I can only get the genefamilies.tsv, but I cannot get the files pathcoverage.tsv and pathabundance.tsv

I ran humann-3.6 with metaphlan-4.0.3 with (–input-format) fastq, I can only get the genefamilies.tsv, but I cannot get the files pathcoverage.tsv and pathabundance.tsv. I assume that it’s the problem of ‘–pathways-database’ or utility mapping database I used, which specific databases or commands should I use to get the files of pathcoverage.tsv and pathabundance.tsv?
When we run humann, which option can I can use to provide utility mapping database location?

conmand used:
humann -i 323TP2_S7_1_SINGLETONS_clean.fq --input-format fastq -o 03_humann_results --threads 24 --metaphlan-options “–input_type fastq --bowtie2db /workdir/databases/metaphlan_database” --nucleotide-database /workdir/databases/chocophlan/ --protein-database /workdir/databases/uniref

.log:
02/20/2023 07:54:03 PM - humann.humann - INFO: Running humann v3.6
02/20/2023 07:54:03 PM - humann.humann - INFO: Output files will be written to: /local/workdir/jd2267/Poole-ME-13641_2023_01_20/01_Clean_reads/03_humann_results
02/20/2023 07:54:03 PM - humann.humann - INFO: Writing temp files to directory: /local/workdir/jd2267/Poole-ME-13641_2023_01_20/01_Clean_reads/03_humann_results/323TP2_S7_1_SINGLETONS_clean_humann_temp
02/20/2023 07:54:03 PM - humann.humann - INFO: Removing spaces from identifiers in input file
02/20/2023 07:55:48 PM - humann.utilities - DEBUG: Check software, metaphlan, for required version, 3.0
02/20/2023 07:55:50 PM - humann.utilities - INFO: Using metaphlan version 4.0
02/20/2023 07:55:50 PM - humann.utilities - DEBUG: Check software, bowtie2, for required version, 2.2
02/20/2023 07:55:50 PM - humann.utilities - INFO: Using bowtie2 version 2.4
02/20/2023 07:55:50 PM - humann.humann - INFO: Search mode set to uniref90 because a uniref90 translated search database is selected
02/20/2023 07:55:50 PM - humann.utilities - DEBUG: Check software, diamond, for required version, 2.0.15
02/20/2023 07:55:50 PM - humann.utilities - INFO: Using diamond version 2.1.1
02/20/2023 07:55:50 PM - humann.config - INFO:
Run config settings:

DATABASE SETTINGS
nucleotide database folder = /workdir/databases/chocophlan
protein database folder = /workdir/databases/uniref
pathways database file 1 = /programs/humann-3.6/lib/python3.9/site-packages/humann/data/pathways/metacyc_reactions_level4ec_only.uniref.bz2
pathways database file 2 = /programs/humann-3.6/lib/python3.9/site-packages/humann/data/pathways/metacyc_pathways_structured_filtered_v24
utility mapping database folder = /programs/humann-3.6/lib/python3.9/site-packages/humann/data/misc

