# MetaPhlAn4 can not profile eukaryote? **URL:** \ **Category:** MetaPhlAn\ **Created:** [June 23, 2023, 1:56am UTC](https://forum.biobakery.org/t/metaphlan4-can-not-profile-eukaryote/5522 "2023-06-23T01:56:05Z")\ **Posts on this page:** 5\ **Page:** 1
**Author:** ![Jiulong-Zhao](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/jiulong-zhao/32/2236_2.png) [@Jiulong-Zhao](https://forum.biobakery.org/u/Jiulong-Zhao)\ **Post date:** [June 23, 2023, 1:56am UTC](https://forum.biobakery.org/t/metaphlan4-can-not-profile-eukaryote/5522/1 "2023-06-23T01:56:05Z")
Hi developers: Thanks for your effects in developing and maintaining MetaPhlAn4! Recently, I installed MetaPhlAn4 and downloaded the database “mpa\_vOct22\_CHOCOPhlAnSGB\_202212” to profile several metagenomes from kelp tissues. However, using the command “metaphlan …/…/2.qc/HK-t\_1\_kneaddata\_paired\_1.fastq,…/…/2.qc/HK-t\_1\_kneaddata\_paired\_2.fastq --input\_type fastq -o K1\_t.txt --nproc 30 --stat\_q 0.1 --bowtie2out bowtie2out\_K1\_t.bz2” (–stat\_q 0.2 also tried), there are many bacterial taxonomies but no eukaryotic taxonomy (especially the kelp) in the result file. So, I wonder if MetaPhlAn4 can profile eukaryotes or not. Or, there is no marker of kelp in the MetaPhlAn4 database, so there is no kelp taxonomy in my result file? Looking forward to your reply! Thank you! Sincerely, Jiulong ---
**Author:** ![aitor.blancomiguez](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/aitor.blancomiguez/32/86_2.png) [@aitor.blancomiguez](https://forum.biobakery.org/u/aitor.blancomiguez)\ **Post date:** [June 28, 2023, 9:10am UTC](https://forum.biobakery.org/t/metaphlan4-can-not-profile-eukaryote/5522/2 "2023-06-28T09:10:37Z")
Dear @Jiulong-Zhao The database mpa\_vOct22 also contains a set of micro-eukaryotic species, you can have a look at the species currently in the database here: [http://cmprod1.cibio.unitn.it/biobakery4/metaphlan\_databases/mpa\_vOct22\_CHOCOPhlAnSGB\_202212\_species.txt.bz2](http://cmprod1.cibio.unitn.it/biobakery4/metaphlan_databases/mpa_vOct22_CHOCOPhlAnSGB_202212_species.txt.bz2) ---
**Author:** ![lzh1982](https://avatars.discourse-cdn.com/v4/letter/l/5fc32e/32.png) [@lzh1982](https://forum.biobakery.org/u/lzh1982)\ **Post date:** [August 4, 2023, 3:18am UTC](https://forum.biobakery.org/t/metaphlan4-can-not-profile-eukaryote/5522/3 "2023-08-04T03:18:45Z")
> [@Jiulong-Zhao](#): > > Hi developers: > Thanks for your effects in developing and maintaining MetaPhlAn4! > Recently, I installed MetaPhlAn4 and downloaded the database “mpa\_vOct22\_CHOCOPhlAnSGB\_202212” to profile several metagenomes from kelp tissues. > However, using the command “metaphlan …/…/2.qc/HK-t\_1\_kneaddata\_paired\_1.fastq,…/…/2.qc/HK-t\_1\_kneaddata\_paired\_2.fastq --input\_type fastq -o K1\_t.txt --nproc 30 --stat\_q 0.1 --bowtie2out bowtie2out\_K1\_t.bz2” (–stat\_q 0.2 also tried), there are many bacterial taxonomies but no eukaryotic taxonomy (especially the kelp) in the result file. > So, I wonder if MetaPhlAn4 can profile eukaryotes or not. Or, there is no marker of kelp in the MetaPhlAn4 database, so there is no kelp taxonomy in my result file? > Looking forward to your reply! > Thank you! > Sincerely, > Jiulong Hi Developers: I also meet these issues. mpa\_vOct22 include the micro-eukaryotic species candida, which I am sure there are many candida species present in my samples, however, the results have not detected the candida when using Metaphlan4 and mpa\_vOct22. ---
**Author:** ![lzh1982](https://avatars.discourse-cdn.com/v4/letter/l/5fc32e/32.png) [@lzh1982](https://forum.biobakery.org/u/lzh1982)\ **Post date:** [August 4, 2023, 3:19am UTC](https://forum.biobakery.org/t/metaphlan4-can-not-profile-eukaryote/5522/4 "2023-08-04T03:19:18Z")
> [@lzh1982](#): > > Hi Developers: > I also meet these issues. mpa\_vOct22 include the micro-eukaryotic species candida, which I am sure there are many candida species present in my samples, however, the results have not detected the candida when using Metaphlan4 and mpa\_vOct22. Hi Developers: I also meet these issues. mpa\_vOct22 include the micro-eukaryotic species candida, which I am sure there are many candida species present in my samples, however, the results have not detected the candida when using Metaphlan4 and mpa\_vOct22. ---
**Author:** ![aitor.blancomiguez](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/aitor.blancomiguez/32/86_2.png) [@aitor.blancomiguez](https://forum.biobakery.org/u/aitor.blancomiguez)\ **Post date:** [September 1, 2023, 12:26pm UTC](https://forum.biobakery.org/t/metaphlan4-can-not-profile-eukaryote/5522/5 "2023-09-01T12:26:29Z")
Hi @lzh1982 this is a tricky question to assess… False negatives in MetaPhlAn can be due to several factors like low abundance, strains not accounted for the building of the database, biased in the extraction protocols, etc. Have you tried to run other profilers to compare the results?