The bioBakery help forum

Humann3 not installing

Hi,

I am getting the following error when trying to install humann3:

Collecting package metadata (repodata.json): done

Solving environment: failed with initial frozen solve. Retrying with flexible solve.

PackagesNotFoundError: The following packages are not available from current channels:

Which version of Python are you using? I’ve seen this error when trying to install into a Python below 3.7 (required for some elements of MetaPhlAn 3.0).

Hi, yes, I am using Python 3.7. I was able to install it with pip install metaphlan but now the checksum is not passing, with an error regarding the md5 file downladed into the metaphlan databases. I tried removing the databases and re-installing them, the default being v30, I changed them to v296, but still am not able to get the humann3 demo to run on the demo.fastq. I hope this is fixable! I have verified that I can properly call metaphlan, diamond, and humann with --version, however bowtie2 gets called a little oddly:
(base) curangalt-osx:metaphlan curanga$ bowtie2 --version
/Users/curanga/bowtie2/bowtie2-align-s version 2.4.1
64-bit
Built on
Fri Feb 28 22:21:49 UTC 2020
Compiler: InstalledDir: /Library/Developer/CommandLineTools/usr/bin
Options: -O3 -msse2 -funroll-loops -g3 -mmacosx-version-min=10.9 -DPOPCNT_CAPABILITY -DWITH_TBB -std=c++11 -DNO_SPINLOCK -DWITH_QUEUELOCK=1
Sizeof {int, long, long long, void*, size_t, off_t}: {4, 8, 8, 8, 8, 8}
(base) curangalt-osx:metaphlan curanga$

Any help to get this working would be wonderful! I really need to get it working for our lab! Thank you in advance.

Best wishes,
Carla

Were you able to get past this point? I see that you have another thread going about MetaPhlAn installation. It’s possible that the conda channel priorities were also to blame here. Let us know if you’re still having install problems (here or on the other thread).

Hi thank you so much for asking! I was able to get past this point and am going through the demos. The fastaq demo worked fine, but I am wanting to apply humann3 to proteomics, which is proving a bit more challenging. I am generating peptide lists and turning them into fastas with R, which I then am feeding into diamond. If I can get this to work it would be super cool. Take care and stay healthy, and thanks again!

Best wishes,

Carla