# No species found from stool.fasta file in HUMAnN tutorial **URL:** \ **Category:** HUMAnN\ **Created:** [April 23, 2024, 1:43pm UTC](https://forum.biobakery.org/t/no-species-found-from-stool-fasta-file-in-humann-tutorial/6952 "2024-04-23T13:43:26Z")\ **Posts on this page:** 2\ **Page:** 1
**Author:** ![CarolineSchouNielsen](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/carolineschounielsen/32/2830_2.png) [@CarolineSchouNielsen](https://forum.biobakery.org/u/CarolineSchouNielsen)\ **Post date:** [April 23, 2024, 1:43pm UTC](https://forum.biobakery.org/t/no-species-found-from-stool-fasta-file-in-humann-tutorial/6952/1 "2024-04-23T13:43:26Z")
Hi! In section 4.2 of the HUMAnN 3.0 tutorial, I had downloaded all 6 fasta files: -rw-r–r-- 1 lnp524 staff 2.6M Apr 22 12:24 763577454-SRS014459-Stool.fasta -rw-r–r-- 1 lnp524 staff 2.6M Apr 22 12:24 763577454-SRS014464-Anterior _nares.fasta -rw-r–r-- 1 lnp524 staff 2.7M Apr 22 12:24 763577454-SRS014470-Tongue\_dorsum.fasta -rw-r–r-- 1 lnp524 staff 2.7M Apr 22 12:24 763577454-SRS014472-Buccal_ mucosa.fasta -rw-r–r-- 1 lnp524 staff 2.6M Apr 22 12:24 763577454-SRS014476-Supragingival \_plaque.fasta -rw-r–r-- 1 lnp524 staff 2.7M Apr 22 12:25 763577454-SRS014494-Posterior \_fornix.fasta Following the tutorial, when I ran this command on the first file (stool.fasta) I did not get any hits with either MetaPhlAn, bowtie2 or diamond: > humann -i 763577454-SRS014459-Stool.fasta -o hmp\_subset Creating output directory: /Users/lnp524/humann\_dbs/HMP\_downloads/hmp\_subset Output files will be written to: /Users/lnp524/humann\_dbs/HMP\_downloads/hmp\_subset Running metaphlan … Total species selected from prescreen: 0 Selected species explain 0.00% of predicted community composition No species were selected from the prescreen. Because of this the custom ChocoPhlAn database is empty. This will result in zero species-specific gene families and pathways. Running diamond … Aligning to reference database: uniref90\_demo\_prots\_v201901b.dmnd Total bugs after translated alignment: 0 Total gene families after translated alignment: 0 Unaligned reads after translated alignment: 100.0000000000 % Computing gene families … Computing pathways abundance and coverage … Output files created: /Users/lnp524/humann\_dbs/HMP\_downloads/hmp\_subset/763577454-SRS014459-Stool\_genefamilies.tsv /Users/lnp524/humann\_dbs/HMP\_downloads/hmp\_subset/763577454-SRS014459-Stool\_pathabundance.tsv /Users/lnp524/humann\_dbs/HMP\_downloads/hmp\_subset/763577454-SRS014459-Stool\_pathcoverage.tsv The other fasta files worked just fine 🙂 Maybe the database should be updated for a smooth tutorial? Have a great day! Caroline ---
**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:** [April 26, 2024, 6:46pm UTC](https://forum.biobakery.org/t/no-species-found-from-stool-fasta-file-in-humann-tutorial/6952/2 "2024-04-26T18:46:45Z")
Good note. I think the issue is that the tiny HUMAnN demo database doesn’t have all of the species present across all of these demo inputs. If you use the full HUMAnN database for this part of the demo you should get some output. The first part of the tutorial (working on the one `demo.fastq` sample) is designed to work with the tiny databases that come with the HUMAnN software.