[2024-01-24 15:10:41,159] [INFO] DFAST_QC pipeline started. [2024-01-24 15:10:41,162] [INFO] DFAST_QC version: 0.5.7 [2024-01-24 15:10:41,163] [INFO] DQC Reference Directory: /var/lib/cwl/stg15f27602-3ab5-4fe7-a556-b971325faf2d/dqc_reference [2024-01-24 15:10:42,519] [INFO] ===== Start taxonomy check using ANI ===== [2024-01-24 15:10:42,520] [INFO] Task started: Prodigal [2024-01-24 15:10:42,520] [INFO] Running command: gunzip -c /var/lib/cwl/stg79e177ef-d35e-4255-8163-84641f17ee6a/GCF_900104845.1_IMG-taxon_2693429824_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900104845.1_IMG-taxon_2693429824_annotated_assembly_genomic.fna/cds.fna -a GCF_900104845.1_IMG-taxon_2693429824_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null [2024-01-24 15:11:04,797] [INFO] Task succeeded: Prodigal [2024-01-24 15:11:04,797] [INFO] Task started: HMMsearch [2024-01-24 15:11:04,798] [INFO] Running command: hmmsearch --tblout GCF_900104845.1_IMG-taxon_2693429824_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg15f27602-3ab5-4fe7-a556-b971325faf2d/dqc_reference/reference_markers.hmm GCF_900104845.1_IMG-taxon_2693429824_annotated_assembly_genomic.fna/protein.faa > /dev/null [2024-01-24 15:11:05,255] [INFO] Task succeeded: HMMsearch [2024-01-24 15:11:05,256] [INFO] Found 6/6 markers. [2024-01-24 15:11:05,325] [INFO] Query marker FASTA was written to GCF_900104845.1_IMG-taxon_2693429824_annotated_assembly_genomic.fna/markers.fasta [2024-01-24 15:11:05,325] [INFO] Task started: Blastn [2024-01-24 15:11:05,325] [INFO] Running command: blastn -query GCF_900104845.1_IMG-taxon_2693429824_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg15f27602-3ab5-4fe7-a556-b971325faf2d/dqc_reference/reference_markers.fasta -out GCF_900104845.1_IMG-taxon_2693429824_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5 [2024-01-24 15:11:06,394] [INFO] Task succeeded: Blastn [2024-01-24 15:11:06,397] [INFO] Selected 27 target genomes. [2024-01-24 15:11:06,397] [INFO] Target genome list was writen to GCF_900104845.1_IMG-taxon_2693429824_annotated_assembly_genomic.fna/target_genomes.txt [2024-01-24 15:11:06,411] [INFO] Task started: fastANI [2024-01-24 15:11:06,412] [INFO] Running command: fastANI --query /var/lib/cwl/stg79e177ef-d35e-4255-8163-84641f17ee6a/GCF_900104845.1_IMG-taxon_2693429824_annotated_assembly_genomic.fna.gz --refList GCF_900104845.1_IMG-taxon_2693429824_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900104845.1_IMG-taxon_2693429824_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1 [2024-01-24 15:11:53,637] [INFO] Task succeeded: fastANI [2024-01-24 15:11:53,637] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg15f27602-3ab5-4fe7-a556-b971325faf2d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt [2024-01-24 15:11:53,638] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg15f27602-3ab5-4fe7-a556-b971325faf2d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt] [2024-01-24 15:11:53,657] [INFO] Found 27 fastANI hits (2 hits with ANI > threshold) [2024-01-24 15:11:53,657] [INFO] The taxonomy check result is classified as 'conclusive'. [2024-01-24 15:11:53,657] [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 Paraburkholderia caballeronis strain=TNe-841 GCA_900104845.1 416943 416943 type True 100.0 2369 2370 95 conclusive Paraburkholderia caballeronis strain=LMG 26416 GCA_900109675.1 416943 416943 type True 99.9858 2326 2370 95 conclusive Paraburkholderia acidipaludis strain=NBRC 101816 GCA_000684975.1 660537 660537 type True 83.6172 1189 2370 95 below_threshold Paraburkholderia lycopersici strain=TNe-862 GCA_900096975.1 416944 416944 type True 83.4463 1323 2370 95 below_threshold Paraburkholderia ferrariae strain=NBRC 106233 GCA_000685035.1 386056 386056 type True 83.3856 1313 2370 95 below_threshold Paraburkholderia tropica strain=LMG 22274 GCA_900109265.1 92647 92647 type True 83.3076 1452 2370 95 below_threshold Paraburkholderia mimosarum strain=NBRC 106338 GCA_000739815.1 312026 312026 type True 83.1321 1209 2370 95 below_threshold Paraburkholderia mimosarum strain=LMG 23256 GCA_902833725.1 312026 312026 type True 83.1287 1231 2370 95 below_threshold Paraburkholderia mimosarum strain=LMG 23256 GCA_000472825.1 312026 312026 type True 83.109 1218 2370 95 below_threshold Paraburkholderia dinghuensis strain=DHOA04 GCA_003837865.1 2305225 2305225 type True 83.0747 1087 2370 95 below_threshold Burkholderia ubonensis strain=LMG 20358 GCA_902833085.1 