[2024-01-25 18:48:05,691] [INFO] DFAST_QC pipeline started. [2024-01-25 18:48:05,693] [INFO] DFAST_QC version: 0.5.7 [2024-01-25 18:48:05,693] [INFO] DQC Reference Directory: /var/lib/cwl/stg3bb84ad5-0bd3-4540-bf87-d6fcc1f7a5a0/dqc_reference [2024-01-25 18:48:06,856] [INFO] ===== Start taxonomy check using ANI ===== [2024-01-25 18:48:06,856] [INFO] Task started: Prodigal [2024-01-25 18:48:06,856] [INFO] Running command: gunzip -c /var/lib/cwl/stg7e57ec6d-bf92-4abd-8974-2c7f5670cce7/GCF_015708085.1_ASM1570808v1_genomic.fna.gz | prodigal -d GCF_015708085.1_ASM1570808v1_genomic.fna/cds.fna -a GCF_015708085.1_ASM1570808v1_genomic.fna/protein.faa -g 11 -q > /dev/null [2024-01-25 18:48:18,663] [INFO] Task succeeded: Prodigal [2024-01-25 18:48:18,664] [INFO] Task started: HMMsearch [2024-01-25 18:48:18,664] [INFO] Running command: hmmsearch --tblout GCF_015708085.1_ASM1570808v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3bb84ad5-0bd3-4540-bf87-d6fcc1f7a5a0/dqc_reference/reference_markers.hmm GCF_015708085.1_ASM1570808v1_genomic.fna/protein.faa > /dev/null [2024-01-25 18:48:18,981] [INFO] Task succeeded: HMMsearch [2024-01-25 18:48:18,983] [INFO] Found 6/6 markers. [2024-01-25 18:48:19,021] [INFO] Query marker FASTA was written to GCF_015708085.1_ASM1570808v1_genomic.fna/markers.fasta [2024-01-25 18:48:19,022] [INFO] Task started: Blastn [2024-01-25 18:48:19,022] [INFO] Running command: blastn -query GCF_015708085.1_ASM1570808v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3bb84ad5-0bd3-4540-bf87-d6fcc1f7a5a0/dqc_reference/reference_markers.fasta -out GCF_015708085.1_ASM1570808v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5 [2024-01-25 18:48:19,824] [INFO] Task succeeded: Blastn [2024-01-25 18:48:19,827] [INFO] Selected 25 target genomes. [2024-01-25 18:48:19,827] [INFO] Target genome list was writen to GCF_015708085.1_ASM1570808v1_genomic.fna/target_genomes.txt [2024-01-25 18:48:19,863] [INFO] Task started: fastANI [2024-01-25 18:48:19,864] [INFO] Running command: fastANI --query /var/lib/cwl/stg7e57ec6d-bf92-4abd-8974-2c7f5670cce7/GCF_015708085.1_ASM1570808v1_genomic.fna.gz --refList GCF_015708085.1_ASM1570808v1_genomic.fna/target_genomes.txt --output GCF_015708085.1_ASM1570808v1_genomic.fna/fastani_result.tsv --threads 1 [2024-01-25 18:48:36,814] [INFO] Task succeeded: fastANI [2024-01-25 18:48:36,815] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3bb84ad5-0bd3-4540-bf87-d6fcc1f7a5a0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt [2024-01-25 18:48:36,815] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3bb84ad5-0bd3-4540-bf87-d6fcc1f7a5a0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt] [2024-01-25 18:48:36,829] [INFO] Found 25 fastANI hits (1 hits with ANI > threshold) [2024-01-25 18:48:36,830] [INFO] The taxonomy check result is classified as 'conclusive'. [2024-01-25 18:48:36,830] [INFO] DFAST Taxonomy check final result -------------------------------------------------------------------------------- organism_name strain accession taxid species_taxid relation_to_type validated ani matched_fragments total_fragments ani_threshold status Arthrobacter terrae strain=Z1-20 GCA_015708085.1 2935737 2935737 type True 100.0 1444 1448 95 conclusive Arthrobacter dokdonellae GCA_003268655.1 2211210 2211210 type True 78.1262 312 1448 95 below_threshold Arthrobacter silviterrae strain=DSM 27180 GCA_011045165.1 2026658 2026658 type True 77.8269 295 1448 95 below_threshold Arthrobacter stackebrandtii strain=DSM 16005 GCA_017876675.1 272161 272161 type True 77.8056 269 1448 95 below_threshold Pseudarthrobacter scleromae strain=CGMCC 1.3601 GCA_014644515.1 158897 158897 type True 77.8012 251 1448 95 below_threshold Arthrobacter ipis strain=IA7 GCA_014694315.1 2716202 2716202 type True 77.6164 248 1448 95 below_threshold Pseudarthrobacter siccitolerans strain=4J27 GCA_001046895.1 861266 861266 type True 77.6119 240 1448 95 below_threshold Pseudarthrobacter phenanthrenivorans strain=Sphe3 GCA_000189535.1 361575 361575 type True 77.6073 232 1448 95 below_threshold Arthrobacter celericrescens strain=NEAU-SA2 GCA_003614925.1 2320851 2320851 type True 77.6043 236 1448 95 below_threshold Arthrobacter ulcerisalmonis GCA_900609065.1 2483813 2483813 type True 77.5868 198 1448 95 below_threshold Pseudarthrobacter sulfonivorans strain=ALL GCA_014712225.1 121292 121292 type True 77.5783 233 1448 