humann v3.8
I’m trying to run humann through my institution’s HPC cluster and running into an issue that they were unsure how to resolve. I’m starting with fastq.gz files and the program runs into an error when trying to run MetaPhlAn. Here is my input:
module load humann/3.8
cd /scratch/g/jkirby/Landon_WGS_reanalysis/Figure_8/
humann --input humann/examples/demo.fastq.gz --output humann_demo
And here is the output including all the error messages:
Creating output directory: /scratch/g/jkirby/Landon_WGS_reanalysis/Figure_8/humann_demo
Output files will be written to: /scratch/g/jkirby/Landon_WGS_reanalysis/Figure_8/humann_demo
Decompressing gzipped file …
Running metaphlan …
CRITICAL ERROR: Error executing: /hpc/apps/miniconda3/4.9.2/envs/humann-3.8/bin/metaphlan /scratch/g/jkirby/Landon_WGS_reanalysis/Figure_8/humann_demo/demo_humann_temp/tmpobntluyw/tmppz5g72wz -t rel_ab -o /scratch/g/jkirby/Landon_WGS_reanalysis/Figure_8/humann_demo/demo_humann_temp/demo_metaphlan_bugs_list.tsv --input_type fastq --bowtie2out /scratch/g/jkirby/Landon_WGS_reanalysis/Figure_8/humann_demo/demo_humann_temp/demo_metaphlan_bowtie2.txt
Error message returned from metaphlan :
Downloading http://cmprod1.cibio.unitn.it/biobakery4/metaphlan_databases/mpa_latest
Warning: Unable to download http://cmprod1.cibio.unitn.it/biobakery4/metaphlan_databases/mpa_latest
Traceback (most recent call last):
File “/hpc/apps/miniconda3/4.9.2/envs/humann-3.8/bin/metaphlan”, line 10, in
sys.exit(main())
File “/hpc/apps/miniconda3/4.9.2/envs/humann-3.8/lib/python3.10/site-packages/metaphlan/metaphlan.py”, line 996, in main
pars[‘index’] = check_and_install_database(pars[‘index’], pars[‘bowtie2db’], pars[‘bowtie2_build’], pars[‘nproc’], pars[‘force_download’], pars[‘offline’])
File “/hpc/apps/miniconda3/4.9.2/envs/humann-3.8/lib/python3.10/site-packages/metaphlan/init.py”, line 303, in check_and_install_database
index = resolve_latest_database(bowtie2_db, mpa_latest, force_redownload_latest, offline)
File “/hpc/apps/miniconda3/4.9.2/envs/humann-3.8/lib/python3.10/site-packages/metaphlan/init.py”, line 267, in resolve_latest_database
with open(os.path.join(bowtie2_db,‘mpa_latest’)) as mpa_latest:
FileNotFoundError: [Errno 2] No such file or directory: ‘/hpc/apps/miniconda3/4.9.2/envs/humann-3.8/lib/python3.10/site-packages/metaphlan/metaphlan_databases/mpa_latest’
I would just download mpa_latest, but there’s nothing downloadable at http://cmprod1.cibio.unitn.it/biobakery4/metaphlan_databases/mpa_latest so I’m not sure what to do.
Does anyone have any suggestions?