08/28/2020 09:04:03 PM - humann.humann - INFO: Running humann v3.0.0.alpha.4 08/28/2020 09:04:03 PM - humann.humann - INFO: Output files will be written to: /tmp/tmpneydg9e9 08/28/2020 09:04:03 PM - humann.humann - INFO: Writing temp files to directory: /tmp/tmpneydg9e9/test_ma_R1.fastq.gz_humann_temp_fzcl9dvi 08/28/2020 09:04:03 PM - humann.utilities - INFO: File ( /home/winkler/humann3_test/test_ma_R2.fastq.gz ) is of format: fastq.gz 08/28/2020 09:04:03 PM - humann.utilities - INFO: Decompressing gzipped file ... 08/28/2020 09:04:04 PM - humann.utilities - DEBUG: Check software, metaphlan, for required version, 3.0 08/28/2020 09:04:04 PM - humann.utilities - INFO: Using metaphlan version 3.0 08/28/2020 09:04:04 PM - humann.utilities - DEBUG: Check software, bowtie2, for required version, 2.2 08/28/2020 09:04:05 PM - humann.utilities - INFO: Using bowtie2 version 2.2 08/28/2020 09:04:05 PM - humann.humann - INFO: Search mode set to uniref90 because a uniref90 translated search database is selected 08/28/2020 09:04:05 PM - humann.utilities - DEBUG: Check software, diamond, for required version, 0.9.24 08/28/2020 09:04:05 PM - humann.utilities - INFO: Using diamond version 0.9.24 08/28/2020 09:04:05 PM - humann.config - INFO: Run config settings: DATABASE SETTINGS nucleotide database folder = /home/annotator/databases protein database folder = /home/annotator/databases pathways database file 1 = /usr/local/lib/python3.6/dist-packages/humann/data/pathways/metacyc_reactions_level4ec_only.uniref.bz2 pathways database file 2 = /usr/local/lib/python3.6/dist-packages/humann/data/pathways/metacyc_pathways_structured_filtered utility mapping database folder = /opt/humann_utility_mapping/utility_mapping 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 = 28 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 08/28/2020 09:04:05 PM - humann.store - DEBUG: Initialize Alignments class instance to minimize memory use 08/28/2020 09:04:05 PM - humann.store - DEBUG: Initialize Reads class instance to minimize memory use 08/28/2020 09:04:21 PM - humann.humann - INFO: Load pathways database part 1: /usr/local/lib/python3.6/dist-packages/humann/data/pathways/metacyc_reactions_level4ec_only.uniref.bz2 08/28/2020 09:04:21 PM - humann.humann - INFO: Load pathways database part 2: /usr/local/lib/python3.6/dist-packages/humann/data/pathways/metacyc_pathways_structured_filtered 08/28/2020 09:04:21 PM - humann.search.prescreen - INFO: Found g__Moorella.s__Moorella_thermoacetica : 100.00% of mapped reads 08/28/2020 09:04:21 PM - humann.search.prescreen - INFO: Total species selected from prescreen: 1 08/28/2020 09:04:21 PM - humann.search.prescreen - DEBUG: Adding file to database: g__Moorella.s__Moorella_thermoacetica.centroids.v296_201901.ffn.gz 08/28/2020 09:04:21 PM - humann.search.prescreen - INFO: Creating custom ChocoPhlAn database ........ 08/28/2020 09:04:21 PM - humann.utilities - DEBUG: Using software: /bin/gunzip 08/28/2020 09:04:21 PM - humann.utilities - INFO: Execute command: /bin/gunzip -c /home/annotator/databases/g__Moorella.s__Moorella_thermoacetica.centroids.v296_201901.ffn.gz 08/28/2020 09:04:21 PM - humann.humann - INFO: TIMESTAMP: Completed custom database creation : 0 seconds 08/28/2020 09:04:21 PM - humann.search.nucleotide - INFO: Running bowtie2-build ........ 08/28/2020 09:04:21 PM - humann.utilities - DEBUG: Using software: /usr/bin/bowtie2-build 08/28/2020 09:04:21 PM - humann.utilities - INFO: Execute command: /usr/bin/bowtie2-build -f /tmp/tmpneydg9e9/test_ma_R1.fastq.gz_humann_temp_fzcl9dvi/test_ma_R1.fastq.gz_custom_chocophlan_database.ffn /tmp/tmpneydg9e9/test_ma_R1.fastq.gz_humann_temp_fzcl9dvi/test_ma_R1.fastq.gz_bowtie2_index 08/28/2020 09:04:24 PM - humann.humann - INFO: TIMESTAMP: Completed database index : 4 seconds 08/28/2020 09:04:24 PM - humann.search.nucleotide - DEBUG: Nucleotide input file is of type: fastq 08/28/2020 09:04:24 PM - humann.utilities - DEBUG: Using software: /usr/bin/bowtie2 08/28/2020 09:04:24 PM - humann.utilities - INFO: Execute command: /usr/bin/bowtie2 -q -x /tmp/tmpneydg9e9/test_ma_R1.fastq.gz_humann_temp_fzcl9dvi/test_ma_R1.fastq.gz_bowtie2_index -U /tmp/tmpneydg9e9/test_ma_R1.fastq.gz_humann_temp_fzcl9dvi/tmpnipd4zv5/tmpainp3vlt -S /tmp/tmpneydg9e9/test_ma_R1.fastq.gz_humann_temp_fzcl9dvi/test_ma_R1.fastq.gz_bowtie2_aligned.sam -p 28 --very-sensitive 08/28/2020 09:04:29 PM - humann.utilities - DEBUG: b'1000000 reads; of these:\n 1000000 (100.00%) were unpaired; of these:\n 201427 (20.14%) aligned 0 times\n 677005 (67.70%) aligned exactly 1 time\n 121568 (12.16%) aligned >1 times\n79.86% overall alignment rate\n' 08/28/2020 09:04:29 PM - humann.humann - INFO: TIMESTAMP: Completed nucleotide alignment : 5 seconds 08/28/2020 09:05:01 PM - humann.utilities - DEBUG: Total alignments where percent identity is not a number: 0 08/28/2020 09:05:01 PM - humann.utilities - DEBUG: Total alignments where alignment length is not a number: 0 08/28/2020 09:05:01 PM - humann.utilities - DEBUG: Total alignments where E-value is not a number: 0 08/28/2020 09:05:01 PM - humann.utilities - DEBUG: Total alignments not included based on large e-value: 0 08/28/2020 09:05:01 PM - humann.utilities - DEBUG: Total alignments not included based on small percent identity: 0 08/28/2020 09:05:01 PM - humann.utilities - DEBUG: Total alignments not included based on small query coverage: 0 08/28/2020 09:05:01 PM - humann.search.blastx_coverage - INFO: Total alignments without coverage information: 0 08/28/2020 09:05:01 PM - humann.search.blastx_coverage - INFO: Total proteins in blastx output: 3455 08/28/2020 09:05:01 PM - humann.search.blastx_coverage - INFO: Total proteins without lengths: 0 08/28/2020 09:05:01 PM - humann.search.blastx_coverage - INFO: Proteins with coverage greater than threshold (50.0): 3161 08/28/2020 09:05:29 PM - humann.search.nucleotide - DEBUG: Total nucleotide alignments not included based on filtered genes: 5337 08/28/2020 09:05:29 PM - humann.search.nucleotide - DEBUG: Total nucleotide alignments not included based on small percent identities: 85 08/28/2020 09:05:29 PM - humann.search.nucleotide - DEBUG: Total nucleotide alignments not included based on query coverage threshold: 0 08/28/2020 09:05:29 PM - humann.search.nucleotide - DEBUG: Keeping sam file 08/28/2020 09:05:29 PM - humann.humann - INFO: TIMESTAMP: Completed nucleotide alignment post-processing : 60 seconds 08/28/2020 09:05:29 PM - humann.humann - INFO: Total bugs from nucleotide alignment: 1 08/28/2020 09:05:29 PM - humann.humann - INFO: g__Moorella.s__Moorella_thermoacetica: 793183 hits 08/28/2020 09:05:29 PM - humann.humann - INFO: Total gene families from nucleotide alignment: 3161 08/28/2020 09:05:29 PM - humann.humann - INFO: Unaligned reads after nucleotide alignment: 20.6817000000 % 08/28/2020 09:05:29 PM - humann.search.translated - INFO: Running diamond ........ 08/28/2020 09:05:29 PM - humann.search.translated - INFO: Aligning to reference database: uniref90_201901.dmnd 08/28/2020 09:05:29 PM - humann.utilities - DEBUG: Remove file: /tmp/tmpneydg9e9/test_ma_R1.fastq.gz_humann_temp_fzcl9dvi/tmpnipd4zv5/diamond_m8_ky17mu7a 08/28/2020 09:05:29 PM - humann.utilities - DEBUG: Using software: /usr/bin/diamond 08/28/2020 09:05:29 PM - humann.utilities - INFO: Execute command: /usr/bin/diamond blastx --query /tmp/tmpneydg9e9/test_ma_R1.fastq.gz_humann_temp_fzcl9dvi/test_ma_R1.fastq.gz_bowtie2_unaligned.fa --evalue 1.0 --threads 28 --top 1 --outfmt 6 --db /home/annotator/databases/uniref90_201901 --out /tmp/tmpneydg9e9/test_ma_R1.fastq.gz_humann_temp_fzcl9dvi/tmpnipd4zv5/diamond_m8_ky17mu7a --tmpdir /tmp/tmpneydg9e9/test_ma_R1.fastq.gz_humann_temp_fzcl9dvi/tmpnipd4zv5 08/28/2020 09:14:04 PM - humann.utilities - DEBUG: b'diamond v0.9.24.125 | by Benjamin Buchfink \nLicensed under the GNU GPL \nCheck http://github.com/bbuchfink/diamond for updates.\n\n#CPU threads: 28\nScoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1)\nTemporary directory: /tmp/tmpneydg9e9/test_ma_R1.fastq.gz_humann_temp_fzcl9dvi/tmpnipd4zv5\nOpening the database... [2.3e-05s]\nPercentage range of top alignment score to report hits: 1\nOpening the input file... [1.5e-05s]\nOpening the output file... [1.3e-05s]\nLoading query sequences... [0.288832s]\nMasking queries... [0.339743s]\nBuilding query seed set... [0.048685s]\nAlgorithm: Double-indexed\nBuilding query histograms... [0.043518s]\nAllocating buffers... [5.8e-05s]\nLoading reference sequences... [2.57509s]\nBuilding reference histograms... [2.35503s]\nAllocating buffers... [0.000159s]\nInitializing temporary storage... [0.015258s]\nProcessing query chunk 0, reference chunk 0, shape 0, index chunk 0.\nBuilding reference index... [3.1428s]\nBuilding query index... [0.046835s]\nBuilding seed filter... [0.174618s]\nSearching alignments... [0.130273s]\nProcessing query chunk 0, reference chunk 0, shape 0, index chunk 1.\nBuilding reference index... [3.27935s]\nBuilding query index... [0.041421s]\nBuilding seed filter... [0.171273s]\nSearching alignments... [0.128154s]\nProcessing query chunk 0, reference chunk 0, shape 0, index chunk 2.\nBuilding reference index... [3.37413s]\nBuilding query index... [0.042942s]\nBuilding seed filter... [0.175384s]\nSearching alignments... [0.127454s]\nProcessing query chunk 0, reference chunk 0, shape 0, index chunk 3.\nBuilding reference index... [3.0964s]\nBuilding query index... [0.039511s]\nBuilding seed filter... [0.175766s]\nSearching alignments... [0.124631s]\nProcessing query chunk 0, reference chunk 0, shape 1, index chunk 0.\nBuilding reference index... [3.04527s]\nBuilding query index... [0.03709s]\nBuilding seed filter... [0.17319s]\nSearching alignments... [0.118039s]\nProcessing query chunk 0, reference chunk 0, shape 1, index chunk 1.\nBuilding reference index... [3.34669s]\nBuilding query index... [0.038546s]\nBuilding seed filter... [0.175109s]\nSearching alignments... [0.118452s]\nProcessing query chunk 0, reference chunk 0, shape 1, index chunk 2.\nBuilding reference index... [3.44365s]\nBuilding query index... [0.040728s]\nBuilding seed filter... [0.178016s]\nSearching alignments... [0.114025s]\nProcessing query chunk 0, reference chunk 0, shape 1, index chunk 3.\nBuilding reference index... [3.1993s]\nBuilding query index... [0.040365s]\nBuilding seed filter... [0.178178s]\nSearching alignments... [0.115363s]\nDeallocating buffers... [0.245794s]\nOpening temporary output file... [0.0001s]\nComputing alignments... [0.662099s]\nDeallocating reference... [0.121102s]\nLoading reference sequences... [2.58387s]\nBuilding reference histograms... [2.30891s]\nAllocating buffers... [8.6e-05s]\nInitializing temporary storage... [0.01484s]\nProcessing query chunk 0, reference chunk 1, shape 0, index chunk 0.\nBuilding reference index... [3.14688s]\nBuilding query index... [0.042536s]\nBuilding seed filter... [0.176107s]\nSearching alignments... [0.131246s]\nProcessing query chunk 0, reference chunk 1, shape 0, index chunk 1.\nBuilding reference index... [3.26381s]\nBuilding query index... [0.043674s]\nBuilding seed filter... [0.173514s]\nSearching alignments... [0.127906s]\nProcessing query chunk 0, reference chunk 1, shape 0, index chunk 2.\nBuilding reference index... [3.44908s]\nBuilding query index... [0.046329s]\nBuilding seed filter... [0.179273s]\nSearching alignments... [0.127417s]\nProcessing query chunk 0, reference chunk 1, shape 0, index chunk 3.\nBuilding reference index... [3.20558s]\nBuilding query index... [0.043774s]\nBuilding seed filter... [0.180201s]\nSearching alignments... [0.126505s]\nProcessing query chunk 0, reference chunk 1, shape 1, index chunk 0.\nBuilding reference index... [3.15703s]\nBuilding query index... [0.040128s]\nBuilding seed filter... [0.175272s]\nSearching alignments... [0.117473s]\nProcessing query chunk 0, reference chunk 1, shape 1, index chunk 1.