95 below_threshold Arthrobacter cupressi strain=DSM 24664 GCA_013409905.1 1045773 1045773 type True 77.5284 248 1448 95 below_threshold Pseudarthrobacter equi strain=IMMIB L-1606 GCA_900105535.1 728066 728066 type True 77.5205 262 1448 95 below_threshold Arthrobacter cupressi strain=CGMCC 1.10783 GCA_900099975.1 1045773 1045773 type True 77.5118 246 1448 95 below_threshold Arthrobacter globiformis strain=NBRC 12137 GCA_000238915.2 1665 1665 type True 77.4911 247 1448 95 below_threshold Arthrobacter silvisoli strain=NEAU-SA1 GCA_003369445.1 2291022 2291022 type True 77.452 230 1448 95 below_threshold Arthrobacter citreus strain=DSM 20133 GCA_009192745.1 1670 1670 type True 77.371 185 1448 95 below_threshold Arthrobacter koreensis strain=DSM 16760 GCA_009193255.1 199136 199136 type True 77.3399 185 1448 95 below_threshold Arthrobacter mobilis strain=E918 GCA_012395835.1 2724944 2724944 type True 77.3342 250 1448 95 below_threshold Arthrobacter jiangjiafuii strain=zg-ZUI227 GCA_018622995.1 2817475 2817475 type True 77.2719 233 1448 95 below_threshold Arthrobacter jiangjiafuii strain=zg-ZUI227 GCA_017898065.1 2817475 2817475 type True 77.2276 230 1448 95 below_threshold Arthrobacter zhaoguopingii strain=J391 GCA_009828595.1 2681491 2681491 type True 77.2023 179 1448 95 below_threshold Arthrobacter tumbae strain=DSM 16406 GCA_016907495.1 163874 163874 type True 76.8796 155 1448 95 below_threshold Kocuria flava strain=HO-9041 GCA_001482365.1 446860 446860 type True 76.5409 125 1448 95 below_threshold Kocuria rosea strain=ATCC 186 GCA_003124035.1 1275 1275 suspected-type True 76.4524 121 1448 95 below_threshold -------------------------------------------------------------------------------- [2024-01-25 18:48:36,831] [INFO] DFAST Taxonomy check result was written to GCF_015708085.1_ASM1570808v1_genomic.fna/tc_result.tsv [2024-01-25 18:48:36,832] [INFO] ===== Taxonomy check completed ===== [2024-01-25 18:48:36,832] [INFO] ===== Start completeness check using CheckM ===== [2024-01-25 18:48:36,832] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3bb84ad5-0bd3-4540-bf87-d6fcc1f7a5a0/dqc_reference/checkm_data [2024-01-25 18:48:36,833] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM [2024-01-25 18:48:36,876] [INFO] Task started: CheckM [2024-01-25 18:48:36,876] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_015708085.1_ASM1570808v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_015708085.1_ASM1570808v1_genomic.fna/checkm_input GCF_015708085.1_ASM1570808v1_genomic.fna/checkm_result [2024-01-25 18:49:11,999] [INFO] Task succeeded: CheckM [2024-01-25 18:49:12,000] [INFO] Completeness check finished. -------------------------------------------------------------------------------- Completeness: 100.00% Contamintation: 4.17% Strain heterogeneity: 0.00% -------------------------------------------------------------------------------- [2024-01-25 18:49:12,018] [INFO] ===== Completeness check finished ===== [2024-01-25 18:49:12,019] [INFO] ===== Start GTDB Search ===== [2024-01-25 18:49:12,019] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_015708085.1_ASM1570808v1_genomic.fna/markers.fasta) [2024-01-25 18:49:12,019] [INFO] Task started: Blastn [2024-01-25 18:49:12,019] [INFO] Running command: blastn -query GCF_015708085.1_ASM1570808v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3bb84ad5-0bd3-4540-bf87-d6fcc1f7a5a0/dqc_reference/reference_markers_gtdb.fasta -out GCF_015708085.1_ASM1570808v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5 [2024-01-25 18:49:13,199] [INFO] Task succeeded: Blastn [2024-01-25 18:49:13,202] [INFO] Selected 24 target genomes. [2024-01-25 18:49:13,203] [INFO] Target genome list was writen to GCF_015708085.1_ASM1570808v1_genomic.fna/target_genomes_gtdb.txt [2024-01-25 18:49:13,220] [INFO] Task started: fastANI [2024-01-25 18:49:13,221] [INFO] Running command: fastANI --query /var/lib/cwl/stg7e57ec6d-bf92-4abd-8974-2c7f5670cce7/GCF_015708085.1_ASM1570808v1_genomic.fna.gz --refList GCF_015708085.1_ASM1570808v1_genomic.fna/target_genomes_gtdb.txt --output GCF_015708085.1_ASM1570808v1_genomic.fna/fastani_result_gtdb.tsv --threads 1 [2024-01-25 18:49:31,067] [INFO] Task succeeded: fastANI [2024-01-25 18:49:31,081] [INFO] Found 24 fastANI hits (1 hits with ANI > circumscription radius) [2024-01-25 18:49:31,081] [INFO] GTDB search result -------------------------------------------------------------------------------- accession gtdb_species ani matched_fragments total_fragments gtdb_taxonomy ani_circumscription_radius mean_intra_species_ani min_intra_species_ani mean_intra_species_af min_intra_species_af num_clustered_genomes status GCF_015708085.1 s__Z1-20 sp015708085 100.0 1444 1448 d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Z1-20 95.0 N/A N/A N/A N/A 1 conclusive GCF_000482545.1 s__Specibacter sp000482545 78.209 371 1448 d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Specibacter 95.0 N/A N/A N/A N/A 1 - GCF_001750145.1 s__Arthrobacter_I sp001750145 77.953 288 1448 d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_I 95.0 N/A N/A N/A N/A 1 - GCF_013359735.1 s__Arthrobacter_I sp013359735 77.8897 268 1448 d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_I 95.0 N/A N/A N/A N/A 1 - GCF_004798705.1 s__Arthrobacter_I sp004798705 77.8651 273 1448 d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_I 95.0 N/A N/A N/A N/A 1 - GCF_003097355.1 s__Arthrobacter_I sp003097355 77.8233 287 1448 d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_I 95.0 95.72 95.72 0.82 0.82 2 - GCF_011045165.1 s__Specibacter silviterrae 77.8037 297 1448 d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Specibacter 95.0 N/A N/A N/A N/A 1 - GCF_000374925.1 s__Arthrobacter_I sp000374925 77.7655 284 1448 d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_I 95.0 97.54 97.54 0.90 0.90 2 - GCF_000876655.1 s__Arthrobacter_I sp000876655 77.7548 252 1448 d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_I 95.0 N/A N/A N/A N/A 1 - GCF_004320525.1 s__Pseudarthrobacter sp004320525 77.736 239 1448 d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Pseudarthrobacter 95.0 N/A N/A N/A N/A 1 - GCF_005937985.2 s__Arthrobacter_I sp005937985 77.7048 273 1448 d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_I 95.0 N/A N/A N/A N/A 1 - GCF_001423745.1 s__Arthrobacter_I sp001423745 77.6605 266 1448 d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_I 95.0 N/A N/A N/A N/A 1 - GCF_005796205.1 s__Pseudarthrobacter sp005796205 77.6539 216 1448 d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Pseudarthrobacter 95.0 N/A N/A N/A N/A 1 - GCF_007858535.1 s__Arthrobacter_I sp007858535 77.6511 290 1448 d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_I 95.0 N/A N/A N/A N/A 1 - GCF_003946885.1 s__Specibacter cremeus 77.6491 311 1448 d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Specibacter 95.0 N/A N/A N/A N/A 1 - GCF_006151685.1 s__Pseudarthrobacter sp006151685 77.6435 237 1448 d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Pseudarthrobacter 95.0 100.00 100.00 1.00 1.00 2 - GCF_001766675.1 s__Arthrobacter_G sp001766675 77.6038 226 1448 d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_G 95.0 N/A N/A N/A N/A 1 - GCF_000374905.1 s__Pseudarthrobacter sp000374905 77.6013 247 1448 d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Pseudarthrobacter 95.0 98.45 96.91 0.92 0.90 5 - GCF_900110595.1 s__Pseudarthrobacter sp900110595 77.5063 259 1448 d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Pseudarthrobacter 95.0 97.13 97.13 0.83 0.83 2 - GCF_000238915.1 s__Arthrobacter globiformis 77.4911 247 1448 d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter 95.0 N/A N/A N/A N/A 1 - GCF_003261175.1 s__Arthrobacter globiformis_A 77.4529 250 1448 d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter 95.0 N/A N/A N/A N/A 1 - GCF_009192745.1 s__Arthrobacter_B citreus 77.371 185 1448 d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_B 95.0 N/A N/A N/A N/A 1 - GCF_009193255.1 s__Arthrobacter_B koreensis 77.3399 185 1448 d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_B 95.0 99.08 99.08 0.97 0.97 2 - GCF_012395835.1 s__Arthrobacter_F mobilis 77.3342 250 1448 d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_F 95.0 N/A N/A N/A N/A 1 - -------------------------------------------------------------------------------- [2024-01-25 18:49:31,083] [INFO] GTDB search result was written to GCF_015708085.1_ASM1570808v1_genomic.fna/result_gtdb.tsv [2024-01-25 18:49:31,083] [INFO] ===== GTDB Search completed ===== [2024-01-25 18:49:31,088] [INFO] DFAST_QC result json was written to GCF_015708085.1_ASM1570808v1_genomic.fna/dqc_result.json [2024-01-25 18:49:31,088] [INFO] DFAST_QC completed! [2024-01-25 18:49:31,088] [INFO] Total running time: 0h1m25s