01/05/2021 04:10:28 PM - humann.humann - INFO: Running humann v3.0.0.alpha.3
01/05/2021 04:10:28 PM - humann.humann - INFO: Output files will be written to: /media/plicht/T7/Samples8-30.5/HumanN/a10
01/05/2021 04:10:28 PM - humann.humann - INFO: Writing temp files to directory: /media/plicht/T7/Samples8-30.5/HumanN/a10/a10_paired_cat_humann_temp_n32zynxi
01/05/2021 04:10:28 PM - humann.utilities - INFO: File ( /media/plicht/T7/Samples8-30.5/KneadData/only_read1_and_read2_paired_kneaddata/a10/a10_paired_cat.fastq ) is of format:  fastq
01/05/2021 04:10:28 PM - humann.utilities - DEBUG: Check software, metaphlan, for required version, 3.0
01/05/2021 04:10:28 PM - humann.utilities - INFO: Using metaphlan version 3.0
01/05/2021 04:10:28 PM - humann.utilities - DEBUG: Check software, bowtie2, for required version, 2.2
01/05/2021 04:10:28 PM - humann.utilities - WARNING: Can not call software version for bowtie2
01/05/2021 04:10:28 PM - humann.utilities - INFO: Using bowtie2 version UNK
01/05/2021 04:10:28 PM - humann.humann - INFO: Search mode set to uniref90 because a uniref90 translated search database is selected
01/05/2021 04:10:28 PM - humann.utilities - DEBUG: Check software, diamond, for required version, 0.9.24
01/05/2021 04:10:28 PM - humann.utilities - INFO: Using diamond version 2.0.2
01/05/2021 04:10:28 PM - humann.config - INFO: 
Run config settings: 

DATABASE SETTINGS
nucleotide database folder = /home/plicht/humann_db/chocophlan
protein database folder = /home/plicht/humann_db/uniref90/uniref
pathways database file 1 = /home/plicht/anaconda3/envs/metaphlan3_env/lib/python3.7/site-packages/humann/data/pathways/metacyc_reactions_level4ec_only.uniref.bz2
pathways database file 2 = /home/plicht/anaconda3/envs/metaphlan3_env/lib/python3.7/site-packages/humann/data/pathways/metacyc_pathways_structured_filtered
utility mapping database folder = /home/plicht/humann_db/utility_mapping

RUN MODES
resume = False
verbose = True
bypass prescreen = False
bypass nucleotide index = False
bypass nucleotide search = False
bypass translated search = False
translated search = diamond
pick frames = off
threads = 12

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

01/05/2021 04:10:28 PM - humann.store - DEBUG: Initialize Alignments class instance to minimize memory use
01/05/2021 04:10:28 PM - humann.store - DEBUG: Initialize Reads class instance to minimize memory use
01/05/2021 04:10:42 PM - humann.humann - INFO: Load pathways database part 1: /home/plicht/anaconda3/envs/metaphlan3_env/lib/python3.7/site-packages/humann/data/pathways/metacyc_reactions_level4ec_only.uniref.bz2
01/05/2021 04:10:42 PM - humann.humann - INFO: Load pathways database part 2: /home/plicht/anaconda3/envs/metaphlan3_env/lib/python3.7/site-packages/humann/data/pathways/metacyc_pathways_structured_filtered
01/05/2021 04:10:42 PM - humann.search.prescreen - INFO: Found g__Cutibacterium.s__Cutibacterium_acnes : 92.39% of mapped reads
01/05/2021 04:10:42 PM - humann.search.prescreen - INFO: Found g__Acinetobacter.s__Acinetobacter_lwoffii : 4.26% of mapped reads
01/05/2021 04:10:42 PM - humann.search.prescreen - INFO: Found g__Staphylococcus.s__Staphylococcus_epidermidis : 0.87% of mapped reads
