# No MetaPhlAn BowTie2 database found (--index option)!
**URL:** https://forum.biobakery.org/t/no-metaphlan-bowtie2-database-found-index-option/1688
**Category:** HUMAnN
**Created:** [February 15, 2021, 3:23pm UTC](https://forum.biobakery.org/t/no-metaphlan-bowtie2-database-found-index-option/1688 "2021-02-15T15:23:24Z")
**Posts on this page:** 20
**Page:** 1
### Author:  [@giacomo42vitali](https://forum.biobakery.org/u/giacomo42vitali)
#### Post date: [February 15, 2021, 3:23pm UTC](https://forum.biobakery.org/t/no-metaphlan-bowtie2-database-found-index-option/1688/1 "2021-02-15T15:23:24Z")
Hi Biobakery community!
I recently upgraded to HUMAnN v3.0 after having used HUMAnN2, but don’t seem to be able to run the demo because of a recurring error.
This text will be hidden
I installed it via conda in a contained environment, as suggested here: [humann3 – The Huttenhower Lab](https://huttenhower.sph.harvard.edu/humann)
```
# create env
conda create --name biobakery3 python=3.7
# activate env
conda activate biobakery3
# update channels
conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge
conda config --add channels biobakery
# install biobakery and metaphlan
conda install -c biobakery human
conda install -c bioconda metaphlan
# test installation
humann_test
```
All of the tests seemed to be fine. I then proceeded to run the demo:
```
humann -i demo.fastq -o demo_outputs
```
The first time I ran it, it took 4 hours, after which the job was killed on the cluster I was using.
After that, it returned the following errors:
```
CRITICAL ERROR: Error executing: /data/home/btx143/.conda/envs/biobakery3/bin/metaphlan /data/home/btx143/shotgun2/demo/data/demo.fastq -t rel_ab -o /data/home/btx143/shotgun2/demo/outputs/demo_output/demo_humann_temp/demo_metaphlan_bugs_list.tsv --input_type fastq --bowtie2out /data/home/btx143/shotgun2/demo/outputs/demo_output/demo_humann_temp/demo_metaphlan_bowtie2.txt
```
and
> Error message returned from metaphlan :
> No MetaPhlAn BowTie2 database found (–index option)!
> Expecting location /data/home/btx143/.conda/envs/biobakery3/lib/python3.7/site-packages/metaphlan/metaphlan\_databases/mpa\_v30\_CHOCOPhlAn\_201901
> Exiting…
The issue is that when I check in the directory where the database indices should be, then I find the following files:
> mpa\_latest
> mpa\_v30\_CHOCOPhlAn\_201901.1.bt2
> mpa\_v30\_CHOCOPhlAn\_201901.2.bt2
> mpa\_v30\_CHOCOPhlAn\_201901.3.bt2
> mpa\_v30\_CHOCOPhlAn\_201901.4.bt2
> mpa\_v30\_CHOCOPhlAn\_201901.fna
> mpa\_v30\_CHOCOPhlAn\_201901.fna.bz2
> mpa\_v30\_CHOCOPhlAn\_201901.md5
> mpa\_v30\_CHOCOPhlAn\_201901.pkl
> mpa\_v30\_CHOCOPhlAn\_201901.rev.1.bt2
> mpa\_v30\_CHOCOPhlAn\_201901.rev.2.bt2
> mpa\_v30\_CHOCOPhlAn\_201901.tar
And the expected “mpa\_v30\_CHOCOPhlAn\_201901” is missing
I found a similar [post](https://forum.biobakery.org/t/difficulties-installing-humann3-metaphlan3/823/2) in this forum and tried the following:
## 1. manually delete metaphlan/bowtie2 databases and re-run demo
From what I unnderstand, humann (through metaphlan and bowtie2) should automatically
## 2. manually delete metaphlan/bowtie2 databases, download the files and use bowtie2 to build the databases
> tar -xvf mpa\_v30\_CHOCOPhlAn\_201901.tar
> bunzip2 \*.bz2
> bowtie2-build mpa\_v30\_CHOCOPhlAn\_201901.fna mpa\_v30\_CHOCOPhlAn\_201901
And even tried to run humann specifying the databases option:
> humann -i demo.fastq -o sample\_results --metaphlan-options “–bowtie2db ${condapath}/${dbpa} -x mpa\_v30\_CHOCOPhlAn\_201901”
After this, I still get the same annoying error:
> No MetaPhlAn BowTie2 database found (–index option)!
