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.