01/05/2021 04:10:42 PM - humann.search.prescreen - INFO: Found g__Enhydrobacter.s__Enhydrobacter_aerosaccus : 0.22% of mapped reads
01/05/2021 04:10:42 PM - humann.search.prescreen - INFO: Found g__Corynebacterium.s__Corynebacterium_kroppenstedtii : 0.22% of mapped reads
01/05/2021 04:10:42 PM - humann.search.prescreen - INFO: Found g__Malassezia.s__Malassezia_restricta : 0.20% of mapped reads
01/05/2021 04:10:42 PM - humann.search.prescreen - INFO: Found g__Moraxella.s__Moraxella_osloensis : 0.17% of mapped reads
01/05/2021 04:10:42 PM - humann.search.prescreen - INFO: Found g__Acinetobacter.s__Acinetobacter_johnsonii : 0.16% of mapped reads
01/05/2021 04:10:42 PM - humann.search.prescreen - INFO: Found g__Cutibacterium.s__Propionibacterium_namnetense : 0.14% of mapped reads
01/05/2021 04:10:42 PM - humann.search.prescreen - INFO: Found g__Staphylococcus.s__Staphylococcus_hominis : 0.14% of mapped reads
01/05/2021 04:10:42 PM - humann.search.prescreen - INFO: Found g__Enterococcus.s__Enterococcus_faecalis : 0.09% of mapped reads
01/05/2021 04:10:42 PM - humann.search.prescreen - INFO: Found g__Prevotella.s__Prevotella_timonensis : 0.09% of mapped reads
01/05/2021 04:10:42 PM - humann.search.prescreen - INFO: Found g__Corynebacterium.s__Corynebacterium_coyleae : 0.08% of mapped reads
01/05/2021 04:10:42 PM - humann.search.prescreen - INFO: Found g__Corynebacterium.s__Corynebacterium_riegelii : 0.07% of mapped reads
01/05/2021 04:10:42 PM - humann.search.prescreen - INFO: Found g__Corynebacterium.s__Corynebacterium_genitalium : 0.07% of mapped reads
01/05/2021 04:10:42 PM - humann.search.prescreen - INFO: Found g__Listeria.s__Listeria_monocytogenes : 0.06% of mapped reads
01/05/2021 04:10:42 PM - humann.search.prescreen - INFO: Found g__Campylobacter.s__Campylobacter_ureolyticus : 0.06% of mapped reads
01/05/2021 04:10:42 PM - humann.search.prescreen - INFO: Found g__Finegoldia.s__Finegoldia_magna : 0.06% of mapped reads
01/05/2021 04:10:42 PM - humann.search.prescreen - INFO: Found g__Veillonella.s__Veillonella_parvula : 0.05% of mapped reads
01/05/2021 04:10:42 PM - humann.search.prescreen - INFO: Found g__Corynebacterium.s__Corynebacterium_amycolatum : 0.05% of mapped reads
01/05/2021 04:10:42 PM - humann.search.prescreen - INFO: Found g__Prolinoborus.s__Prolinoborus_fasciculus : 0.05% of mapped reads
01/05/2021 04:10:42 PM - humann.search.prescreen - INFO: Found g__Peptoniphilus.s__Peptoniphilus_harei : 0.05% of mapped reads
01/05/2021 04:10:42 PM - humann.search.prescreen - INFO: Found g__Streptococcus.s__Streptococcus_gordonii : 0.05% of mapped reads
01/05/2021 04:10:42 PM - humann.search.prescreen - INFO: Found g__Cutibacterium.s__Cutibacterium_granulosum : 0.05% of mapped reads
01/05/2021 04:10:42 PM - humann.search.prescreen - INFO: Found g__Peptoniphilus.s__Peptoniphilus_lacrimalis : 0.04% of mapped reads
01/05/2021 04:10:42 PM - humann.search.prescreen - INFO: Found g__Anaerococcus.s__Anaerococcus_lactolyticus : 0.04% of mapped reads
01/05/2021 04:10:42 PM - humann.search.prescreen - INFO: Found g__Actinomyces.s__Actinomyces_oris : 0.03% of mapped reads
01/05/2021 04:10:42 PM - humann.search.prescreen - INFO: Found g__Malassezia.s__Malassezia_globosa : 0.03% of mapped reads
