Full log below.
These reads don’t add up for a full accounting. What’s going on?
12/21/2020 04:24:49 PM - humann.humann - INFO: Running humann v3.0.0.alpha.4
12/21/2020 04:24:49 PM - humann.humann - INFO: Output files will be written to: /scratch/j/jparkin/billyc59/kneaddata_run/h3/NOD_no_bypass/503_cmn
12/21/2020 04:24:49 PM - humann.humann - INFO: Writing temp files to directory: /scratch/j/jparkin/billyc59/kneaddata_run/h3/NOD_no_bypass/503_cmn/NOD503CecMN_r1_new_kneaddata_unmatched_1_humann_temp
12/21/2020 04:24:49 PM - humann.utilities - INFO: File ( /scratch/j/jparkin/billyc59/kneaddata_run/cleaned_NOD/NOD503CecMN_r1_new_kneaddata_unmatched_1.fastq ) is of format: fastq
12/21/2020 04:24:50 PM - humann.utilities - DEBUG: Check software, metaphlan, for required version, 3.0
12/21/2020 04:24:52 PM - humann.utilities - INFO: Using metaphlan version 3.0
12/21/2020 04:24:52 PM - humann.utilities - DEBUG: Check software, bowtie2, for required version, 2.2
12/21/2020 04:24:54 PM - humann.utilities - INFO: Using bowtie2 version 2.2
12/21/2020 04:24:54 PM - humann.humann - INFO: Search mode set to uniref90 because a uniref90 translated search database is selected
12/21/2020 04:24:54 PM - humann.utilities - DEBUG: Check software, diamond, for required version, 0.9.24
12/21/2020 04:24:54 PM - humann.utilities - INFO: Using diamond version 0.9.24
12/21/2020 04:24:54 PM - humann.config - INFO:
Run config settings:
DATABASE SETTINGS
nucleotide database folder = /scratch/j/jparkin/billyc59/h3_db/chocophlan
protein database folder = /scratch/j/jparkin/billyc59/h3_db/uniref
pathways database file 1 = /gpfs/fs1/home/j/jparkin/billyc59/.virtualenvs/h3/lib/python3.8/site-packages/humann/data/pathways/metacyc_reactions_level4ec_only.uniref.bz2
pathways database file 2 = /gpfs/fs1/home/j/jparkin/billyc59/.virtualenvs/h3/lib/python3.8/site-packages/humann/data/pathways/metacyc_pathways_structured_filtered
utility mapping database folder = /gpfs/fs1/home/j/jparkin/billyc59/.virtualenvs/h3/lib/python3.8/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
pick frames = off
threads = 40
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
12/21/2020 04:24:54 PM - humann.store - DEBUG: Initialize Alignments class instance to minimize memory use
12/21/2020 04:24:54 PM - humann.store - DEBUG: Initialize Reads class instance to minimize memory use
12/21/2020 04:25:12 PM - humann.humann - INFO: Load pathways database part 1: /gpfs/fs1/home/j/jparkin/billyc59/.virtualenvs/h3/lib/python3.8/site-packages/humann/data/pathways/metacyc_reactions_level4ec_only.uniref.bz2
12/21/2020 04:25:12 PM - humann.humann - INFO: Load pathways database part 2: /gpfs/fs1/home/j/jparkin/billyc59/.virtualenvs/h3/lib/python3.8/site-packages/humann/data/pathways/metacyc_pathways_structured_filtered
12/21/2020 04:25:12 PM - humann.search.prescreen - INFO: Running metaphlan …
12/21/2020 04:25:12 PM - humann.utilities - DEBUG: Using software: /gpfs/fs1/home/j/jparkin/billyc59/.virtualenvs/h3/bin/metaphlan
12/21/2020 04:25:12 PM - humann.utilities - DEBUG: Remove file: /scratch/j/jparkin/billyc59/kneaddata_run/h3/NOD_no_bypass/503_cmn/NOD503CecMN_r1_new_kneaddata_unmatched_1_humann_temp/NOD503CecMN_r1_new_kneaddata_unmatched_1_metaphlan_bugs_list.tsv
12/21/2020 04:25:12 PM - humann.utilities - DEBUG: Remove file: /scratch/j/jparkin/billyc59/kneaddata_run/h3/NOD_no_bypass/503_cmn/NOD503CecMN_r1_new_kneaddata_unmatched_1_humann_temp/NOD503CecMN_r1_new_kneaddata_unmatched_1_metaphlan_bowtie2.txt
