[2024-01-24 11:05:25,410] [INFO] DFAST_QC pipeline started. [2024-01-24 11:05:25,418] [INFO] DFAST_QC version: 0.5.7 [2024-01-24 11:05:25,419] [INFO] DQC Reference Directory: /var/lib/cwl/stg94499d16-0e22-4590-84ab-29cd9acc42be/dqc_reference [2024-01-24 11:05:26,841] [INFO] ===== Start taxonomy check using ANI ===== [2024-01-24 11:05:26,842] [INFO] Task started: Prodigal [2024-01-24 11:05:26,842] [INFO] Running command: gunzip -c /var/lib/cwl/stg209017d3-751e-4eb2-9d46-88e0d613d1d6/GCF_004359985.1_ASM435998v1_genomic.fna.gz | prodigal -d GCF_004359985.1_ASM435998v1_genomic.fna/cds.fna -a GCF_004359985.1_ASM435998v1_genomic.fna/protein.faa -g 11 -q > /dev/null [2024-01-24 11:05:48,170] [INFO] Task succeeded: Prodigal [2024-01-24 11:05:48,171] [INFO] Task started: HMMsearch [2024-01-24 11:05:48,171] [INFO] Running command: hmmsearch --tblout GCF_004359985.1_ASM435998v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg94499d16-0e22-4590-84ab-29cd9acc42be/dqc_reference/reference_markers.hmm GCF_004359985.1_ASM435998v1_genomic.fna/protein.faa > /dev/null [2024-01-24 11:05:48,512] [INFO] Task succeeded: HMMsearch [2024-01-24 11:05:48,514] [INFO] Found 6/6 markers. [2024-01-24 11:05:48,569] [INFO] Query marker FASTA was written to GCF_004359985.1_ASM435998v1_genomic.fna/markers.fasta [2024-01-24 11:05:48,569] [INFO] Task started: Blastn [2024-01-24 11:05:48,570] [INFO] Running command: blastn -query GCF_004359985.1_ASM435998v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg94499d16-0e22-4590-84ab-29cd9acc42be/dqc_reference/reference_markers.fasta -out GCF_004359985.1_ASM435998v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5 [2024-01-24 11:05:49,575] [INFO] Task succeeded: Blastn [2024-01-24 11:05:49,579] [INFO] Selected 18 target genomes. [2024-01-24 11:05:49,580] [INFO] Target genome list was writen to GCF_004359985.1_ASM435998v1_genomic.fna/target_genomes.txt [2024-01-24 11:05:49,587] [INFO] Task started: fastANI [2024-01-24 11:05:49,588] [INFO] Running command: fastANI --query /var/lib/cwl/stg209017d3-751e-4eb2-9d46-88e0d613d1d6/GCF_004359985.1_ASM435998v1_genomic.fna.gz --refList GCF_004359985.1_ASM435998v1_genomic.fna/target_genomes.txt --output GCF_004359985.1_ASM435998v1_genomic.fna/fastani_result.tsv --threads 1 [2024-01-24 11:06:21,388] [INFO] Task succeeded: fastANI [2024-01-24 11:06:21,389] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg94499d16-0e22-4590-84ab-29cd9acc42be/dqc_reference/prokaryote_ANI_species_specific_threshold.txt [2024-01-24 11:06:21,389] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg94499d16-0e22-4590-84ab-29cd9acc42be/dqc_reference/prokaryote_ANI_species_specific_threshold.txt] [2024-01-24 11:06:21,408] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold) [2024-01-24 11:06:21,408] [INFO] The taxonomy check result is classified as 'conclusive'. [2024-01-24 11:06:21,408] [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 flava strain=LD6 GCA_004359985.1 2547393 2547393 type True 100.0 2318 2319 95 conclusive Paraburkholderia acidicola strain=ATCC 31363 GCA_002362315.1 1912599 1912599 type True 84.7217 1427 2319 95 below_threshold Paraburkholderia megapolitana strain=LMG 23650 GCA_900113825.1 420953 420953 type True 84.4221 1480 2319 95 below_threshold Paraburkholderia megapolitana strain=LMG 23650 GCA_007556815.1 420953 420953 type True 84.418 1509 2319 95 below_threshold Paraburkholderia ginsengisoli strain=NBRC 100965 GCA_000739735.1 311231 311231 type True 83.4698 1224 2319 95 below_threshold Paraburkholderia monticola strain=JC2948 GCA_001580545.1 1399968 1399968 type True 83.3323 1268 2319 95 below_threshold Paraburkholderia caballeronis strain=LMG 26416 GCA_900109675.1 416943 416943 type True 83.3026 1172 2319 95 