01/05/2021 04:10:42 PM - humann.search.prescreen - INFO: Found g__Streptococcus.s__Streptococcus_mitis : 0.03% of mapped reads
01/05/2021 04:10:42 PM - humann.search.prescreen - INFO: Found g__Corynebacterium.s__Corynebacterium_aurimucosum : 0.03% of mapped reads
01/05/2021 04:10:42 PM - humann.search.prescreen - INFO: Found g__Prevotella.s__Prevotella_colorans : 0.03% of mapped reads
01/05/2021 04:10:42 PM - humann.search.prescreen - INFO: Found g__Anaerococcus.s__Anaerococcus_octavius : 0.02% of mapped reads
01/05/2021 04:10:42 PM - humann.search.prescreen - INFO: Found g__Corynebacterium.s__Corynebacterium_sp_NML140438 : 0.02% of mapped reads
01/05/2021 04:10:42 PM - humann.search.prescreen - INFO: Found g__Streptococcus.s__Streptococcus_oralis : 0.01% of mapped reads
01/05/2021 04:10:42 PM - humann.search.prescreen - INFO: Total species selected from prescreen: 34
01/05/2021 04:10:42 PM - humann.search.prescreen - DEBUG: Adding file to database: g__Peptoniphilus.s__Peptoniphilus_harei.centroids.v296_201901.ffn.gz
01/05/2021 04:10:42 PM - humann.search.prescreen - DEBUG: Adding file to database: g__Streptococcus.s__Streptococcus_mitis.centroids.v296_201901.ffn.gz
01/05/2021 04:10:42 PM - humann.search.prescreen - DEBUG: Adding file to database: g__Listeria.s__Listeria_monocytogenes.centroids.v296_201901.ffn.gz
01/05/2021 04:10:42 PM - humann.search.prescreen - DEBUG: Adding file to database: g__Peptoniphilus.s__Peptoniphilus_lacrimalis.centroids.v296_201901.ffn.gz
01/05/2021 04:10:42 PM - humann.search.prescreen - DEBUG: Adding file to database: g__Staphylococcus.s__Staphylococcus_hominis.centroids.v296_201901.ffn.gz
01/05/2021 04:10:42 PM - humann.search.prescreen - DEBUG: Adding file to database: g__Cutibacterium.s__Cutibacterium_granulosum.centroids.v296_201901.ffn.gz
01/05/2021 04:10:42 PM - humann.search.prescreen - DEBUG: Adding file to database: g__Cutibacterium.s__Propionibacterium_namnetense.centroids.v296_201901.ffn.gz
01/05/2021 04:10:42 PM - humann.search.prescreen - DEBUG: Adding file to database: g__Corynebacterium.s__Corynebacterium_sp_NML140438.centroids.v296_201901.ffn.gz
01/05/2021 04:10:42 PM - humann.search.prescreen - DEBUG: Adding file to database: g__Prevotella.s__Prevotella_timonensis.centroids.v296_201901.ffn.gz
01/05/2021 04:10:42 PM - humann.search.prescreen - DEBUG: Adding file to database: g__Actinomyces.s__Actinomyces_oris.centroids.v296_201901.ffn.gz
01/05/2021 04:10:42 PM - humann.search.prescreen - DEBUG: Adding file to database: g__Acinetobacter.s__Acinetobacter_johnsonii.centroids.v296_201901.ffn.gz
01/05/2021 04:10:42 PM - humann.search.prescreen - DEBUG: Adding file to database: g__Corynebacterium.s__Corynebacterium_kroppenstedtii.centroids.v296_201901.ffn.gz
01/05/2021 04:10:42 PM - humann.search.prescreen - DEBUG: Adding file to database: g__Cutibacterium.s__Cutibacterium_acnes.centroids.v296_201901.ffn.gz
01/05/2021 04:10:42 PM - humann.search.prescreen - DEBUG: Adding file to database: g__Corynebacterium.s__Corynebacterium_amycolatum.centroids.v296_201901.ffn.gz
01/05/2021 04:10:42 PM - humann.search.prescreen - DEBUG: Adding file to database: g__Streptococcus.s__Streptococcus_gordonii.centroids.v296_201901.ffn.gz
