10/06/2021 08:57:48 PM - humann.humann - INFO: Running humann v3.0.0
10/06/2021 08:57:48 PM - humann.humann - INFO: Output files will be written to: /local/ifs2_projdata/0780/projects/SMU_MUC/curanga/RNAseq/hmp_subset
10/06/2021 08:57:48 PM - humann.humann - INFO: Writing temp files to directory: /local/ifs2_projdata/0780/projects/SMU_MUC/curanga/RNAseq/hmp_subset/B2A-PE-B10I7-B10I5-1_S10_R1_001_humann_temp
10/06/2021 08:57:48 PM - humann.utilities - INFO: File ( /usr/local/JTC/data/prod/solexa_depot/210930_A00588_0079_AH57C3DMXY/Unaligned_Lane1_05-10-2021/SOLEXASEQ-1579/B2A-PE-B10I7-B10I5-1_S10_R1_001.fastq.gz ) is of format:  fastq.gz
10/06/2021 08:57:48 PM - humann.utilities - INFO: Decompressing gzipped file ...
10/06/2021 09:02:20 PM - humann.humann - INFO: Removing spaces from identifiers in input file
10/06/2021 09:07:28 PM - humann.utilities - DEBUG: Check software, metaphlan, for required version, 3.0
10/06/2021 09:07:30 PM - humann.utilities - INFO: Using metaphlan version 3.0
10/06/2021 09:07:30 PM - humann.utilities - DEBUG: Check software, bowtie2, for required version, 2.2
10/06/2021 09:07:30 PM - humann.utilities - INFO: Using bowtie2 version 2.4
10/06/2021 09:07:30 PM - humann.humann - INFO: Search mode set to uniref90 because a uniref90 translated search database is selected
10/06/2021 09:07:30 PM - humann.utilities - DEBUG: Check software, diamond, for required version, 0.9.36
10/06/2021 09:07:30 PM - humann.utilities - INFO: Using diamond version 2.0.11
10/06/2021 09:07:30 PM - humann.config - INFO: 
Run config settings: 

DATABASE SETTINGS
nucleotide database folder = /local/ifs2_projdata/0780/projects/SMU_MUC/curanga/RNAseq/chocophlan1
protein database folder = /local/ifs2_projdata/0780/projects/SMU_MUC/curanga/RNAseq/uniref
pathways database file 1 = /local/ifs2_projdata/0780/projects/SMU_MUC/curanga/miniconda3/envs/mpa/lib/python3.7/site-packages/humann/data/pathways/metacyc_reactions_level4ec_only.uniref.bz2
pathways database file 2 = /local/ifs2_projdata/0780/projects/SMU_MUC/curanga/miniconda3/envs/mpa/lib/python3.7/site-packages/humann/data/pathways/metacyc_pathways_structured_filtered
utility mapping database folder = /local/ifs2_projdata/0780/projects/SMU_MUC/curanga/miniconda3/envs/mpa/lib/python3.7/site-packages/humann/data/misc

RUN MODES
resume = False
verbose = False
bypass prescreen = False
bypass nucleotide index = False
bypass nucleotide search = False
bypass translated search = False
translated search = diamond
threads = 1

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.gz
output file format = tsv
output max decimals = 10
remove stratified output = False
remove column description output = False
log level = DEBUG

10/06/2021 09:07:30 PM - humann.store - DEBUG: Initialize Alignments class instance to minimize memory use
10/06/2021 09:07:30 PM - humann.store - DEBUG: Initialize Reads class instance to minimize memory use
10/06/2021 09:07:50 PM - humann.humann - INFO: Load pathways database part 1: /local/ifs2_projdata/0780/projects/SMU_MUC/curanga/miniconda3/envs/mpa/lib/python3.7/site-packages/humann/data/pathways/metacyc_reactions_level4ec_only.uniref.bz2
10/06/2021 09:07:50 PM - humann.humann - INFO: Load pathways database part 2: /local/ifs2_projdata/0780/projects/SMU_MUC/curanga/miniconda3/envs/mpa/lib/python3.7/site-packages/humann/data/pathways/metacyc_pathways_structured_filtered
10/06/2021 09:07:50 PM - humann.search.prescreen - INFO: Running metaphlan ........
