Metaphlan 3.0
I encountered the following error message while running the tutorial for the Humann.
Following is the command i used and the error message.
humann --input demo.fastq.gz --output demo_fastq --nucleotide-database /scratch/user/sal/Humann_projects/humann_dbs/chocophl
an --protein-database /scratch/user/sal/Humann_projects/humann_dbs/uniref
Output files will be written to: /scratch/user/sal/Humann_projects/Tutorials/humann3/input/demo_fastq
Decompressing gzipped file …
Running metaphlan …
CRITICAL ERROR: Error executing: /scratch/user/sal/.conda/envs/Salenv/bin/metaphlan /scratch/user/sal/Humann_projects/Tutorials/humann3/input/demo_fastq/
demo_humann_temp/tmpal5xx8vc/tmp295_lrf4 -t rel_ab -o /scratch/user/sal/Humann_projects/Tutorials/humann3/input/demo_fastq/demo_humann_temp/demo_metaphla
n_bugs_list.tsv --input_type fastq --bowtie2out /scratch/user/sal/Humann_projects/Tutorials/humann3/input/demo_fastq/demo_humann_temp/demo_metaphlan_bowt
ie2.txt
Error message returned from metaphlan :
Downloading https://www.dropbox.com/sh/7qze7m7g9fe2xjg/AAA4XDP85WHon_eHvztxkamTa/file_list.txt?dl=1
Warning: Unable to download https://www.dropbox.com/sh/7qze7m7g9fe2xjg/AAA4XDP85WHon_eHvztxkamTa/file_list.txt?dl=1
Traceback (most recent call last):
File “/scratch/user/sal/.conda/envs/Salenv/bin/metaphlan”, line 10, in
sys.exit(main())
File “/scratch/user/sal/.conda/envs/Salenv/lib/python3.6/site-packages/metaphlan/metaphlan.py”, line 1187, in main
pars[‘index’] = check_and_install_database(pars[‘index’], pars[‘bowtie2db’], pars[‘bowtie2_build’], pars[‘nproc’], pars[‘force_download’])
File “/scratch/user/sal/.conda/envs/Salenv/lib/python3.6/site-packages/metaphlan/metaphlan.py”, line 589, in check_and_install_database
index = resolve_latest_database(bowtie2_db, ls_f[‘mpa_latest’], force_redownload_latest)
UnboundLocalError: local variable ‘ls_f’ referenced before assignment