01/05/2021 04:10:42 PM - humann.search.prescreen - DEBUG: Adding file to database: g__Acinetobacter.s__Acinetobacter_lwoffii.centroids.v296_201901.ffn.gz
01/05/2021 04:10:42 PM - humann.search.prescreen - DEBUG: Adding file to database: g__Staphylococcus.s__Staphylococcus_epidermidis.centroids.v296_201901.ffn.gz
01/05/2021 04:10:42 PM - humann.search.prescreen - DEBUG: Adding file to database: g__Streptococcus.s__Streptococcus_oralis.centroids.v296_201901.ffn.gz
01/05/2021 04:10:42 PM - humann.search.prescreen - DEBUG: Adding file to database: g__Veillonella.s__Veillonella_parvula.centroids.v296_201901.ffn.gz
01/05/2021 04:10:42 PM - humann.search.prescreen - DEBUG: Adding file to database: g__Prevotella.s__Prevotella_colorans.centroids.v296_201901.ffn.gz
01/05/2021 04:10:42 PM - humann.search.prescreen - DEBUG: Adding file to database: g__Corynebacterium.s__Corynebacterium_aurimucosum.centroids.v296_201901.ffn.gz
01/05/2021 04:10:42 PM - humann.search.prescreen - DEBUG: Adding file to database: g__Malassezia.s__Malassezia_globosa.centroids.v296_201901.ffn.gz
01/05/2021 04:10:42 PM - humann.search.prescreen - DEBUG: Adding file to database: g__Moraxella.s__Moraxella_osloensis.centroids.v296_201901.ffn.gz
01/05/2021 04:10:42 PM - humann.search.prescreen - DEBUG: Adding file to database: g__Enhydrobacter.s__Enhydrobacter_aerosaccus.centroids.v296_201901.ffn.gz
01/05/2021 04:10:42 PM - humann.search.prescreen - DEBUG: Adding file to database: g__Anaerococcus.s__Anaerococcus_lactolyticus.centroids.v296_201901.ffn.gz
01/05/2021 04:10:42 PM - humann.search.prescreen - DEBUG: Adding file to database: g__Finegoldia.s__Finegoldia_magna.centroids.v296_201901.ffn.gz
01/05/2021 04:10:42 PM - humann.search.prescreen - DEBUG: Adding file to database: g__Corynebacterium.s__Corynebacterium_riegelii.centroids.v296_201901.ffn.gz
01/05/2021 04:10:42 PM - humann.search.prescreen - DEBUG: Adding file to database: g__Corynebacterium.s__Corynebacterium_coyleae.centroids.v296_201901.ffn.gz
01/05/2021 04:10:42 PM - humann.search.prescreen - DEBUG: Adding file to database: g__Anaerococcus.s__Anaerococcus_octavius.centroids.v296_201901.ffn.gz
01/05/2021 04:10:42 PM - humann.search.prescreen - DEBUG: Adding file to database: g__Enterococcus.s__Enterococcus_faecalis.centroids.v296_201901.ffn.gz
01/05/2021 04:10:42 PM - humann.search.prescreen - DEBUG: Adding file to database: g__Corynebacterium.s__Corynebacterium_genitalium.centroids.v296_201901.ffn.gz
01/05/2021 04:10:42 PM - humann.search.prescreen - DEBUG: Adding file to database: g__Campylobacter.s__Campylobacter_ureolyticus.centroids.v296_201901.ffn.gz
01/05/2021 04:10:42 PM - humann.search.prescreen - INFO: Creating custom ChocoPhlAn database ........
01/05/2021 04:10:42 PM - humann.utilities - DEBUG: Using software: /bin/gunzip