10/06/2021 09:07:50 PM - humann.utilities - DEBUG: Using software: /local/ifs2_projdata/0780/projects/SMU_MUC/curanga/miniconda3/envs/mpa/bin/metaphlan
10/06/2021 09:07:50 PM - humann.utilities - INFO: Execute command: /local/ifs2_projdata/0780/projects/SMU_MUC/curanga/miniconda3/envs/mpa/bin/metaphlan /local/ifs2_projdata/0780/projects/SMU_MUC/curanga/RNAseq/hmp_subset/B2A-PE-B10I7-B10I5-1_S10_R1_001_humann_temp/tmpbmi62t5r/tmpi0slz6vl -t rel_ab -o /local/ifs2_projdata/0780/projects/SMU_MUC/curanga/RNAseq/hmp_subset/B2A-PE-B10I7-B10I5-1_S10_R1_001_humann_temp/B2A-PE-B10I7-B10I5-1_S10_R1_001_metaphlan_bugs_list.tsv --input_type fastq --bowtie2out /local/ifs2_projdata/0780/projects/SMU_MUC/curanga/RNAseq/hmp_subset/B2A-PE-B10I7-B10I5-1_S10_R1_001_humann_temp/B2A-PE-B10I7-B10I5-1_S10_R1_001_metaphlan_bowtie2.txt
10/06/2021 10:41:05 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'
10/06/2021 10:41:05 PM - humann.humann - INFO: TIMESTAMP: Completed 	prescreen 	:	 5595	 seconds
10/06/2021 10:41:05 PM - humann.search.prescreen - INFO: Found g__Lactobacillus.s__Lactobacillus_fermentum : 86.21% of mapped reads
10/06/2021 10:41:05 PM - humann.search.prescreen - INFO: Found g__Streptococcus.s__Streptococcus_oralis : 3.61% of mapped reads
10/06/2021 10:41:05 PM - humann.search.prescreen - INFO: Found g__Streptococcus.s__Streptococcus_salivarius : 3.53% of mapped reads
10/06/2021 10:41:05 PM - humann.search.prescreen - INFO: Found g__Streptococcus.s__Streptococcus_mutans : 2.58% of mapped reads
10/06/2021 10:41:05 PM - humann.search.prescreen - INFO: Found g__Veillonella.s__Veillonella_atypica : 2.42% of mapped reads
10/06/2021 10:41:05 PM - humann.search.prescreen - INFO: Found g__Streptococcus.s__Streptococcus_parasanguinis : 1.29% of mapped reads
10/06/2021 10:41:05 PM - humann.search.prescreen - INFO: Found g__Streptococcus.s__Streptococcus_cristatus : 0.07% of mapped reads
10/06/2021 10:41:05 PM - humann.search.prescreen - INFO: Found g__Streptococcus.s__Streptococcus_anginosus_group : 0.06% of mapped reads
10/06/2021 10:41:05 PM - humann.search.prescreen - INFO: Found g__Veillonella.s__Veillonella_dispar : 0.06% of mapped reads
10/06/2021 10:41:05 PM - humann.search.prescreen - INFO: Found g__Veillonella.s__Veillonella_parvula : 0.04% of mapped reads
10/06/2021 10:41:05 PM - humann.search.prescreen - INFO: Found g__Streptococcus.s__Streptococcus_mitis : 0.03% of mapped reads
10/06/2021 10:41:05 PM - humann.search.prescreen - INFO: Found g__Gemella.s__Gemella_sanguinis : 0.03% of mapped reads
10/06/2021 10:41:05 PM - humann.search.prescreen - INFO: Found g__Streptococcus.s__Streptococcus_infantis : 0.02% of mapped reads
10/06/2021 10:41:05 PM - humann.search.prescreen - INFO: Found g__Streptococcus.s__Streptococcus_sp_HMSC034E03 : 0.01% of mapped reads
10/06/2021 10:41:05 PM - humann.search.prescreen - INFO: Total species selected from prescreen: 14
10/06/2021 10:41:05 PM - humann.search.prescreen - DEBUG: Adding file to database: g__Streptococcus.s__Streptococcus_sp_HMSC034E03.centroids.v296_v201901b.ffn.gz
10/06/2021 10:41:05 PM - humann.search.prescreen - DEBUG: Adding file to database: g__Veillonella.s__Veillonella_parvula.centroids.v296_v201901b.ffn.gz
