Hello,
I had the same issue reported here. I have installed humann3 using a humann3.yml file. I git clone the humann3 from github and tryed to run the test samples within the ~/humann/examples folder. I used this command:
humann --input demo.fastq.gz --output demo_fastq --threads 16
and I got this output
Creating output directory: /panfs/roc/groups/11/noyes046/diazo005/humann/examples/demo_fastq
Output files will be written to: /panfs/roc/groups/11/noyes046/diazo005/humann/examples/demo_fastq
Decompressing gzipped file ...
Running metaphlan ........
CRITICAL ERROR: Error executing: /home/noyes046/diazo005/.conda/envs/humann3/bin/metaphlan /panfs/roc/groups/11/
noyes046/diazo005/humann/examples/demo_fastq/demo_humann_temp/tmpp_ptudn3/tmpzbt96zmj -t rel_ab -o /panfs/roc/gr
oups/11/noyes046/diazo005/humann/examples/demo_fastq/demo_humann_temp/demo_metaphlan_bugs_list.tsv --input_type
fastq --bowtie2out /panfs/roc/groups/11/noyes046/diazo005/humann/examples/demo_fastq/demo_humann_temp/demo_metap
hlan_bowtie2.txt --nproc 16
Error message returned from metaphlan :
No MetaPhlAn BowTie2 database found (--index option)!
Expecting location bowtie2db
Exiting...
Then I just looked in several forums and ended up doing a fresh installation of the new release of Humann3, as indicated in the release note: Announcing MetaPhlAn 3.1 and HUMAnN 3.1
The following steps are detailed here (humann3 – The Huttenhower Lab), briefly:
Create and activate a new conda environment called “biobakery3”
conda create --name biobakery3 python=3.7
conda activate biobakery3
Set conda channel priority
conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge
conda config --add channels biobakery
Install HUMAnN 3.1 software with demo databases:
conda install humann -c biobakery
Tested my INSTALLATION
humann_test
I moved to examples directory (within the already copied humann directory):
cd ~/humann/examples
I ran the following code in the “examples” folder
humann --input demo.fastq.gz --output demo_fastq --threads 16
Everything worked out and I got the following OUTPUT:
Creating output directory: /panfs/roc/groups/11/noyes046/diazo005/humann/examples/demo_fastq
Output files will be written to: /panfs/roc/groups/11/noyes046/diazo005/humann/examples/demo_fastq
Decompressing gzipped file ...
Running metaphlan ........
Found t__SGB1815 : 53.72% of mapped reads ( s__Bacteroides_dorei,s__Phocaeicola_vulgatus,s__Bacteroides_v$
lgatus,s__Bacteroides_sp_9_1_42FAA,s__Bacteroides_sp_3_1_33FAA,s__Bacteroides_sp_NMBE5,s__Phocaeicola_dor$
i,s__Bacteroidaceae_bacterium,g__Phocaeicola.s__Phocaeicola_vulgatus,g__Bacteroides.s__Bacteroides_sp_9_1$
42FAA,g__Bacteroides.s__Bacteroides_sp_3_1_33FAA,g__Bacteroides.s__Bacteroides_sp_NMBE5,g__Bacteroidaceae$
unclassified.s__Bacteroidaceae_bacterium )
Found t__SGB1814 : 46.28% of mapped reads ( s__Bacteroides_vulgatus,s__Bacteroides_dorei,s__Phocaeicola_d$
rei,s__Bacteroides_sp_3_1_33FAA,s__Bacteroides_sp_4_3_47FAA,s__Bacteroides_sp_3_1_40A,s__Bacteroides_sp_A$
18_9,s__Bacteroides_sp_AM23_18,s__Bacteroides_sp_AF39_10AT,s__Bacteroides_sp_AF32_15BH,s__Bacteroides_sp_$
F25_18,s__Bacteroides_sp_AF16_29,s__Bacteroides_sp_AM28_6,s__Bacteroides_sp_AM27_13,s__Bacteroides_sp_AM2$
_11,s__Bacteroides_sp_AF15_23LB,s__Bacteroides_sp_AF17_1,g__Phocaeicola.s__Phocaeicola_dorei,g__Bacteroid$
s.s__Bacteroides_sp_3_1_33FAA,g__Bacteroides.s__Bacteroides_sp_4_3_47FAA,g__Bacteroides.s__Bacteroides_sp$
3_1_40A,g__Bacteroides.s__Bacteroides_sp_AM18_9,g__Bacteroides.s__Bacteroides_sp_AM23_18,g__Bacteroides.s_
_Bacteroides_sp_AF39_10AT,g__Bacteroides.s__Bacteroides_sp_AF32_15BH,g__Bacteroides.s__Bacteroides_sp_AF25
_18,g__Bacteroides.s__Bacteroides_sp_AF16_29,g__Bacteroides.s__Bacteroides_sp_AM28_6,g__Bacteroides.s__Bac
teroides_sp_AM27_13,g__Bacteroides.s__Bacteroides_sp_AM26_11,g__Bacteroides.s__Bacteroides_sp_AF15_23LB,g_
_Bacteroides.s__Bacteroides_sp_AF17_1 )
Total species selected from prescreen: 47
Selected species explain 100.00% of predicted community composition
Creating custom ChocoPhlAn database ........
Running bowtie2-build ........ [870/1996]
Running bowtie2 ........
Total bugs from nucleotide alignment: 2
g__Bacteroides.s__Bacteroides_dorei: 1270 hits
g__Bacteroides.s__Bacteroides_vulgatus: 1335 hits
Total gene families from nucleotide alignment: 572
Unaligned reads after nucleotide alignment: 87.5952380952 %
Running diamond ........
Aligning to reference database: uniref90_demo_prots_v201901b.dmnd
Total bugs after translated alignment: 3
g__Bacteroides.s__Bacteroides_dorei: 1270 hits
g__Bacteroides.s__Bacteroides_vulgatus: 1335 hits
unclassified: 1017 hits
Total gene families after translated alignment: 615
Unaligned reads after translated alignment: 82.8857142857 %
Computing gene families ...
Computing pathways abundance and coverage ...
Output files created:
/panfs/roc/groups/11/noyes046/diazo005/humann/examples/demo_fastq/demo_genefamilies.tsv
/panfs/roc/groups/11/noyes046/diazo005/humann/examples/demo_fastq/demo_pathabundance.tsv
/panfs/roc/groups/11/noyes046/diazo005/humann/examples/demo_fastq/demo_pathcoverage.tsv
I obtained the 3 output files from the tutorial. So, suggestion: Download the new Humann 3.1 (with the new Metaphlan release).
Gerardo R Diaz
CVM-UMN