\nBuilding reference index... [3.35273s]\nBuilding query index... [0.04169s]\nBuilding seed filter... [0.17189s]\nSearching alignments... [0.11495s]\nProcessing query chunk 0, reference chunk 1, shape 1, index chunk 2.\nBuilding reference index... [3.50846s]\nBuilding query index... [0.036912s]\nBuilding seed filter... [0.171383s]\nSearching alignments... [0.117324s]\nProcessing query chunk 0, reference chunk 1, shape 1, index chunk 3.\nBuilding reference index... [3.17436s]\nBuilding query index... [0.036003s]\nBuilding seed filter... [0.172522s]\nSearching alignments... [0.115292s]\nDeallocating buffers... [0.248657s]\nOpening temporary output file... [9.8e-05s]\nComputing alignments... [0.664122s]\nDeallocating reference... [0.123355s]\nLoading reference sequences... [2.52545s]\nBuilding reference histograms... [2.41881s]\nAllocating buffers... [9.9e-05s]\nInitializing temporary storage... [0.00923s]\nProcessing query chunk 0, reference chunk 2, shape 0, index chunk 0.\nBuilding reference index... [3.14207s]\nBuilding query index... [0.040122s]\nBuilding seed filter... [0.170791s]\nSearching alignments... [0.133708s]\nProcessing query chunk 0, reference chunk 2, shape 0, index chunk 1.\nBuilding reference index... [3.26569s]\nBuilding query index... [0.046493s]\nBuilding seed filter... [0.181171s]\nSearching alignments... [0.130482s]\nProcessing query chunk 0, reference chunk 2, shape 0, index chunk 2.\nBuilding reference index... [3.46358s]\nBuilding query index... [0.043572s]\nBuilding seed filter... [0.175785s]\nSearching alignments... [0.127755s]\nProcessing query chunk 0, reference chunk 2, shape 0, index chunk 3.\nBuilding reference index... [3.20902s]\nBuilding query index... [0.04011s]\nBuilding seed filter... [0.176578s]\nSearching alignments... [0.123628s]\nProcessing query chunk 0, reference chunk 2, shape 1, index chunk 0.\nBuilding reference index... [3.17734s]\nBuilding query index... [0.039316s]\nBuilding seed filter... [0.176609s]\nSearching alignments... [0.117991s]\nProcessing query chunk 0, reference chunk 2, shape 1, index chunk 1.\nBuilding reference index... [3.377s]\nBuilding query index... [0.04114s]\nBuilding seed filter... [0.173476s]\nSearching alignments... [0.115045s]\nProcessing query chunk 0, reference chunk 2, shape 1, index chunk 2.\nBuilding reference index... [3.46597s]\nBuilding query index... [0.036848s]\nBuilding seed filter... [0.172315s]\nSearching alignments... [0.118528s]\nProcessing query chunk 0, reference chunk 2, shape 1, index chunk 3.\nBuilding reference index... [3.19877s]\nBuilding query index... [0.034072s]\nBuilding seed filter... [0.174043s]\nSearching alignments... [0.115715s]\nDeallocating buffers... [0.249743s]\nOpening temporary output file... [9.3e-05s]\nComputing alignments... [0.673013s]\nDeallocating reference... [0.121245s]\nLoading reference sequences... [2.5936s]\nBuilding reference histograms... [2.35996s]\nAllocating buffers... [8.8e-05s]\nInitializing temporary storage... [0.008252s]\nProcessing query chunk 0, reference chunk 3, shape 0, index chunk 0.\nBuilding reference index... [3.1456s]\nBuilding query index... [0.044583s]\nBuilding seed filter... [0.176797s]\nSearching alignments... [0.1296s]\nProcessing query chunk 0, reference chunk 3, shape 0, index chunk 1.\nBuilding reference index... [3.25978s]\nBuilding query index... [0.043219s]\nBuilding seed filter... [0.172773s]\nSearching alignments... [0.128813s]\nProcessing query chunk 0, reference chunk 3, shape 0, index chunk 2.\nBuilding reference index... [3.4354s]\nBuilding query index... [0.048621s]\nBuilding seed filter... [0.174646s]\nSearching alignments... [0.128755s]\nProcessing query chunk 0, reference chunk 3, shape 0, index chunk 3.\nBuilding reference index... [3.22986s]\nBuilding query index... [0.040665s]\nBuilding seed filter... [0.175295s]\nSearching alignments... [0.1265s]\nProcessing query chunk 0, reference chunk 3, shape 1, index chunk 0.\nBuilding reference index... [3.19954s]\nBuilding query index... [0.038258s]\nBuilding seed filter... [0.178542s]\nSearching alignments... [0.116309s]\nProcessing query chunk 0, reference chunk 3, shape 1, index chunk 1.\nBuilding reference index... [3.3471s]\nBuilding query index... [0.039544s]\nBuilding seed filter... [0.17709s]\nSearching alignments... [0.117761s]\nProcessing query chunk 0, reference chunk 3, shape 1, index chunk 2.\nBuilding reference index... [3.4929s]\nBuilding query index... [0.03816s]\nBuilding seed filter... [0.173882s]\nSearching alignments... [0.119822s]\nProcessing query chunk 0, reference chunk 3, shape 1, index chunk 3.\nBuilding reference index... [3.20323s]\nBuilding query index... [0.039043s]\nBuilding seed filter... [0.18414s]\nSearching alignments... [0.116578s]\nDeallocating buffers... [0.248015s]\nOpening temporary output file... [9.9e-05s]\nComputing alignments... [0.658315s]\nDeallocating reference... [0.121953s]\nLoading reference sequences... [2.57711s]\nBuilding reference histograms... [2.3352s]\nAllocating buffers... [0.000106s]\nInitializing temporary storage... [0.008472s]\nProcessing query chunk 0, reference chunk 4, shape 0, index chunk 0.\nBuilding reference index... [3.17445s]\nBuilding query index... [0.041522s]\nBuilding seed filter... [0.17307s]\nSearching alignments... [0.128411s]\nProcessing query chunk 0, reference chunk 4, shape 0, index chunk 1.\nBuilding reference index... [3.2843s]\nBuilding query index... [0.044348s]\nBuilding seed filter... [0.174813s]\nSearching alignments... [0.126756s]\nProcessing query chunk 0, reference chunk 4, shape 0, index chunk 2.\nBuilding reference index... [3.45536s]\nBuilding query index... [0.046097s]\nBuilding seed filter... [0.182174s]\nSearching alignments... [0.128635s]\nProcessing query chunk 0, reference chunk 4, shape 0, index chunk 3.\nBuilding reference index... [3.23093s]\nBuilding query index... [0.040869s]\nBuilding seed filter... [0.172593s]\nSearching alignments... [0.12579s]\nProcessing query chunk 0, reference chunk 4, shape 1, index chunk 0.