12/21/2020 04:25:12 PM - humann.utilities - INFO: Execute command: /gpfs/fs1/home/j/jparkin/billyc59/.virtualenvs/h3/bin/metaphlan /scratch/j/jparkin/billyc59/kneaddata_run/cleaned_NOD/NOD503CecMN_r1_new_kneaddata_unmatched_1.fastq -t rel_ab -o /scratch/j/jparkin/billyc59/kneaddata_run/h3/NOD_no_bypass/503_cmn/NOD503CecMN_r1_new_kneaddata_unmatched_1_humann_temp/NOD503CecMN_r1_new_kneaddata_unmatched_1_metaphlan_bugs_list.tsv --input_type fastq --bowtie2out /scratch/j/jparkin/billyc59/kneaddata_run/h3/NOD_no_bypass/503_cmn/NOD503CecMN_r1_new_kneaddata_unmatched_1_humann_temp/NOD503CecMN_r1_new_kneaddata_unmatched_1_metaphlan_bowtie2.txt --nproc 40
12/21/2020 04:28:54 PM - humann.utilities - DEBUG: b’Warning! Biom python library not detected!\n Exporting to biom format will not work!\nWARNING: 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.\nWARNING: It seems that you do not have Internet access.\nWARNING: Cannot connect to the database server. The latest available local database will be used.\n’
12/21/2020 04:28:54 PM - humann.humann - INFO: TIMESTAMP: Completed prescreen : 222 seconds
12/21/2020 04:28:54 PM - humann.search.prescreen - INFO: Found g__Parabacteroides.s__Parabacteroides_goldsteinii : 73.88% of mapped reads
12/21/2020 04:28:54 PM - humann.search.prescreen - INFO: Found g__Clostridium.s__Clostridium_sp_ASF356 : 15.14% of mapped reads
12/21/2020 04:28:54 PM - humann.search.prescreen - INFO: Found g__Blautia.s__Blautia_coccoides : 5.54% of mapped reads
12/21/2020 04:28:54 PM - humann.search.prescreen - INFO: Found g__Mucispirillum.s__Mucispirillum_schaedleri : 5.11% of mapped reads
12/21/2020 04:28:54 PM - humann.search.prescreen - INFO: Found g__Lactobacillus.s__Lactobacillus_murinus : 0.33% of mapped reads
12/21/2020 04:28:54 PM - humann.search.prescreen - INFO: Total species selected from prescreen: 5
12/21/2020 04:28:54 PM - humann.search.prescreen - DEBUG: Adding file to database: g__Clostridium.s__Clostridium_sp_ASF356.centroids.v296_201901.ffn.gz
12/21/2020 04:28:54 PM - humann.search.prescreen - DEBUG: Adding file to database: g__Lactobacillus.s__Lactobacillus_murinus.centroids.v296_201901.ffn.gz
12/21/2020 04:28:54 PM - humann.search.prescreen - DEBUG: Adding file to database: g__Mucispirillum.s__Mucispirillum_schaedleri.centroids.v296_201901.ffn.gz
12/21/2020 04:28:54 PM - humann.search.prescreen - DEBUG: Adding file to database: g__Blautia.s__Blautia_coccoides.centroids.v296_201901.ffn.gz
12/21/2020 04:28:54 PM - humann.search.prescreen - DEBUG: Adding file to database: g__Parabacteroides.s__Parabacteroides_goldsteinii.centroids.v296_201901.ffn.gz
12/21/2020 04:28:54 PM - humann.search.prescreen - INFO: Creating custom ChocoPhlAn database …
12/21/2020 04:28:54 PM - humann.utilities - DEBUG: Remove file: /scratch/j/jparkin/billyc59/kneaddata_run/h3/NOD_no_bypass/503_cmn/NOD503CecMN_r1_new_kneaddata_unmatched_1_humann_temp/NOD503CecMN_r1_new_kneaddata_unmatched_1_custom_chocophlan_database.ffn
12/21/2020 04:28:54 PM - humann.utilities - DEBUG: Using software: /cvmfs/soft.computecanada.ca/nix/var/nix/profiles/16.09/bin/gunzip
12/21/2020 04:28:54 PM - humann.utilities - INFO: Execute command: /cvmfs/soft.computecanada.ca/nix/var/nix/profiles/16.09/bin/gunzip -c /scratch/j/jparkin/billyc59/h3_db/chocophlan/g__Clostridium.s__Clostridium_sp_ASF356.centroids.v296_201901.ffn.gz /scratch/j/jparkin/billyc59/h3_db/chocophlan/g__Lactobacillus.s__Lactobacillus_murinus.centroids.v296_201901.ffn.gz /scratch/j/jparkin/billyc59/h3_db/chocophlan/g__Mucispirillum.s__Mucispirillum_schaedleri.centroids.v296_201901.ffn.gz /scratch/j/jparkin/billyc59/h3_db/chocophlan/g__Blautia.s__Blautia_coccoides.centroids.v296_201901.ffn.gz /scratch/j/jparkin/billyc59/h3_db/chocophlan/g__Parabacteroides.s__Parabacteroides_goldsteinii.centroids.v296_201901.ffn.gz