01/05/2021 04:10:42 PM - humann.utilities - INFO: Execute command: /bin/gunzip -c /home/plicht/humann_db/chocophlan/g__Peptoniphilus.s__Peptoniphilus_harei.centroids.v296_201901.ffn.gz /home/plicht/humann_db/chocophlan/g__Streptococcus.s__Streptococcus_mitis.centroids.v296_201901.ffn.gz /home/plicht/humann_db/chocophlan/g__Listeria.s__Listeria_monocytogenes.centroids.v296_201901.ffn.gz /home/plicht/humann_db/chocophlan/g__Peptoniphilus.s__Peptoniphilus_lacrimalis.centroids.v296_201901.ffn.gz /home/plicht/humann_db/chocophlan/g__Staphylococcus.s__Staphylococcus_hominis.centroids.v296_201901.ffn.gz /home/plicht/humann_db/chocophlan/g__Cutibacterium.s__Cutibacterium_granulosum.centroids.v296_201901.ffn.gz /home/plicht/humann_db/chocophlan/g__Cutibacterium.s__Propionibacterium_namnetense.centroids.v296_201901.ffn.gz /home/plicht/humann_db/chocophlan/g__Corynebacterium.s__Corynebacterium_sp_NML140438.centroids.v296_201901.ffn.gz /home/plicht/humann_db/chocophlan/g__Prevotella.s__Prevotella_timonensis.centroids.v296_201901.ffn.gz /home/plicht/humann_db/chocophlan/g__Actinomyces.s__Actinomyces_oris.centroids.v296_201901.ffn.gz /home/plicht/humann_db/chocophlan/g__Acinetobacter.s__Acinetobacter_johnsonii.centroids.v296_201901.ffn.gz /home/plicht/humann_db/chocophlan/g__Corynebacterium.s__Corynebacterium_kroppenstedtii.centroids.v296_201901.ffn.gz /home/plicht/humann_db/chocophlan/g__Cutibacterium.s__Cutibacterium_acnes.centroids.v296_201901.ffn.gz /home/plicht/humann_db/chocophlan/g__Corynebacterium.s__Corynebacterium_amycolatum.centroids.v296_201901.ffn.gz /home/plicht/humann_db/chocophlan/g__Streptococcus.s__Streptococcus_gordonii.centroids.v296_201901.ffn.gz /home/plicht/humann_db/chocophlan/g__Acinetobacter.s__Acinetobacter_lwoffii.centroids.v296_201901.ffn.gz /home/plicht/humann_db/chocophlan/g__Staphylococcus.s__Staphylococcus_epidermidis.centroids.v296_201901.ffn.gz /home/plicht/humann_db/chocophlan/g__Streptococcus.s__Streptococcus_oralis.centroids.v296_201901.ffn.gz /home/plicht/humann_db/chocophlan/g__Veillonella.s__Veillonella_parvula.centroids.v296_201901.ffn.gz /home/plicht/humann_db/chocophlan/g__Prevotella.s__Prevotella_colorans.centroids.v296_201901.ffn.gz /home/plicht/humann_db/chocophlan/g__Corynebacterium.s__Corynebacterium_aurimucosum.centroids.v296_201901.ffn.gz /home/plicht/humann_db/chocophlan/g__Malassezia.s__Malassezia_globosa.centroids.v296_201901.ffn.gz /home/plicht/humann_db/chocophlan/g__Moraxella.s__Moraxella_osloensis.centroids.v296_201901.ffn.gz /home/plicht/humann_db/chocophlan/g__Enhydrobacter.s__Enhydrobacter_aerosaccus.centroids.v296_201901.ffn.gz /home/plicht/humann_db/chocophlan/g__Anaerococcus.s__Anaerococcus_lactolyticus.centroids.v296_201901.ffn.gz /home/plicht/humann_db/chocophlan/g__Finegoldia.s__Finegoldia_magna.centroids.v296_201901.ffn.gz /home/plicht/humann_db/chocophlan/g__Corynebacterium.s__Corynebacterium_riegelii.centroids.v296_201901.ffn.gz /home/plicht/humann_db/chocophlan/g__Corynebacterium.s__Corynebacterium_coyleae.centroids.v296_201901.ffn.gz /home/plicht/humann_db/chocophlan/g__Anaerococcus.s__Anaerococcus_octavius.centroids.v296_201901.ffn.gz /home/plicht/humann_db/chocophlan/g__Enterococcus.s__Enterococcus_faecalis.centroids.v296_201901.ffn.gz /home/plicht/humann_db/chocophlan/g__Corynebacterium.s__Corynebacterium_genitalium.centroids.v296_201901.ffn.gz /home/plicht/humann_db/chocophlan/g__Campylobacter.s__Campylobacter_ureolyticus.centroids.v296_201901.ffn.gz
01/05/2021 04:10:43 PM - humann.humann - INFO: TIMESTAMP: Completed 	custom database creation 	:	 2	 seconds
01/05/2021 04:10:43 PM - humann.search.nucleotide - INFO: Running bowtie2-build ........
