__S2 __METABAT2__ E.1__bin.2 22562.8012692604 UNINTEGRATED|d __Bacteria;p__ Pseudomonadota;c __Alphaproteobacteria;o__ Rhodobacterales;f __Rhodobacteraceae;g__ Aliishimia;s __;t__ S3 __METABAT2__ P.1__bin.4 9215.3696142461 UNINTEGRATED|d __Bacteria;p__ Pseudomonadota;c __Alphaproteobacteria;o__ Rhodobacterales;f __Rhodobacteraceae;g__ JALEFY01;s __;t__ S3 __MAXBIN2-107__ P.1__bin.005 820.2588789283 LIPASYN-PWY: phospholipases 240.5774367950 LIPASYN-PWY: phospholipases|c __Bacillariophyceae;o__ Bacillariales;f __Bacillariaceae;g__ ;s __;t__ S4 __METABAT2__ E.1__bin.2 196.3624498706 LIPASYN-PWY: phospholipases|c __Bacillariophyceae;o__ Naviculales;f __Phaeodactylaceae;g__ Phaeodactylum;s__Phaeodactylum tricornutum [CCAP 1055/1];t__S1 __METABAT2__ E.1__bin.1 22.1074934622 LIPASYN-PWY: phospholipases|c __Bacillariophyceae;o__ Naviculales;f __Phaeodactylaceae;g__ Phaeodactylum;s__Phaeodactylum tricornutum [CCAP 1055/1];t__S2 __METABAT2__ E.1__bin.2 22.1074934622 PANTO-PWY: phosphopantothenate biosynthesis I 137.1807208031 PWY-7208: superpathway of pyrimidine nucleobases salvage 133.8841119258 PWY-5667: CDP-diacylglycerol biosynthesis I 111.6144003857 PWY0-1319: CDP-diacylglycerol biosynthesis II 111.6144003857 P41-PWY: pyruvate fermentation to acetate and (S)-lactate I 102.5586344296 PWY-5100: pyruvate fermentation to acetate and lactate II 102.5586344296 PWY-5100: pyruvate fermentation to acetate and lactate II|c __Bacillariophyceae;o__ Bacillariales;f __Bacillariaceae;g__ ;s __;t__ S4 __METABAT2__ E.1__bin.2 83.8098433960 SER-GLYSYN-PWY: superpathway of L-serine and glycine biosynthesis I 97.7258146256 ``` `LIPASYN-PWY: phospholipases` makes sense because it’s literally just the sum of the other `LIPASYN-PWY: phospholipases` that have taxonomy. However, this one doesn’t have any taxonomy anywhere in the file: ```auto PANTO-PWY: phosphopantothenate biosynthesis I 137.1807208031 ``` Then there is this one: ```auto (base) [jespinoz@login02 TestVEBA]$ cat test_output/joined_pathabundance.tsv | grep "PWY-3781" PWY-3781: aerobic respiration I (cytochrome c) 36.1384257683 PWY-3781: aerobic respiration I (cytochrome c)|d __Bacteria;p__ Pseudomonadota;c __Alphaproteobacteria;o__ Rhodobacterales;f __Rhodobacteraceae;g__ Aliishimia;s __;t__ S3 __METABAT2__ P.1__bin.4 17.5489594619 PWY-3781: aerobic respiration I (cytochrome c)|d __Bacteria;p__ Pseudomonadota;c __Alphaproteobacteria;o__ Rhodobacterales;f __Rhodobacteraceae;g__ JALEFY01;s __;t__ S3 __MAXBIN2-107__ P.1__bin.005 2.3236692546 ``` Where the ones with taxonomy don’t sum up to the one without taxonomy. **My main question is why some don’t have taxonomy assigned to them when all of the protein identifiers are linked to a specific taxa in the --id-mapping table.** ---
**Author:** ![franzosa](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/franzosa/32/3511_2.png) [@franzosa](https://forum.biobakery.org/u/franzosa)\ **Post date:** [October 20, 2023, 8:23pm UTC](https://forum.biobakery.org/t/why-are-some-humann-features-in-name-pathabundance-tsv-missing-taxonomy/6057/2 "2023-10-20T20:23:52Z")
Because we report the abundance of _complete_ pathways, it’s possible/common for the community total to be larger than the sum of complete contributions from individual species. Consider a tiny pathway A → B. Species 1 contributes 2As and 1B, so it has one complete pathway copy. Species 2 contributes 1A and 2Bs, so it also has one complete copy. But at the community level there are three complete copies (not just two). In the extreme case, no single species has a complete copy of the pathway, but the pathway is still satisfied at the community level (e.g. species 1 contributes only A and species 2 contributes only B). In this case, you will see a community (unstratified) abundance for the pathway but not species-level stratifications. These phenomena are a consequence of the way that pathways are reconstructed compared to other functional units. For any other function profiled by HUMAnN (e.g. an EC), the strata will sum to the total.