12/21/2020 04:28:55 PM - humann.humann - INFO: TIMESTAMP: Completed custom database creation : 1 seconds
12/21/2020 04:28:55 PM - humann.search.nucleotide - INFO: Running bowtie2-build …
12/21/2020 04:28:55 PM - humann.utilities - DEBUG: Using software: /gpfs/fs1/home/j/jparkin/billyc59/.virtualenvs/h3/bin/bowtie2-build
12/21/2020 04:28:55 PM - humann.utilities - DEBUG: Remove file: /scratch/j/jparkin/billyc59/kneaddata_run/h3/NOD_no_bypass/503_cmn/NOD503CecMN_r1_new_kneaddata_unmatched_1_humann_temp/NOD503CecMN_r1_new_kneaddata_unmatched_1_bowtie2_index.1.bt2
12/21/2020 04:28:55 PM - humann.utilities - DEBUG: Remove file: /scratch/j/jparkin/billyc59/kneaddata_run/h3/NOD_no_bypass/503_cmn/NOD503CecMN_r1_new_kneaddata_unmatched_1_humann_temp/NOD503CecMN_r1_new_kneaddata_unmatched_1_bowtie2_index.2.bt2
12/21/2020 04:28:55 PM - humann.utilities - DEBUG: Remove file: /scratch/j/jparkin/billyc59/kneaddata_run/h3/NOD_no_bypass/503_cmn/NOD503CecMN_r1_new_kneaddata_unmatched_1_humann_temp/NOD503CecMN_r1_new_kneaddata_unmatched_1_bowtie2_index.3.bt2
12/21/2020 04:28:55 PM - humann.utilities - DEBUG: Remove file: /scratch/j/jparkin/billyc59/kneaddata_run/h3/NOD_no_bypass/503_cmn/NOD503CecMN_r1_new_kneaddata_unmatched_1_humann_temp/NOD503CecMN_r1_new_kneaddata_unmatched_1_bowtie2_index.4.bt2
12/21/2020 04:28:55 PM - humann.utilities - DEBUG: Remove file: /scratch/j/jparkin/billyc59/kneaddata_run/h3/NOD_no_bypass/503_cmn/NOD503CecMN_r1_new_kneaddata_unmatched_1_humann_temp/NOD503CecMN_r1_new_kneaddata_unmatched_1_bowtie2_index.rev.1.bt2
12/21/2020 04:28:55 PM - humann.utilities - DEBUG: Remove file: /scratch/j/jparkin/billyc59/kneaddata_run/h3/NOD_no_bypass/503_cmn/NOD503CecMN_r1_new_kneaddata_unmatched_1_humann_temp/NOD503CecMN_r1_new_kneaddata_unmatched_1_bowtie2_index.rev.2.bt2
12/21/2020 04:28:55 PM - humann.utilities - INFO: Execute command: /gpfs/fs1/home/j/jparkin/billyc59/.virtualenvs/h3/bin/bowtie2-build -f /scratch/j/jparkin/billyc59/kneaddata_run/h3/NOD_no_bypass/503_cmn/NOD503CecMN_r1_new_kneaddata_unmatched_1_humann_temp/NOD503CecMN_r1_new_kneaddata_unmatched_1_custom_chocophlan_database.ffn /scratch/j/jparkin/billyc59/kneaddata_run/h3/NOD_no_bypass/503_cmn/NOD503CecMN_r1_new_kneaddata_unmatched_1_humann_temp/NOD503CecMN_r1_new_kneaddata_unmatched_1_bowtie2_index
12/21/2020 04:29:19 PM - humann.humann - INFO: TIMESTAMP: Completed database index : 24 seconds
12/21/2020 04:29:19 PM - humann.search.nucleotide - DEBUG: Nucleotide input file is of type: fastq
12/21/2020 04:29:19 PM - humann.utilities - DEBUG: Using software: /gpfs/fs1/home/j/jparkin/billyc59/.virtualenvs/h3/bin/bowtie2
12/21/2020 04:29:19 PM - humann.utilities - DEBUG: Remove file: /scratch/j/jparkin/billyc59/kneaddata_run/h3/NOD_no_bypass/503_cmn/NOD503CecMN_r1_new_kneaddata_unmatched_1_humann_temp/NOD503CecMN_r1_new_kneaddata_unmatched_1_bowtie2_aligned.sam
