[2024-01-24 14:15:00,905] [INFO] DFAST_QC pipeline started. [2024-01-24 14:15:00,907] [INFO] DFAST_QC version: 0.5.7 [2024-01-24 14:15:00,907] [INFO] DQC Reference Directory: /var/lib/cwl/stg02212ced-ae1f-4620-afb1-9338f49cf2f1/dqc_reference [2024-01-24 14:15:02,391] [INFO] ===== Start taxonomy check using ANI ===== [2024-01-24 14:15:02,392] [INFO] Task started: Prodigal [2024-01-24 14:15:02,393] [INFO] Running command: gunzip -c /var/lib/cwl/stg96f9fa75-c9a0-4c3a-82d0-94f39c2c10df/GCF_900142685.1_IMG-taxon_2700988709_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900142685.1_IMG-taxon_2700988709_annotated_assembly_genomic.fna/cds.fna -a GCF_900142685.1_IMG-taxon_2700988709_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null [2024-01-24 14:15:23,931] [INFO] Task succeeded: Prodigal [2024-01-24 14:15:23,932] [INFO] Task started: HMMsearch [2024-01-24 14:15:23,932] [INFO] Running command: hmmsearch --tblout GCF_900142685.1_IMG-taxon_2700988709_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg02212ced-ae1f-4620-afb1-9338f49cf2f1/dqc_reference/reference_markers.hmm GCF_900142685.1_IMG-taxon_2700988709_annotated_assembly_genomic.fna/protein.faa > /dev/null [2024-01-24 14:15:24,294] [INFO] Task succeeded: HMMsearch [2024-01-24 14:15:24,296] [INFO] Found 6/6 markers. [2024-01-24 14:15:24,348] [INFO] Query marker FASTA was written to GCF_900142685.1_IMG-taxon_2700988709_annotated_assembly_genomic.fna/markers.fasta [2024-01-24 14:15:24,348] [INFO] Task started: Blastn [2024-01-24 14:15:24,348] [INFO] Running command: blastn -query GCF_900142685.1_IMG-taxon_2700988709_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg02212ced-ae1f-4620-afb1-9338f49cf2f1/dqc_reference/reference_markers.fasta -out GCF_900142685.1_IMG-taxon_2700988709_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5 [2024-01-24 14:15:25,076] [INFO] Task succeeded: Blastn [2024-01-24 14:15:25,081] [INFO] Selected 19 target genomes. [2024-01-24 14:15:25,081] [INFO] Target genome list was writen to GCF_900142685.1_IMG-taxon_2700988709_annotated_assembly_genomic.fna/target_genomes.txt [2024-01-24 14:15:25,089] [INFO] Task started: fastANI [2024-01-24 14:15:25,089] [INFO] Running command: fastANI --query /var/lib/cwl/stg96f9fa75-c9a0-4c3a-82d0-94f39c2c10df/GCF_900142685.1_IMG-taxon_2700988709_annotated_assembly_genomic.fna.gz --refList GCF_900142685.1_IMG-taxon_2700988709_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900142685.1_IMG-taxon_2700988709_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1 [2024-01-24 14:15:49,088] [INFO] Task succeeded: fastANI [2024-01-24 14:15:49,089] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg02212ced-ae1f-4620-afb1-9338f49cf2f1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt [2024-01-24 14:15:49,090] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg02212ced-ae1f-4620-afb1-9338f49cf2f1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt] [2024-01-24 14:15:49,106] [INFO] Found 19 fastANI hits (2 hits with ANI > threshold) [2024-01-24 14:15:49,107] [INFO] The taxonomy check result is classified as 'conclusive'. [2024-01-24 14:15:49,107] [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 Flavobacterium chilense strain=DSM 24724 GCA_900142685.1 946677 946677 type True 100.0 2021 2024 95 conclusive Flavobacterium chilense strain=LMG 26360 GCA_001602525.1 946677 946677 type True 99.9957 1958 2024 95 conclusive Flavobacterium bizetiae strain=CIP 105534 GCA_904425415.1 2704140 2704140 type True 84.7351 1249 2024 95 below_threshold Flavobacterium bizetiae strain=CIP 105534 GCA_902804475.1 2704140 2704140 type True 84.7348 1221 2024 95 below_threshold Flavobacterium aquidurense strain=DSM 18293 GCA_002217195.1 362413 362413 type True 84.1852 1227 2024 95 below_threshold Flavobacterium piscis strain=CCUG 60099 GCA_002222045.1 1114874 1114874 type True 84.1731 1175 2024 95 below_threshold Flavobacterium piscis strain=CCUG 60099 GCA_001686925.1 1114874 1114874 type True 84.1438 1206 2024 95 below_threshold Flavobacterium psychroterrae strain=CCM 8827 GCA_018380615.1 2133767 2133767 type True 84.12 1274 2024 95 below_threshold Flavobacterium panici GCA_903819335.1 2654843 2654843 