101571 101571 type True 83.0609 1205 2370 95 below_threshold Burkholderia ubonensis GCA_902499185.1 101571 101571 type True 83.0406 1173 2370 95 below_threshold Burkholderia latens strain=CCUG 54555 GCA_008802135.1 488446 488446 suspected-type True 83.0221 1119 2370 95 below_threshold Paraburkholderia acidisoli strain=DHF22 GCA_009789675.1 2571748 2571748 type True 82.9746 1353 2370 95 below_threshold Burkholderia vietnamiensis strain=FDAARGOS_1488 GCA_020099355.1 60552 60552 type True 82.9373 1188 2370 95 below_threshold Paraburkholderia eburnea strain=JCM 18070 GCA_002917095.1 1189126 1189126 type True 82.9316 1284 2370 95 below_threshold Paraburkholderia pallida strain=7MH5 GCA_004524855.1 2547399 2547399 type True 82.9265 1330 2370 95 below_threshold Burkholderia latens GCA_902499045.1 488446 488446 suspected-type True 82.885 1168 2370 95 below_threshold Paraburkholderia oxyphila strain=NBRC 105797 GCA_000685075.1 614212 614212 type True 82.8558 1311 2370 95 below_threshold Paraburkholderia silviterrae strain=4M-K11 GCA_004353915.1 2528715 2528715 type True 82.8278 1268 2370 95 below_threshold Paraburkholderia sacchari strain=LMG 19450 GCA_902833715.1 159450 159450 type True 82.767 1220 2370 95 below_threshold Paraburkholderia podalyriae strain=WC7.3b GCA_014397785.1 1938811 1938811 type True 82.6561 1179 2370 95 below_threshold Pseudoduganella dura strain=DSM 17513 GCA_009727155.1 321982 321982 type True 77.4605 527 2370 95 below_threshold Pseudoduganella dura strain=KCTC 12342 GCA_014651395.1 321982 321982 type True 77.2703 515 2370 95 below_threshold Chromobacterium violaceum strain=NCTC9757 GCA_900446805.1 536 536 type True 76.9337 284 2370 95 below_threshold Massilia glaciei strain=B448-2 GCA_003011895.2 1524097 1524097 type True 76.9245 440 2370 95 below_threshold Chromobacterium violaceum strain=ATCC 12472 GCA_000007705.1 536 536 type True 76.8193 306 2370 95 below_threshold -------------------------------------------------------------------------------- [2024-01-24 15:11:53,659] [INFO] DFAST Taxonomy check result was written to GCF_900104845.1_IMG-taxon_2693429824_annotated_assembly_genomic.fna/tc_result.tsv [2024-01-24 15:11:53,660] [INFO] ===== Taxonomy check completed ===== [2024-01-24 15:11:53,660] [INFO] ===== Start completeness check using CheckM ===== [2024-01-24 15:11:53,660] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg15f27602-3ab5-4fe7-a556-b971325faf2d/dqc_reference/checkm_data [2024-01-24 15:11:53,661] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM [2024-01-24 15:11:53,727] [INFO] Task started: CheckM [2024-01-24 15:11:53,727] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900104845.1_IMG-taxon_2693429824_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900104845.1_IMG-taxon_2693429824_annotated_assembly_genomic.fna/checkm_input GCF_900104845.1_IMG-taxon_2693429824_annotated_assembly_genomic.fna/checkm_result [2024-01-24 15:12:56,965] [INFO] Task succeeded: CheckM [2024-01-24 15:12:56,967] [INFO] Completeness check finished. -------------------------------------------------------------------------------- Completeness: 100.00% Contamintation: 0.00% Strain heterogeneity: 0.00% -------------------------------------------------------------------------------- [2024-01-24 15:12:56,992] [INFO] ===== Completeness check finished ===== [2024-01-24 15:12:56,992] [INFO] ===== Start GTDB Search ===== [2024-01-24 15:12:56,993] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900104845.1_IMG-taxon_2693429824_annotated_assembly_genomic.fna/markers.fasta) [2024-01-24 15:12:56,993] [INFO] Task started: Blastn [2024-01-24 15:12:56,993] [INFO] Running command: blastn -query GCF_900104845.1_IMG-taxon_2693429824_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg15f27602-3ab5-4fe7-a556-b971325faf2d/dqc_reference/reference_markers_gtdb.fasta -out GCF_900104845.1_IMG-taxon_2693429824_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5 [2024-01-24 15:12:58,662] [INFO] Task succeeded: Blastn [2024-01-24 15:12:58,666] [INFO] Selected 23 target genomes. [2024-01-24 15:12:58,667] [INFO] Target genome list was writen to GCF_900104845.1_IMG-taxon_2693429824_annotated_assembly_genomic.fna/target_genomes_gtdb.txt [2024-01-24 15:12:58,684] [INFO] Task started: fastANI [2024-01-24 15:12:58,684] [INFO] Running command: fastANI --query /var/lib/cwl/stg79e177ef-d35e-4255-8163-84641f17ee6a/GCF_900104845.1_IMG-taxon_2693429824_annotated_assembly_genomic.fna.gz --refList GCF_900104845.1_IMG-taxon_2693429824_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900104845.1_IMG-taxon_2693429824_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1 [2024-01-24 15:13:38,340] [INFO] Task succeeded: fastANI [2024-01-24 15:13:38,363] [INFO] Found 23 fastANI hits (1 hits with ANI > circumscription radius) [2024-01-24 15:13:38,363] [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_900104845.1 s__Paraburkholderia caballeronis 100.0 2369 2370 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia 95.0 99.48 98.95 0.97 0.92 9 conclusive GCF_003253405.1 s__Paraburkholderia sp003253405 87.574 1489 2370 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia 95.0 N/A N/A N/A N/A 1 - GCA_004298475.1 s__Paraburkholderia sp004298475 83.8519 978 2370 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia 95.0 99.94 99.94 0.88 0.88 2 - GCF_002870125.1 s__Paraburkholderia sp002870125 83.6283 1069 2370 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia 95.0 N/A N/A N/A N/A 1 - GCF_000684975.1 s__Paraburkholderia acidipaludis 83.5833 1194 2370 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia 95.0 N/A N/A N/A N/A 1 - GCF_900096975.1 s__Paraburkholderia lycopersici 83.4641 1320 2370 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia 95.0 N/A N/A N/A N/A 1 - GCF_000685035.1 s__Paraburkholderia ferrariae 83.4116 1309 2370 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia 95.0 N/A N/A N/A N/A 1 - GCF_900109265.1 s__Paraburkholderia tropica 83.3477 1445 2370 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia 95.0 99.07 95.97 0.93 0.85 14 - GCF_003837865.1 s__Paraburkholderia dinghuensis 83.0949 1084 2370 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia 95.0 N/A N/A N/A N/A 1 - GCF_000739815.1 s__Paraburkholderia mimosarum 83.0748 1217 2370 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia 95.0 99.63 98.93 0.95 0.86 4 - GCF_001718195.1 s__Paraburkholderia nodosa_A 83.0189 1313 2370 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia 95.0 N/A N/A N/A N/A 1 - GCF_009789675.1 s__Paraburkholderia acidisoli 82.9617 1358 2370 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia 95.0 N/A N/A N/A N/A 1 - GCF_002917095.1 s__Paraburkholderia eburnea 82.9316 1284 2370 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia 95.0 99.11 98.22 0.96 0.92 3 - GCF_902499045.1 s__Burkholderia latens 82.9262 1158 2370 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 99.69 99.09 0.97 0.92 4 - GCF_000685075.1 s__Paraburkholderia oxyphila 82.8661 1309 2370 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia 95.0 95.32 95.32 0.74 0.74 2 - GCF_000959445.1 s__Burkholderia vietnamiensis 82.8122 1188 2370 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 98.93 97.91 0.90 0.83 111 - GCF_000011705.1 s__Burkholderia mallei 82.6458 1094 2370 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 99.31 98.71 0.94 0.78 1780 - GCF_005144415.1 s__Trinickia sp005144415 82.4641 1098 2370 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Trinickia 95.0 N/A N/A N/A N/A 1 - GCF_017315705.1 s__Trinickia sp017315705 82.3707 1068 2370 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Trinickia 95.0 N/A N/A N/A N/A 1 - GCF_003986935.1 s__Paraburkholderia kururiensis 81.9832 1164 2370 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia 95.0 98.16 96.06 0.93 0.91 5 - GCF_009727155.1 s__Pseudoduganella dura 77.4494 522 2370 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudoduganella 95.0 99.99 99.99 1.00 1.00 2 - GCF_000007705.1 s__Chromobacterium violaceum 76.7904 308 2370 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Chromobacterium 95.0 98.58 98.16 0.94 0.91 26 - GCF_000428465.1 s__Chitinimonas koreensis 76.4368 486 2370 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinimonadaceae;g__Chitinimonas 95.0 N/A N/A N/A N/A 1 - -------------------------------------------------------------------------------- [2024-01-24 15:13:38,365] [INFO] GTDB search result was written to GCF_900104845.1_IMG-taxon_2693429824_annotated_assembly_genomic.fna/result_gtdb.tsv [2024-01-24 15:13:38,366] [INFO] ===== GTDB Search completed ===== [2024-01-24 15:13:38,371] [INFO] DFAST_QC result json was written to GCF_900104845.1_IMG-taxon_2693429824_annotated_assembly_genomic.fna/dqc_result.json [2024-01-24 15:13:38,371] [INFO] DFAST_QC completed! [2024-01-24 15:13:38,371] [INFO] Total running time: 0h2m57s