\nBuilding reference index... [3.18134s]\nBuilding query index... [0.035822s]\nBuilding seed filter... [0.174154s]\nSearching alignments... [0.117652s]\nProcessing query chunk 0, reference chunk 4, shape 1, index chunk 1.\nBuilding reference index... [3.34105s]\nBuilding query index... [0.040589s]\nBuilding seed filter... [0.177366s]\nSearching alignments... [0.118117s]\nProcessing query chunk 0, reference chunk 4, shape 1, index chunk 2.\nBuilding reference index... [3.48731s]\nBuilding query index... [0.037596s]\nBuilding seed filter... [0.17646s]\nSearching alignments... [0.117357s]\nProcessing query chunk 0, reference chunk 4, shape 1, index chunk 3.\nBuilding reference index... [3.17892s]\nBuilding query index... [0.03988s]\nBuilding seed filter... [0.177369s]\nSearching alignments... [0.116017s]\nDeallocating buffers... [0.248851s]\nOpening temporary output file... [9.8e-05s]\nComputing alignments... [0.651793s]\nDeallocating reference... [0.119584s]\nLoading reference sequences... [2.54707s]\nBuilding reference histograms... [2.4118s]\nAllocating buffers... [0.000113s]\nInitializing temporary storage... [0.008455s]\nProcessing query chunk 0, reference chunk 5, shape 0, index chunk 0.\nBuilding reference index... [3.17087s]\nBuilding query index... [0.038707s]\nBuilding seed filter... [0.179409s]\nSearching alignments... [0.133534s]\nProcessing query chunk 0, reference chunk 5, shape 0, index chunk 1.\nBuilding reference index... [3.25398s]\nBuilding query index... [0.043206s]\nBuilding seed filter... [0.181482s]\nSearching alignments... [0.130011s]\nProcessing query chunk 0, reference chunk 5, shape 0, index chunk 2.\nBuilding reference index... [3.4465s]\nBuilding query index... [0.044932s]\nBuilding seed filter... [0.176406s]\nSearching alignments... [0.127706s]\nProcessing query chunk 0, reference chunk 5, shape 0, index chunk 3.\nBuilding reference index... [3.22561s]\nBuilding query index... [0.040959s]\nBuilding seed filter... [0.175775s]\nSearching alignments... [0.125909s]\nProcessing query chunk 0, reference chunk 5, shape 1, index chunk 0.\nBuilding reference index... [3.18301s]\nBuilding query index... [0.042164s]\nBuilding seed filter... [0.176764s]\nSearching alignments... [0.118747s]\nProcessing query chunk 0, reference chunk 5, shape 1, index chunk 1.\nBuilding reference index... [3.38181s]\nBuilding query index... [0.039745s]\nBuilding seed filter... [0.175278s]\nSearching alignments... [0.11928s]\nProcessing query chunk 0, reference chunk 5, shape 1, index chunk 2.\nBuilding reference index... [3.48122s]\nBuilding query index... [0.037424s]\nBuilding seed filter... [0.172824s]\nSearching alignments... [0.116071s]\nProcessing query chunk 0, reference chunk 5, shape 1, index chunk 3.\nBuilding reference index... [3.22127s]\nBuilding query index... [0.037451s]\nBuilding seed filter... [0.173174s]\nSearching alignments... [0.115716s]\nDeallocating buffers... [0.245711s]\nOpening temporary output file... [9.7e-05s]\nComputing alignments... [0.658479s]\nDeallocating reference... [0.123615s]\nLoading reference sequences... [2.56434s]\nBuilding reference histograms... [2.39219s]\nAllocating buffers... [0.000101s]\nInitializing temporary storage... [0.00891s]\nProcessing query chunk 0, reference chunk 6, shape 0, index chunk 0.\nBuilding reference index... [3.16263s]\nBuilding query index... [0.040606s]\nBuilding seed filter... [0.175101s]\nSearching alignments... [0.13134s]\nProcessing query chunk 0, reference chunk 6, shape 0, index chunk 1.\nBuilding reference index... [3.30503s]\nBuilding query index... [0.040269s]\nBuilding seed filter... [0.173759s]\nSearching alignments... [0.128202s]\nProcessing query chunk 0, reference chunk 6, shape 0, index chunk 2.\nBuilding reference index... [3.4479s]\nBuilding query index... [0.044727s]\nBuilding seed filter... [0.172562s]\nSearching alignments... [0.126045s]\nProcessing query chunk 0, reference chunk 6, shape 0, index chunk 3.\nBuilding reference index... [3.25393s]\nBuilding query index... [0.043524s]\nBuilding seed filter... [0.175632s]\nSearching alignments... [0.125889s]\nProcessing query chunk 0, reference chunk 6, shape 1, index chunk 0.\nBuilding reference index... [3.19992s]\nBuilding query index... [0.040075s]\nBuilding seed filter... [0.178194s]\nSearching alignments... [0.120155s]\nProcessing query chunk 0, reference chunk 6, shape 1, index chunk 1.\nBuilding reference index... [3.36786s]\nBuilding query index... [0.038567s]\nBuilding seed filter... [0.177796s]\nSearching alignments... [0.120363s]\nProcessing query chunk 0, reference chunk 6, shape 1, index chunk 2.\nBuilding reference index... [3.46585s]\nBuilding query index... [0.039668s]\nBuilding seed filter... [0.175061s]\nSearching alignments... [0.117664s]\nProcessing query chunk 0, reference chunk 6, shape 1, index chunk 3.\nBuilding reference index... [3.20506s]\nBuilding query index... [0.038502s]\nBuilding seed filter... [0.174292s]\nSearching alignments... [0.116243s]\nDeallocating buffers... [0.247291s]\nOpening temporary output file... [9.5e-05s]\nComputing alignments... [0.648271s]\nDeallocating reference... [0.122419s]\nLoading reference sequences... [2.5674s]\nBuilding reference histograms... [2.41511s]\nAllocating buffers... [0.000115s]\nInitializing temporary storage... [0.008428s]\nProcessing query chunk 0, reference chunk 7, shape 0, index chunk 0.\nBuilding reference index... [3.18215s]\nBuilding query index... [0.038964s]\nBuilding seed filter... [0.169069s]\nSearching alignments... [0.129325s]\nProcessing query chunk 0, reference chunk 7, shape 0, index chunk 1.\nBuilding reference index... [3.2875s]\nBuilding query index... [0.044761s]\nBuilding seed filter... [0.171228s]\nSearching alignments... [0.127827s]\nProcessing query chunk 0, reference chunk 7, shape 0, index chunk 2.\nBuilding reference index... [3.49093s]\nBuilding query index... [0.041342s]\nBuilding seed filter... [0.172552s]\nSearching alignments... [0.124801s]\nProcessing query chunk 0, reference chunk 7, shape 0, index chunk 3.