12/21/2020 04:29:19 PM - humann.utilities - INFO: Execute command: /gpfs/fs1/home/j/jparkin/billyc59/.virtualenvs/h3/bin/bowtie2 -q -x /scratch/j/jparkin/billyc59/kneaddata_run/h3/NOD_no_bypass/503_cmn/NOD503CecMN_r1_new_kneaddata_unmatched_1_humann_temp/NOD503CecMN_r1_new_kneaddata_unmatched_1_bowtie2_index -U /scratch/j/jparkin/billyc59/kneaddata_run/cleaned_NOD/NOD503CecMN_r1_new_kneaddata_unmatched_1.fastq -S /scratch/j/jparkin/billyc59/kneaddata_run/h3/NOD_no_bypass/503_cmn/NOD503CecMN_r1_new_kneaddata_unmatched_1_humann_temp/NOD503CecMN_r1_new_kneaddata_unmatched_1_bowtie2_aligned.sam -p 40 --very-sensitive
12/21/2020 04:29:40 PM - humann.utilities - DEBUG: b’5237875 reads; of these:\n 5237875 (100.00%) were unpaired; of these:\n 4296874 (82.03%) aligned 0 times\n 885884 (16.91%) aligned exactly 1 time\n 55117 (1.05%) aligned >1 times\n17.97% overall alignment rate\n’
12/21/2020 04:29:40 PM - humann.humann - INFO: TIMESTAMP: Completed nucleotide alignment : 21 seconds
12/21/2020 04:30:43 PM - humann.utilities - DEBUG: Total alignments where percent identity is not a number: 0
12/21/2020 04:30:43 PM - humann.utilities - DEBUG: Total alignments where alignment length is not a number: 0
12/21/2020 04:30:43 PM - humann.utilities - DEBUG: Total alignments where E-value is not a number: 0
12/21/2020 04:30:43 PM - humann.utilities - DEBUG: Total alignments not included based on large e-value: 0
12/21/2020 04:30:43 PM - humann.utilities - DEBUG: Total alignments not included based on small percent identity: 0
12/21/2020 04:30:43 PM - humann.utilities - DEBUG: Total alignments not included based on small query coverage: 0
12/21/2020 04:30:43 PM - humann.search.blastx_coverage - INFO: Total alignments without coverage information: 0
12/21/2020 04:30:43 PM - humann.search.blastx_coverage - INFO: Total proteins in blastx output: 14716
12/21/2020 04:30:43 PM - humann.search.blastx_coverage - INFO: Total proteins without lengths: 0
12/21/2020 04:30:43 PM - humann.search.blastx_coverage - INFO: Proteins with coverage greater than threshold (50.0): 9071
12/21/2020 04:32:00 PM - humann.search.nucleotide - DEBUG: Total nucleotide alignments not included based on filtered genes: 64249
12/21/2020 04:32:00 PM - humann.search.nucleotide - DEBUG: Total nucleotide alignments not included based on small percent identities: 0
12/21/2020 04:32:00 PM - humann.search.nucleotide - DEBUG: Total nucleotide alignments not included based on query coverage threshold: 0
12/21/2020 04:32:00 PM - humann.search.nucleotide - DEBUG: Keeping sam file
12/21/2020 04:32:00 PM - humann.humann - INFO: TIMESTAMP: Completed nucleotide alignment post-processing : 140 seconds
12/21/2020 04:32:00 PM - humann.humann - INFO: Total bugs from nucleotide alignment: 5
12/21/2020 04:32:00 PM - humann.humann - INFO:
g__Parabacteroides.s__Parabacteroides_goldsteinii: 733486 hits
g__Clostridium.s__Clostridium_sp_ASF356: 67630 hits
g__Blautia.s__Blautia_coccoides: 66534 hits
g__Mucispirillum.s__Mucispirillum_schaedleri: 9038 hits
g__Lactobacillus.s__Lactobacillus_murinus: 64 hits
12/21/2020 04:32:00 PM - humann.humann - INFO: Total gene families from nucleotide alignment: 9071
12/21/2020 04:32:00 PM - humann.humann - INFO: Unaligned reads after nucleotide alignment: 85.0070015157 %
12/21/2020 04:32:00 PM - humann.utilities - DEBUG: Remove file: /scratch/j/jparkin/billyc59/kneaddata_run/h3/NOD_no_bypass/503_cmn/NOD503CecMN_r1_new_kneaddata_unmatched_1_humann_temp/NOD503CecMN_r1_new_kneaddata_unmatched_1_diamond_aligned.tsv
12/21/2020 04:32:00 PM - humann.search.translated - INFO: Running diamond …
12/21/2020 04:32:00 PM - humann.search.translated - INFO: Aligning to reference database: uniref90_201901.dmnd