01/05/2021 04:10:43 PM - humann.utilities - DEBUG: Using software: /home/plicht/anaconda3/envs/metaphlan3_env/bin/bowtie2-build
01/05/2021 04:10:43 PM - humann.utilities - INFO: Execute command: /home/plicht/anaconda3/envs/metaphlan3_env/bin/bowtie2-build -f /media/plicht/T7/Samples8-30.5/HumanN/a10/a10_paired_cat_humann_temp_n32zynxi/a10_paired_cat_custom_chocophlan_database.ffn /media/plicht/T7/Samples8-30.5/HumanN/a10/a10_paired_cat_humann_temp_n32zynxi/a10_paired_cat_bowtie2_index
01/05/2021 04:14:02 PM - humann.humann - INFO: TIMESTAMP: Completed 	database index 	:	 199	 seconds
01/05/2021 04:14:02 PM - humann.search.nucleotide - DEBUG: Nucleotide input file is of type: fastq
01/05/2021 04:14:02 PM - humann.utilities - DEBUG: Using software: /home/plicht/anaconda3/envs/metaphlan3_env/bin/bowtie2
01/05/2021 04:14:02 PM - humann.utilities - INFO: Execute command: /home/plicht/anaconda3/envs/metaphlan3_env/bin/bowtie2 -q -x /media/plicht/T7/Samples8-30.5/HumanN/a10/a10_paired_cat_humann_temp_n32zynxi/a10_paired_cat_bowtie2_index -U /media/plicht/T7/Samples8-30.5/KneadData/only_read1_and_read2_paired_kneaddata/a10/a10_paired_cat.fastq -S /media/plicht/T7/Samples8-30.5/HumanN/a10/a10_paired_cat_humann_temp_n32zynxi/a10_paired_cat_bowtie2_aligned.sam -p 12 --very-sensitive
01/05/2021 04:15:29 PM - humann.utilities - DEBUG: b'4849228 reads; of these:\n  4849228 (100.00%) were unpaired; of these:\n    2193229 (45.23%) aligned 0 times\n    1147361 (23.66%) aligned exactly 1 time\n    1508638 (31.11%) aligned >1 times\n54.77% overall alignment rate\n'
01/05/2021 04:15:29 PM - humann.humann - INFO: TIMESTAMP: Completed 	nucleotide alignment 	:	 87	 seconds
01/05/2021 04:17:17 PM - humann.utilities - DEBUG: Total alignments where percent identity is not a number: 0
01/05/2021 04:17:17 PM - humann.utilities - DEBUG: Total alignments where alignment length is not a number: 0
01/05/2021 04:17:17 PM - humann.utilities - DEBUG: Total alignments where E-value is not a number: 0
01/05/2021 04:17:17 PM - humann.utilities - DEBUG: Total alignments not included based on large e-value: 0
01/05/2021 04:17:17 PM - humann.utilities - DEBUG: Total alignments not included based on small percent identity: 0
01/05/2021 04:17:17 PM - humann.utilities - DEBUG: Total alignments not included based on small query coverage: 0
01/05/2021 04:17:17 PM - humann.search.blastx_coverage - INFO: Total alignments without coverage information: 0
01/05/2021 04:17:17 PM - humann.search.blastx_coverage - INFO: Total proteins in blastx output: 42956
01/05/2021 04:17:17 PM - humann.search.blastx_coverage - INFO: Total proteins without lengths: 0
01/05/2021 04:17:17 PM - humann.search.blastx_coverage - INFO: Proteins with coverage greater than threshold (50.0): 12639
01/05/2021 04:18:59 PM - humann.search.nucleotide - DEBUG: Total nucleotide alignments not included based on filtered genes: 115123
01/05/2021 04:18:59 PM - humann.search.nucleotide - DEBUG: Total nucleotide alignments not included based on small percent identities: 0
01/05/2021 04:18:59 PM - humann.search.nucleotide - DEBUG: Total nucleotide alignments not included based on query coverage threshold: 0
01/05/2021 04:18:59 PM - humann.search.nucleotide - DEBUG: Keeping sam file
01/05/2021 04:18:59 PM - humann.humann - INFO: TIMESTAMP: Completed 	nucleotide alignment post-processing 	:	 209	 seconds
01/05/2021 04:18:59 PM - humann.humann - INFO: Total bugs from nucleotide alignment: 32
01/05/2021 04:18:59 PM - humann.humann - INFO: 
g__Cutibacterium.s__Cutibacterium_acnes: 2257486 hits
g__Acinetobacter.s__Acinetobacter_lwoffii: 162919 hits
g__Staphylococcus.s__Staphylococcus_epidermidis: 29549 hits
g__Cutibacterium.s__Propionibacterium_namnetense: 43932 hits
g__Corynebacterium.s__Corynebacterium_kroppenstedtii: 2953 hits
g__Acinetobacter.s__Acinetobacter_johnsonii: 17171 hits
g__Cutibacterium.s__Cutibacterium_granulosum: 3146 hits
g__Corynebacterium.s__Corynebacterium_aurimucosum: 743 hits
g__Listeria.s__Listeria_monocytogenes: 1349 hits
g__Moraxella.s__Moraxella_osloensis: 6969 hits
g__Enterococcus.s__Enterococcus_faecalis: 928 hits
g__Streptococcus.s__Streptococcus_oralis: 235 hits