\nBuilding reference index... [3.21322s]\nBuilding query index... [0.041547s]\nBuilding seed filter... [0.179711s]\nSearching alignments... [0.126354s]\nProcessing query chunk 0, reference chunk 7, shape 1, index chunk 0.\nBuilding reference index... [3.20345s]\nBuilding query index... [0.038966s]\nBuilding seed filter... [0.17621s]\nSearching alignments... [0.118619s]\nProcessing query chunk 0, reference chunk 7, shape 1, index chunk 1.\nBuilding reference index... [3.35755s]\nBuilding query index... [0.034655s]\nBuilding seed filter... [0.175107s]\nSearching alignments... [0.11591s]\nProcessing query chunk 0, reference chunk 7, shape 1, index chunk 2.\nBuilding reference index... [3.47489s]\nBuilding query index... [0.039037s]\nBuilding seed filter... [0.176098s]\nSearching alignments... [0.117103s]\nProcessing query chunk 0, reference chunk 7, shape 1, index chunk 3.\nBuilding reference index... [3.19958s]\nBuilding query index... [0.03556s]\nBuilding seed filter... [0.175115s]\nSearching alignments... [0.1162s]\nDeallocating buffers... [0.246724s]\nOpening temporary output file... [9.7e-05s]\nComputing alignments... [0.661542s]\nDeallocating reference... [0.118997s]\nLoading reference sequences... [2.55603s]\nBuilding reference histograms... [2.38237s]\nAllocating buffers... [9.6e-05s]\nInitializing temporary storage... [0.009194s]\nProcessing query chunk 0, reference chunk 8, shape 0, index chunk 0.\nBuilding reference index... [3.17195s]\nBuilding query index... [0.044067s]\nBuilding seed filter... [0.17418s]\nSearching alignments... [0.130977s]\nProcessing query chunk 0, reference chunk 8, shape 0, index chunk 1.\nBuilding reference index... [3.30214s]\nBuilding query index... [0.043394s]\nBuilding seed filter... [0.178004s]\nSearching alignments... [0.131598s]\nProcessing query chunk 0, reference chunk 8, shape 0, index chunk 2.\nBuilding reference index... [3.4577s]\nBuilding query index... [0.043674s]\nBuilding seed filter... [0.175461s]\nSearching alignments... [0.125158s]\nProcessing query chunk 0, reference chunk 8, shape 0, index chunk 3.\nBuilding reference index... [3.24428s]\nBuilding query index... [0.042013s]\nBuilding seed filter... [0.175027s]\nSearching alignments... [0.127014s]\nProcessing query chunk 0, reference chunk 8, shape 1, index chunk 0.\nBuilding reference index... [3.16055s]\nBuilding query index... [0.036947s]\nBuilding seed filter... [0.1795s]\nSearching alignments... [0.119629s]\nProcessing query chunk 0, reference chunk 8, shape 1, index chunk 1.\nBuilding reference index... [3.39053s]\nBuilding query index... [0.038775s]\nBuilding seed filter... [0.181171s]\nSearching alignments... [0.119769s]\nProcessing query chunk 0, reference chunk 8, shape 1, index chunk 2.\nBuilding reference index... [3.48221s]\nBuilding query index... [0.040054s]\nBuilding seed filter... [0.180626s]\nSearching alignments... [0.11902s]\nProcessing query chunk 0, reference chunk 8, shape 1, index chunk 3.\nBuilding reference index... [3.18478s]\nBuilding query index... [0.040564s]\nBuilding seed filter... [0.17764s]\nSearching alignments... [0.116599s]\nDeallocating buffers... [0.247256s]\nOpening temporary output file... [7.8e-05s]\nComputing alignments... [0.647351s]\nDeallocating reference... [0.121975s]\nLoading reference sequences... [2.54889s]\nBuilding reference histograms... [2.41241s]\nAllocating buffers... [9.2e-05s]\nInitializing temporary storage... [0.009143s]\nProcessing query chunk 0, reference chunk 9, shape 0, index chunk 0.\nBuilding reference index... [3.15891s]\nBuilding query index... [0.042744s]\nBuilding seed filter... [0.171726s]\nSearching alignments... [0.130063s]\nProcessing query chunk 0, reference chunk 9, shape 0, index chunk 1.\nBuilding reference index... [3.28444s]\nBuilding query index... [0.043326s]\nBuilding seed filter... [0.170186s]\nSearching alignments... [0.129477s]\nProcessing query chunk 0, reference chunk 9, shape 0, index chunk 2.\nBuilding reference index... [3.46588s]\nBuilding query index... [0.042997s]\nBuilding seed filter... [0.178822s]\nSearching alignments... [0.125918s]\nProcessing query chunk 0, reference chunk 9, shape 0, index chunk 3.\nBuilding reference index... [3.25485s]\nBuilding query index... [0.043395s]\nBuilding seed filter... [0.176519s]\nSearching alignments... [0.125443s]\nProcessing query chunk 0, reference chunk 9, shape 1, index chunk 0.\nBuilding reference index... [3.18038s]\nBuilding query index... [0.038813s]\nBuilding seed filter... [0.178351s]\nSearching alignments... [0.118136s]\nProcessing query chunk 0, reference chunk 9, shape 1, index chunk 1.\nBuilding reference index... [3.37791s]\nBuilding query index... [0.037326s]\nBuilding seed filter... [0.17291s]\nSearching alignments... [0.116909s]\nProcessing query chunk 0, reference chunk 9, shape 1, index chunk 2.\nBuilding reference index... [3.48948s]\nBuilding query index... [0.038856s]\nBuilding seed filter... [0.182845s]\nSearching alignments... [0.117488s]\nProcessing query chunk 0, reference chunk 9, shape 1, index chunk 3.\nBuilding reference index... [3.21625s]\nBuilding query index... [0.039485s]\nBuilding seed filter... [0.179097s]\nSearching alignments... [0.116472s]\nDeallocating buffers... [0.250094s]\nOpening temporary output file... [8.2e-05s]\nComputing alignments... [0.654189s]\nDeallocating reference... [0.12213s]\nLoading reference sequences... [2.56016s]\nBuilding reference histograms... [2.37082s]\nAllocating buffers... [5.6e-05s]\nInitializing temporary storage... [0.004956s]\nProcessing query chunk 0, reference chunk 10, shape 0, index chunk 0.\nBuilding reference index... [3.19166s]\nBuilding query index... [0.043932s]\nBuilding seed filter... [0.178774s]\nSearching alignments... [0.129794s]\nProcessing query chunk 0, reference chunk 10, shape 0, index chunk 1.\nBuilding reference index... [3.31128s]\nBuilding query index... [0.041572s]\nBuilding seed filter... [0.175777s]\nSearching alignments... [0.12853s]\nProcessing query chunk 0, reference chunk 10, shape 0, index chunk 2.