08/07/2021 06:14:37 PM - humann.humann - INFO: Running humann v3.0.0.alpha.4
08/07/2021 06:14:37 PM - humann.humann - INFO: Output files will be written to: ./OUT/SRR88998813
08/07/2021 06:14:37 PM - humann.humann - INFO: Writing temp files to directory: ./OUT/SRR88998813/SRR88998813_paired_1_humann_temp
08/07/2021 06:14:37 PM - humann.utilities - DEBUG: Check software, metaphlan, for required version, 3.0
08/07/2021 06:14:43 PM - humann.utilities - INFO: Using metaphlan version 3.0
08/07/2021 06:14:43 PM - humann.utilities - DEBUG: Check software, bowtie2, for required version, 2.2
08/07/2021 06:14:44 PM - humann.utilities - INFO: Using bowtie2 version 2.2
08/07/2021 06:14:44 PM - humann.humann - INFO: Search mode set to uniref50 because a uniref50 translated search database is selected
08/07/2021 06:14:44 PM - humann.utilities - DEBUG: Check software, diamond, for required version, 0.9.24
08/07/2021 06:14:44 PM - humann.utilities - INFO: Using diamond version 0.9.24
08/07/2021 06:14:44 PM - humann.config - INFO: 
Run config settings: 

DATABASE SETTINGS
nucleotide database folder = /humann/DB/chocophlan
protein database folder = /humann/DB/uniref
pathways database file 1 = /usr/local/lib/python3.6/dist-packages/humann/data/pathways/metacyc_reactions_level4ec_only.uniref.bz2
pathways database file 2 = /usr/local/lib/python3.6/dist-packages/humann/data/pathways/metacyc_pathways_structured_filtered
utility mapping database folder = /lustre/scratch118/infgen/pathogen/pathpipe/utility_mapping/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 = 20

SEARCH MODE
search mode = uniref50
nucleotide identity threshold = 0.0
translated identity threshold = 50.0

ALIGNMENT SETTINGS
bowtie2 options = --very-sensitive
diamond options = --top 1 --sensitive --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

08/07/2021 06:14:44 PM - humann.store - DEBUG: Initialize Alignments class instance to minimize memory use
08/07/2021 06:14:44 PM - humann.store - DEBUG: Initialize Reads class instance to minimize memory use
08/07/2021 06:15:19 PM - humann.humann - INFO: Load pathways database part 1: /usr/local/lib/python3.6/dist-packages/humann/data/pathways/metacyc_reactions_level4ec_only.uniref.bz2
08/07/2021 06:15:19 PM - humann.humann - INFO: Load pathways database part 2: /usr/local/lib/python3.6/dist-packages/humann/data/pathways/metacyc_pathways_structured_filtered
08/07/2021 06:15:19 PM - humann.search.prescreen - INFO: Running metaphlan ........
08/07/2021 06:15:19 PM - humann.utilities - DEBUG: Using software: /usr/local/bin/metaphlan
08/07/2021 06:15:19 PM - humann.utilities - INFO: Execute command: /usr/local/bin/metaphlan ./IN/SRR88998813_paired_1.fastq --bowtie2db /metaphlan/database296/ --index mpa_v296_CHOCOPhlAn_201901 -o ./OUT/SRR88998813/SRR88998813_paired_1_humann_temp/SRR88998813_paired_1_metaphlan_bugs_list.tsv --input_type fastq --bowtie2out ./OUT/SRR88998813/SRR88998813_paired_1_humann_temp/SRR88998813_paired_1_metaphlan_bowtie2.txt --nproc 20
08/07/2021 06:25:24 PM - humann.utilities - DEBUG: b'WARNING: The metagenome profile contains clades that represent multiple species merged into a single representant.\nAn additional column listing the merged species is added to the MetaPhlAn output.\n'