12/21/2020 04:32:00 PM - humann.utilities - DEBUG: Remove file: /scratch/j/jparkin/billyc59/kneaddata_run/h3/NOD_no_bypass/503_cmn/NOD503CecMN_r1_new_kneaddata_unmatched_1_humann_temp/tmpc5enxr3g/diamond_m8_9emeeup5
12/21/2020 04:32:00 PM - humann.utilities - DEBUG: Using software: /gpfs/fs1/home/j/jparkin/billyc59/.virtualenvs/h3/bin/diamond
12/21/2020 04:32:00 PM - humann.utilities - INFO: Execute command: /gpfs/fs1/home/j/jparkin/billyc59/.virtualenvs/h3/bin/diamond blastx --query /scratch/j/jparkin/billyc59/kneaddata_run/h3/NOD_no_bypass/503_cmn/NOD503CecMN_r1_new_kneaddata_unmatched_1_humann_temp/NOD503CecMN_r1_new_kneaddata_unmatched_1_bowtie2_unaligned.fa --evalue 1.0 --threads 40 --top 1 --outfmt 6 --db /scratch/j/jparkin/billyc59/h3_db/uniref/uniref90_201901 --out /scratch/j/jparkin/billyc59/kneaddata_run/h3/NOD_no_bypass/503_cmn/NOD503CecMN_r1_new_kneaddata_unmatched_1_humann_temp/tmpc5enxr3g/diamond_m8_9emeeup5 --tmpdir /scratch/j/jparkin/billyc59/kneaddata_run/h3/NOD_no_bypass/503_cmn/NOD503CecMN_r1_new_kneaddata_unmatched_1_humann_temp/tmpc5enxr3g
12/21/2020 04:33:19 PM - humann.utilities - DEBUG: b’diamond v0.9.24.125 | by Benjamin Buchfink buchfink@gmail.com\nLicensed under the GNU GPL https://www.gnu.org/licenses/gpl.txt\nCheck http://github.com/bbuchfink/diamond for updates.\n\n#CPU threads: 40\nScoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1)\nTemporary directory: /scratch/j/jparkin/billyc59/kneaddata_run/h3/NOD_no_bypass/503_cmn/NOD503CecMN_r1_new_kneaddata_unmatched_1_humann_temp/tmpc5enxr3g\nOpening the database… [0.048518s]\nPercentage range of top alignment score to report hits: 1\nOpening the input file… [4.8e-05s]\nOpening the output file… [0.00016s]\nLoading query sequences… [6.07824s]\nMasking queries… [9.25263s]\nBuilding query seed set… [0.096469s]\nAlgorithm: Double-indexed\nBuilding query histograms… [0.332385s]\nAllocating buffers… [0.00065s]\nLoading reference sequences… [6.78216s]\nBuilding reference histograms… [0.93041s]\nAllocating buffers… [0.000143s]\nInitializing temporary storage… [0.30558s]\nProcessing query chunk 0, reference chunk 0, shape 0, index chunk 0.\nBuilding reference index… [1.32846s]\nBuilding query index… [0.228905s]\nBuilding seed filter… [0.078927s]\nSearching alignments… [0.976783s]\nProcessing query chunk 0, reference chunk 0, shape 0, index chunk 1.\nBuilding reference index… [1.3904s]\nBuilding query index… [0.288476s]\nBuilding seed filter… [0.078824s]\nSearching alignments… [0.207263s]\nProcessing query chunk 0, reference chunk 0, shape 0, index chunk 2.\nBuilding reference index… [1.47163s]\nBuilding query index… [0.303348s]\nBuilding seed filter… [0.079271s]\nSearching alignments… [0.212712s]\nProcessing query chunk 0, reference chunk 0, shape 0, index chunk 3.\nBuilding reference index… [1.28992s]\nBuilding query index… [0.222088s]\nBuilding seed filter… [0.078896s]\nSearching alignments… [0.222324s]\nProcessing query chunk 0, reference chunk 0, shape 1, index chunk 0.\nBuilding reference index… [1.24914s]\nBuilding query index… [0.233302s]\nBuilding seed filter… [0.077608s]\nSearching alignments… [0.146752s]\nProcessing query chunk 0, reference chunk 0, shape 1, index chunk 1.\nBuilding reference index… [1.39514s]\nBuilding query index… [0.250647s]\nBuilding seed filter… [0.077068s]\nSearching alignments… [0.149504s]\nProcessing query chunk 0, reference chunk 0, shape 1, index chunk 2.