below_threshold Paraburkholderia caballeronis strain=TNe-841 GCA_900104845.1 416943 416943 type True 83.2453 1194 2319 95 below_threshold Paraburkholderia podalyriae strain=WC7.3b GCA_014397785.1 1938811 1938811 type True 83.1501 1222 2319 95 below_threshold Paraburkholderia ultramafica strain=LMG 28614 GCA_902859915.1 1544867 1544867 type True 83.132 1176 2319 95 below_threshold Paraburkholderia gardini strain=LMG 32171 GCA_907164575.1 2823469 2823469 type True 83.0612 1166 2319 95 below_threshold Paraburkholderia panacisoli strain=DCY113 GCA_008369935.1 2603818 2603818 type True 82.9806 1278 2319 95 below_threshold Paraburkholderia azotifigens strain=NF 2-5-3 GCA_007995085.1 2057004 2057004 type True 82.8186 1325 2319 95 below_threshold Paraburkholderia saeva strain=LMG 31841 GCA_907164555.1 2777537 2777537 type True 82.7872 1120 2319 95 below_threshold Paraburkholderia elongata strain=5N GCA_013177735.1 2675747 2675747 type True 82.3707 1177 2319 95 below_threshold Burkholderia pseudomultivorans GCA_902499075.1 1207504 1207504 suspected-type True 82.2491 1099 2319 95 below_threshold Burkholderia stagnalis GCA_902499155.1 1503054 1503054 type True 82.201 1089 2319 95 below_threshold Burkholderia stagnalis strain=LMG 28156 GCA_902830275.1 1503054 1503054 type True 82.1838 1131 2319 95 below_threshold -------------------------------------------------------------------------------- [2024-01-24 11:06:21,415] [INFO] DFAST Taxonomy check result was written to GCF_004359985.1_ASM435998v1_genomic.fna/tc_result.tsv [2024-01-24 11:06:21,416] [INFO] ===== Taxonomy check completed ===== [2024-01-24 11:06:21,416] [INFO] ===== Start completeness check using CheckM ===== [2024-01-24 11:06:21,416] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg94499d16-0e22-4590-84ab-29cd9acc42be/dqc_reference/checkm_data [2024-01-24 11:06:21,417] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM [2024-01-24 11:06:21,485] [INFO] Task started: CheckM [2024-01-24 11:06:21,485] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004359985.1_ASM435998v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004359985.1_ASM435998v1_genomic.fna/checkm_input GCF_004359985.1_ASM435998v1_genomic.fna/checkm_result [2024-01-24 11:07:24,028] [INFO] Task succeeded: CheckM [2024-01-24 11:07:24,029] [INFO] Completeness check finished. -------------------------------------------------------------------------------- Completeness: 100.00% Contamintation: 0.00% Strain heterogeneity: 0.00% -------------------------------------------------------------------------------- [2024-01-24 11:07:24,050] [INFO] ===== Completeness check finished ===== [2024-01-24 11:07:24,051] [INFO] ===== Start GTDB Search ===== [2024-01-24 11:07:24,051] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004359985.1_ASM435998v1_genomic.fna/markers.fasta) [2024-01-24 11:07:24,051] [INFO] Task started: Blastn [2024-01-24 11:07:24,052] [INFO] Running command: blastn -query GCF_004359985.1_ASM435998v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg94499d16-0e22-4590-84ab-29cd9acc42be/dqc_reference/reference_markers_gtdb.fasta -out GCF_004359985.1_ASM435998v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5 [2024-01-24 11:07:26,013] [INFO] Task succeeded: Blastn [2024-01-24 11:07:26,018] [INFO] Selected 20 target genomes. [2024-01-24 11:07:26,018] [INFO] Target genome list was writen to GCF_004359985.1_ASM435998v1_genomic.fna/target_genomes_gtdb.txt [2024-01-24 11:07:26,057] [INFO] Task started: fastANI [2024-01-24 11:07:26,057] [INFO] Running command: fastANI --query /var/lib/cwl/stg209017d3-751e-4eb2-9d46-88e0d613d1d6/GCF_004359985.1_ASM435998v1_genomic.fna.gz --refList GCF_004359985.1_ASM435998v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004359985.1_ASM435998v1_genomic.fna/fastani_result_gtdb.tsv --threads 1 [2024-01-24 11:07:58,717] [INFO] Task succeeded: fastANI [2024-01-24 11:07:58,745] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius) [2024-01-24 11:07:58,745] [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_004359985.1 s__Paraburkholderia sp004359985 100.0 2318 2319 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia 95.0 N/A N/A N/A N/A 1 conclusive GCF_002362315.1 s__Paraburkholderia acidophila 84.6805 1433 2319 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia 95.0 N/A N/A N/A N/A 1 - GCF_007556815.1 s__Paraburkholderia megapolitana 84.4194 1509 2319 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia 95.0 99.99 99.99 1.00 1.00 2 - GCF_012927125.1 s__Paraburkholderia sp012927125 83.6981 1260 2319 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia 95.0 N/A N/A N/A N/A 1 - GCF_011752995.1 s__Paraburkholderia sp011752995 83.5217 1209 2319 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia 95.0 99.23 99.21 0.92 0.90 4 - GCF_001931485.1 s__Paraburkholderia sp001931485 83.5117 1209 2319 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia 95.0 N/A N/A N/A N/A 1 - GCF_900177725.1 s__Paraburkholderia susongensis 83.4967 1223 2319 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia 95.0 N/A N/A N/A N/A 1 - GCF_000739735.1 s__Paraburkholderia ginsengisoli 83.475 1223 2319 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia 95.0 100.00 100.00 1.00 1.00 2 - GCF_900107685.1 s__Paraburkholderia sartisoli 83.3342 1149 2319 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia 95.0 96.92 96.92 0.85 0.85 2 - GCF_001580545.1 s__Paraburkholderia monticola 83.3222 1270 2319 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia 95.0 N/A N/A N/A N/A 1 - GCF_900104845.1 s__Paraburkholderia caballeronis 83.2482 1194 2319 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia 95.0 99.48 98.95 0.97 0.92 9 - GCF_902859915.1 s__Paraburkholderia ultramafica 83.105 1180 2319 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia 95.0 N/A N/A N/A N/A 1 - GCF_008369935.1 s__Paraburkholderia panacisoli 83.0136 1273 2319 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia 95.0 N/A N/A N/A N/A 1 - GCF_900996225.1 s__Paraburkholderia sp900996225 82.3878 1203 2319 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia 95.0 N/A N/A N/A N/A 1 - GCF_013177735.1 s__Paraburkholderia sp013177735 82.3456 1183 2319 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia 95.0 N/A N/A N/A N/A 1 - GCF_902830275.1 s__Burkholderia stagnalis 82.195 1130 2319 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 98.76 95.48 0.93 0.80 113 - GCF_005280735.1 s__Trinickia sp005280735 82.1689 1169 2319 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Trinickia 95.0 N/A N/A N/A N/A 1 - GCF_003854275.1 s__Burkholderia sp003854275 82.1083 1093 2319 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 95.08 95.08 0.74 0.74 2 - GCF_000687455.2 s__Burkholderia sp000687455 81.9115 932 2319 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 N/A N/A N/A N/A 1 - GCF_003429005.1 s__Paraburkholderia sp003429005 81.6648 1092 2319 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia 95.0 N/A N/A N/A N/A 1 - -------------------------------------------------------------------------------- [2024-01-24 11:07:58,747] [INFO] GTDB search result was written to GCF_004359985.1_ASM435998v1_genomic.fna/result_gtdb.tsv [2024-01-24 11:07:58,748] [INFO] ===== GTDB Search completed ===== [2024-01-24 11:07:58,752] [INFO] DFAST_QC result json was written to GCF_004359985.1_ASM435998v1_genomic.fna/dqc_result.json [2024-01-24 11:07:58,752] [INFO] DFAST_QC completed! [2024-01-24 11:07:58,752] [INFO] Total running time: 0h2m33s