08/07/2021 06:25:24 PM - humann.humann - INFO: TIMESTAMP: Completed 	prescreen 	:	 605	 seconds
08/07/2021 06:25:24 PM - humann.search.prescreen - INFO: Found g__Bifidobacterium.s__Bifidobacterium_longum : 14.53% of mapped reads
08/07/2021 06:25:24 PM - humann.search.prescreen - INFO: Found g__Faecalibacterium.s__Faecalibacterium_prausnitzii : 13.57% of mapped reads
08/07/2021 06:25:24 PM - humann.search.prescreen - INFO: Found g__Escherichia.s__Escherichia_coli : 6.96% of mapped reads
08/07/2021 06:25:24 PM - humann.search.prescreen - INFO: Found g__Collinsella.s__Collinsella_aerofaciens : 6.87% of mapped reads
08/07/2021 06:25:24 PM - humann.search.prescreen - INFO: Found g__Dialister.s__Dialister_sp_CAG_357 : 6.41% of mapped reads
08/07/2021 06:25:24 PM - humann.search.prescreen - INFO: Found g__Bifidobacterium.s__Bifidobacterium_dentium : 5.32% of mapped reads
08/07/2021 06:25:24 PM - humann.search.prescreen - INFO: Found g__Veillonella.s__Veillonella_parvula : 4.76% of mapped reads
08/07/2021 06:25:24 PM - humann.search.prescreen - INFO: Found g__Bacteroides.s__Bacteroides_vulgatus : 4.27% of mapped reads
08/07/2021 06:25:24 PM - humann.search.prescreen - INFO: Found g__Dorea.s__Dorea_longicatena : 4.17% of mapped reads
08/07/2021 06:25:24 PM - humann.search.prescreen - INFO: Found g__Lachnospiraceae_unclassified.s__Eubacterium_rectale : 3.84% of mapped reads
08/07/2021 06:25:24 PM - humann.search.prescreen - INFO: Found g__Bacteroides.s__Bacteroides_uniformis : 2.70% of mapped reads
08/07/2021 06:25:24 PM - humann.search.prescreen - INFO: Found g__Eggerthella.s__Eggerthella_lenta : 2.48% of mapped reads
08/07/2021 06:25:24 PM - humann.search.prescreen - INFO: Found g__Alistipes.s__Alistipes_putredinis : 2.04% of mapped reads
08/07/2021 06:25:24 PM - humann.search.prescreen - INFO: Found g__Bifidobacterium.s__Bifidobacterium_pseudocatenulatum : 1.97% of mapped reads
08/07/2021 06:25:24 PM - humann.search.prescreen - INFO: Found g__Blautia.s__Ruminococcus_gnavus : 1.84% of mapped reads
08/07/2021 06:25:24 PM - humann.search.prescreen - INFO: Found g__Lactobacillus.s__Lactobacillus_ruminis : 1.74% of mapped reads
08/07/2021 06:25:24 PM - humann.search.prescreen - INFO: Found g__Barnesiella.s__Barnesiella_intestinihominis : 1.42% of mapped reads
08/07/2021 06:25:24 PM - humann.search.prescreen - INFO: Found g__Anaerostipes.s__Anaerostipes_hadrus : 1.20% of mapped reads
08/07/2021 06:25:24 PM - humann.search.prescreen - INFO: Found g__Dorea.s__Dorea_formicigenerans : 1.06% of mapped reads
08/07/2021 06:25:24 PM - humann.search.prescreen - INFO: Found g__Roseburia.s__Roseburia_inulinivorans : 1.03% of mapped reads
08/07/2021 06:25:24 PM - humann.search.prescreen - INFO: Found g__Prevotella.s__Prevotella_copri : 0.72% of mapped reads
08/07/2021 06:25:24 PM - humann.search.prescreen - INFO: Found g__Fusicatenibacter.s__Fusicatenibacter_saccharivorans : 0.67% of mapped reads
08/07/2021 06:25:24 PM - humann.search.prescreen - INFO: Found g__Agathobaculum.s__Agathobaculum_butyriciproducens : 0.60% of mapped reads