\nBuilding reference index… [1.46274s]\nBuilding query index… [0.24851s]\nBuilding seed filter… [0.077118s]\nSearching alignments… [0.142223s]\nProcessing query chunk 0, reference chunk 0, shape 1, index chunk 3.\nBuilding reference index… [1.35164s]\nBuilding query index… [0.233226s]\nBuilding seed filter… [0.077712s]\nSearching alignments… [0.15188s]\nDeallocating buffers… [0.007416s]\nComputing alignments… [39.8387s]\nDeallocating reference… [0.004772s]\nLoading reference sequences… [0.000397s]\nDeallocating buffers… [0.001428s]\nDeallocating queries… [0.004989s]\nLoading query sequences… [2.5e-05s]\nClosing the input file… [2.1e-05s]\nClosing the output file… [0.000155s]\nClosing the database file… [2e-05s]\nDeallocating taxonomy… [3e-06s]\nTotal time = 79.4698s\nReported 214621 pairwise alignments, 214659 HSPs.\n99556 queries aligned.\n’
12/21/2020 04:33:19 PM - humann.utilities - DEBUG: Using software: /cvmfs/soft.computecanada.ca/nix/var/nix/profiles/16.09/bin/cat
12/21/2020 04:33:19 PM - humann.utilities - INFO: Execute command: /cvmfs/soft.computecanada.ca/nix/var/nix/profiles/16.09/bin/cat /scratch/j/jparkin/billyc59/kneaddata_run/h3/NOD_no_bypass/503_cmn/NOD503CecMN_r1_new_kneaddata_unmatched_1_humann_temp/tmpc5enxr3g/diamond_m8_9emeeup5
12/21/2020 04:33:20 PM - humann.humann - INFO: TIMESTAMP: Completed translated alignment : 80 seconds
12/21/2020 04:33:22 PM - humann.utilities - DEBUG: Total alignments where percent identity is not a number: 0
12/21/2020 04:33:22 PM - humann.utilities - DEBUG: Total alignments where alignment length is not a number: 0
12/21/2020 04:33:22 PM - humann.utilities - DEBUG: Total alignments where E-value is not a number: 0
12/21/2020 04:33:22 PM - humann.utilities - DEBUG: Total alignments not included based on large e-value: 17
12/21/2020 04:33:22 PM - humann.utilities - DEBUG: Total alignments not included based on small percent identity: 30213
12/21/2020 04:33:22 PM - humann.utilities - DEBUG: Total alignments not included based on small query coverage: 126996
12/21/2020 04:33:22 PM - humann.search.blastx_coverage - INFO: Total alignments without coverage information: 0
12/21/2020 04:33:22 PM - humann.search.blastx_coverage - INFO: Total proteins in blastx output: 18349
12/21/2020 04:33:22 PM - humann.search.blastx_coverage - INFO: Total proteins without lengths: 0
12/21/2020 04:33:22 PM - humann.search.blastx_coverage - INFO: Proteins with coverage greater than threshold (50.0): 120
12/21/2020 04:33:24 PM - humann.utilities - DEBUG: Total alignments where percent identity is not a number: 0
12/21/2020 04:33:24 PM - humann.utilities - DEBUG: Total alignments where alignment length is not a number: 0
12/21/2020 04:33:24 PM - humann.utilities - DEBUG: Total alignments where E-value is not a number: 0
12/21/2020 04:33:24 PM - humann.utilities - DEBUG: Total alignments not included based on large e-value: 17
12/21/2020 04:33:24 PM - humann.utilities - DEBUG: Total alignments not included based on small percent identity: 30213
12/21/2020 04:33:24 PM - humann.utilities - DEBUG: Total alignments not included based on small query coverage: 126996
12/21/2020 04:33:24 PM - humann.search.translated - DEBUG: Total translated alignments not included based on small subject coverage value: 61831
12/21/2020 04:33:43 PM - humann.humann - INFO: TIMESTAMP: Completed translated alignment post-processing : 23 seconds
12/21/2020 04:33:43 PM - humann.humann - INFO: Total bugs after translated alignment: 6
12/21/2020 04:33:43 PM - humann.humann - INFO:
g__Parabacteroides.s__Parabacteroides_goldsteinii: 733486 hits