type True 83.8894 1158 2024 95 below_threshold Flavobacterium soyae strain=SCIV07 GCA_021245985.1 2903098 2903098 type True 83.7193 1106 2024 95 below_threshold Flavobacterium plurextorum strain=CCUG 60112 GCA_002217395.1 1114867 1114867 type True 83.6527 1097 2024 95 below_threshold Flavobacterium oncorhynchi strain=CCUG 59446 GCA_002217355.1 728056 728056 type True 83.5477 1113 2024 95 below_threshold Flavobacterium collinsii GCA_902804485.1 1114861 1114861 type True 83.133 1144 2024 95 below_threshold Flavobacterium tyrosinilyticum strain=KCTC 42726 GCA_023656565.1 1658740 1658740 type True 82.5805 1093 2024 95 below_threshold Flavobacterium quisquiliarum strain=EA-12 GCA_019308285.1 1834436 1834436 type True 82.5616 1120 2024 95 below_threshold Flavobacterium endoglycinae strain=BB8 GCA_017352115.1 2816357 2816357 type True 82.3126 1103 2024 95 below_threshold Flavobacterium phragmitis strain=CGMCC 1.10370 GCA_900112575.1 739143 739143 type True 82.2979 1090 2024 95 below_threshold Flavobacterium panacis strain=DCY106 GCA_024649945.1 2962567 2962567 type True 82.1181 1110 2024 95 below_threshold Flavobacterium sediminilitoris strain=YSM-43 GCA_023008245.1 2024526 2024526 type True 76.7938 239 2024 95 below_threshold -------------------------------------------------------------------------------- [2024-01-24 14:15:49,108] [INFO] DFAST Taxonomy check result was written to GCF_900142685.1_IMG-taxon_2700988709_annotated_assembly_genomic.fna/tc_result.tsv [2024-01-24 14:15:49,109] [INFO] ===== Taxonomy check completed ===== [2024-01-24 14:15:49,109] [INFO] ===== Start completeness check using CheckM ===== [2024-01-24 14:15:49,109] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg02212ced-ae1f-4620-afb1-9338f49cf2f1/dqc_reference/checkm_data [2024-01-24 14:15:49,110] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM [2024-01-24 14:15:49,167] [INFO] Task started: CheckM [2024-01-24 14:15:49,167] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900142685.1_IMG-taxon_2700988709_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900142685.1_IMG-taxon_2700988709_annotated_assembly_genomic.fna/checkm_input GCF_900142685.1_IMG-taxon_2700988709_annotated_assembly_genomic.fna/checkm_result [2024-01-24 14:16:47,866] [INFO] Task succeeded: CheckM [2024-01-24 14:16:47,868] [INFO] Completeness check finished. -------------------------------------------------------------------------------- Completeness: 100.00% Contamintation: 0.00% Strain heterogeneity: 0.00% -------------------------------------------------------------------------------- [2024-01-24 14:16:47,894] [INFO] ===== Completeness check finished ===== [2024-01-24 14:16:47,895] [INFO] ===== Start GTDB Search ===== [2024-01-24 14:16:47,895] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900142685.1_IMG-taxon_2700988709_annotated_assembly_genomic.fna/markers.fasta) [2024-01-24 14:16:47,895] [INFO] Task started: Blastn [2024-01-24 14:16:47,896] [INFO] Running command: blastn -query GCF_900142685.1_IMG-taxon_2700988709_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg02212ced-ae1f-4620-afb1-9338f49cf2f1/dqc_reference/reference_markers_gtdb.fasta -out GCF_900142685.1_IMG-taxon_2700988709_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5 [2024-01-24 14:16:48,974] [INFO] Task succeeded: Blastn [2024-01-24 14:16:48,978] [INFO] Selected 24 target genomes. [2024-01-24 14:16:48,978] [INFO] Target genome list was writen to GCF_900142685.1_IMG-taxon_2700988709_annotated_assembly_genomic.fna/target_genomes_gtdb.txt [2024-01-24 14:16:48,990] [INFO] Task started: fastANI [2024-01-24 14:16:48,991] [INFO] Running command: fastANI --query /var/lib/cwl/stg96f9fa75-c9a0-4c3a-82d0-94f39c2c10df/GCF_900142685.1_IMG-taxon_2700988709_annotated_assembly_genomic.fna.gz --refList GCF_900142685.1_IMG-taxon_2700988709_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900142685.1_IMG-taxon_2700988709_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1 [2024-01-24 14:17:19,965] [INFO] Task succeeded: fastANI [2024-01-24 14:17:19,989] [INFO] Found 24 fastANI hits (1 hits with ANI > circumscription radius) [2024-01-24 14:17:19,990] [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_001602525.1 