08/07/2021 06:25:24 PM - humann.search.prescreen - INFO: Found g__Roseburia.s__Roseburia_hominis : 0.60% of mapped reads
08/07/2021 06:25:24 PM - humann.search.prescreen - INFO: Found g__Bifidobacterium.s__Bifidobacterium_adolescentis : 0.52% of mapped reads
08/07/2021 06:25:24 PM - humann.search.prescreen - INFO: Found g__Blautia.s__Blautia_sp_CAG_257 : 0.47% of mapped reads
08/07/2021 06:25:24 PM - humann.search.prescreen - INFO: Found g__Bacteroides.s__Bacteroides_massiliensis : 0.46% of mapped reads
08/07/2021 06:25:24 PM - humann.search.prescreen - INFO: Found g__Streptococcus.s__Streptococcus_salivarius : 0.45% of mapped reads
08/07/2021 06:25:24 PM - humann.search.prescreen - INFO: Found g__Streptococcus.s__Streptococcus_anginosus_group : 0.42% of mapped reads
08/07/2021 06:25:24 PM - humann.search.prescreen - INFO: Found g__Gordonibacter.s__Gordonibacter_pamelaeae : 0.39% of mapped reads
08/07/2021 06:25:24 PM - humann.search.prescreen - INFO: Found g__Megamonas.s__Megamonas_funiformis : 0.38% of mapped reads
08/07/2021 06:25:24 PM - humann.search.prescreen - INFO: Found g__Parabacteroides.s__Parabacteroides_distasonis : 0.38% of mapped reads
08/07/2021 06:25:24 PM - humann.search.prescreen - INFO: Found g__Parabacteroides.s__Parabacteroides_merdae : 0.35% of mapped reads
08/07/2021 06:25:24 PM - humann.search.prescreen - INFO: Found g__Phascolarctobacterium.s__Phascolarctobacterium_faecium : 0.34% of mapped reads
08/07/2021 06:25:24 PM - humann.search.prescreen - INFO: Found g__Staphylococcus.s__Staphylococcus_aureus : 0.32% of mapped reads
08/07/2021 06:25:24 PM - humann.search.prescreen - INFO: Found g__Alistipes.s__Alistipes_shahii : 0.30% of mapped reads
08/07/2021 06:25:24 PM - humann.search.prescreen - INFO: Found g__Flavonifractor.s__Flavonifractor_plautii : 0.24% of mapped reads
08/07/2021 06:25:24 PM - humann.search.prescreen - INFO: Found g__Streptococcus.s__Streptococcus_parasanguinis : 0.23% of mapped reads
08/07/2021 06:25:24 PM - humann.search.prescreen - INFO: Found g__Paraprevotella.s__Paraprevotella_xylaniphila : 0.20% of mapped reads
08/07/2021 06:25:24 PM - humann.search.prescreen - INFO: Found g__Alistipes.s__Alistipes_finegoldii : 0.19% of mapped reads
08/07/2021 06:25:24 PM - humann.search.prescreen - INFO: Found g__Sellimonas.s__Sellimonas_intestinalis : 0.18% of mapped reads
08/07/2021 06:25:24 PM - humann.search.prescreen - INFO: Found g__Erysipelatoclostridium.s__Clostridium_innocuum : 0.17% of mapped reads
08/07/2021 06:25:24 PM - humann.search.prescreen - INFO: Found g__Acidaminococcus.s__Acidaminococcus_intestini : 0.16% of mapped reads
08/07/2021 06:25:24 PM - humann.search.prescreen - INFO: Found g__Blautia.s__Blautia_wexlerae : 0.16% of mapped reads
08/07/2021 06:25:24 PM - humann.search.prescreen - INFO: Found g__Bacteroides.s__Bacteroides_caccae : 0.16% of mapped reads
08/07/2021 06:25:24 PM - humann.search.prescreen - INFO: Found g__Clostridium.s__Clostridium_disporicum : 0.15% of mapped reads
08/07/2021 06:25:24 PM - humann.search.prescreen - INFO: Found g__Ruthenibacterium.s__Ruthenibacterium_lactatiformans : 0.15% of mapped reads