g__Clostridium.s__Clostridium_sp_ASF356: 67630 hits
g__Blautia.s__Blautia_coccoides: 66534 hits
g__Mucispirillum.s__Mucispirillum_schaedleri: 9038 hits
g__Lactobacillus.s__Lactobacillus_murinus: 64 hits
unclassified: 5418 hits
12/21/2020 04:33:43 PM - humann.humann - INFO: Total gene families after translated alignment: 9187
12/21/2020 04:33:43 PM - humann.humann - INFO: Unaligned reads after translated alignment: 84.8843132833 %
12/21/2020 04:33:43 PM - humann.humann - INFO: Computing gene families …
12/21/2020 04:33:43 PM - humann.quantify.families - DEBUG: Compute gene families
12/21/2020 04:33:45 PM - humann.store - INFO:
Total gene families : 9187
g__Parabacteroides.s__Parabacteroides_goldsteinii : 5368 gene families
g__Clostridium.s__Clostridium_sp_ASF356 : 1429 gene families
g__Blautia.s__Blautia_coccoides : 1941 gene families
g__Mucispirillum.s__Mucispirillum_schaedleri : 324 gene families
g__Lactobacillus.s__Lactobacillus_murinus : 12 gene families
unclassified : 120 gene families
12/21/2020 04:33:59 PM - humann.humann - INFO: TIMESTAMP: Completed computing gene families : 16 seconds
12/21/2020 04:33:59 PM - humann.humann - INFO: Computing pathways abundance and coverage …
12/21/2020 04:33:59 PM - humann.quantify.modules - DEBUG: Write flat reactions to pathways file for Minpath
12/21/2020 04:33:59 PM - humann.quantify.modules - INFO: Compute reaction scores for bug: g__Parabacteroides.s__Parabacteroides_goldsteinii
12/21/2020 04:34:01 PM - humann.quantify.modules - INFO: Run MinPath on g__Parabacteroides.s__Parabacteroides_goldsteinii
12/21/2020 04:34:01 PM - humann.quantify.modules - INFO: Compute reaction scores for bug: g__Clostridium.s__Clostridium_sp_ASF356
12/21/2020 04:34:03 PM - humann.quantify.modules - INFO: Run MinPath on g__Clostridium.s__Clostridium_sp_ASF356
12/21/2020 04:34:03 PM - humann.quantify.modules - INFO: Compute reaction scores for bug: g__Blautia.s__Blautia_coccoides
12/21/2020 04:34:04 PM - humann.quantify.modules - INFO: Run MinPath on g__Blautia.s__Blautia_coccoides
12/21/2020 04:34:04 PM - humann.quantify.modules - INFO: Compute reaction scores for bug: g__Mucispirillum.s__Mucispirillum_schaedleri
12/21/2020 04:34:06 PM - humann.quantify.modules - INFO: Run MinPath on g__Mucispirillum.s__Mucispirillum_schaedleri
12/21/2020 04:34:06 PM - humann.quantify.modules - INFO: Compute reaction scores for bug: g__Lactobacillus.s__Lactobacillus_murinus
12/21/2020 04:34:07 PM - humann.quantify.modules - INFO: Compute reaction scores for bug: unclassified
12/21/2020 04:34:08 PM - humann.quantify.modules - INFO: Run MinPath on unclassified
12/21/2020 04:34:08 PM - humann.quantify.modules - INFO: Compute reaction scores for bug: all
12/21/2020 04:34:10 PM - humann.quantify.modules - INFO: Run MinPath on all
12/21/2020 04:34:10 PM - humann.utilities - DEBUG: Using python module : /gpfs/fs1/home/j/jparkin/billyc59/.virtualenvs/h3/lib/python3.8/site-packages/humann/quantify/MinPath12hmp.py
12/21/2020 04:34:10 PM - humann.utilities - DEBUG: Using python module : /gpfs/fs1/home/j/jparkin/billyc59/.virtualenvs/h3/lib/python3.8/site-packages/humann/quantify/MinPath12hmp.py
12/21/2020 04:34:10 PM - humann.utilities - DEBUG: Using python module : /gpfs/fs1/home/j/jparkin/billyc59/.virtualenvs/h3/lib/python3.8/site-packages/humann/quantify/MinPath12hmp.py
12/21/2020 04:34:10 PM - humann.utilities - DEBUG: Using python module : /gpfs/fs1/home/j/jparkin/billyc59/.virtualenvs/h3/lib/python3.8/site-packages/humann/quantify/MinPath12hmp.py
