# Metaphlan2 trial run result **URL:** \ **Category:** MetaPhlAn\ **Created:** [March 26, 2020, 7:56am UTC](https://forum.biobakery.org/t/metaphlan2-trial-run-result/302 "2020-03-26T07:56:04Z")\ **Posts on this page:** 17\ **Page:** 1
**Author:** ![DEEPCHANDA7](https://avatars.discourse-cdn.com/v4/letter/d/eb9ed0/32.png) [@DEEPCHANDA7](https://forum.biobakery.org/u/DEEPCHANDA7)\ **Post date:** [March 26, 2020, 7:56am UTC](https://forum.biobakery.org/t/metaphlan2-trial-run-result/302/1 "2020-03-26T07:56:04Z")
I am running **Metaphlan2 (2.96.1)** with the **mpa\_v296\_CHOCOPhlAn** database. When I analyzed the subsampled data (`https://bitbucket.org/biobakery/biobakery/raw/tip/demos/biobakery_demos/data/metaphlan2/input/SRS014476-Supragingival_plaque.fasta.gz`) provided in the tutorial with my installed software, I found the result is different from what given in the tutorial. Here I’m attaching my output file. Please tell me why I am getting discrepancies in my result? ![MY_output](https://canada1.discourse-cdn.com/flex027/uploads/biobakery/original/1X/95f5342fadfbe04ebb2e8f5956f565c63f0f1b4b.png) Link to tutorial output file: [https://bitbucket.org/biobakery/biobakery/raw/tip/demos/biobakery\_demos/data/metaphlan2/output/SRS014476-Supragingival\_plaque\_profile.txt](https://bitbucket.org/biobakery/biobakery/raw/tip/demos/biobakery_demos/data/metaphlan2/output/SRS014476-Supragingival_plaque_profile.txt) Thank You, DEEP CHANDA ---
**Author:** ![fbeghini](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/fbeghini/32/81_2.png) [@fbeghini](https://forum.biobakery.org/u/fbeghini)\ **Post date:** [April 6, 2020, 4:18pm UTC](https://forum.biobakery.org/t/metaphlan2-trial-run-result/302/2 "2020-04-06T16:18:36Z")
Hi, the results showed in the tutorial were computed with a previous version of the MetaPhlAn2 database (v20\_m200), while yours are obtained with a more recent and updated one. The new database includes more species, compared to the previous one, so this is the reason of why more species are now present. Best ---
**Author:** ![DEEPCHANDA7](https://avatars.discourse-cdn.com/v4/letter/d/eb9ed0/32.png) [@DEEPCHANDA7](https://forum.biobakery.org/u/DEEPCHANDA7)\ **Post date:** [April 26, 2020, 12:53pm UTC](https://forum.biobakery.org/t/metaphlan2-trial-run-result/302/3 "2020-04-26T12:53:36Z")
Hi fbeghini!!! Can I use this output profiled by this database ( **mpa\_v296\_CHOCOPhlAn\_201901** ) as input for **Humann2**? I am using **MetaPhlAn version 2.96.1 (02 Feb 2020)** Thanks and Regards, DC7 ---
**Author:** ![fbeghini](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/fbeghini/32/81_2.png) [@fbeghini](https://forum.biobakery.org/u/fbeghini)\ **Post date:** [April 27, 2020, 2:27pm UTC](https://forum.biobakery.org/t/metaphlan2-trial-run-result/302/4 "2020-04-27T14:27:04Z")
Hi, yes, you can use the 2.9 version of HUMAnN [https://github.com/biobakery/humann/tree/2.9](https://github.com/biobakery/humann/tree/2.9) ---
**Author:** ![Toan](https://avatars.discourse-cdn.com/v4/letter/t/b3f665/32.png) [@Toan](https://forum.biobakery.org/u/Toan)\ **Post date:** [April 28, 2020, 9:54pm UTC](https://forum.biobakery.org/t/metaphlan2-trial-run-result/302/5 "2020-04-28T21:54:00Z")
Hi there, I am new with Metaphlan. I am trying to follow the tutorial of metaphlan2 at bitbucket, but when I ran the command: metaphlan2.py SRS014476-Supragingival\_plaque.fasta.gz --input\_type fasta \> SRS014476-Supragingival\_plaque\_profile.txt I got an error as following: Downloading [https://bitbucket.org/biobakery/metaphlan2/downloads/mpa\_latest](https://bitbucket.org/biobakery/metaphlan2/downloads/mpa_latest) Warning: Unable to download [https://bitbucket.org/biobakery/metaphlan2/downloads/mpa\_latest](https://bitbucket.org/biobakery/metaphlan2/downloads/mpa_latest) Traceback (most recent call last): File “/usr/local/bin/metaphlan2.py”, line 1442, in metaphlan2() File “/usr/local/bin/metaphlan2.py”, line 1164, in metaphlan2 pars[‘index’] = check\_and\_install\_database(pars[‘index’], pars[‘bowtie2db’], pars[‘bowtie2\_build’], pars[‘nproc’], pars[‘force\_download’]) File “/usr/local/bin/metaphlan2.py”, line 570, in check\_and\_install\_database index = resolve\_latest\_database(bowtie2\_db, force\_redownload\_latest) File “/usr/local/bin/metaphlan2.py”, line 549, in resolve\_latest\_database with open(os.path.join(bowtie2\_db,‘mpa\_latest’)) as mpa\_latest: FileNotFoundError: [Errno 2] No such file or directory: ‘/usr/local/bin/metaphlan\_databases/mpa\_latest’ Could you please advise me how to solve it? Thank you very much, Best, Toan ---