> Expecting location /data/home/btx143/.conda/envs/biobakery3/lib/python3.7/site-packages/metaphlan/metaphlan\_databases/mpa\_v30\_CHOCOPhlAn\_201901
> Exiting…
Did anyone run into the same or similar error?
Cheers,
Giacomo
---
### Author:  [@lauren.j.mciver](https://forum.biobakery.org/u/lauren.j.mciver)
#### Post date: [February 17, 2021, 8:48pm UTC](https://forum.biobakery.org/t/no-metaphlan-bowtie2-database-found-index-option/1688/2 "2021-02-17T20:48:51Z")
Hello, Sorry you are having issues running the demo. Thank you for your detailed and organized post! I think you might have an older version of MetaPhlAn installed. Can you check the version number? If it is an older version if you update to the latest version and then run `$ metaphlan --install` it should download and install the database. Once you have the database installed, you should hopefully be set! If you still see errors double check you have the latest version of HUMAnN installed. Sometimes conda does not always install the latest version but instead it installs an older version that is compatible with the current conda environment.
Thank you,
Lauren
---
### Author:  [@giacomo42vitali](https://forum.biobakery.org/u/giacomo42vitali)
#### Post date: [March 1, 2021, 7:30am UTC](https://forum.biobakery.org/t/no-metaphlan-bowtie2-database-found-index-option/1688/3 "2021-03-01T07:30:36Z")
Hi Lauren,
Thank you for your reply, and sorry for late answer!
I did have metaphlan v3.0.7 installed already. All it took was to run:
> metaphlan --install
(as you sugested)
and the correct databases were installed!
Thank you so much!
Giacomo
---
### Author:  [@lauren.j.mciver](https://forum.biobakery.org/u/lauren.j.mciver)
#### Post date: [March 1, 2021, 9:14pm UTC](https://forum.biobakery.org/t/no-metaphlan-bowtie2-database-found-index-option/1688/4 "2021-03-01T21:14:31Z")
Hi Giacomo, Awesome! Thanks for the follow up and glad to hear you are all set! Please post again if you have other issues.
Thank you,
Lauren
---
### Author:  [@kmorten](https://forum.biobakery.org/u/kmorten)
#### Post date: [March 22, 2021, 4:35pm UTC](https://forum.biobakery.org/t/no-metaphlan-bowtie2-database-found-index-option/1688/5 "2021-03-22T16:35:12Z")
Hi there!
I’m having trouble running the demo as well. For context, I’m on linux server and I’ve tried the exact commands listed on the humann3 site ([link here](https://huttenhower.sph.harvard.edu/humann)). I’ve made sure that metaphlan is correct version, as well as humann. I’ve tried both the conda installation and the pip installation but consistently run into the same error when I try to run the demo. For fun, I tried running metaphlan --install but got the same error again. The error reads as follows:
###########################################
Downloading MetaPhlAn database
Please note due to the size this might take a few minutes
File /home/kmorten/bin/anaconda3/envs/biobakery3/lib/python3.7/site-packages/metaphlan/metaphlan\_databases/mpa\_v30\_CHOCOPhlAn\_201901.tar already present!
File /home/kmorten/bin/anaconda3/envs/biobakery3/lib/python3.7/site-packages/metaphlan/metaphlan\_databases/mpa\_v30\_CHOCOPhlAn\_201901.md5 already present!