12/21/2020 04:34:10 PM - humann.utilities - DEBUG: Using python module : /gpfs/fs1/home/j/jparkin/billyc59/.virtualenvs/h3/lib/python3.8/site-packages/humann/quantify/MinPath12hmp.py
12/21/2020 04:34:10 PM - humann.utilities - DEBUG: Using python module : /gpfs/fs1/home/j/jparkin/billyc59/.virtualenvs/h3/lib/python3.8/site-packages/humann/quantify/MinPath12hmp.py
12/21/2020 04:34:10 PM - humann.utilities - INFO: Execute command: /gpfs/fs1/home/j/jparkin/billyc59/.virtualenvs/h3/bin/python /gpfs/fs1/home/j/jparkin/billyc59/.virtualenvs/h3/lib/python3.8/site-packages/humann/quantify/MinPath12hmp.py -any /scratch/j/jparkin/billyc59/kneaddata_run/h3/NOD_no_bypass/503_cmn/NOD503CecMN_r1_new_kneaddata_unmatched_1_humann_temp/tmpc5enxr3g/tmp_9s0t4me -map /scratch/j/jparkin/billyc59/kneaddata_run/h3/NOD_no_bypass/503_cmn/NOD503CecMN_r1_new_kneaddata_unmatched_1_humann_temp/tmpc5enxr3g/tmp1foe8dg8 -report /scratch/j/jparkin/billyc59/kneaddata_run/h3/NOD_no_bypass/503_cmn/NOD503CecMN_r1_new_kneaddata_unmatched_1_humann_temp/tmpc5enxr3g/tmp959ocj0u -details /scratch/j/jparkin/billyc59/kneaddata_run/h3/NOD_no_bypass/503_cmn/NOD503CecMN_r1_new_kneaddata_unmatched_1_humann_temp/tmpc5enxr3g/tmpg12rjf5n -mps /scratch/j/jparkin/billyc59/kneaddata_run/h3/NOD_no_bypass/503_cmn/NOD503CecMN_r1_new_kneaddata_unmatched_1_humann_temp/tmpc5enxr3g/tmpqohag_dn
12/21/2020 04:34:10 PM - humann.utilities - INFO: Execute command: /gpfs/fs1/home/j/jparkin/billyc59/.virtualenvs/h3/bin/python /gpfs/fs1/home/j/jparkin/billyc59/.virtualenvs/h3/lib/python3.8/site-packages/humann/quantify/MinPath12hmp.py -any /scratch/j/jparkin/billyc59/kneaddata_run/h3/NOD_no_bypass/503_cmn/NOD503CecMN_r1_new_kneaddata_unmatched_1_humann_temp/tmpc5enxr3g/tmp4uu1sp8b -map /scratch/j/jparkin/billyc59/kneaddata_run/h3/NOD_no_bypass/503_cmn/NOD503CecMN_r1_new_kneaddata_unmatched_1_humann_temp/tmpc5enxr3g/tmp1foe8dg8 -report /scratch/j/jparkin/billyc59/kneaddata_run/h3/NOD_no_bypass/503_cmn/NOD503CecMN_r1_new_kneaddata_unmatched_1_humann_temp/tmpc5enxr3g/tmps025ntok -details /scratch/j/jparkin/billyc59/kneaddata_run/h3/NOD_no_bypass/503_cmn/NOD503CecMN_r1_new_kneaddata_unmatched_1_humann_temp/tmpc5enxr3g/tmpdr9f345o -mps /scratch/j/jparkin/billyc59/kneaddata_run/h3/NOD_no_bypass/503_cmn/NOD503CecMN_r1_new_kneaddata_unmatched_1_humann_temp/tmpc5enxr3g/tmplj5lc9dg
12/21/2020 04:34:10 PM - humann.utilities - INFO: Execute command: /gpfs/fs1/home/j/jparkin/billyc59/.virtualenvs/h3/bin/python /gpfs/fs1/home/j/jparkin/billyc59/.virtualenvs/h3/lib/python3.8/site-packages/humann/quantify/MinPath12hmp.py -any /scratch/j/jparkin/billyc59/kneaddata_run/h3/NOD_no_bypass/503_cmn/NOD503CecMN_r1_new_kneaddata_unmatched_1_humann_temp/tmpc5enxr3g/tmpp5qlh8xm -map /scratch/j/jparkin/billyc59/kneaddata_run/h3/NOD_no_bypass/503_cmn/NOD503CecMN_r1_new_kneaddata_unmatched_1_humann_temp/tmpc5enxr3g/tmp1foe8dg8 -report /scratch/j/jparkin/billyc59/kneaddata_run/h3/NOD_no_bypass/503_cmn/NOD503CecMN_r1_new_kneaddata_unmatched_1_humann_temp/tmpc5enxr3g/tmpxeis4tvo -details /scratch/j/jparkin/billyc59/kneaddata_run/h3/NOD_no_bypass/503_cmn/NOD503CecMN_r1_new_kneaddata_unmatched_1_humann_temp/tmpc5enxr3g/tmpopjin027 -mps /scratch/j/jparkin/billyc59/kneaddata_run/h3/NOD_no_bypass/503_cmn/NOD503CecMN_r1_new_kneaddata_unmatched_1_humann_temp/tmpc5enxr3g/tmpztghywjr
12/21/2020 04:34:10 PM - humann.utilities - INFO: Execute command: /gpfs/fs1/home/j/jparkin/billyc59/.virtualenvs/h3/bin/python