01/05/2021 04:29:19 PM - humann.humann - INFO: Running humann v3.0.0.alpha.3 01/05/2021 04:29:19 PM - humann.humann - INFO: Output files will be written to: /media/plicht/T7/Samples8-30.5/HumanN/a10 01/05/2021 04:29:19 PM - humann.humann - INFO: Writing temp files to directory: /media/plicht/T7/Samples8-30.5/HumanN/a10/a10_paired_cat_humann_temp_2cqhe285 01/05/2021 04:29:19 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 04:29:19 PM - humann.utilities - DEBUG: Check software, metaphlan, for required version, 3.0 01/05/2021 04:29:19 PM - humann.utilities - INFO: Using metaphlan version 3.0 01/05/2021 04:29:19 PM - humann.utilities - DEBUG: Check software, bowtie2, for required version, 2.2 01/05/2021 04:29:19 PM - humann.utilities - WARNING: Can not call software version for bowtie2 01/05/2021 04:29:19 PM - humann.utilities - INFO: Using bowtie2 version UNK 01/05/2021 04:29:19 PM - humann.humann - INFO: Search mode set to uniref90 because a uniref90 translated search database is selected 01/05/2021 04:29:19 PM - humann.utilities - DEBUG: Check software, diamond, for required version, 0.9.24 01/05/2021 04:29:19 PM - humann.utilities - INFO: Using diamond version 0.9.24 01/05/2021 04:29:19 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 04:29:19 PM - humann.store - DEBUG: Initialize Alignments class instance to maximize memory use 01/05/2021 04:29:19 PM - humann.store - DEBUG: Initialize Reads class instance to maximize memory use 01/05/2021 04:29:33 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 04:29:33 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 04:29:33 PM - humann.search.prescreen - INFO: Found g__Cutibacterium.s__Cutibacterium_acnes : 92.39% of mapped reads 01/05/2021 04:29:33 PM - humann.search.prescreen - INFO: Found g__Acinetobacter.s__Acinetobacter_lwoffii : 4.26% of mapped reads 01/05/2021 04:29:33 PM - humann.search.prescreen - INFO: Found g__Staphylococcus.s__Staphylococcus_epidermidis : 0.87% of mapped reads 01/05/2021 04:29:33 PM - humann.search.prescreen - INFO: Found g__Enhydrobacter.s__Enhydrobacter_aerosaccus : 0.22% of mapped reads 01/05/2021 04:29:33 PM - humann.search.prescreen - INFO: Found g__Corynebacterium.s__Corynebacterium_kroppenstedtii : 0.22% of mapped reads 01/05/2021 04:29:33 PM - humann.search.prescreen - INFO: Found g__Malassezia.s__Malassezia_restricta : 0.20% of mapped reads 01/05/2021 04:29:33 PM - humann.search.prescreen - INFO: Found g__Moraxella.s__Moraxella_osloensis : 0.17% of mapped reads 01/05/2021 04:29:33 PM - humann.search.prescreen - INFO: Found g__Acinetobacter.s__Acinetobacter_johnsonii : 0.16% of mapped reads 01/05/2021 04:29:33 PM - humann.search.prescreen - INFO: Found g__Cutibacterium.s__Propionibacterium_namnetense : 0.14% of mapped reads 01/05/2021 04:29:33 PM - humann.search.prescreen - INFO: Found g__Staphylococcus.s__Staphylococcus_hominis : 0.14% of mapped reads 01/05/2021 04:29:33 PM - humann.search.prescreen - INFO: Found g__Enterococcus.s__Enterococcus_faecalis : 0.09% of mapped reads 01/05/2021 04:29:33 PM - humann.search.prescreen - INFO: Found g__Prevotella.s__Prevotella_timonensis : 0.09% of mapped reads 01/05/2021 04:29:33 PM - humann.search.prescreen - INFO: Found g__Corynebacterium.s__Corynebacterium_coyleae : 0.08% of mapped reads 01/05/2021 04:29:33 PM - humann.search.prescreen - INFO: Found g__Corynebacterium.s__Corynebacterium_riegelii : 0.07% of mapped reads 01/05/2021 04:29:33 PM - humann.search.prescreen - INFO: Found g__Corynebacterium.s__Corynebacterium_genitalium : 0.07% of mapped reads 01/05/2021 04:29:33 PM - humann.search.prescreen - INFO: Found g__Listeria.s__Listeria_monocytogenes : 0.06% of mapped reads 01/05/2021 04:29:33 PM - humann.search.prescreen - INFO: Found g__Campylobacter.s__Campylobacter_ureolyticus : 0.06% of mapped reads 01/05/2021 04:29:33 PM - humann.search.prescreen - INFO: Found g__Finegoldia.s__Finegoldia_magna : 0.06% of mapped reads 01/05/2021 04:29:33 PM - humann.search.prescreen - INFO: Found g__Veillonella.s__Veillonella_parvula : 0.05% of mapped reads 01/05/2021 04:29:33 PM - humann.search.prescreen - INFO: Found g__Corynebacterium.s__Corynebacterium_amycolatum : 0.05% of mapped reads 01/05/2021 04:29:33 PM - humann.search.prescreen - INFO: Found g__Prolinoborus.s__Prolinoborus_fasciculus : 0.05% of mapped reads 01/05/2021 04:29:33 PM - humann.search.prescreen - INFO: Found g__Peptoniphilus.s__Peptoniphilus_harei : 0.05% of mapped reads 01/05/2021 04:29:33 PM - humann.search.prescreen - INFO: Found g__Streptococcus.s__Streptococcus_gordonii : 0.05% of mapped reads 01/05/2021 04:29:33 PM - humann.search.prescreen - INFO: Found g__Cutibacterium.s__Cutibacterium_granulosum : 0.05% of mapped reads 01/05/2021 04:29:33 PM - humann.search.prescreen - INFO: Found g__Peptoniphilus.s__Peptoniphilus_lacrimalis : 0.04% of mapped reads 01/05/2021 04:29:33 PM - humann.search.prescreen - INFO: Found g__Anaerococcus.s__Anaerococcus_lactolyticus : 0.04% of mapped reads 01/05/2021 04:29:33 PM - humann.search.prescreen - INFO: Found g__Actinomyces.s__Actinomyces_oris : 0.03% of mapped reads 01/05/2021 04:29:33 PM - humann.search.prescreen - INFO: Found g__Malassezia.s__Malassezia_globosa : 0.03% of mapped reads 01/05/2021 04:29:33 PM - humann.search.prescreen - INFO: Found g__Streptococcus.s__Streptococcus_mitis : 0.03% of mapped reads 01/05/2021 04:29:33 PM - humann.search.prescreen - INFO: Found g__Corynebacterium.s__Corynebacterium_aurimucosum : 0.03% of mapped reads 01/05/2021 04:29:33 PM - humann.search.prescreen - INFO: Found g__Prevotella.s__Prevotella_colorans : 0.03% of mapped reads 01/05/2021 04:29:33 PM - humann.search.prescreen - INFO: Found g__Anaerococcus.s__Anaerococcus_octavius : 0.02% of mapped reads 01/05/2021 04:29:33 PM - humann.search.prescreen - INFO: Found g__Corynebacterium.s__Corynebacterium_sp_NML140438 : 0.02% of mapped reads 01/05/2021 04:29:33 PM - humann.search.prescreen - INFO: Found g__Streptococcus.s__Streptococcus_oralis : 0.01% of mapped reads 01/05/2021 04:29:33 PM - humann.search.prescreen - INFO: Total species selected from prescreen: 34 01/05/2021 04:29:33 PM - humann.search.prescreen - DEBUG: Adding file to database: g__Peptoniphilus.s__Peptoniphilus_harei.centroids.v296_201901.ffn.gz 01/05/2021 04:29:33 PM - humann.search.prescreen - DEBUG: Adding file to database: g__Streptococcus.s__Streptococcus_mitis.centroids.v296_201901.ffn.gz 01/05/2021 04:29:33 PM - humann.search.prescreen - DEBUG: Adding file to database: g__Listeria.s__Listeria_monocytogenes.centroids.v296_201901.ffn.gz 01/05/2021 04:29:33 PM - humann.search.prescreen - DEBUG: Adding file to database: g__Peptoniphilus.s__Peptoniphilus_lacrimalis.centroids.v296_201901.ffn.gz 01/05/2021 04:29:33 PM - humann.search.prescreen - DEBUG: Adding file to database: g__Staphylococcus.s__Staphylococcus_hominis.centroids.v296_201901.ffn.gz 01/05/2021 04:29:33 PM - humann.search.prescreen - DEBUG: Adding file to database: g__Cutibacterium.s__Cutibacterium_granulosum.centroids.v296_201901.ffn.gz 01/05/2021 04:29:33 PM - humann.search.prescreen - DEBUG: Adding file to database: g__Cutibacterium.s__Propionibacterium_namnetense.centroids.v296_201901.ffn.gz 01/05/2021 04:29:33 PM - humann.search.prescreen - DEBUG: Adding file to database: g__Corynebacterium.s__Corynebacterium_sp_NML140438.centroids.v296_201901.ffn.gz 01/05/2021 04:29:33 PM - humann.search.prescreen - DEBUG: Adding file to database: g__Prevotella.s__Prevotella_timonensis.centroids.v296_201901.ffn.gz 01/05/2021 04:29:33 PM - humann.search.prescreen - DEBUG: Adding file to database: g__Actinomyces.s__Actinomyces_oris.centroids.v296_201901.ffn.gz 01/05/2021 04:29:33 PM - humann.search.prescreen - DEBUG: Adding file to database: g__Acinetobacter.s__Acinetobacter_johnsonii.centroids.v296_201901.ffn.gz 01/05/2021 04:29:33 PM - humann.search.prescreen - DEBUG: Adding file to database: g__Corynebacterium.s__Corynebacterium_kroppenstedtii.centroids.v296_201901.ffn.gz 01/05/2021 04:29:33 PM - humann.search.prescreen - DEBUG: Adding file to database: g__Cutibacterium.s__Cutibacterium_acnes.centroids.v296_201901.ffn.gz 01/05/2021 04:29:33 PM - humann.search.prescreen - DEBUG: Adding file to database: g__Corynebacterium.s__Corynebacterium_amycolatum.centroids.v296_201901.ffn.gz 01/05/2021 04:29:33 PM - humann.search.prescreen - DEBUG: Adding file to database: g__Streptococcus.s__Streptococcus_gordonii.centroids.v296_201901.ffn.gz 01/05/2021 04:29:33 PM - humann.search.prescreen - DEBUG: Adding file to database: g__Acinetobacter.s__Acinetobacter_lwoffii.centroids.v296_201901.ffn.gz 01/05/2021 04:29:33 PM - humann.search.prescreen - DEBUG: Adding file to database: g__Staphylococcus.s__Staphylococcus_epidermidis.centroids.v296_201901.ffn.gz 01/05/2021 04:29:33 PM - humann.search.prescreen - DEBUG: Adding file to database: g__Streptococcus.s__Streptococcus_oralis.centroids.v296_201901.ffn.gz 01/05/2021 04:29:33 PM - humann.search.prescreen - DEBUG: Adding file to database: g__Veillonella.s__Veillonella_parvula.centroids.v296_201901.ffn.gz 01/05/2021 04:29:33 PM - humann.search.prescreen - DEBUG: Adding file to database: g__Prevotella.s__Prevotella_colorans.centroids.v296_201901.ffn.gz 01/05/2021 04:29:33 PM - humann.search.prescreen - DEBUG: Adding file to database: g__Corynebacterium.s__Corynebacterium_aurimucosum.centroids.v296_201901.ffn.gz 01/05/2021 04:29:33 PM - humann.search.prescreen - DEBUG: Adding file to database: g__Malassezia.s__Malassezia_globosa.centroids.v296_201901.ffn.gz 01/05/2021 04:29:33 PM - humann.search.prescreen - DEBUG: Adding file to database: g__Moraxella.s__Moraxella_osloensis.centroids.v296_201901.ffn.gz 01/05/2021 04:29:33 PM - humann.search.prescreen - DEBUG: Adding file to database: g__Enhydrobacter.s__Enhydrobacter_aerosaccus.centroids.v296_201901.ffn.gz 01/05/2021 04:29:33 PM - humann.search.prescreen - DEBUG: Adding file to database: g__Anaerococcus.s__Anaerococcus_lactolyticus.centroids.v296_201901.ffn.gz 01/05/2021 04:29:33 PM - humann.search.prescreen - DEBUG: Adding file to database: g__Finegoldia.s__Finegoldia_magna.centroids.v296_201901.ffn.gz 01/05/2021 04:29:33 PM - humann.search.prescreen - DEBUG: Adding file to database: g__Corynebacterium.s__Corynebacterium_riegelii.centroids.v296_201901.ffn.gz 01/05/2021 04:29:33 PM - humann.search.prescreen - DEBUG: Adding file to database: g__Corynebacterium.s__Corynebacterium_coyleae.centroids.v296_201901.ffn.gz 01/05/2021 04:29:33 PM - humann.search.prescreen - DEBUG: Adding file to database: g__Anaerococcus.s__Anaerococcus_octavius.centroids.v296_201901.ffn.gz 01/05/2021 04:29:33 PM - humann.search.prescreen - DEBUG: Adding file to database: g__Enterococcus.s__Enterococcus_faecalis.centroids.v296_201901.ffn.gz 01/05/2021 04:29:33 PM - humann.search.prescreen - DEBUG: Adding file to database: g__Corynebacterium.s__Corynebacterium_genitalium.centroids.v296_201901.ffn.gz 01/05/2021 04:29:33 PM - humann.search.prescreen - DEBUG: Adding file to database: g__Campylobacter.s__Campylobacter_ureolyticus.centroids.v296_201901.ffn.gz 01/05/2021 04:29:33 PM - humann.search.prescreen - INFO: Creating custom ChocoPhlAn database ........ 01/05/2021 04:29:33 PM - humann.utilities - DEBUG: Using software: /bin/gunzip 01/05/2021 04:29:33 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 04:29:35 PM - humann.humann - INFO: TIMESTAMP: Completed custom database creation : 2 seconds 01/05/2021 04:29:35 PM - humann.search.nucleotide - INFO: Running bowtie2-build ........ 01/05/2021 04:29:35 PM - humann.utilities - DEBUG: Using software: /home/plicht/anaconda3/envs/metaphlan3_env/bin/bowtie2-build 01/05/2021 04:29:35 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_2cqhe285/a10_paired_cat_custom_chocophlan_database.ffn /media/plicht/T7/Samples8-30.5/HumanN/a10/a10_paired_cat_humann_temp_2cqhe285/a10_paired_cat_bowtie2_index 01/05/2021 04:32:56 PM - humann.humann - INFO: TIMESTAMP: Completed database index : 202 seconds 01/05/2021 04:32:56 PM - humann.search.nucleotide - DEBUG: Nucleotide input file is of type: fastq 01/05/2021 04:32:56 PM - humann.utilities - DEBUG: Using software: /home/plicht/anaconda3/envs/metaphlan3_env/bin/bowtie2 01/05/2021 04:32:56 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_2cqhe285/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_2cqhe285/a10_paired_cat_bowtie2_aligned.sam -p 12 --very-sensitive 01/05/2021 04:34:29 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 04:34:29 PM - humann.humann - INFO: TIMESTAMP: Completed nucleotide alignment : 93 seconds 01/05/2021 04:36:17 PM - humann.utilities - DEBUG: Total alignments where percent identity is not a number: 0 01/05/2021 04:36:17 PM - humann.utilities - DEBUG: Total alignments where alignment length is not a number: 0 01/05/2021 04:36:17 PM - humann.utilities - DEBUG: Total alignments where E-value is not a number: 0 01/05/2021 04:36:17 PM - humann.utilities - DEBUG: Total alignments not included based on large e-value: 0 01/05/2021 04:36:17 PM - humann.utilities - DEBUG: Total alignments not included based on small percent identity: 0 01/05/2021 04:36:17 PM - humann.utilities - DEBUG: Total alignments not included based on small query coverage: 0 01/05/2021 04:36:17 PM - humann.search.blastx_coverage - INFO: Total alignments without coverage information: 0 01/05/2021 04:36:17 PM - humann.search.blastx_coverage - INFO: Total proteins in blastx output: 42956 01/05/2021 04:36:17 PM - humann.search.blastx_coverage - INFO: Total proteins without lengths: 0 01/05/2021 04:36:17 PM - humann.search.blastx_coverage - INFO: Proteins with coverage greater than threshold (50.0): 12639 01/05/2021 04:37:55 PM - humann.search.nucleotide - DEBUG: Total nucleotide alignments not included based on filtered genes: 115123 01/05/2021 04:37:55 PM - humann.search.nucleotide - DEBUG: Total nucleotide