Traceback (most recent call last):
File “/home/kmorten/bin/anaconda3/envs/biobakery3/bin/metaphlan”, line 10, in
sys.exit(main())
File “/home/kmorten/bin/anaconda3/envs/biobakery3/lib/python3.7/site-packages/metaphlan/metaphlan.py”, line 925, in main
pars[‘index’] = check\_and\_install\_database(pars[‘index’], pars[‘bowtie2db’], pars[‘bowtie2\_build’], pars[‘nproc’], pars[‘force\_download’])
File “/home/kmorten/bin/anaconda3/envs/biobakery3/lib/python3.7/site-packages/metaphlan/ **init**.py”, line 301, in check\_and\_install\_database
download\_unpack\_tar(index, bowtie2\_db, bowtie2\_build, nproc, use\_zenodo)
File “/home/kmorten/bin/anaconda3/envs/biobakery3/lib/python3.7/site-packages/metaphlan/ **init**.py”, line 180, in download\_unpack\_tar
bt2\_build\_output = subp.check\_output([bowtie2\_build, ‘–usage’], stderr=subp.STDOUT)
File “/home/kmorten/bin/anaconda3/envs/biobakery3/lib/python3.7/subprocess.py”, line 411, in check\_output
\*\*kwargs).stdout
File “/home/kmorten/bin/anaconda3/envs/biobakery3/lib/python3.7/subprocess.py”, line 512, in run
output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command ‘[‘bowtie2-build’, ‘–usage’]’ returned non-zero exit status 127.
############################################
I’ve read a lot of the posts that seem to have traces of the issue I’m experiencing, but no luck. Any suggestions would be much appreciated!
Thank you!
Kate
---
### Author:  [@Massoud\_Maher](https://forum.biobakery.org/u/Massoud_Maher)
#### Post date: [July 14, 2021, 5:15am UTC](https://forum.biobakery.org/t/no-metaphlan-bowtie2-database-found-index-option/1688/6 "2021-07-14T05:15:03Z")
I was getting this error when I was running HumanN3. I fixed it (and am now getting OP’s error) by running
```auto
conda install bowtie2
```
for some reason bowtie2 wasn’t installed.
Also I didn’t have tbb installed and had to do that as well
---
### Author:  [@Massoud\_Maher](https://forum.biobakery.org/u/Massoud_Maher)
#### Post date: [July 14, 2021, 4:56pm UTC](https://forum.biobakery.org/t/no-metaphlan-bowtie2-database-found-index-option/1688/7 "2021-07-14T16:56:57Z")
I’m getting this error and
```auto
metaphlan —install
```
does not solve it. I do have the latest versions of metaphlan and humann
---
### Author:  [@Billy\_Law](https://forum.biobakery.org/u/Billy_Law)
#### Post date: [November 4, 2021, 4:52pm UTC](https://forum.biobakery.org/t/no-metaphlan-bowtie2-database-found-index-option/1688/8 "2021-11-04T16:52:15Z")
I am also running into this error. Just installed today
It might be a fault of the new database.
I managed to trick metaphlan into downloading an earlier version, by editing the mpa\_latest file in the databases folder. we’ll see how that goes
no luck at all
---
### Author:  [@Daniel\_Thomas](https://forum.biobakery.org/u/Daniel_Thomas)
#### Post date: [February 17, 2022, 4:05pm UTC](https://forum.biobakery.org/t/no-metaphlan-bowtie2-database-found-index-option/1688/9 "2022-02-17T16:05:05Z")
Like @Massoud_Maher, for me this error was due to the lack of a particular threading library for C++, called tbb2. I think Bowtie needs it. I couldn’t find tbb2 on Conda. I’m in an Ubuntu environment, so I installed it outside of conda with apt:
`sudo apt-get install libtbb2`
---
### Author:  [@YikeShen](https://forum.biobakery.org/u/YikeShen)
#### Post date: [April 17, 2022, 2:07pm UTC](https://forum.biobakery.org/t/no-metaphlan-bowtie2-database-found-index-option/1688/10 "2022-04-17T14:07:04Z")
Hello biobakery community,
I used alpha version of humann3 and an older version of MetaPhlAn it worked.