g__Enhydrobacter.s__Enhydrobacter_aerosaccus: 4421 hits
g__Anaerococcus.s__Anaerococcus_lactolyticus: 330 hits
g__Prevotella.s__Prevotella_timonensis: 468 hits
g__Staphylococcus.s__Staphylococcus_hominis: 1457 hits
g__Anaerococcus.s__Anaerococcus_octavius: 187 hits
g__Corynebacterium.s__Corynebacterium_coyleae: 1745 hits
g__Actinomyces.s__Actinomyces_oris: 134 hits
g__Corynebacterium.s__Corynebacterium_riegelii: 804 hits
g__Campylobacter.s__Campylobacter_ureolyticus: 147 hits
g__Finegoldia.s__Finegoldia_magna: 844 hits
g__Peptoniphilus.s__Peptoniphilus_lacrimalis: 406 hits
g__Peptoniphilus.s__Peptoniphilus_harei: 437 hits
g__Corynebacterium.s__Corynebacterium_genitalium: 609 hits
g__Streptococcus.s__Streptococcus_mitis: 152 hits
g__Prevotella.s__Prevotella_colorans: 276 hits
g__Corynebacterium.s__Corynebacterium_amycolatum: 342 hits
g__Corynebacterium.s__Corynebacterium_sp_NML140438: 295 hits
g__Streptococcus.s__Streptococcus_gordonii: 180 hits
g__Malassezia.s__Malassezia_globosa: 102 hits
g__Veillonella.s__Veillonella_parvula: 160 hits
01/05/2021 04:18:59 PM - humann.humann - INFO: Total gene families from nucleotide alignment: 12639
01/05/2021 04:18:59 PM - humann.humann - INFO: Unaligned reads after nucleotide alignment: 47.6024637324 %
01/05/2021 04:18:59 PM - humann.search.translated - INFO: Running diamond ........
01/05/2021 04:18:59 PM - humann.search.translated - INFO: Aligning to reference database: uniref90_201901.dmnd
01/05/2021 04:18:59 PM - humann.utilities - DEBUG: Remove file: /media/plicht/T7/Samples8-30.5/HumanN/a10/a10_paired_cat_humann_temp_n32zynxi/tmpzqicxha6/diamond_m8_s_v2abi6
01/05/2021 04:18:59 PM - humann.utilities - DEBUG: Using software: /home/plicht/anaconda3/envs/metaphlan3_env/bin/diamond
01/05/2021 04:18:59 PM - humann.utilities - INFO: Execute command: /home/plicht/anaconda3/envs/metaphlan3_env/bin/diamond blastx --query /media/plicht/T7/Samples8-30.5/HumanN/a10/a10_paired_cat_humann_temp_n32zynxi/a10_paired_cat_bowtie2_unaligned.fa --evalue 1.0 --threads 12 --top 1 --outfmt 6 --db /home/plicht/humann_db/uniref90/uniref/uniref90_201901 --out /media/plicht/T7/Samples8-30.5/HumanN/a10/a10_paired_cat_humann_temp_n32zynxi/tmpzqicxha6/diamond_m8_s_v2abi6 --tmpdir /media/plicht/T7/Samples8-30.5/HumanN/a10/a10_paired_cat_humann_temp_n32zynxi/tmpzqicxha6
01/05/2021 04:20:34 PM - humann.utilities - CRITICAL: Error executing: /home/plicht/anaconda3/envs/metaphlan3_env/bin/diamond blastx --query /media/plicht/T7/Samples8-30.5/HumanN/a10/a10_paired_cat_humann_temp_n32zynxi/a10_paired_cat_bowtie2_unaligned.fa --evalue 1.0 --threads 12 --top 1 --outfmt 6 --db /home/plicht/humann_db/uniref90/uniref/uniref90_201901 --out /media/plicht/T7/Samples8-30.5/HumanN/a10/a10_paired_cat_humann_temp_n32zynxi/tmpzqicxha6/diamond_m8_s_v2abi6 --tmpdir /media/plicht/T7/Samples8-30.5/HumanN/a10/a10_paired_cat_humann_temp_n32zynxi/tmpzqicxha6

Error message returned from diamond :
diamond v2.0.2.140 (C) Max Planck Society for the Advancement of Science
Documentation, support and updates available at http://www.diamondsearch.org

#CPU threads: 12
Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1)
Temporary directory: /media/plicht/T7/Samples8-30.5/HumanN/a10/a10_paired_cat_humann_temp_n32zynxi/tmpzqicxha6
Opening the database...  [0.05s]
Percentage range of top alignment score to report hits: 1
Reference = /home/plicht/humann_db/uniref90/uniref/uniref90_201901.dmnd
Sequences = 87296736
Letters = 29247941583
Block size = 2000000000
Opening the input file...  [0.023s]
Opening the output file...  [0s]
Loading query sequences...  [3.583s]
Masking queries...  [5.065s]
Building query seed set...  [0.046s]
The host system is detected to have 67 GB of RAM. It is recommended to increase the block size for better performance using these parameters: -b6
Algorithm: Double-indexed
Building query histograms...  [1.077s]
Allocating buffers...  [0s]
Loading reference sequences...  [2.682s]
Masking reference...  [13.92s]
Initializing temporary storage...  [0s]
Building reference histograms...  [5.473s]
Allocating buffers...  [0s]
Processing query block 0, reference block 0, shape 0, index chunk 0.