s__Flavobacterium chilense 99.9829 1959 2024 d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium 95.0 98.30 96.61 0.93 0.86 3 conclusive GCF_001422725.1 s__Flavobacterium sp001422725 84.607 1272 2024 d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium 95.0 N/A N/A N/A N/A 1 - GCF_001975985.1 s__Flavobacterium sp001975985 84.5435 1298 2024 d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium 95.0 N/A N/A N/A N/A 1 - GCF_009664855.1 s__Flavobacterium sp009664855 84.3449 1250 2024 d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium 95.0 98.90 98.90 0.89 0.89 2 - GCA_900129595.1 s__Flavobacterium frigidimaris 84.2098 1230 2024 d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium 95.0 99.99 99.99 1.00 1.00 2 - GCF_002754195.1 s__Flavobacterium sp002754195 84.0479 1237 2024 d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium 95.0 N/A N/A N/A N/A 1 - GCF_004339525.1 s__Flavobacterium sp004339525 83.9673 1243 2024 d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium 95.0 99.99 99.99 1.00 1.00 2 - GCF_006438875.1 s__Flavobacterium pectinovorum_A 83.9067 1250 2024 d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium 95.0 N/A N/A N/A N/A 1 - GCF_003217415.1 s__Flavobacterium sp003217415 83.8154 1214 2024 d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium 95.0 99.56 98.67 0.98 0.94 4 - GCF_002210235.1 s__Flavobacterium sp002210235 83.7895 1173 2024 d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium 95.0 98.80 96.54 0.96 0.91 4 - GCF_900129795.1 s__Flavobacterium sp900129795 83.7726 1167 2024 d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium 95.0 99.99 99.99 0.98 0.98 2 - GCA_002482975.1 s__Flavobacterium sp002482975 83.6849 1178 2024 d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium 95.0 N/A N/A N/A N/A 1 - GCF_002217395.1 s__Flavobacterium plurextorum 83.6503 1098 2024 d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium 95.0 98.27 98.27 0.92 0.92 2 - GCF_004119495.1 s__Flavobacterium sp004119495 83.5767 1071 2024 d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium 95.0 N/A N/A N/A N/A 1 - GCF_001879205.1 s__Flavobacterium johnsoniae_A 83.5496 1198 2024 d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium 95.0 N/A N/A N/A N/A 1 - GCF_000745775.1 s__Flavobacterium sp000745775 83.2282 1068 2024 d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium 95.0 N/A N/A N/A N/A 1 - GCF_900182645.1 s__Flavobacterium resistens 83.1757 1067 2024 d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium 95.0 99.98 99.98 1.00 1.00 2 - GCF_018383905.1 s__Flavobacterium branchiicola 83.0469 1144 2024 d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium 95.0 N/A N/A N/A N/A 1 - GCF_004368785.1 s__Flavobacterium sp004368785 82.7386 1120 2024 d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium 95.0 N/A N/A N/A N/A 1 - GCF_003105115.1 s__Flavobacterium sp003105115 82.7335 990 2024 d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium 95.0 N/A N/A N/A N/A 1 - GCF_009711165.2 s__Flavobacterium sp009711165 82.5992 1146 2024 d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium 95.0 N/A N/A N/A N/A 1 - GCF_002303885.1 s__Flavobacterium sp002303885 82.4929 1095 2024 d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium 95.0 N/A N/A N/A N/A 1 - GCF_014207905.1 s__Flavobacterium notoginsengisoli 82.4486 1064 2024 d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium 95.0 100.00 100.00 1.00 1.00 2 - GCF_900112575.1 s__Flavobacterium phragmitis 82.2906 1091 2024 d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium 95.0 N/A N/A N/A N/A 1 - -------------------------------------------------------------------------------- [2024-01-24 14:17:19,992] [INFO] GTDB search result was written to GCF_900142685.1_IMG-taxon_2700988709_annotated_assembly_genomic.fna/result_gtdb.tsv [2024-01-24 14:17:19,992] [INFO] ===== GTDB Search completed ===== [2024-01-24 14:17:19,997] [INFO] DFAST_QC result json was written to GCF_900142685.1_IMG-taxon_2700988709_annotated_assembly_genomic.fna/dqc_result.json [2024-01-24 14:17:19,997] [INFO] DFAST_QC completed! [2024-01-24 14:17:19,997] [INFO] Total running time: 0h2m19s