No MetaPhlAn BowTie2 database found (--index option)!

Microbial community profiling HUMAnN
21

I am also stuck on this step. I followed the recommended installation

conda create --name biobakery3 python=3.7
conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge
conda config --add channels biobakery
conda install humann -c biobakery```

I then downloaded all the databases:

humann_databases --download chocophlan full /scratch4/jsuez1/week12/chocophlan --update-config yes
humann_databases --download uniref uniref90_diamond/scratch4/jsuez1/week12/diamond --update-config yes
humann_databases --download utility_mapping full /scratch4/jsuez1/week12/diamond --update-config yes

Then when I try to run either a sample of mine or the demo.fastq.gz, i get this error:

Running metaphlan ........

CRITICAL ERROR: Error executing: /home/hhallow1/.conda/envs/biobakery3/bin/metaphlan /scratch4/jsuez1/week12_virome/sample_results/demo_humann_temp/tmpm6r5uqir/tmpe2u0gnbk -t rel_ab -o /scratch4/jsuez1/week12_virome/sample_results/demo_humann_temp/demo_metaphlan_bugs_list.tsv --input_type fastq --bowtie2out /scratch4/jsuez1/week12_virome/sample_results/demo_humann_temp/demo_metaphlan_bowtie2.txt

Error message returned from metaphlan :

No MetaPhlAn BowTie2 database found (--index option)!

Expecting location bowtie2db

Exiting...

Ive tried re-installing the databases, resinstalling humann completely, nothing is working. After some digging, it seems that when i download the database using

humann_databases --download chocophlan full /scratch4/jsuez1/week12/chocophlan --update-config yes

The file becomes unzipped. I tried manually combining all files into one .fna by doing this

cat chocophlan/* > mpa_v30_CHOCOPhlAn_201901.fna

then using bowtie-build to build my index

bowtie2-build mpa_v30_CHOCOPhlAn_201901.fna mpa_v30_CHOCOPhlAn_201901

I got about 1000 warnings from bowtie that each reference was empty, i.e contains all Ns rather than ATCG, before i killed the job

So my question is, why is the database unzipping when i download it? what is the correct why to cat these files together to be indexed?

I am running Metaphlan 4.0.2 and Humann 3.6

*I should note that i was able to run Humann before with no problem but lost my install because we started using a new cluster.

Thanks!

1 Like
22

Hello!
I used anaconda2 to install humann2 for analysis, but when running, I suddenly reported an error
（CRITICAL ERROR: Error executing: /home/hlli/anaconda2/envs/metagenome_env/bin/metaphlan2.py /home/hlli/AUC/temp/concat/ERR688551.fq -t rel_ab -o /home/hlli/AUC/temp/humann2/ERR688551_humann2_temp/ERR688551_metaphlan_bugs_list.tsv --input_type multifastq --bowtie2out /home/hlli/AUC/temp/humann2/ERR688551_humann2_temp/ERR688551_metaphlan_bowtie2.txt --nproc 8

Error message returned from metaphlan2.py :
No MetaPhlAn BowTie2 database found [–bowtie2db option]! (or wrong path provided).
Expecting location ${mpa_dir}/db_v20/map_v20_m200
Exiting…
）
I have downloaded related related databases and placed them in the specified path, but the same problem still occurs
微信截图_20230201200708
微信截图_20230201200719
I would like to ask the professor what is the best way to solve this problem

23

Can you try running the MetaPhlAn command external to HUMAnN? If you’re manually specifying an index path (or expecting to) HUMAnN won’t have that information. You can pass additional information to MetaPhlAn within the HUMAnN CLI using the --metaphlan-options flag.