[2024-01-24 13:17:34,769] [INFO] DFAST_QC pipeline started. [2024-01-24 13:17:34,773] [INFO] DFAST_QC version: 0.5.7 [2024-01-24 13:17:34,773] [INFO] DQC Reference Directory: /var/lib/cwl/stgfb1d4354-9529-480a-83c3-a47ecbcb14fe/dqc_reference [2024-01-24 13:17:36,137] [INFO] ===== Start taxonomy check using ANI ===== [2024-01-24 13:17:36,138] [INFO] Task started: Prodigal [2024-01-24 13:17:36,138] [INFO] Running command: gunzip -c /var/lib/cwl/stg834a375a-1196-499e-8fb1-26b128021ac9/GCF_000950575.1_ASM95057v1_genomic.fna.gz | prodigal -d GCF_000950575.1_ASM95057v1_genomic.fna/cds.fna -a GCF_000950575.1_ASM95057v1_genomic.fna/protein.faa -g 11 -q > /dev/null [2024-01-24 13:17:47,126] [INFO] Task succeeded: Prodigal [2024-01-24 13:17:47,126] [INFO] Task started: HMMsearch [2024-01-24 13:17:47,126] [INFO] Running command: hmmsearch --tblout GCF_000950575.1_ASM95057v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfb1d4354-9529-480a-83c3-a47ecbcb14fe/dqc_reference/reference_markers.hmm GCF_000950575.1_ASM95057v1_genomic.fna/protein.faa > /dev/null [2024-01-24 13:17:47,385] [INFO] Task succeeded: HMMsearch [2024-01-24 13:17:47,387] [INFO] Found 6/6 markers. [2024-01-24 13:17:47,422] [INFO] Query marker FASTA was written to GCF_000950575.1_ASM95057v1_genomic.fna/markers.fasta [2024-01-24 13:17:47,423] [INFO] Task started: Blastn [2024-01-24 13:17:47,423] [INFO] Running command: blastn -query GCF_000950575.1_ASM95057v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfb1d4354-9529-480a-83c3-a47ecbcb14fe/dqc_reference/reference_markers.fasta -out GCF_000950575.1_ASM95057v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5 [2024-01-24 13:17:48,295] [INFO] Task succeeded: Blastn [2024-01-24 13:17:48,298] [INFO] Selected 24 target genomes. [2024-01-24 13:17:48,299] [INFO] Target genome list was writen to GCF_000950575.1_ASM95057v1_genomic.fna/target_genomes.txt [2024-01-24 13:17:48,307] [INFO] Task started: fastANI [2024-01-24 13:17:48,308] [INFO] Running command: fastANI --query /var/lib/cwl/stg834a375a-1196-499e-8fb1-26b128021ac9/GCF_000950575.1_ASM95057v1_genomic.fna.gz --refList GCF_000950575.1_ASM95057v1_genomic.fna/target_genomes.txt --output GCF_000950575.1_ASM95057v1_genomic.fna/fastani_result.tsv --threads 1 [2024-01-24 13:18:03,076] [INFO] Task succeeded: fastANI [2024-01-24 13:18:03,076] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfb1d4354-9529-480a-83c3-a47ecbcb14fe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt [2024-01-24 13:18:03,077] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfb1d4354-9529-480a-83c3-a47ecbcb14fe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt] [2024-01-24 13:18:03,096] [INFO] Found 24 fastANI hits (1 hits with ANI > threshold) [2024-01-24 13:18:03,096] [INFO] The taxonomy check result is classified as 'conclusive'. [2024-01-24 13:18:03,096] [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 lacuslunae strain=IHBB 11108 GCA_000950575.1 1618207 1618207 type True 100.0 1198 1199 95 conclusive Psychromicrobium silvestre strain=DSM 102047 GCA_013408295.1 1645614 1645614 type True 78.783 402 1199 95 below_threshold Renibacterium salmoninarum strain=ATCC 33209 GCA_000018885.1 1646 1646 type True 78.5591 179 1199 95 below_threshold Paenarthrobacter nicotinovorans strain=DSM 420 GCA_017876445.1 29320 29320 suspected-type True 78.3997 116 1199 95 below_threshold Paenarthrobacter nicotinovorans strain=ATCC 49919 GCA_021919345.1 29320 29320 suspected-type True 78.3042 117 1199 95 below_threshold Arthrobacter cupressi strain=DSM 24664 GCA_013409905.1 1045773 1045773 type True 78.1254 140 1199 95 below_threshold Arthrobacter sunyaminii strain=zg-ZUI122 GCA_018866305.1 2816859 2816859 type True 77.9282 108 1199 95 below_threshold Arthrobacter globiformis strain=NBRC 12137 GCA_000238915.2 1665 1665 type True 77.9246 134 1199 95 below_threshold Arthrobacter yangruifuii strain=785 GCA_009192775.1 2606616 2606616 type True 77.8886 112 1199 95 below_threshold Arthrobacter sunyaminii