10/06/2021 10:41:05 PM - humann.search.prescreen - DEBUG: Adding file to database: g__Streptococcus.s__Streptococcus_oralis.centroids.v296_v201901b.ffn.gz
10/06/2021 10:41:05 PM - humann.search.prescreen - DEBUG: Adding file to database: g__Streptococcus.s__Streptococcus_parasanguinis.centroids.v296_v201901b.ffn.gz
10/06/2021 10:41:05 PM - humann.search.prescreen - DEBUG: Adding file to database: g__Streptococcus.s__Streptococcus_mitis.centroids.v296_v201901b.ffn.gz
10/06/2021 10:41:05 PM - humann.search.prescreen - DEBUG: Adding file to database: g__Streptococcus.s__Streptococcus_cristatus.centroids.v296_v201901b.ffn.gz
10/06/2021 10:41:05 PM - humann.search.prescreen - DEBUG: Adding file to database: g__Streptococcus.s__Streptococcus_mutans.centroids.v296_v201901b.ffn.gz
10/06/2021 10:41:05 PM - humann.search.prescreen - DEBUG: Adding file to database: g__Lactobacillus.s__Lactobacillus_fermentum.centroids.v296_v201901b.ffn.gz
10/06/2021 10:41:05 PM - humann.search.prescreen - DEBUG: Adding file to database: g__Veillonella.s__Veillonella_atypica.centroids.v296_v201901b.ffn.gz
10/06/2021 10:41:05 PM - humann.search.prescreen - DEBUG: Adding file to database: g__Streptococcus.s__Streptococcus_salivarius.centroids.v296_v201901b.ffn.gz
10/06/2021 10:41:05 PM - humann.search.prescreen - DEBUG: Adding file to database: g__Streptococcus.s__Streptococcus_anginosus_group.centroids.v296_v201901b.ffn.gz
10/06/2021 10:41:05 PM - humann.search.prescreen - DEBUG: Adding file to database: g__Gemella.s__Gemella_sanguinis.centroids.v201901b.ffn.gz
10/06/2021 10:41:05 PM - humann.search.prescreen - DEBUG: Adding file to database: g__Veillonella.s__Veillonella_dispar.centroids.v296_v201901b.ffn.gz
10/06/2021 10:41:05 PM - humann.search.prescreen - DEBUG: Adding file to database: g__Streptococcus.s__Streptococcus_infantis.centroids.v296_v201901b.ffn.gz
10/06/2021 10:41:05 PM - humann.search.prescreen - INFO: Creating custom ChocoPhlAn database ........
10/06/2021 10:41:06 PM - humann.utilities - DEBUG: Using software: /bin/gunzip
10/06/2021 10:41:06 PM - humann.utilities - INFO: Execute command: /bin/gunzip -c /local/ifs2_projdata/0780/projects/SMU_MUC/curanga/RNAseq/chocophlan1/g__Streptococcus.s__Streptococcus_sp_HMSC034E03.centroids.v296_v201901b.ffn.gz /local/ifs2_projdata/0780/projects/SMU_MUC/curanga/RNAseq/chocophlan1/g__Veillonella.s__Veillonella_parvula.centroids.v296_v201901b.ffn.gz /local/ifs2_projdata/0780/projects/SMU_MUC/curanga/RNAseq/chocophlan1/g__Streptococcus.s__Streptococcus_oralis.centroids.v296_v201901b.ffn.gz /local/ifs2_projdata/0780/projects/SMU_MUC/curanga/RNAseq/chocophlan1/g__Streptococcus.s__Streptococcus_parasanguinis.centroids.v296_v201901b.ffn.gz /local/ifs2_projdata/0780/projects/SMU_MUC/curanga/RNAseq/chocophlan1/g__Streptococcus.s__Streptococcus_mitis.centroids.v296_v201901b.ffn.gz /local/ifs2_projdata/0780/projects/SMU_MUC/curanga/RNAseq/chocophlan1/g__Streptococcus.s__Streptococcus_cristatus.centroids.v296_v201901b.ffn.gz /local/ifs2_projdata/0780/projects/SMU_MUC/curanga/RNAseq/chocophlan1/g__Streptococcus.s__Streptococcus_mutans.centroids.v296_v201901b.ffn.gz /local/ifs2_projdata/0780/projects/SMU_MUC/curanga/RNAseq/chocophlan1/g__Lactobacillus.s__Lactobacillus_fermentum.centroids.v296_v201901b.ffn.gz /local/ifs2_projdata/0780/projects/SMU_MUC/curanga/RNAseq/chocophlan1/g__Veillonella.s__Veillonella_atypica.centroids.v296_v201901b.ffn.gz /local/ifs2_projdata/0780/projects/SMU_MUC/curanga/RNAseq/chocophlan1/g__Streptococcus.s__Streptococcus_salivarius.centroids.v296_v201901b.ffn.gz /local/ifs2_projdata/0780/projects/SMU_MUC/curanga/RNAseq/chocophlan1/g__Streptococcus.s__Streptococcus_anginosus_group.centroids.v296_v201901b.ffn.gz /local/ifs2_projdata/0780/projects/SMU_MUC/curanga/RNAseq/chocophlan1/g__Gemella.s__Gemella_sanguinis.centroids.v201901b.ffn.gz /local/ifs2_projdata/0780/projects/SMU_MUC/curanga/RNAseq/chocophlan1/g__Veillonella.s__Veillonella_dispar.centroids.v296_v201901b.ffn.gz /local/ifs2_projdata/0780/projects/SMU_MUC/curanga/RNAseq/chocophlan1/g__Streptococcus.s__Streptococcus_infantis.centroids.v296_v201901b.ffn.gz
10/06/2021 10:41:07 PM - humann.humann - INFO: TIMESTAMP: Completed 	custom database creation 	:	 2	 seconds
10/06/2021 10:41:07 PM - humann.search.nucleotide - INFO: Running bowtie2-build ........
10/06/2021 10:41:07 PM - humann.utilities - DEBUG: Using software: /local/ifs2_projdata/0780/projects/SMU_MUC/curanga/miniconda3/envs/mpa/bin/bowtie2-build
10/06/2021 10:41:07 PM - humann.utilities - INFO: Execute command: /local/ifs2_projdata/0780/projects/SMU_MUC/curanga/miniconda3/envs/mpa/bin/bowtie2-build -f /local/ifs2_projdata/0780/projects/SMU_MUC/curanga/RNAseq/hmp_subset/B2A-PE-B10I7-B10I5-1_S10_R1_001_humann_temp/B2A-PE-B10I7-B10I5-1_S10_R1_001_custom_chocophlan_database.ffn /local/ifs2_projdata/0780/projects/SMU_MUC/curanga/RNAseq/hmp_subset/B2A-PE-B10I7-B10I5-1_S10_R1_001_humann_temp/B2A-PE-B10I7-B10I5-1_S10_R1_001_bowtie2_index
10/06/2021 10:43:01 PM - humann.humann - INFO: TIMESTAMP: Completed 	database index 	:	 114	 seconds
10/06/2021 10:43:01 PM - humann.search.nucleotide - DEBUG: Nucleotide input file is of type: fastq
10/06/2021 10:43:01 PM - humann.utilities - DEBUG: Using software: /local/ifs2_projdata/0780/projects/SMU_MUC/curanga/miniconda3/envs/mpa/bin/bowtie2
10/06/2021 10:43:01 PM - humann.utilities - INFO: Execute command: /local/ifs2_projdata/0780/projects/SMU_MUC/curanga/miniconda3/envs/mpa/bin/bowtie2 -q -x /local/ifs2_projdata/0780/projects/SMU_MUC/curanga/RNAseq/hmp_subset/B2A-PE-B10I7-B10I5-1_S10_R1_001_humann_temp/B2A-PE-B10I7-B10I5-1_S10_R1_001_bowtie2_index -U /local/ifs2_projdata/0780/projects/SMU_MUC/curanga/RNAseq/hmp_subset/B2A-PE-B10I7-B10I5-1_S10_R1_001_humann_temp/tmpbmi62t5r/tmpi0slz6vl -S /local/ifs2_projdata/0780/projects/SMU_MUC/curanga/RNAseq/hmp_subset/B2A-PE-B10I7-B10I5-1_S10_R1_001_humann_temp/B2A-PE-B10I7-B10I5-1_S10_R1_001_bowtie2_aligned.sam --very-sensitive
10/07/2021 03:48:20 AM - humann.utilities - DEBUG: b'127080025 reads; of these:\n  127080025 (100.00%) were unpaired; of these:\n    54435191 (42.84%) aligned 0 times\n    57318959 (45.10%) aligned exactly 1 time\n    15325875 (12.06%) aligned >1 times\n57.16% overall alignment rate\n'
10/07/2021 03:48:20 AM - humann.humann - INFO: TIMESTAMP: Completed 	nucleotide alignment 	:	 18319	 seconds