**Author:** ![fbeghini](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/fbeghini/32/81_2.png) [@fbeghini](https://forum.biobakery.org/u/fbeghini)\ **Post date:** [April 29, 2020, 9:41am UTC](https://forum.biobakery.org/t/metaphlan2-trial-run-result/302/6 "2020-04-29T09:41:27Z")
Hi Toan, which version of MetaPhlAn2 have you downloaded? The latest working and updated version is MetaPhlAn2 2.8, you can get it from GitHub [here](https://github.com/biobakery/MetaPhlAn/releases/tag/2.8) The version you are running probably is an older one, still pointing to the BitBucket resources ---
**Author:** ![Toan](https://avatars.discourse-cdn.com/v4/letter/t/b3f665/32.png) [@Toan](https://forum.biobakery.org/u/Toan)\ **Post date:** [April 29, 2020, 9:37pm UTC](https://forum.biobakery.org/t/metaphlan2-trial-run-result/302/7 "2020-04-29T21:37:24Z")
Hi Francesco, Thanks a lot for your reply! I installed it with bioconda, so maybe I got an old version. I will try with the the latest one now. Do you have it in bioconda yet (I can’t find it)? Cheers, Toan ---
**Author:** ![Toan](https://avatars.discourse-cdn.com/v4/letter/t/b3f665/32.png) [@Toan](https://forum.biobakery.org/u/Toan)\ **Post date:** [April 29, 2020, 11:45pm UTC](https://forum.biobakery.org/t/metaphlan2-trial-run-result/302/8 "2020-04-29T23:45:37Z")
Hi Francesco, It is working with the updated version MetaPhlAn2 2.8. I am running it on google colab. How long it usually takes to complete the run of a sample in the tutorial (it is taking quite long for me)? And what is the message when it is done? Thank you, Toan ---
**Author:** ![DEEPCHANDA7](https://avatars.discourse-cdn.com/v4/letter/d/eb9ed0/32.png) [@DEEPCHANDA7](https://forum.biobakery.org/u/DEEPCHANDA7)\ **Post date:** [April 30, 2020, 5:53am UTC](https://forum.biobakery.org/t/metaphlan2-trial-run-result/302/9 "2020-04-30T05:53:38Z")
But why I’m seeing `MetaPhlAn version 2.96.1 (02 Feb 2020)` !!! 🙄 🙄 ---
**Author:** ![fbeghini](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/fbeghini/32/81_2.png) [@fbeghini](https://forum.biobakery.org/u/fbeghini)\ **Post date:** [April 30, 2020, 11:48am UTC](https://forum.biobakery.org/t/metaphlan2-trial-run-result/302/10 "2020-04-30T11:48:39Z")
It depends on how many threads have you specified, it can take up to one hour. Nothing is prompted when the profiling is finished, you’ll have back your shell ---
**Author:** ![fbeghini](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/fbeghini/32/81_2.png) [@fbeghini](https://forum.biobakery.org/u/fbeghini)\ **Post date:** [April 30, 2020, 11:49am UTC](https://forum.biobakery.org/t/metaphlan2-trial-run-result/302/11 "2020-04-30T11:49:05Z")
You have to specify that you need to install version 2.8 (metaphlan2=2.8) ---
**Author:** ![Toan](https://avatars.discourse-cdn.com/v4/letter/t/b3f665/32.png) [@Toan](https://forum.biobakery.org/u/Toan)\ **Post date:** [April 30, 2020, 12:00pm UTC](https://forum.biobakery.org/t/metaphlan2-trial-run-result/302/12 "2020-04-30T12:00:33Z")
Hi Francesco, Thank you for your reply! I could make it done! Cheers, Toan ---
**Author:** ![Toan](https://avatars.discourse-cdn.com/v4/letter/t/b3f665/32.png) [@Toan](https://forum.biobakery.org/u/Toan)\ **Post date:** [May 2, 2020, 11:15am UTC](https://forum.biobakery.org/t/metaphlan2-trial-run-result/302/13 "2020-05-02T11:15:23Z")
Hi Francesco, Sorry for many questions! I am trying to re-generate the heatmap and cladogram from the tutorial of MetaPhlan2, but I could not install hclust2 and GraPhlAn either from biobakery or directly from source. I also tried with metaphlan\_hclust\_heatmap.py from the Metaphlan 2.8, but it showed: ![image](https://canada1.discourse-cdn.com/flex027/uploads/biobakery/original/1X/ae8ff3fb9d4837658f85842e39ff2c18065e1d07.png) Could you please explain to me how to solve this? Thank you very much, Best, Toan ---
