Dear all,
Humann3 fail to re-produce the pathabundance and pathcoverage like the toturial in my machine by following command while the genefamilies is right:
humann -i demo.fastq.gz -o functions --diamond …/…/ --thread 4
The part log of running is
11/25/2021 03:25:33 PM - humann.utilities - DEBUG: Check software, metaphlan, for required version, 3.0
11/25/2021 03:25:48 PM - humann.utilities - INFO: Using metaphlan version 3.0
11/25/2021 03:25:48 PM - humann.utilities - DEBUG: Check software, bowtie2, for required version, 2.2
11/25/2021 03:25:48 PM - humann.utilities - INFO: Using bowtie2 version 2.3
11/25/2021 03:25:48 PM - humann.humann - INFO: Search mode set to uniref90 because a uniref90 translated search database is selected
11/25/2021 03:25:48 PM - humann.utilities - DEBUG: Check software, diamond, for required version, 0.9.36
11/25/2021 03:25:49 PM - humann.utilities - INFO: Using diamond version 0.9.36
11/25/2021 03:29:08 PM - humann.search.prescreen - INFO: Found g__Bacteroides.s__Bacteroides_dorei : 57.96% of mapped reads
11/25/2021 03:29:08 PM - humann.search.prescreen - INFO: Found g__Bacteroides.s__Bacteroides_vulgatus : 42.04% of mapped reads
11/25/2021 03:29:08 PM - humann.search.prescreen - INFO: Total species selected from prescreen: 2
g__Bacteroides.s__Bacteroides_vulgatus: 1195 hits
g__Bacteroides.s__Bacteroides_dorei: 1260 hits
unclassified: 252 hits
11/25/2021 03:29:53 PM - humann.humann - INFO: Total gene families after translated alignment: 559
11/25/2021 03:29:53 PM - humann.humann - INFO: Unaligned reads after translated alignment: 87.2000000000 %
pathabundance.tsv
/# Pathway demo_Abundance
UNMAPPED 5736.8494011104
UNINTEGRATED 2558.6999771082
UNINTEGRATED|unclassified 38.3748531259
PWY-4203: volatile benzenoid biosynthesis I (ester formation) 13.3772872602
PWY-4203: volatile benzenoid biosynthesis I (ester formation)|unclassified 13.3772872602
pathcoverage.tsv
/# Pathway demo_Coverage
UNMAPPED 1.0000000000
UNINTEGRATED 1.0000000000
UNINTEGRATED|unclassified 1.0000000000
PWY-4203: volatile benzenoid biosynthesis I (ester formation) 0.8361658544
PWY-4203: volatile benzenoid biosynthesis I (ester formation)|unclassified 0.6438577695
My envirionment is as following:
huaman_config
HUMAnN Configuration ( Section : Name = Value )
database_folders : nucleotide = /data/home/xjsjfengweibing/wanghao/wjk/blast/tools/humann-3.0.1/humann/data/chocophlan_DEMO
database_folders : protein = /data/home/xjsjfengweibing/wanghao/wjk/blast/tools/humann-3.0.1/humann/data/uniref_DEMO
database_folders : utility_mapping = /data/home/xjsjfengweibing/wanghao/wjk/blast/tools/humann-3.0.1/humann/data/misc
run_modes : resume = False
run_modes : verbose = False
run_modes : bypass_prescreen = False
run_modes : bypass_nucleotide_index = False
run_modes : bypass_nucleotide_search = False
run_modes : bypass_translated_search = False
run_modes : threads = 1
alignment_settings : evalue_threshold = 1.0
alignment_settings : prescreen_threshold = 0.01
alignment_settings : translated_subject_coverage_threshold = 50.0
alignment_settings : translated_query_coverage_threshold = 90.0
alignment_settings : nucleotide_subject_coverage_threshold = 50.0
alignment_settings : nucleotide_query_coverage_threshold = 90.0
output_format : output_max_decimals = 10
output_format : remove_stratified_output = False
output_format : remove_column_description_output = False
humann_test
Ran 186 tests in 92.333s
OK
./diamond version
diamond version 0.9.36
metaphlan -v
MetaPhlAn version 3.0.13 (27 Jul 2021)