alignments not included based on small percent identities: 0 01/05/2021 04:37:55 PM - humann.search.nucleotide - DEBUG: Total nucleotide alignments not included based on query coverage threshold: 0 01/05/2021 04:37:55 PM - humann.search.nucleotide - DEBUG: Keeping sam file 01/05/2021 04:37:55 PM - humann.humann - INFO: TIMESTAMP: Completed nucleotide alignment post-processing : 206 seconds 01/05/2021 04:37:55 PM - humann.humann - INFO: Total bugs from nucleotide alignment: 32 01/05/2021 04:37:55 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__Corynebacterium.s__Corynebacterium_kroppenstedtii: 2953 hits g__Cutibacterium.s__Propionibacterium_namnetense: 43932 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 04:37:55 PM - humann.humann - INFO: Total gene families from nucleotide alignment: 12639 01/05/2021 04:37:55 PM - humann.humann - INFO: Unaligned reads after nucleotide alignment: 47.6024637324 % 01/05/2021 04:37:55 PM - humann.search.translated - INFO: Running diamond ........ 01/05/2021 04:37:55 PM - humann.search.translated - INFO: Aligning to reference database: uniref90_201901.dmnd 01/05/2021 04:37:55 PM - humann.utilities - DEBUG: Remove file: /media/plicht/T7/Samples8-30.5/HumanN/a10/a10_paired_cat_humann_temp_2cqhe285/tmpdq05it2l/diamond_m8_duk6r4gg 01/05/2021 04:37:55 PM - humann.utilities - DEBUG: Using software: /home/plicht/anaconda3/envs/metaphlan3_env/bin/diamond 01/05/2021 04:37:55 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_2cqhe285/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_2cqhe285/tmpdq05it2l/diamond_m8_duk6r4gg --tmpdir /media/plicht/T7/Samples8-30.5/HumanN/a10/a10_paired_cat_humann_temp_2cqhe285/tmpdq05it2l 01/05/2021 04:38:32 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_2cqhe285/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_2cqhe285/tmpdq05it2l/diamond_m8_duk6r4gg --tmpdir /media/plicht/T7/Samples8-30.5/HumanN/a10/a10_paired_cat_humann_temp_2cqhe285/tmpdq05it2l Error message returned from diamond : diamond v0.9.24.125 | by Benjamin Buchfink Licensed under the GNU GPL Check http://github.com/bbuchfink/diamond for updates. #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_2cqhe285/tmpdq05it2l Opening the database... [1.6e-05s] Percentage range of top alignment score to report hits: 1 Opening the input file... [1.4e-05s] Opening the output file... [1.3e-05s] Loading query sequences... [3.73777s] Masking queries... [15.5913s] Building query seed set... [0.042783s] Algorithm: Double-indexed Building query histograms... [0.903827s] Allocating buffers... [4.6e-05s] Loading reference sequences... [2.69293s] Building reference histograms... [4.4737s] Allocating buffers... [3.7e-05s] Initializing temporary storage... [0.001966s] Processing query chunk 0, reference chunk 0, shape 0, index chunk 0. Building reference index... [7.23267s] Building query index... [1.09464s] Building seed filter... [0.443503s] Searching alignments... Input/output error terminate called after throwing an instance of 'File_write_exception' what(): Error writing file /media/plicht/T7/Samples8-30.5/HumanN/a10/a10_paired_cat_humann_temp_2cqhe285/tmpdq05it2l/diamond-tmp-bJh6AG 01/05/2021 04:38:32 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_2cqhe285/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_2cqhe285/tmpdq05it2l/diamond_m8_duk6r4gg', '--tmpdir', '/media/plicht/T7/Samples8-30.5/HumanN/a10/a10_paired_cat_humann_temp_2cqhe285/tmpdq05it2l']' died with .