\nBuilding reference index... [3.47551s]\nBuilding query index... [0.041197s]\nBuilding seed filter... [0.180163s]\nSearching alignments... [0.125721s]\nProcessing query chunk 0, reference chunk 10, shape 0, index chunk 3.\nBuilding reference index... [3.2561s]\nBuilding query index... [0.041199s]\nBuilding seed filter... [0.170642s]\nSearching alignments... [0.128s]\nProcessing query chunk 0, reference chunk 10, shape 1, index chunk 0.\nBuilding reference index... [3.18641s]\nBuilding query index... [0.038571s]\nBuilding seed filter... [0.179726s]\nSearching alignments... [0.11889s]\nProcessing query chunk 0, reference chunk 10, shape 1, index chunk 1.\nBuilding reference index... [3.38867s]\nBuilding query index... [0.037494s]\nBuilding seed filter... [0.175164s]\nSearching alignments... [0.116659s]\nProcessing query chunk 0, reference chunk 10, shape 1, index chunk 2.\nBuilding reference index... [3.49622s]\nBuilding query index... [0.041547s]\nBuilding seed filter... [0.176776s]\nSearching alignments... [0.116706s]\nProcessing query chunk 0, reference chunk 10, shape 1, index chunk 3.\nBuilding reference index... [3.19839s]\nBuilding query index... [0.039067s]\nBuilding seed filter... [0.178814s]\nSearching alignments... [0.115407s]\nDeallocating buffers... [0.248299s]\nOpening temporary output file... [0.0001s]\nComputing alignments... [0.669946s]\nDeallocating reference... [0.122687s]\nLoading reference sequences... [2.62958s]\nBuilding reference histograms... [2.4054s]\nAllocating buffers... [0.000103s]\nInitializing temporary storage... [0.009851s]\nProcessing query chunk 0, reference chunk 11, shape 0, index chunk 0.\nBuilding reference index... [3.17401s]\nBuilding query index... [0.039848s]\nBuilding seed filter... [0.17435s]\nSearching alignments... [0.131972s]\nProcessing query chunk 0, reference chunk 11, shape 0, index chunk 1.\nBuilding reference index... [3.27312s]\nBuilding query index... [0.04319s]\nBuilding seed filter... [0.177057s]\nSearching alignments... [0.129799s]\nProcessing query chunk 0, reference chunk 11, shape 0, index chunk 2.\nBuilding reference index... [3.47294s]\nBuilding query index... [0.045381s]\nBuilding seed filter... [0.172164s]\nSearching alignments... [0.128576s]\nProcessing query chunk 0, reference chunk 11, shape 0, index chunk 3.\nBuilding reference index... [3.23393s]\nBuilding query index... [0.041174s]\nBuilding seed filter... [0.171138s]\nSearching alignments... [0.126903s]\nProcessing query chunk 0, reference chunk 11, shape 1, index chunk 0.\nBuilding reference index... [3.20778s]\nBuilding query index... [0.037419s]\nBuilding seed filter... [0.177034s]\nSearching alignments... [0.116647s]\nProcessing query chunk 0, reference chunk 11, shape 1, index chunk 1.\nBuilding reference index... [3.36138s]\nBuilding query index... [0.036317s]\nBuilding seed filter... [0.175506s]\nSearching alignments... [0.116712s]\nProcessing query chunk 0, reference chunk 11, shape 1, index chunk 2.\nBuilding reference index... [3.4792s]\nBuilding query index... [0.041424s]\nBuilding seed filter... [0.179335s]\nSearching alignments... [0.116504s]\nProcessing query chunk 0, reference chunk 11, shape 1, index chunk 3.\nBuilding reference index... [3.20693s]\nBuilding query index... [0.035361s]\nBuilding seed filter... [0.176258s]\nSearching alignments... [0.116038s]\nDeallocating buffers... [0.245099s]\nOpening temporary output file... [8.1e-05s]\nComputing alignments... [0.650626s]\nDeallocating reference... [0.120776s]\nLoading reference sequences... [2.62549s]\nBuilding reference histograms... [2.39772s]\nAllocating buffers... [0.000102s]\nInitializing temporary storage... [0.008102s]\nProcessing query chunk 0, reference chunk 12, shape 0, index chunk 0.\nBuilding reference index... [3.19456s]\nBuilding query index... [0.044406s]\nBuilding seed filter... [0.174129s]\nSearching alignments... [0.129354s]\nProcessing query chunk 0, reference chunk 12, shape 0, index chunk 1.\nBuilding reference index... [3.29524s]\nBuilding query index... [0.043302s]\nBuilding seed filter... [0.171296s]\nSearching alignments... [0.131267s]\nProcessing query chunk 0, reference chunk 12, shape 0, index chunk 2.\nBuilding reference index... [3.44984s]\nBuilding query index... [0.040116s]\nBuilding seed filter... [0.171935s]\nSearching alignments... [0.126135s]\nProcessing query chunk 0, reference chunk 12, shape 0, index chunk 3.\nBuilding reference index... [3.27393s]\nBuilding query index... [0.043162s]\nBuilding seed filter... [0.172626s]\nSearching alignments... [0.12762s]\nProcessing query chunk 0, reference chunk 12, shape 1, index chunk 0.\nBuilding reference index... [3.18561s]\nBuilding query index... [0.038024s]\nBuilding seed filter... [0.177108s]\nSearching alignments... [0.116754s]\nProcessing query chunk 0, reference chunk 12, shape 1, index chunk 1.\nBuilding reference index... [3.37472s]\nBuilding query index... [0.035153s]\nBuilding seed filter... [0.171566s]\nSearching alignments... [0.118353s]\nProcessing query chunk 0, reference chunk 12, shape 1, index chunk 2.\nBuilding reference index... [3.4735s]\nBuilding query index... [0.039988s]\nBuilding seed filter... [0.180272s]\nSearching alignments... [0.116736s]\nProcessing query chunk 0, reference chunk 12, shape 1, index chunk 3.\nBuilding reference index... [3.22045s]\nBuilding query index... [0.039384s]\nBuilding seed filter... [0.175534s]\nSearching alignments... [0.117072s]\nDeallocating buffers... [0.248162s]\nOpening temporary output file... [9.8e-05s]\nComputing alignments... [0.664242s]\nDeallocating reference... [0.120855s]\nLoading reference sequences... [2.60822s]\nBuilding reference histograms... [2.43613s]\nAllocating buffers... [9.6e-05s]\nInitializing temporary storage... [0.009205s]\nProcessing query chunk 0, reference chunk 13, shape 0, index chunk 0.