08/07/2021 06:25:24 PM - humann.search.prescreen - INFO: Found g__Streptococcus.s__Streptococcus_viridans : 0.14% of mapped reads
08/07/2021 06:25:24 PM - humann.search.prescreen - INFO: Found g__Eubacterium.s__Eubacterium_hallii : 0.13% of mapped reads
08/07/2021 06:25:24 PM - humann.search.prescreen - INFO: Found g__Alistipes.s__Alistipes_indistinctus : 0.12% of mapped reads
08/07/2021 06:25:24 PM - humann.search.prescreen - INFO: Found g__Actinomyces.s__Actinomyces_sp_oral_taxon_181 : 0.12% of mapped reads
08/07/2021 06:25:24 PM - humann.search.prescreen - INFO: Found g__Roseburia.s__Roseburia_faecis : 0.11% of mapped reads
08/07/2021 06:25:24 PM - humann.search.prescreen - INFO: Found g__Odoribacter.s__Odoribacter_splanchnicus : 0.11% of mapped reads
08/07/2021 06:25:24 PM - humann.search.prescreen - INFO: Found g__Asaccharobacter.s__Asaccharobacter_celatus : 0.11% of mapped reads
08/07/2021 06:25:24 PM - humann.search.prescreen - INFO: Found g__Lachnoclostridium.s__Clostridium_bolteae : 0.10% of mapped reads
08/07/2021 06:25:24 PM - humann.search.prescreen - INFO: Found g__Bacteroides.s__Bacteroides_ovatus : 0.09% of mapped reads
08/07/2021 06:25:24 PM - humann.search.prescreen - INFO: Found g__Rothia.s__Rothia_mucilaginosa : 0.07% of mapped reads
08/07/2021 06:25:24 PM - humann.search.prescreen - INFO: Found g__Anaerotruncus.s__Anaerotruncus_colihominis : 0.07% of mapped reads
08/07/2021 06:25:24 PM - humann.search.prescreen - INFO: Found g__Bacteroides.s__Bacteroides_cellulosilyticus : 0.06% of mapped reads
08/07/2021 06:25:24 PM - humann.search.prescreen - INFO: Found g__Actinomyces.s__Actinomyces_graevenitzii : 0.06% of mapped reads
08/07/2021 06:25:24 PM - humann.search.prescreen - INFO: Found g__Haemophilus.s__Haemophilus_pittmaniae : 0.06% of mapped reads
08/07/2021 06:25:24 PM - humann.search.prescreen - INFO: Found g__Actinomyces.s__Actinomyces_sp_HMSC035G02 : 0.06% of mapped reads
08/07/2021 06:25:24 PM - humann.search.prescreen - INFO: Found g__Bacteroides.s__Bacteroides_stercoris : 0.05% of mapped reads
08/07/2021 06:25:24 PM - humann.search.prescreen - INFO: Found g__Collinsella.s__Collinsella_stercoris : 0.05% of mapped reads
08/07/2021 06:25:24 PM - humann.search.prescreen - INFO: Found g__Actinomyces.s__Actinomyces_odontolyticus : 0.05% of mapped reads
08/07/2021 06:25:24 PM - humann.search.prescreen - INFO: Found g__Eubacterium.s__Eubacterium_eligens : 0.05% of mapped reads
08/07/2021 06:25:24 PM - humann.search.prescreen - INFO: Found g__Anaeromassilibacillus.s__Anaeromassilibacillus_sp_An250 : 0.05% of mapped reads
08/07/2021 06:25:24 PM - humann.search.prescreen - INFO: Found g__Clostridiales_Family_XIII_Incertae_Sedis_unclassified.s__Eubacterium_sulci : 0.05% of mapped reads
08/07/2021 06:25:24 PM - humann.search.prescreen - INFO: Found g__Actinomyces.s__Actinomyces_sp_S6_Spd3 : 0.05% of mapped reads
08/07/2021 06:25:24 PM - humann.search.prescreen - INFO: Found g__Atopobium.s__Atopobium_parvulum : 0.04% of mapped reads
08/07/2021 06:25:24 PM - humann.search.prescreen - INFO: Found g__Veillonella.s__Veillonella_dispar : 0.04% of mapped reads