However, I installed the newest version of both, installed the most up to date chocoplan, uniref databases, it shows the same error message.
> Error message returned from metaphlan :
> No MetaPhlAn BowTie2 database found (–index option)!
> Expecting location bowtie2db
Is there a way to use the newer version and still be able to run?
Thanks!!
Yike
---
### Author:  [@angelolimeta](https://forum.biobakery.org/u/angelolimeta)
#### Post date: [April 21, 2022, 1:38pm UTC](https://forum.biobakery.org/t/no-metaphlan-bowtie2-database-found-index-option/1688/11 "2022-04-21T13:38:32Z")
Hi!
Just wanted to chime in and say that im getting the same error as @YikeShen. Im using humann v3.0.1 and metaphlan 3.0.14.
Running metaphlan --install returns “The database is installed”. I checked the metaphlan\_databases folder in my metaphlan installation on conda and the following files are there, so it looks ok:
> README.txt
> mpa\_latest
> mpa\_v30\_CHOCOPhlAn\_201901.1.bt2.tmp
> mpa\_v30\_CHOCOPhlAn\_201901.2.bt2.tmp
> mpa\_v30\_CHOCOPhlAn\_201901.3.bt2.tmp
> mpa\_v30\_CHOCOPhlAn\_201901.4.bt2.tmp
> mpa\_v30\_CHOCOPhlAn\_201901.76.sa
> mpa\_v30\_CHOCOPhlAn\_201901.77.sa
> mpa\_v30\_CHOCOPhlAn\_201901.78.sa
> mpa\_v30\_CHOCOPhlAn\_201901.79.sa
> mpa\_v30\_CHOCOPhlAn\_201901.80.sa
> mpa\_v30\_CHOCOPhlAn\_201901.81.sa
> mpa\_v30\_CHOCOPhlAn\_201901.82.sa
> mpa\_v30\_CHOCOPhlAn\_201901.83.sa
> mpa\_v30\_CHOCOPhlAn\_201901.84.sa
> mpa\_v30\_CHOCOPhlAn\_201901.85.sa
> mpa\_v30\_CHOCOPhlAn\_201901.86.sa
> mpa\_v30\_CHOCOPhlAn\_201901.87.sa
> mpa\_v30\_CHOCOPhlAn\_201901.88.sa
> mpa\_v30\_CHOCOPhlAn\_201901.89.sa
> mpa\_v30\_CHOCOPhlAn\_201901.90.sa
> mpa\_v30\_CHOCOPhlAn\_201901.91.sa
> mpa\_v30\_CHOCOPhlAn\_201901.92.sa
> mpa\_v30\_CHOCOPhlAn\_201901.93.sa
> mpa\_v30\_CHOCOPhlAn\_201901.94.sa
> mpa\_v30\_CHOCOPhlAn\_201901.95.sa
> mpa\_v30\_CHOCOPhlAn\_201901.96.sa
> mpa\_v30\_CHOCOPhlAn\_201901.fna
> mpa\_v30\_CHOCOPhlAn\_201901.fna.bz2
> mpa\_v30\_CHOCOPhlAn\_201901.md5
> mpa\_v30\_CHOCOPhlAn\_201901.pkl
> mpa\_v30\_CHOCOPhlAn\_201901.tar
Ive tried manually specifying the --index and --bowtie2db paths in --metaphlan-options but it still returns the same error messsage:
> Error message returned from metaphlan :
> No MetaPhlAn BowTie2 database found (–index option)!