\nBuilding reference index... [3.20539s]\nBuilding query index... [0.039117s]\nBuilding seed filter... [0.170826s]\nSearching alignments... [0.130583s]\nProcessing query chunk 0, reference chunk 13, shape 0, index chunk 1.\nBuilding reference index... [3.2715s]\nBuilding query index... [0.042243s]\nBuilding seed filter... [0.177817s]\nSearching alignments... [0.130482s]\nProcessing query chunk 0, reference chunk 13, shape 0, index chunk 2.\nBuilding reference index... [3.45297s]\nBuilding query index... [0.0471s]\nBuilding seed filter... [0.181186s]\nSearching alignments... [0.127168s]\nProcessing query chunk 0, reference chunk 13, shape 0, index chunk 3.\nBuilding reference index... [3.2508s]\nBuilding query index... [0.043716s]\nBuilding seed filter... [0.181014s]\nSearching alignments... [0.128225s]\nProcessing query chunk 0, reference chunk 13, shape 1, index chunk 0.\nBuilding reference index... [3.18182s]\nBuilding query index... [0.040056s]\nBuilding seed filter... [0.172439s]\nSearching alignments... [0.118025s]\nProcessing query chunk 0, reference chunk 13, shape 1, index chunk 1.\nBuilding reference index... [3.38067s]\nBuilding query index... [0.040948s]\nBuilding seed filter... [0.180654s]\nSearching alignments... [0.119887s]\nProcessing query chunk 0, reference chunk 13, shape 1, index chunk 2.\nBuilding reference index... [3.47322s]\nBuilding query index... [0.04106s]\nBuilding seed filter... [0.184178s]\nSearching alignments... [0.118255s]\nProcessing query chunk 0, reference chunk 13, shape 1, index chunk 3.\nBuilding reference index... [3.20005s]\nBuilding query index... [0.034979s]\nBuilding seed filter... [0.172516s]\nSearching alignments... [0.116097s]\nDeallocating buffers... [0.2493s]\nOpening temporary output file... [9.5e-05s]\nComputing alignments... [0.663563s]\nDeallocating reference... [0.121126s]\nLoading reference sequences... [1.67553s]\nBuilding reference histograms... [1.4825s]\nAllocating buffers... [6.8e-05s]\nInitializing temporary storage... [0.005607s]\nProcessing query chunk 0, reference chunk 14, shape 0, index chunk 0.\nBuilding reference index... [1.97014s]\nBuilding query index... [0.038482s]\nBuilding seed filter... [0.114055s]\nSearching alignments... [0.085951s]\nProcessing query chunk 0, reference chunk 14, shape 0, index chunk 1.\nBuilding reference index... [2.03564s]\nBuilding query index... [0.044973s]\nBuilding seed filter... [0.117654s]\nSearching alignments... [0.085665s]\nProcessing query chunk 0, reference chunk 14, shape 0, index chunk 2.\nBuilding reference index... [2.08292s]\nBuilding query index... [0.04555s]\nBuilding seed filter... [0.126883s]\nSearching alignments... [0.085007s]\nProcessing query chunk 0, reference chunk 14, shape 0, index chunk 3.\nBuilding reference index... [1.94291s]\nBuilding query index... [0.045819s]\nBuilding seed filter... [0.121721s]\nSearching alignments... [0.085511s]\nProcessing query chunk 0, reference chunk 14, shape 1, index chunk 0.\nBuilding reference index... [1.96976s]\nBuilding query index... [0.035172s]\nBuilding seed filter... [0.122553s]\nSearching alignments... [0.08259s]\nProcessing query chunk 0, reference chunk 14, shape 1, index chunk 1.\nBuilding reference index... [2.08562s]\nBuilding query index... [0.043172s]\nBuilding seed filter... [0.123355s]\nSearching alignments... [0.08032s]\nProcessing query chunk 0, reference chunk 14, shape 1, index chunk 2.\nBuilding reference index... [2.16057s]\nBuilding query index... [0.041429s]\nBuilding seed filter... [0.1171s]\nSearching alignments... [0.078718s]\nProcessing query chunk 0, reference chunk 14, shape 1, index chunk 3.\nBuilding reference index... [1.97867s]\nBuilding query index... [0.038891s]\nBuilding seed filter... [0.12064s]\nSearching alignments... [0.077831s]\nDeallocating buffers... [0.144709s]\nOpening temporary output file... [9.2e-05s]\nComputing alignments... [0.641047s]\nDeallocating reference... [0.083305s]\nLoading reference sequences... [3.1e-05s]\nDeallocating buffers... [0.001055s]\nJoining output blocks... [0.677068s]\nDeallocating queries... [0.048114s]\nLoading query sequences... [1.4e-05s]\nClosing the input file... [6e-06s]\nClosing the output file... [2.4e-05s]\nClosing the database file... [4e-06s]\nDeallocating taxonomy... [2e-06s]\nTotal time = 514.626s\nReported 98893 pairwise alignments, 98893 HSPs.\n59066 queries aligned.\n' 08/28/2020 09:14:04 PM - humann.utilities - DEBUG: Using software: /bin/cat 08/28/2020 09:14:04 PM - humann.utilities - INFO: Execute command: /bin/cat /tmp/tmpneydg9e9/test_ma_R1.fastq.gz_humann_temp_fzcl9dvi/tmpnipd4zv5/diamond_m8_ky17mu7a 08/28/2020 09:14:04 PM - humann.humann - INFO: TIMESTAMP: Completed translated alignment : 515 seconds 08/28/2020 09:14:05 PM - humann.utilities - DEBUG: Total alignments where percent identity is not a number: 0 08/28/2020 09:14:05 PM - humann.utilities - DEBUG: Total alignments where alignment length is not a number: 0 08/28/2020 09:14:05 PM - humann.utilities - DEBUG: Total alignments where E-value is not a number: 0 08/28/2020 09:14:05 PM - humann.utilities - DEBUG: Total alignments not included based on large e-value: 0 08/28/2020 09:14:05 PM - humann.utilities - DEBUG: Total alignments not included based on small percent identity: 1398 08/28/2020 09:14:05 PM - humann.utilities - DEBUG: Total alignments not included based on small query coverage: 15549 08/28/2020 09:14:05 PM - humann.search.blastx_coverage - INFO: Total alignments without coverage information: 0 08/28/2020 09:14:05 PM - humann.search.blastx_coverage - INFO: Total proteins in blastx output: 14684 08/28/2020 09:14:05 PM - humann.search.blastx_coverage - INFO: Total proteins without lengths: 0 08/28/2020 09:14:05 PM - humann.search.blastx_coverage - INFO: Proteins with coverage greater than threshold (50.0): 463 08/28/2020 09:14:07 PM - humann.utilities - DEBUG: Total alignments where percent identity is not a number: 0 08/28/2020 09:14:07 PM - humann.utilities - DEBUG: Total alignments where alignment length is not a number: 0 