**Author:** ![fbeghini](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/fbeghini/32/81_2.png) [@fbeghini](https://forum.biobakery.org/u/fbeghini)\ **Post date:** [May 4, 2020, 8:18am UTC](https://forum.biobakery.org/t/metaphlan2-trial-run-result/302/14 "2020-05-04T08:18:56Z")
`metaphlan_hclust_heatmap.py` is a older version of hclust2 and was not updated anymore, which problems have you encountered while installing hclust2 and/or graphlan? hclust2 is also available on bioconda, you can install it with `conda install -c bioconda hclust2` ---
**Author:** ![DEEPCHANDA7](https://avatars.discourse-cdn.com/v4/letter/d/eb9ed0/32.png) [@DEEPCHANDA7](https://forum.biobakery.org/u/DEEPCHANDA7)\ **Post date:** [May 8, 2020, 2:28pm UTC](https://forum.biobakery.org/t/metaphlan2-trial-run-result/302/15 "2020-05-08T14:28:20Z")
Sir @fbeghini, can I run HUMAnN 2.9 with python version 3.7.6? ---
**Author:** ![Toan](https://avatars.discourse-cdn.com/v4/letter/t/b3f665/32.png) [@Toan](https://forum.biobakery.org/u/Toan)\ **Post date:** [May 10, 2020, 10:05pm UTC](https://forum.biobakery.org/t/metaphlan2-trial-run-result/302/16 "2020-05-10T22:05:18Z")
## Hi @fbeghini, I follow the tutorial on [https://bitbucket.org/biobakery/biobakery/wiki/metaphlan2](https://bitbucket.org/biobakery/biobakery/wiki/metaphlan2), I don’t understand why I could not install hclust2 either via bioconda or biobakery. Even I tried to download it but the link also has error. Here is the error message when I installed it with bioconda or biobakery: Collecting package metadata (current\_repodata.json): done Solving environment: failed with initial frozen solve. Retrying with flexible solve. Solving environment: failed with repodata from current\_repodata.json, will retry with next repodata source. Collecting package metadata (repodata.json): done Solving environment: failed with initial frozen solve. Retrying with flexible solve. Solving environment: - Found conflicts! Looking for incompatible packages. This can take several minutes. Press CTRL-C to abortfailed UnsatisfiableError: The following specifications were found to be incompatible with the existing python installation in your environment: Specifications: - hclust2 -\> python[version=‘2.7.\*|\<3|\>=2.7,\<2.8.0a0’] Your python: python=3.7 If python is on the left-most side of the chain, that’s the version you’ve asked for. When python appears to the right, that indicates that the thing on the left is somehow not available for the python version you are constrained to. Note that conda will not change your python version to a different minor version unless you explicitly specify that. The following specifications were found to be incompatible with your CUDA driver: - feature:/linux-64::\_\_cuda==10.1=0 ## Your installed CUDA driver is: 10.1 Could you please help me to check it? Many thanks! Toan ---
**Author:** ![Carolina\_Diaz](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/carolina_diaz/32/535_2.png) [@Carolina\_Diaz](https://forum.biobakery.org/u/Carolina_Diaz)\ **Post date:** [December 17, 2020, 3:04pm UTC](https://forum.biobakery.org/t/metaphlan2-trial-run-result/302/17 "2020-12-17T15:04:10Z")
I am having a problem with hclust2 too. I installed it via Conda and it finishes the installation apparently without problems. I then run the commands as in the Metaphlan tutorial (mentioned above) and nothing happens, when I call hclust2 from the terminal it says that it is not an instance. When I open anaconda and search for it, it is there. I reinstalled again and this time around it says “The condensed distance matrix must contain only finite values” I will do a google search to try to solve the issue. Is this an hclust2 issue, or a data issue? Any pointers would help. I am new to this. Thanks in advance.