> Expecting location bowtie2db
The exact call i used is the following:
`humann --metaphlan-options "-t rel_ab --index mpa_v30_CHOCOPhlAn_201901 --bowtie2db /priv/c3-sysbio/sysbio/LeaversData_Omics/MetabogenMelanoma/ici_env/lib/python3.9/site-packages/metaphlan/metaphlan_databases" --input /priv/c3-sysbio/sysbio/LeaversData_Omics/MetabogenMelanoma/fastq_filt_cat/D9_FDPL210411324-1a_HWWWJDSX2_L3_cat.fq.gz --output /priv/c3-sysbio/sysbio/LeaversData_Omics/MetabogenMelanoma/test_out --threads 18`
Best,
Angelo
---
### Author:  [@angelolimeta](https://forum.biobakery.org/u/angelolimeta)
#### Post date: [April 21, 2022, 4:31pm UTC](https://forum.biobakery.org/t/no-metaphlan-bowtie2-database-found-index-option/1688/12 "2022-04-21T16:31:48Z")
I looked through the metaphlan.py source code now and it looks like the database files i have are incorrect. The first 4 should end with .bt2 and not .bt2.tmp, also the rev1.bt2 and rev2.bt2 are missing. Gonna see if i can re-download these somehow.
EDIT:
Managed to fix it now! simply re-downloaded the databases and re-built the bowtie2 index in a separate folder using metaphlan --install --bowtie2db /path/to/mpa\_dbs
I managed to run the humann\_test function a few days ago without any problems, using just the installation instructions on your website ([humann3 – The Huttenhower Lab](https://huttenhower.sph.harvard.edu/humann/)). Also, just runnning metaphlan --install returns that the databases have already been installed, even though in my case they still had the .tmp extension as well. Might be good to add an extra check in these functions in a future release.
**For any of u having similar issues, maybe double check that the metaphlan\_databases folder in your conda installation contains the following files:**
> mpa\_v30\_CHOCOPhlAn\_201901.1.bt2
> mpa\_v30\_CHOCOPhlAn\_201901.2.bt2
> mpa\_v30\_CHOCOPhlAn\_201901.3.bt2
> mpa\_v30\_CHOCOPhlAn\_201901.4.bt2
> mpa\_v30\_CHOCOPhlAn\_201901.rev1.bt2
> mpa\_v30\_CHOCOPhlAn\_201901.rev2.bt2
> mpa\_v30\_CHOCOPhlAn\_201901.fna.bz2
> mpa\_v30\_CHOCOPhlAn\_201901.md5
> mpa\_v30\_CHOCOPhlAn\_201901.pkl
> mpa\_v30\_CHOCOPhlAn\_201901.tar
---
### Author:  [@rburten](https://forum.biobakery.org/u/rburten)
#### Post date: [May 3, 2022, 10:10pm UTC](https://forum.biobakery.org/t/no-metaphlan-bowtie2-database-found-index-option/1688/13 "2022-05-03T22:10:25Z")
Hi everyone,
I am running HUMAnN3 on an ssh client and dealing with the same error when I run the demo:
Error message returned from metaphlan :
No MetaPhlAn BowTie2 database found (–index option)!
Expecting location bowtie2db
I have updated or tried updating humann, metaphlan, bowtie2, and tbb, and the issue still occurs when I have the latest version of all of these packages.
I attempted @angelolimeta’s solution to re-download the databases and rebuild the bowtie2 index using metaphlan --install --bowtie2db mpa\_dbs and that partially failed (therefore not resolving the issue), with this error message:
Building Bowtie2 indexes
Fatal error running ‘bowtie2-build --quiet --threads 4 -f mpa\_dbs/mpa\_v30\_CHOCOPhlAn\_201901.fna mpa\_dbs/mpa\_v30\_CHOCOPhlAn\_201901’
Error message: ‘Command ‘[‘bowtie2-build’, ‘–quiet’, ‘–threads’, ‘4’, ‘-f’, ‘mpa\_dbs/mpa\_v30\_CHOCOPhlAn\_201901.fna’, ‘mpa\_dbs/mpa\_v30\_CHOCOPhlAn\_201901’]’ returned non-zero exit status 247.’