08/07/2021 06:25:24 PM - humann.search.prescreen - INFO: Found g__Adlercreutzia.s__Adlercreutzia_equolifaciens : 0.04% of mapped reads
08/07/2021 06:25:24 PM - humann.search.prescreen - INFO: Found g__Intestinimonas.s__Intestinimonas_butyriciproducens : 0.03% of mapped reads
08/07/2021 06:25:24 PM - humann.search.prescreen - INFO: Found g__Haemophilus.s__Haemophilus_parainfluenzae : 0.03% of mapped reads
08/07/2021 06:25:24 PM - humann.search.prescreen - INFO: Found g__Lachnoclostridium.s__Clostridium_citroniae : 0.03% of mapped reads
08/07/2021 06:25:24 PM - humann.search.prescreen - INFO: Found g__Actinomyces.s__Actinomyces_sp_ICM47 : 0.03% of mapped reads
08/07/2021 06:25:24 PM - humann.search.prescreen - INFO: Found g__Tyzzerella.s__Tyzzerella_nexilis : 0.03% of mapped reads
08/07/2021 06:25:24 PM - humann.search.prescreen - INFO: Found g__Bacteroides.s__Bacteroides_faecis : 0.02% of mapped reads
08/07/2021 06:25:24 PM - humann.search.prescreen - INFO: Found g__Atopobium.s__Atopobium_rimae : 0.02% of mapped reads
08/07/2021 06:25:24 PM - humann.search.prescreen - INFO: Found g__Klebsiella.s__Klebsiella_pneumoniae : 0.02% of mapped reads
08/07/2021 06:25:24 PM - humann.search.prescreen - INFO: Found g__Megamonas.s__Megamonas_hypermegale : 0.02% of mapped reads
08/07/2021 06:25:24 PM - humann.search.prescreen - INFO: Found g__Erysipelatoclostridium.s__Erysipelatoclostridium_ramosum : 0.02% of mapped reads
08/07/2021 06:25:24 PM - humann.search.prescreen - INFO: Found g__Lachnoclostridium.s__Clostridium_lavalense : 0.02% of mapped reads
08/07/2021 06:25:24 PM - humann.search.prescreen - INFO: Found g__Collinsella.s__Collinsella_intestinalis : 0.02% of mapped reads
08/07/2021 06:25:24 PM - humann.search.prescreen - INFO: Found g__Veillonella.s__Veillonella_atypica : 0.02% of mapped reads
08/07/2021 06:25:24 PM - humann.search.prescreen - INFO: Found g__Bilophila.s__Bilophila_wadsworthia : 0.02% of mapped reads
08/07/2021 06:25:24 PM - humann.search.prescreen - INFO: Found g__Bacteroides.s__Bacteroides_dorei : 0.02% of mapped reads
08/07/2021 06:25:24 PM - humann.search.prescreen - INFO: Found g__Anaerotignum.s__Anaerotignum_lactatifermentans : 0.02% of mapped reads
08/07/2021 06:25:24 PM - humann.search.prescreen - INFO: Found g__Veillonella.s__Veillonella_infantium : 0.02% of mapped reads
08/07/2021 06:25:24 PM - humann.search.prescreen - INFO: Found g__Rothia.s__Rothia_dentocariosa : 0.01% of mapped reads
08/07/2021 06:25:24 PM - humann.search.prescreen - INFO: Found g__Streptococcus.s__Streptococcus_gordonii : 0.01% of mapped reads
08/07/2021 06:25:24 PM - humann.search.prescreen - INFO: Found g__Streptococcus.s__Streptococcus_oralis : 0.01% of mapped reads
08/07/2021 06:25:24 PM - humann.search.prescreen - INFO: Found g__Klebsiella.s__Klebsiella_variicola : 0.01% of mapped reads
08/07/2021 06:25:24 PM - humann.search.prescreen - INFO: Found g__Clostridium.s__Clostridium_paraputrificum : 0.01% of mapped reads
08/07/2021 06:25:24 PM - humann.search.prescreen - ERROR: The MetaPhlAn2 taxonomic profile provided was not generated with the database version v30 . Please update your version of MetaPhlAn2 to v3.0.