[2024-01-25 18:02:05,664] [INFO] DFAST_QC pipeline started. [2024-01-25 18:02:05,666] [INFO] DFAST_QC version: 0.5.7 [2024-01-25 18:02:05,666] [INFO] DQC Reference Directory: /var/lib/cwl/stgc44e8880-acda-4189-877a-53831b5cfc5d/dqc_reference [2024-01-25 18:02:06,790] [INFO] ===== Start taxonomy check using ANI ===== [2024-01-25 18:02:06,790] [INFO] Task started: Prodigal [2024-01-25 18:02:06,791] [INFO] Running command: gunzip -c /var/lib/cwl/stg6daef812-e689-452e-ab85-760ed1b20d75/GCF_013408295.1_ASM1340829v1_genomic.fna.gz | prodigal -d GCF_013408295.1_ASM1340829v1_genomic.fna/cds.fna -a GCF_013408295.1_ASM1340829v1_genomic.fna/protein.faa -g 11 -q > /dev/null [2024-01-25 18:02:14,984] [INFO] Task succeeded: Prodigal [2024-01-25 18:02:14,985] [INFO] Task started: HMMsearch [2024-01-25 18:02:14,985] [INFO] Running command: hmmsearch --tblout GCF_013408295.1_ASM1340829v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc44e8880-acda-4189-877a-53831b5cfc5d/dqc_reference/reference_markers.hmm GCF_013408295.1_ASM1340829v1_genomic.fna/protein.faa > /dev/null [2024-01-25 18:02:15,203] [INFO] Task succeeded: HMMsearch [2024-01-25 18:02:15,204] [INFO] Found 6/6 markers. [2024-01-25 18:02:15,230] [INFO] Query marker FASTA was written to GCF_013408295.1_ASM1340829v1_genomic.fna/markers.fasta [2024-01-25 18:02:15,230] [INFO] Task started: Blastn [2024-01-25 18:02:15,230] [INFO] Running command: blastn -query GCF_013408295.1_ASM1340829v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc44e8880-acda-4189-877a-53831b5cfc5d/dqc_reference/reference_markers.fasta -out GCF_013408295.1_ASM1340829v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5 [2024-01-25 18:02:16,023] [INFO] Task succeeded: Blastn [2024-01-25 18:02:16,026] [INFO] Selected 23 target genomes. [2024-01-25 18:02:16,026] [INFO] Target genome list was writen to GCF_013408295.1_ASM1340829v1_genomic.fna/target_genomes.txt [2024-01-25 18:02:16,034] [INFO] Task started: fastANI [2024-01-25 18:02:16,035] [INFO] Running command: fastANI --query /var/lib/cwl/stg6daef812-e689-452e-ab85-760ed1b20d75/GCF_013408295.1_ASM1340829v1_genomic.fna.gz --refList GCF_013408295.1_ASM1340829v1_genomic.fna/target_genomes.txt --output GCF_013408295.1_ASM1340829v1_genomic.fna/fastani_result.tsv --threads 1 [2024-01-25 18:02:30,909] [INFO] Task succeeded: fastANI [2024-01-25 18:02:30,909] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc44e8880-acda-4189-877a-53831b5cfc5d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt [2024-01-25 18:02:30,910] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc44e8880-acda-4189-877a-53831b5cfc5d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt] [2024-01-25 18:02:30,922] [INFO] Found 22 fastANI hits (1 hits with ANI > threshold) [2024-01-25 18:02:30,922] [INFO] The taxonomy check result is classified as 'conclusive'. [2024-01-25 18:02:30,922] [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 Psychromicrobium silvestre strain=DSM 102047 GCA_013408295.1 1645614 1645614 type True 100.0 1052 1054 95 conclusive Psychromicrobium lacuslunae strain=IHBB 11108 GCA_000950575.1 1618207 1618207 type True 78.8802 399 1054 95 below_threshold Renibacterium salmoninarum strain=ATCC 33209 GCA_000018885.1 1646 1646 type True 78.5353 179 1054 95 below_threshold Paenarthrobacter ilicis strain=DSM 20138 GCA_016907545.1 43665 43665 type True 78.4482 131 1054 95 below_threshold Pseudarthrobacter equi strain=IMMIB L-1606 GCA_900105535.1 728066 728066 type True 78.0786 149 1054 95 below_threshold Arthrobacter dokdonellae GCA_003268655.1 2211210 2211210 type True 77.9893 159 1054 95 below_threshold Arthrobacter jiangjiafuii strain=zg-ZUI227 GCA_018622995.1 2817475 2817475 type True 77.9735 140 1054 95 below_threshold Paeniglutamicibacter psychrophenolicus strain=DSM 15454 GCA_017876575.1 257454 257454 type True 77.8974 118 1054 95 below_threshold Arthrobacter tumbae strain=DSM 16406 