The bioBakery help forum

Error running sample fasta with Humann2/metaphlan

Hi I am getting metaphlan3 errors. Is there a way you can help me with this? Thank you!

Best,
Carla

Error message returned from metaphlan :
Warning! Biom python library not detected!
Exporting to biom format will not work!

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 “/Library/Frameworks/Python.framework/Versions/3.8/bin/metaphlan”, line 8, in
sys.exit(main())
File “/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/metaphlan/metaphlan.py”, line 916, in main
pars[‘index’] = check_and_install_database(pars[‘index’], pars[‘bowtie2db’], pars[‘bowtie2_build’], pars[‘nproc’], pars[‘force_download’])
File “/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/metaphlan/init.py”, line 271, 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

Here is the log file text:

06/18/2020 02:27:43 PM - humann.humann - INFO: Running humann v3.0.0.alpha.2
06/18/2020 02:27:43 PM - humann.humann - INFO: Output files will be written to: /Users/curanga/Desktop/humann3/databases/demo_fastq
06/18/2020 02:27:43 PM - humann.humann - INFO: Writing temp files to directory: /Users/curanga/Desktop/humann3/databases/demo_fastq/demo_humann_temp
06/18/2020 02:27:43 PM - humann.utilities - INFO: File ( /Users/curanga/Desktop/humann3/databases/demo.fastq ) is of format: fastq
06/18/2020 02:27:43 PM - humann.utilities - DEBUG: Check software, metaphlan, for required version, 3.0
06/18/2020 02:27:43 PM - humann.utilities - INFO: Using metaphlan version 3.0
06/18/2020 02:27:43 PM - humann.utilities - DEBUG: Check software, bowtie2, for required version, 2.2
06/18/2020 02:27:43 PM - humann.utilities - INFO: Using bowtie2 version 2.3
06/18/2020 02:27:43 PM - humann.humann - INFO: Search mode set to uniref90 because a uniref90 translated search database is selected
06/18/2020 02:27:43 PM - humann.utilities - DEBUG: Check software, diamond, for required version, 0.9.24
06/18/2020 02:27:43 PM - humann.utilities - INFO: Using diamond version 0.9.34
06/18/2020 02:27:43 PM - humann.config - INFO:
Run config settings:

DATABASE SETTINGS
nucleotide database folder = /Users/curanga/Desktop/humann3/databases/chocophlan
protein database folder = /Users/curanga/Desktop/humann3/databases/uniref
pathways database file 1 = /Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/humann/data/pathways/metacyc_reactions_level4ec_only.uniref.bz2
pathways database file 2 = /Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/humann/data/pathways/metacyc_pathways_structured_filtered
utility mapping database folder = /Users/curanga/Desktop/humann3/databases/utility_mapping

RUN MODES
resume = False
verbose = False
bypass prescreen = False
bypass nucleotide index = False
bypass nucleotide search = False
bypass translated search = False
translated search = diamond
pick frames = off
threads = 1

SEARCH MODE
search mode = uniref90
nucleotide identity threshold = 0.0
translated identity threshold = 80.0

ALIGNMENT SETTINGS
bowtie2 options = --very-sensitive
diamond options = --top 1 --outfmt 6
evalue threshold = 1.0
prescreen threshold = 0.01
translated subject coverage threshold = 50.0
translated query coverage threshold = 90.0
nucleotide subject coverage threshold = 50.0
nucleotide query coverage threshold = 90.0

PATHWAYS SETTINGS
minpath = on
xipe = off
gap fill = on

INPUT AND OUTPUT FORMATS
input file format = fastq
output file format = tsv
output max decimals = 10
remove stratified output = False
remove column description output = False
log level = DEBUG

06/18/2020 02:27:43 PM - humann.store - DEBUG: Initialize Alignments class instance to minimize memory use
06/18/2020 02:27:43 PM - humann.store - DEBUG: Initialize Reads class instance to minimize memory use
06/18/2020 02:28:00 PM - humann.humann - INFO: Load pathways database part 1: /Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/humann/data/pathways/metacyc_reactions_level4ec_only.uniref.bz2
06/18/2020 02:28:00 PM - humann.humann - INFO: Load pathways database part 2: /Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/humann/data/pathways/metacyc_pathways_structured_filtered
06/18/2020 02:28:00 PM - humann.search.prescreen - INFO: Running metaphlan …
06/18/2020 02:28:00 PM - humann.utilities - DEBUG: Using software: /Library/Frameworks/Python.framework/Versions/3.8/bin/metaphlan
06/18/2020 02:28:00 PM - humann.utilities - INFO: Execute command: /Library/Frameworks/Python.framework/Versions/3.8/bin/metaphlan /Users/curanga/Desktop/humann3/databases/demo.fastq -t rel_ab -o /Users/curanga/Desktop/humann3/databases/demo_fastq/demo_humann_temp/demo_metaphlan_bugs_list.tsv --input_type fastq --bowtie2out /Users/curanga/Desktop/humann3/databases/demo_fastq/demo_humann_temp/demo_metaphlan_bowtie2.txt
06/18/2020 02:28:01 PM - humann.utilities - CRITICAL: Error executing: /Library/Frameworks/Python.framework/Versions/3.8/bin/metaphlan /Users/curanga/Desktop/humann3/databases/demo.fastq -t rel_ab -o /Users/curanga/Desktop/humann3/databases/demo_fastq/demo_humann_temp/demo_metaphlan_bugs_list.tsv --input_type fastq --bowtie2out /Users/curanga/Desktop/humann3/databases/demo_fastq/demo_humann_temp/demo_metaphlan_bowtie2.txt

Error message returned from metaphlan :
Warning! Biom python library not detected!
Exporting to biom format will not work!

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 “/Library/Frameworks/Python.framework/Versions/3.8/bin/metaphlan”, line 8, in
sys.exit(main())
File “/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/metaphlan/metaphlan.py”, line 916, in main
pars[‘index’] = check_and_install_database(pars[‘index’], pars[‘bowtie2db’], pars[‘bowtie2_build’], pars[‘nproc’], pars[‘force_download’])
File “/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/metaphlan/init.py”, line 271, 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

06/18/2020 02:28:01 PM - humann.utilities - CRITICAL: TRACEBACK:
Traceback (most recent call last):
File “/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/humann/utilities.py”, line 734, in execute_command
p_out = subprocess.check_output(cmd, stderr=subprocess.STDOUT)
File “/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/subprocess.py”, line 411, in check_output
return run(*popenargs, stdout=PIPE, timeout=timeout, check=True,
File “/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/subprocess.py”, line 512, in run
raise CalledProcessError(retcode, process.args,
subprocess.CalledProcessError: Command ‘[’/Library/Frameworks/Python.framework/Versions/3.8/bin/metaphlan’, ‘/Users/curanga/Desktop/humann3/databases/demo.fastq’, ‘-t’, ‘rel_ab’, ‘-o’, ‘/Users/curanga/Desktop/humann3/databases/demo_fastq/demo_humann_temp/demo_metaphlan_bugs_list.tsv’, ‘–input_type’, ‘fastq’, ‘–bowtie2out’, ‘/Users/curanga/Desktop/humann3/databases/demo_fastq/demo_humann_temp/demo_metaphlan_bowtie2.txt’]’ returned non-zero exit status 1.

I know you’ve got another thread going now for install help. Please let us know if your issues have been resolved there or if you need additional help.