Any assistance would be very appreciated!
---
### Author:  [@YikeShen](https://forum.biobakery.org/u/YikeShen)
#### Post date: [May 5, 2022, 6:19pm UTC](https://forum.biobakery.org/t/no-metaphlan-bowtie2-database-found-index-option/1688/14 "2022-05-05T18:19:47Z")
Those two versions I installed in December 2020 works for me.
---
### Author:  [@sabrinaarif](https://forum.biobakery.org/u/sabrinaarif)
#### Post date: [May 6, 2022, 5:10am UTC](https://forum.biobakery.org/t/no-metaphlan-bowtie2-database-found-index-option/1688/15 "2022-05-06T05:10:52Z")
I have encountered the same error and find that every time I try to manually download the databases, I get different results. Sometimes the mpa\_v30\_CHOCOPhlAn\_201901.rev.1.bt2/ mpa\_v30\_CHOCOPhlAn\_201901.rev.2.bt2 files are just not included. Sometimes one or more of the file sizes are zero. I have followed another thread ([Humann 3 bowtie error - #9 by nasnuvens](https://forum.biobakery.org/t/humann-3-bowtie-error/610/9)) that suggested deleting the .bt2 files and manually rebuilding the index. This seemed to work for me but I am not sure if the files are complete.
**For someone who has successfully used these databases:** what are the final sizes of each file in the metaphlan\_databases directory?
---
### Author:  [@angelolimeta](https://forum.biobakery.org/u/angelolimeta)
#### Post date: [May 22, 2022, 3:03pm UTC](https://forum.biobakery.org/t/no-metaphlan-bowtie2-database-found-index-option/1688/16 "2022-05-22T15:03:51Z")
Hi @sabrinaarif
Here’s a screenshot of the file sizes in my metaphlan db folders
---
### Author:  [@diazo005](https://forum.biobakery.org/u/diazo005)
#### Post date: [September 27, 2022, 3:53am UTC](https://forum.biobakery.org/t/no-metaphlan-bowtie2-database-found-index-option/1688/17 "2022-09-27T03:53:39Z")
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:
```auto
humann --input demo.fastq.gz --output demo_fastq --threads 16
```
and I got this output
```auto
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](https://forum.biobakery.org/t/announcing-metaphlan-3-1-and-humann-3-1/3881)
The following steps are detailed here ([humann3 – The Huttenhower Lab](https://huttenhower.sph.harvard.edu/humann)), 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:
```auto
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
---
### Author:  [@cquxiaoy](https://forum.biobakery.org/u/cquxiaoy)
#### Post date: [October 14, 2022, 1:14am UTC](https://forum.biobakery.org/t/no-metaphlan-bowtie2-database-found-index-option/1688/18 "2022-10-14T01:14:21Z")
I got the same problem yesterday. I solved it by installing specific versions of metaphlan.
The version humann 3.0.0.alpha.3 & metaphlan 3.0.9 would work perfectly.
---
### Author:  [@Heba\_Allah\_Mohamed\_H](https://forum.biobakery.org/u/Heba_Allah_Mohamed_H)
#### Post date: [October 26, 2022, 12:42pm UTC](https://forum.biobakery.org/t/no-metaphlan-bowtie2-database-found-index-option/1688/19 "2022-10-26T12:42:27Z")
what’s the command of installing specific versions of metaphlan?
---
### Author:  [@cquxiaoy](https://forum.biobakery.org/u/cquxiaoy)
#### Post date: [October 27, 2022, 5:09am UTC](https://forum.biobakery.org/t/no-metaphlan-bowtie2-database-found-index-option/1688/20 "2022-10-27T05:09:05Z")
pip install metaphlan==[here is version string]
Such as, `pip install metaphlan==3.0.9`
_\>=, \<=, vice versa._
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