strain=zg-ZUI122 GCA_017353495.1 2816859 2816859 type True 77.8459 108 1199 95 below_threshold Galactobacter caseinivorans strain=JZ R-183 GCA_003640665.1 2676123 2676123 type True 77.7864 55 1199 95 below_threshold Arthrobacter ulcerisalmonis GCA_900609065.1 2483813 2483813 type True 77.7782 127 1199 95 below_threshold Paenarthrobacter nicotinovorans strain=JCM 3874 GCA_014648735.1 29320 29320 suspected-type True 77.7735 114 1199 95 below_threshold Pseudarthrobacter scleromae strain=CGMCC 1.3601 GCA_014644515.1 158897 158897 type True 77.7685 127 1199 95 below_threshold Arthrobacter cupressi strain=CGMCC 1.10783 GCA_900099975.1 1045773 1045773 type True 77.7325 142 1199 95 below_threshold Arthrobacter silviterrae strain=DSM 27180 GCA_011045165.1 2026658 2026658 type True 77.6505 118 1199 95 below_threshold Pseudarthrobacter enclensis strain=NIO-1008 GCA_900094675.1 993070 993070 type True 77.5703 133 1199 95 below_threshold Pseudarthrobacter enclensis strain=NIO-1008 GCA_001457025.1 993070 993070 type True 77.5703 133 1199 95 below_threshold Arthrobacter silvisoli strain=NEAU-SA1 GCA_003369445.1 2291022 2291022 type True 77.559 148 1199 95 below_threshold Arthrobacter jiangjiafuii strain=zg-ZUI227 GCA_018622995.1 2817475 2817475 type True 77.5325 127 1199 95 below_threshold Arthrobacter gallicola strain=Sa2CUA1 GCA_014836775.1 2762225 2762225 type True 77.4898 117 1199 95 below_threshold Acaricomes phytoseiuli strain=DSM 14247 GCA_000376245.1 291968 291968 type True 77.3981 155 1199 95 below_threshold Arthrobacter jiangjiafuii strain=zg-ZUI227 GCA_017898065.1 2817475 2817475 type True 77.3371 126 1199 95 below_threshold Arthrobacter mobilis strain=E918 GCA_012395835.1 2724944 2724944 type True 77.1539 131 1199 95 below_threshold -------------------------------------------------------------------------------- [2024-01-24 13:18:03,098] [INFO] DFAST Taxonomy check result was written to GCF_000950575.1_ASM95057v1_genomic.fna/tc_result.tsv [2024-01-24 13:18:03,099] [INFO] ===== Taxonomy check completed ===== [2024-01-24 13:18:03,099] [INFO] ===== Start completeness check using CheckM ===== [2024-01-24 13:18:03,099] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfb1d4354-9529-480a-83c3-a47ecbcb14fe/dqc_reference/checkm_data [2024-01-24 13:18:03,100] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM [2024-01-24 13:18:03,139] [INFO] Task started: CheckM [2024-01-24 13:18:03,139] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000950575.1_ASM95057v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000950575.1_ASM95057v1_genomic.fna/checkm_input GCF_000950575.1_ASM95057v1_genomic.fna/checkm_result [2024-01-24 13:18:39,962] [INFO] Task succeeded: CheckM [2024-01-24 13:18:39,964] [INFO] Completeness check finished. -------------------------------------------------------------------------------- Completeness: 100.00% Contamintation: 0.00% Strain heterogeneity: 0.00% -------------------------------------------------------------------------------- [2024-01-24 13:18:39,998] [INFO] ===== Completeness check finished ===== [2024-01-24 13:18:39,998] [INFO] ===== Start GTDB Search ===== [2024-01-24 13:18:39,999] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000950575.1_ASM95057v1_genomic.fna/markers.fasta) [2024-01-24 13:18:39,999] [INFO] Task started: Blastn [2024-01-24 13:18:39,999] [INFO] Running command: blastn -query GCF_000950575.1_ASM95057v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfb1d4354-9529-480a-83c3-a47ecbcb14fe/dqc_reference/reference_markers_gtdb.fasta -out GCF_000950575.1_ASM95057v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5 [2024-01-24 13:18:41,275] [INFO] Task succeeded: Blastn [2024-01-24 13:18:41,281] [INFO] Selected 22 target genomes. [2024-01-24 13:18:41,282] [INFO] Target genome list was writen to GCF_000950575.1_ASM95057v1_genomic.fna/target_genomes_gtdb.txt [2024-01-24 13:18:41,331] [INFO] Task started: fastANI [2024-01-24 13:18:41,332] [INFO] Running command: fastANI --query /var/lib/cwl/stg834a375a-1196-499e-8fb1-26b128021ac9/GCF_000950575.1_ASM95057v1_genomic.fna.gz --refList GCF_000950575.1_ASM95057v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000950575.1_ASM95057v1_genomic.fna/fastani_result_gtdb.tsv --threads 1 [2024-01-24 13:18:56,569] [INFO] Task succeeded: fastANI [2024-01-24 13:18:56,591] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius) [2024-01-24 13:18:56,592] [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_000950575.1 s__Psychromicrobium lacuslunae 100.0 1197 1199 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_013408295.1 s__Psychromicrobium silvestre 78.8159 402 1199 d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Psychromicrobium 95.0 N/A N/A N/A N/A 1 - GCF_004028095.1 s__Paenarthrobacter ureafaciens 78.538 112 1199 d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Paenarthrobacter 95.0 98.49 97.15 0.88 0.82 19 - GCF_000018885.1 s__Renibacterium salmoninarum 78.4964 179 1199 d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Renibacterium 95.0 99.99 99.99 1.00 1.00 3 - GCF_002953935.1 s__Pseudarthrobacter sp002953935 78.2592 131 1199 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 78.1382 167 1199 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_001641125.1 s__Pseudarthrobacter sp001641125 78.0796 127 1199 d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Pseudarthrobacter 95.0 N/A N/A N/A N/A 1 - GCA_017419405.1 s__Renibacterium sp005809195 78.0526 298 1199 d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Renibacterium 95.0 99.49 97.56 0.99 0.96 6 - GCF_001484605.1 s__Pseudarthrobacter sulfonivorans_A 78.0422 141 1199 d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Pseudarthrobacter 95.0 N/A N/A N/A N/A 1 - GCF_018531425.1 s__DKR-5 sp018531425 78.0055 138 1199 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_000238915.1 s__Arthrobacter globiformis 77.9246 134 1199 d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter 95.0 N/A N/A N/A N/A 1 - GCF_009192775.1 s__Arthrobacter_B yangruifuii 77.8587 113 1199 d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_B 95.0 97.52 97.52 0.93 0.93 2 - GCF_000332815.1 s__Pseudarthrobacter nitrophenolicus 77.7863 115 1199 d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Pseudarthrobacter 95.0 97.22 97.22 0.86 0.86 2 - GCF_000514015.1 s__Paenarthrobacter nicotinovorans_A 77.784 116 1199 d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Paenarthrobacter 95.0 98.33 98.25 0.94 0.92 3 - GCF_900609065.1 s__Pseudarthrobacter ulcerisalmonis 77.7527 128 1199 d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Pseudarthrobacter 95.0 N/A N/A N/A N/A 1 - GCF_013376095.1 s__Specibacter sp013376095 77.7391 125 1199 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 77.723 149 1199 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_018622995.1 s__Arthrobacter_B sp018622995 77.662 128 1199 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_004798705.1 s__Arthrobacter_I sp004798705 77.6369 157 1199 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_003287955.1 s__Pseudarthrobacter sp003287955 77.5819 131 1199 d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Pseudarthrobacter 95.0 N/A N/A N/A N/A 1 - GCF_003369445.1 s__Arthrobacter_G silvisoli 77.559 148 1199 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_014836775.1 s__Arthrobacter_B sp014836775 77.4898 117 1199 d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_B 95.0 N/A N/A N/A N/A 1 - -------------------------------------------------------------------------------- [2024-01-24 13:18:56,595] [INFO] GTDB search result was written to GCF_000950575.1_ASM95057v1_genomic.fna/result_gtdb.tsv [2024-01-24 13:18:56,596] [INFO] ===== GTDB Search completed ===== [2024-01-24 13:18:56,603] [INFO] DFAST_QC result json was written to GCF_000950575.1_ASM95057v1_genomic.fna/dqc_result.json [2024-01-24 13:18:56,604] [INFO] DFAST_QC completed! [2024-01-24 13:18:56,604] [INFO] Total running time: 0h1m22s