Demo HUMAnN3 Run Fails in conda environment on SSH Server

Microbial community profiling HUMAnN
1

Hi there,

This is my first time using the HUMAnN pipeline. I am trying to run the basic HUMAnN3 demo in the conda environment on an SSH server, but am dealing with a database download error. Downloading the demo databases and the demo.fastq.gz file to my account on the SSH server is successful, but when I enter this command:
humann --input demo.fastq.gz --output demo_fastq

I receive this output:
Creating output directory: /home/rb64a/humann_analysis/demo_fastq
Output files will be written to: /home/rb64a/humann_analysis/demo_fastq
Decompressing gzipped file …

Running metaphlan …

CRITICAL ERROR: Error executing: /share/pkg/condas/2018-05-11/envs/humann_3.0.0/bin/metaphlan /home/rb64a/humann_analysis/demo_fastq/demo_humann_temp/tmpxufulhyj/tmpziyl8ipv -t rel_ab -o /home/rb64a/humann_analysis/demo_fastq/demo_humann_temp/demo_metaphlan_bugs_list.tsv --input_type fastq --bowtie2out /home/rb64a/humann_analysis/demo_fastq/demo_humann_temp/demo_metaphlan_bowtie2.txt

Error message returned from metaphlan :

Downloading http://cmprod1.cibio.unitn.it/biobakery3/metaphlan_databases/mpa_latest

Warning: Unable to download http://cmprod1.cibio.unitn.it/biobakery3/metaphlan_databases/mpa_latest
Traceback (most recent call last):
File “/share/pkg/condas/2018-05-11/envs/humann_3.0.0/bin/metaphlan”, line 10, in
sys.exit(main())
File “/share/pkg/condas/2018-05-11/envs/humann_3.0.0/lib/python3.9/site-packages/metaphlan/metaphlan.py”, line 926, in main
pars[‘index’] = check_and_install_database(pars[‘index’], pars[‘bowtie2db’], pars[‘bowtie2_build’], pars[‘nproc’], pars[‘force_download’])
File “/share/pkg/condas/2018-05-11/envs/humann_3.0.0/lib/python3.9/site-packages/metaphlan/init.py”, line 280, in check_and_install_database
index = resolve_latest_database(bowtie2_db, mpa_latest, force_redownload_latest)
File “/share/pkg/condas/2018-05-11/envs/humann_3.0.0/lib/python3.9/site-packages/metaphlan/init.py”, line 241, in resolve_latest_database
with open(os.path.join(bowtie2_db,‘mpa_latest’)) as mpa_latest:
FileNotFoundError: [Errno 2] No such file or directory: ‘/share/pkg/condas/2018-05-11/envs/humann_3.0.0/lib/python3.9/site-packages/metaphlan/metaphlan_databases/mpa_latest’

Any advice would be much appreciated. I’m worried that this issue could be because I’m trying to run this command on an SSH server, but I’m not sure.

2

Hello, Thank you for your detailed post. Is it possible you are running out of space or do not have write permissions to the location the database is being installed? /share/pkg/condas/2018-05-11/envs/humann_3.0.0/lib/python3.9/site-packages/metaphlan/metaphlan_databases/ If that is not the case, I would check to see if you have the latest MetaPhlAn version installed.

Thanks!
Lauren

3

Hi Lauren,

Thank you very much for your response! The most recent version of MetaPhlAn is installed in the conda environment. It seems like the shared conda environment on the SSH server isn’t writable. Does this mean I should try running HUMAnN3 on a local environment instead of on an SSH server?

4

Hello - Is it possible a sysadmin of your SSH server (or the person that installed MetaPhlAn on the server) can install the MetaPhlAn database? If you can get it installed once you should be set!

Thanks!
Lauren