Here are the errors:
02/21/2023 12:00:11 AM - humann.utilities - DEBUG: Using python module : /programs/humann-3.6/lib/python3.9/site-packages/humann/quantify/MinPath12hmp.py
02/21/2023 12:00:11 AM - humann.utilities - INFO: Process memory RSS = 7.682777404785156 GB
02/21/2023 12:00:11 AM - humann.utilities - CRITICAL: TRACEBACK:
Traceback (most recent call last):
File “/programs/humann-3.6/lib/python3.9/site-packages/humann/utilities.py”, line 759, in execute_command
p = subprocess.check_call(cmd, stdin=stdin, stdout=stdout, stderr=stderr)
File “/usr/lib64/python3.9/subprocess.py”, line 373, in check_call
raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command ‘[’/usr/bin/python3’, ‘/programs/humann-3.6/lib/python3.9/site-packages/humann/quantify/MinPath12hmp.py’, ‘-any’, ‘/local/workdir/jd2267/Poole-ME-13641_2023_01_20/01_Clean_reads/03_humann_results/323TP2_S7_1_SINGLETONS_clean_humann_temp/tmp5ktg_u73/tmpjxsokwkt’, ‘-map’, ‘/local/workdir/jd2267/Poole-ME-13641_2023_01_20/01_Clean_reads/03_humann_results/323TP2_S7_1_SINGLETONS_clean_humann_temp/tmp5ktg_u73/tmpfpfxi63f’, ‘-report’, ‘/local/workdir/jd2267/Poole-ME-13641_2023_01_20/01_Clean_reads/03_humann_results/323TP2_S7_1_SINGLETONS_clean_humann_temp/tmp5ktg_u73/tmpdgp1b82m’, ‘-details’, ‘/local/workdir/jd2267/Poole-ME-13641_2023_01_20/01_Clean_reads/03_humann_results/323TP2_S7_1_SINGLETONS_clean_humann_temp/tmp5ktg_u73/tmpqlc4imbv’, ‘-mps’, ‘/local/workdir/jd2267/Poole-ME-13641_2023_01_20/01_Clean_reads/03_humann_results/323TP2_S7_1_SINGLETONS_clean_humann_temp/tmp5ktg_u73/tmpaulda36a’]’ returned non-zero exit status 1.

02/21/2023 12:00:11 AM - humann.utilities - CRITICAL: TRACEBACK:
Traceback (most recent call last):
File “/programs/humann-3.6/lib/python3.9/site-packages/humann/utilities.py”, line 759, in execute_command
p = subprocess.check_call(cmd, stdin=stdin, stdout=stdout, stderr=stderr)
File “/usr/lib64/python3.9/subprocess.py”, line 373, in check_call
raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command ‘[’/usr/bin/python3’, ‘/programs/humann-3.6/lib/python3.9/site-packages/humann/quantify/MinPath12hmp.py’, ‘-any’, ‘/local/workdir/jd2267/Poole-ME-13641_2023_01_20/01_Clean_reads/03_humann_results/323TP2_S7_1_SINGLETONS_clean_humann_temp/tmp5ktg_u73/tmphebfga0i’, ‘-map’, ‘/local/workdir/jd2267/Poole-ME-13641_2023_01_20/01_Clean_reads/03_humann_results/323TP2_S7_1_SINGLETONS_clean_humann_temp/tmp5ktg_u73/tmpfpfxi63f’, ‘-report’, ‘/local/workdir/jd2267/Poole-ME-13641_2023_01_20/01_Clean_reads/03_humann_results/323TP2_S7_1_SINGLETONS_clean_humann_temp/tmp5ktg_u73/tmpblnnw4c0’, ‘-details’, ‘/local/workdir/jd2267/Poole-ME-13641_2023_01_20/01_Clean_reads/03_humann_results/323TP2_S7_1_SINGLETONS_clean_humann_temp/tmp5ktg_u73/tmp1_0081ek’, ‘-mps’, ‘/local/workdir/jd2267/Poole-ME-13641_2023_01_20/01_Clean_reads/03_humann_results/323TP2_S7_1_SINGLETONS_clean_humann_temp/tmp5ktg_u73/tmpsd8w9brk’]’ returned non-zero exit status 1.

Hello, Thank you for the detailed post! It looks like the error is during the MinPath call which in turn calls glpsol (part of glpk). If you would try updating your version of glpk it might resolve the issue as I have seen errors with older versions of this tool. You can install HUMAnN with pip adding the option --no-binary :all: and it will install all of the dependencies it needs (including a newer version of glpk).

Thank you,
Lauren

Thank you, Lauren!
It works fine now!

Best,
Jingjie

Fantastic! Thanks for the follow up post!
Lauren

Hi! I also come across this problem. I used conda install humann2,and after running humann2, I only got a genefamilies.tsv. here is the error report:CRITICAL: Error executing: ~/.conda/envs/metagenome_env/bin/python ~/.conda/envs/metagenome_env/lib/python2.7/site-packages/humann2/quantify/MinPath12hmp.py ,I have updated glpsol, but it did not work out