# Humann3 output logs: total bugs **URL:** \ **Category:** HUMAnN\ **Created:** [December 21, 2020, 10:08pm UTC](https://forum.biobakery.org/t/humann3-output-logs-total-bugs/1466 "2020-12-21T22:08:27Z")\ **Posts on this page:** 3\ **Page:** 1
**Author:** ![Billy\_Law](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/billy_law/32/85_2.png) [@Billy\_Law](https://forum.biobakery.org/u/Billy_Law)\ **Post date:** [December 21, 2020, 10:08pm UTC](https://forum.biobakery.org/t/humann3-output-logs-total-bugs/1466/1 "2020-12-21T22:08:27Z")
Hi! I’m trying to understand the HUMAnN3 printouts. I see there’s now sections like the portion below that refer to hits. Are these hits “reads”? If not, how can I get read counts, instead of RPKs from HUMAnN3? > Running metaphlan … > Found g\_\_Parabacteroides.s\_\_Parabacteroides\_goldsteinii : 73.88% of mapped reads > Found g\_\_Clostridium.s\_\_Clostridium\_sp\_ASF356 : 15.14% of mapped reads > Found g\_\_Blautia.s\_\_Blautia\_coccoides : 5.54% of mapped reads > Found g\_\_Mucispirillum.s\_\_Mucispirillum\_schaedleri : 5.11% of mapped reads > Found g\_\_Lactobacillus.s\_\_Lactobacillus\_murinus : 0.33% of mapped reads > Total species selected from prescreen: 5 > Selected species explain 100.00% of predicted community composition > Creating custom ChocoPhlAn database … > Running bowtie2-build … > Running bowtie2 … > Total bugs from nucleotide alignment: 5 > 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 > Total gene families from nucleotide alignment: 9071 > Unaligned reads after nucleotide alignment: 85.0070015157 % > Running diamond … > Aligning to reference database: uniref90\_201901.dmnd > Total bugs after translated alignment: 6 > 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 > Total gene families after translated alignment: 9187 > Unaligned reads after translated alignment: 84.8843132833 % > Computing gene families … > Computing pathways abundance and coverage … ---
**Author:** ![Billy\_Law](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/billy_law/32/85_2.png) [@Billy\_Law](https://forum.biobakery.org/u/Billy_Law)\ **Post date:** [December 22, 2020, 6:01pm UTC](https://forum.biobakery.org/t/humann3-output-logs-total-bugs/1466/2 "2020-12-22T18:01:26Z")
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](mailto:buchfink@gmail.com)\nLicensed under the GNU GPL [https://www.gnu.org/licenses/gpl.txt](https://www.gnu.org/licenses/gpl.txt)\nCheck [http://github.com/bbuchfink/diamond](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 ---
**Author:** ![franzosa](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/franzosa/32/3511_2.png) [@franzosa](https://forum.biobakery.org/u/franzosa)\ **Post date:** [January 4, 2021, 7:42pm UTC](https://forum.biobakery.org/t/humann3-output-logs-total-bugs/1466/3 "2021-01-04T19:42:58Z")
HUMAnN’s rawest outputs are RPK units; we don’t have a mode to output integer counts because we allow reads to map to multiple genes (and then divide the read’s weight over those genes). The “hits” you are seeing in the log files are raw counts of alignments of reads by bowtie2 and diamond. A read can in principle participate in multiple hits that HUMAnN counts, especially in the translated search phase (diamond).