Building reference seed array...  [3.698s]
Building query seed array...  [0.692s]
Computing hash join...  [0.959s]
Building seed filter...  [0.043s]
Searching alignments...  [2.531s]
Processing query block 0, reference block 0, shape 0, index chunk 1.
Building reference seed array...  [4.209s]
Building query seed array...  [0.751s]
Computing hash join...  [0.949s]
Building seed filter...  [0.041s]
Searching alignments...  [2.449s]
Processing query block 0, reference block 0, shape 0, index chunk 2.
Building reference seed array...  [4.441s]
Building query seed array...  [0.775s]
Computing hash join...  [0.969s]
Building seed filter...  [0.043s]
Searching alignments...  [2.439s]
Processing query block 0, reference block 0, shape 0, index chunk 3.
Building reference seed array...  [3.515s]
Building query seed array...  [0.668s]
Computing hash join...  [0.951s]
Building seed filter...  [0.041s]
Searching alignments...  [2.343s]
Processing query block 0, reference block 0, shape 1, index chunk 0.
Building reference seed array...  [3.453s]
Building query seed array...  [0.618s]
Computing hash join...  [0.919s]
Building seed filter...  [0.036s]
Searching alignments...  [2.078s]
Processing query block 0, reference block 0, shape 1, index chunk 1.
Building reference seed array...  [4.169s]
Building query seed array...  [0.703s]
Computing hash join...  [0.922s]
Building seed filter...  [0.04s]
Searching alignments...  [2.12s]
Processing query block 0, reference block 0, shape 1, index chunk 2.
Building reference seed array...  [4.441s]
Building query seed array...  [0.732s]
Computing hash join...  [0.908s]
Building seed filter...  [0.038s]
Searching alignments...  [2.023s]
Processing query block 0, reference block 0, shape 1, index chunk 3.
Building reference seed array...  [3.461s]
Building query seed array...  [0.646s]
Computing hash join...  [0.912s]
Building seed filter...  [0.036s]
Searching alignments...  [2.004s]
Deallocating buffers...  [0.209s]
Clearing query masking...  [0.195s]
Opening temporary output file...  [0s]
Computing alignments... Input/output error
 [0s]
Error: Error writing file /media/plicht/T7/Samples8-30.5/HumanN/a10/a10_paired_cat_humann_temp_n32zynxi/tmpzqicxha6/diamond-tmp-HCMDRd

01/05/2021 04:20:34 PM - humann.utilities - CRITICAL: TRACEBACK: 
Traceback (most recent call last):
  File "/home/plicht/anaconda3/envs/metaphlan3_env/lib/python3.7/site-packages/humann/utilities.py", line 744, in execute_command
    p_out = subprocess.check_output(cmd, stderr=subprocess.STDOUT)
  File "/home/plicht/anaconda3/envs/metaphlan3_env/lib/python3.7/subprocess.py", line 411, in check_output
    **kwargs).stdout
  File "/home/plicht/anaconda3/envs/metaphlan3_env/lib/python3.7/subprocess.py", line 512, in run
    output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command '['/home/plicht/anaconda3/envs/metaphlan3_env/bin/diamond', 'blastx', '--query', '/media/plicht/T7/Samples8-30.5/HumanN/a10/a10_paired_cat_humann_temp_n32zynxi/a10_paired_cat_bowtie2_unaligned.fa', '--evalue', '1.0', '--threads', '12', '--top', '1', '--outfmt', '6', '--db', '/home/plicht/humann_db/uniref90/uniref/uniref90_201901', '--out', '/media/plicht/T7/Samples8-30.5/HumanN/a10/a10_paired_cat_humann_temp_n32zynxi/tmpzqicxha6/diamond_m8_s_v2abi6', '--tmpdir', '/media/plicht/T7/Samples8-30.5/HumanN/a10/a10_paired_cat_humann_temp_n32zynxi/tmpzqicxha6']' returned non-zero exit status 1.