GCA_016907495.1 163874 163874 type True 77.8756 109 1054 95 below_threshold Arthrobacter gallicola strain=Sa2CUA1 GCA_014836775.1 2762225 2762225 type True 77.7476 127 1054 95 below_threshold Arthrobacter pascens strain=DSM 20545 GCA_017052465.1 1677 1677 type True 77.6923 149 1054 95 below_threshold Arthrobacter ulcerisalmonis GCA_900609065.1 2483813 2483813 type True 77.6822 136 1054 95 below_threshold Arthrobacter cupressi strain=DSM 24664 GCA_013409905.1 1045773 1045773 type True 77.631 181 1054 95 below_threshold Arthrobacter terricola strain=JH1-1 GCA_004354015.1 2547396 2547396 type True 77.5152 121 1054 95 below_threshold Pseudarthrobacter siccitolerans strain=4J27 GCA_001046895.1 861266 861266 type True 77.4383 150 1054 95 below_threshold Arthrobacter jiangjiafuii strain=zg-ZUI227 GCA_017898065.1 2817475 2817475 type True 77.4312 131 1054 95 below_threshold Arthrobacter wenxiniae strain=AETb3-4 GCA_013376105.1 2713570 2713570 type True 77.3699 148 1054 95 below_threshold Arthrobacter cupressi strain=CGMCC 1.10783 GCA_900099975.1 1045773 1045773 type True 77.3629 177 1054 95 below_threshold Microbacterium cremeum strain=NY27 GCA_015277855.1 2782169 2782169 type True 77.1939 51 1054 95 below_threshold Arthrobacter ruber strain=MDB1-42 GCA_002954225.1 1258893 1258893 type True 77.1836 117 1054 95 below_threshold Nesterenkonia ebinurensis strain=MD2 GCA_008711175.1 2608252 2608252 type True 76.6886 62 1054 95 below_threshold Sinomonas notoginsengisoli strain=KCTC 29237 GCA_021554725.1 1457311 1457311 type True 76.6728 94 1054 95 below_threshold -------------------------------------------------------------------------------- [2024-01-25 18:02:30,924] [INFO] DFAST Taxonomy check result was written to GCF_013408295.1_ASM1340829v1_genomic.fna/tc_result.tsv [2024-01-25 18:02:30,924] [INFO] ===== Taxonomy check completed ===== [2024-01-25 18:02:30,924] [INFO] ===== Start completeness check using CheckM ===== [2024-01-25 18:02:30,925] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc44e8880-acda-4189-877a-53831b5cfc5d/dqc_reference/checkm_data [2024-01-25 18:02:30,925] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM [2024-01-25 18:02:30,958] [INFO] Task started: CheckM [2024-01-25 18:02:30,958] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013408295.1_ASM1340829v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013408295.1_ASM1340829v1_genomic.fna/checkm_input GCF_013408295.1_ASM1340829v1_genomic.fna/checkm_result [2024-01-25 18:02:58,875] [INFO] Task succeeded: CheckM [2024-01-25 18:02:58,876] [INFO] Completeness check finished. -------------------------------------------------------------------------------- Completeness: 100.00% Contamintation: 0.00% Strain heterogeneity: 0.00% -------------------------------------------------------------------------------- [2024-01-25 18:02:58,897] [INFO] ===== Completeness check finished ===== [2024-01-25 18:02:58,897] [INFO] ===== Start GTDB Search ===== [2024-01-25 18:02:58,897] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013408295.1_ASM1340829v1_genomic.fna/markers.fasta) [2024-01-25 18:02:58,897] [INFO] Task started: Blastn [2024-01-25 18:02:58,897] [INFO] Running command: blastn -query GCF_013408295.1_ASM1340829v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc44e8880-acda-4189-877a-53831b5cfc5d/dqc_reference/reference_markers_gtdb.fasta -out GCF_013408295.1_ASM1340829v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5 [2024-01-25 18:03:00,105] [INFO] Task succeeded: Blastn [2024-01-25 18:03:00,108] [INFO] Selected 21 target genomes. [2024-01-25 18:03:00,108] [INFO] Target genome list was writen to GCF_013408295.1_ASM1340829v1_genomic.fna/target_genomes_gtdb.txt [2024-01-25 18:03:00,127] [INFO] Task started: fastANI [2024-01-25 18:03:00,127] [INFO] Running command: fastANI --query /var/lib/cwl/stg6daef812-e689-452e-ab85-760ed1b20d75/GCF_013408295.1_ASM1340829v1_genomic.fna.gz --refList GCF_013408295.1_ASM1340829v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013408295.1_ASM1340829v1_genomic.fna/fastani_result_gtdb.tsv --threads 1 [2024-01-25 18:03:14,131] [INFO] Task succeeded: fastANI [2024-01-25 18:03:14,143] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius) [2024-01-25 18:03:14,144] [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_013408295.1 s__Psychromicrobium silvestre 100.0 1051 1054 d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Psychromicrobium 95.0 N/A N/A N/A N/A 1 conclusive GCF_000950575.1 s__Psychromicrobium lacuslunae 78.8802 399 1054 d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Psychromicrobium 95.0 N/A N/A N/A N/A 1 - GCF_000018885.1 s__Renibacterium salmoninarum 78.5353 179 1054 d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Renibacterium 95.0 99.99 99.99 1.00 1.00 3 - GCA_017419405.1 s__Renibacterium sp005809195 78.2275 320 1054 d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Renibacterium 95.0 99.49 97.56 0.99 0.96 6 - GCF_004320525.1 s__Pseudarthrobacter sp004320525 78.0003 149 1054 d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Pseudarthrobacter 95.0 N/A N/A N/A N/A 1 - GCF_013359735.1 s__Arthrobacter_I sp013359735 77.9873 178 1054 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_001307035.1 s__Arthrobacter_B sp001307035 77.9271 127 1054 d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_B 95.0 98.39 98.39 0.92 0.92 2 - GCF_018622995.1 s__Arthrobacter_B sp018622995 77.913 139 1054 d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_B 95.0 99.13 98.27 0.96 0.92 3 - GCF_017876575.1 s__Paeniglutamicibacter psychrophenolicus 77.8975 118 1054 d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Paeniglutamicibacter 95.0 N/A N/A N/A N/A 1 - GCF_018531425.1 s__DKR-5 sp018531425 77.8473 171 1054 d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__DKR-5 95.0 N/A N/A N/A N/A 1 - GCF_001428365.1 s__Arthrobacter_I sp001428365 77.8403 176 1054 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_005937985.2 s__Arthrobacter_I sp005937985 77.7962 186 1054 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_001512305.1 s__Arthrobacter_I sp001512305 77.7671 166 1054 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_014836775.1 s__Arthrobacter_B sp014836775 77.7476 127 1054 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_900537115.1 s__Pseudarthrobacter sp900537115 77.7473 143 1054 d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Pseudarthrobacter 95.0 N/A N/A N/A N/A 1 - GCA_900016675.1 s__Arthrobacter_B saudimassiliensis 77.746 155 1054 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_003287975.1 s__Paeniglutamicibacter sp003287975 77.7248 113 1054 d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Paeniglutamicibacter 95.0 N/A N/A N/A N/A 1 - GCF_017052465.1 s__Arthrobacter pascens 77.6979 148 1054 d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter 95.0 N/A N/A N/A N/A 1 - GCF_018224015.1 s__Arthrobacter_I sp018224015 77.5415 162 1054 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_001046895.1 s__Pseudarthrobacter siccitolerans 77.4383 150 1054 d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Pseudarthrobacter 95.0 N/A N/A N/A N/A 1 - GCF_008580665.1 s__Zafaria cholistanensis 77.3143 120 1054 d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Zafaria 95.0 N/A N/A N/A N/A 1 - -------------------------------------------------------------------------------- [2024-01-25 18:03:14,145] [INFO] GTDB search result was written to GCF_013408295.1_ASM1340829v1_genomic.fna/result_gtdb.tsv [2024-01-25 18:03:14,146] [INFO] ===== GTDB Search completed ===== [2024-01-25 18:03:14,149] [INFO] DFAST_QC result json was written to GCF_013408295.1_ASM1340829v1_genomic.fna/dqc_result.json [2024-01-25 18:03:14,149] [INFO] DFAST_QC completed! [2024-01-25 18:03:14,150] [INFO] Total running time: 0h1m8s