08/28/2020 09:14:07 PM - humann.utilities - DEBUG: Total alignments where E-value is not a number: 0 08/28/2020 09:14:07 PM - humann.utilities - DEBUG: Total alignments not included based on large e-value: 0 08/28/2020 09:14:07 PM - humann.utilities - DEBUG: Total alignments not included based on small percent identity: 1398 08/28/2020 09:14:07 PM - humann.utilities - DEBUG: Total alignments not included based on small query coverage: 15549 08/28/2020 09:14:07 PM - humann.search.translated - DEBUG: Total translated alignments not included based on small subject coverage value: 48132 08/28/2020 09:14:08 PM - humann.humann - INFO: TIMESTAMP: Completed translated alignment post-processing : 4 seconds 08/28/2020 09:14:08 PM - humann.humann - INFO: Total bugs after translated alignment: 2 08/28/2020 09:14:08 PM - humann.humann - INFO: g__Moorella.s__Moorella_thermoacetica: 793183 hits unclassified: 33838 hits 08/28/2020 09:14:08 PM - humann.humann - INFO: Total gene families after translated alignment: 3321 08/28/2020 09:14:08 PM - humann.humann - INFO: Unaligned reads after translated alignment: 17.4637000000 % 08/28/2020 09:14:08 PM - humann.humann - INFO: Computing gene families ... 08/28/2020 09:14:08 PM - humann.quantify.families - DEBUG: Compute gene families 08/28/2020 09:14:08 PM - humann.store - INFO: Total gene families : 3321 g__Moorella.s__Moorella_thermoacetica : 3161 gene families unclassified : 463 gene families 08/28/2020 09:14:22 PM - humann.humann - INFO: TIMESTAMP: Completed computing gene families : 14 seconds 08/28/2020 09:14:22 PM - humann.humann - INFO: Computing pathways abundance and coverage ... 08/28/2020 09:14:22 PM - humann.quantify.modules - DEBUG: Write flat reactions to pathways file for Minpath 08/28/2020 09:14:22 PM - humann.quantify.modules - INFO: Compute reaction scores for bug: g__Moorella.s__Moorella_thermoacetica 08/28/2020 09:14:24 PM - humann.quantify.modules - INFO: Run MinPath on g__Moorella.s__Moorella_thermoacetica 08/28/2020 09:14:24 PM - humann.quantify.modules - INFO: Compute reaction scores for bug: unclassified 08/28/2020 09:14:27 PM - humann.quantify.modules - INFO: Run MinPath on unclassified 08/28/2020 09:14:27 PM - humann.quantify.modules - INFO: Compute reaction scores for bug: all 08/28/2020 09:14:29 PM - humann.quantify.modules - INFO: Run MinPath on all 08/28/2020 09:14:29 PM - humann.utilities - DEBUG: Using python module : /usr/local/lib/python3.6/dist-packages/humann/quantify/MinPath12hmp.py 08/28/2020 09:14:29 PM - humann.utilities - DEBUG: Using python module : /usr/local/lib/python3.6/dist-packages/humann/quantify/MinPath12hmp.py 08/28/2020 09:14:29 PM - humann.utilities - DEBUG: Using python module : /usr/local/lib/python3.6/dist-packages/humann/quantify/MinPath12hmp.py 08/28/2020 09:14:29 PM - humann.utilities - INFO: Execute command: /usr/bin/python3 /usr/local/lib/python3.6/dist-packages/humann/quantify/MinPath12hmp.py -any /tmp/tmpneydg9e9/test_ma_R1.fastq.gz_humann_temp_fzcl9dvi/tmpnipd4zv5/tmpt8wcmhhx -map /tmp/tmpneydg9e9/test_ma_R1.fastq.gz_humann_temp_fzcl9dvi/tmpnipd4zv5/tmpx83f0a7z -report /tmp/tmpneydg9e9/test_ma_R1.fastq.gz_humann_temp_fzcl9dvi/tmpnipd4zv5/tmpxr6yy4ro -details /tmp/tmpneydg9e9/test_ma_R1.fastq.gz_humann_temp_fzcl9dvi/tmpnipd4zv5/tmpmcu6bewf -mps /tmp/tmpneydg9e9/test_ma_R1.fastq.gz_humann_temp_fzcl9dvi/tmpnipd4zv5/tmpzm984sya 08/28/2020 09:14:29 PM - humann.utilities - INFO: Execute command: /usr/bin/python3 /usr/local/lib/python3.6/dist-packages/humann/quantify/MinPath12hmp.py -any /tmp/tmpneydg9e9/test_ma_R1.fastq.gz_humann_temp_fzcl9dvi/tmpnipd4zv5/tmpos57ygng -map /tmp/tmpneydg9e9/test_ma_R1.fastq.gz_humann_temp_fzcl9dvi/tmpnipd4zv5/tmpx83f0a7z -report /tmp/tmpneydg9e9/test_ma_R1.fastq.gz_humann_temp_fzcl9dvi/tmpnipd4zv5/tmpo07fvg4c -details /tmp/tmpneydg9e9/test_ma_R1.fastq.gz_humann_temp_fzcl9dvi/tmpnipd4zv5/tmpo8r_y58c -mps /tmp/tmpneydg9e9/test_ma_R1.fastq.gz_humann_temp_fzcl9dvi/tmpnipd4zv5/tmp57hahdia 08/28/2020 09:14:29 PM - humann.utilities - INFO: Execute command: /usr/bin/python3 /usr/local/lib/python3.6/dist-packages/humann/quantify/MinPath12hmp.py -any /tmp/tmpneydg9e9/test_ma_R1.fastq.gz_humann_temp_fzcl9dvi/tmpnipd4zv5/tmplztussjr -map /tmp/tmpneydg9e9/test_ma_R1.fastq.gz_humann_temp_fzcl9dvi/tmpnipd4zv5/tmpx83f0a7z -report /tmp/tmpneydg9e9/test_ma_R1.fastq.gz_humann_temp_fzcl9dvi/tmpnipd4zv5/tmpfpeyldmn -details /tmp/tmpneydg9e9/test_ma_R1.fastq.gz_humann_temp_fzcl9dvi/tmpnipd4zv5/tmp49d26909 -mps /tmp/tmpneydg9e9/test_ma_R1.fastq.gz_humann_temp_fzcl9dvi/tmpnipd4zv5/tmp6tqq56by 08/28/2020 09:14:30 PM - humann.quantify.modules - DEBUG: Compute pathway abundance for bug: g__Moorella.s__Moorella_thermoacetica 08/28/2020 09:14:30 PM - humann.quantify.modules - DEBUG: Compute pathway abundance for bug: unclassified 08/28/2020 09:14:30 PM - humann.quantify.modules - DEBUG: Compute pathway abundance for bug: all 08/28/2020 09:14:32 PM - humann.quantify.modules - DEBUG: Compute pathway coverage for bug: g__Moorella.s__Moorella_thermoacetica 08/28/2020 09:14:32 PM - humann.quantify.modules - DEBUG: Compute pathway coverage for bug: unclassified 08/28/2020 09:14:32 PM - humann.quantify.modules - DEBUG: Compute pathway coverage for bug: all 08/28/2020 09:14:33 PM - humann.quantify.modules - DEBUG: Print pathways _Abundance 08/28/2020 09:14:33 PM - humann.quantify.modules - DEBUG: Print pathways _Coverage 08/28/2020 09:14:33 PM - humann.humann - INFO: TIMESTAMP: Completed computing pathways : 11 seconds 08/28/2020 09:14:33 PM - humann.humann - INFO: Output files created: /tmp/tmpneydg9e9/test_ma_R1.fastq.gz_genefamilies.tsv /tmp/tmpneydg9e9/test_ma_R1.fastq.gz_pathabundance.tsv /tmp/tmpneydg9e9/test_ma_R1.fastq.gz_pathcoverage.tsv 08/28/2020 09:14:33 PM - humann.utilities - DEBUG: Remove directory: /tmp/tmpneydg9e9/test_ma_R1.fastq.gz_humann_temp_fzcl9dvi/tmpnipd4zv5 08/28/2020 09:14:33 PM - humann.utilities - DEBUG: Remove directory: /tmp/tmpneydg9e9/test_ma_R1.fastq.gz_humann_temp_fzcl9dvi