[2024-01-24 14:03:08,572] [INFO] DFAST_QC pipeline started. [2024-01-24 14:03:08,574] [INFO] DFAST_QC version: 0.5.7 [2024-01-24 14:03:08,575] [INFO] DQC Reference Directory: /var/lib/cwl/stg62e8049b-4f29-4861-bea9-440439f11885/dqc_reference [2024-01-24 14:03:10,027] [INFO] ===== Start taxonomy check using ANI ===== [2024-01-24 14:03:10,028] [INFO] Task started: Prodigal [2024-01-24 14:03:10,028] [INFO] Running command: gunzip -c /var/lib/cwl/stg5fa80b45-e0da-4a9b-819a-844df9c0f1ba/GCF_902833845.1_ASM90283384v1_genomic.fna.gz | prodigal -d GCF_902833845.1_ASM90283384v1_genomic.fna/cds.fna -a GCF_902833845.1_ASM90283384v1_genomic.fna/protein.faa -g 11 -q > /dev/null [2024-01-24 14:03:31,192] [INFO] Task succeeded: Prodigal [2024-01-24 14:03:31,192] [INFO] Task started: HMMsearch [2024-01-24 14:03:31,192] [INFO] Running command: hmmsearch --tblout GCF_902833845.1_ASM90283384v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg62e8049b-4f29-4861-bea9-440439f11885/dqc_reference/reference_markers.hmm GCF_902833845.1_ASM90283384v1_genomic.fna/protein.faa > /dev/null [2024-01-24 14:03:31,574] [INFO] Task succeeded: HMMsearch [2024-01-24 14:03:31,576] [INFO] Found 6/6 markers. [2024-01-24 14:03:31,628] [INFO] Query marker FASTA was written to GCF_902833845.1_ASM90283384v1_genomic.fna/markers.fasta [2024-01-24 14:03:31,629] [INFO] Task started: Blastn [2024-01-24 14:03:31,629] [INFO] Running command: blastn -query GCF_902833845.1_ASM90283384v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg62e8049b-4f29-4861-bea9-440439f11885/dqc_reference/reference_markers.fasta -out GCF_902833845.1_ASM90283384v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5 [2024-01-24 14:03:32,421] [INFO] Task succeeded: Blastn [2024-01-24 14:03:32,426] [INFO] Selected 24 target genomes. [2024-01-24 14:03:32,426] [INFO] Target genome list was writen to GCF_902833845.1_ASM90283384v1_genomic.fna/target_genomes.txt [2024-01-24 14:03:32,441] [INFO] Task started: fastANI [2024-01-24 14:03:32,442] [INFO] Running command: fastANI --query /var/lib/cwl/stg5fa80b45-e0da-4a9b-819a-844df9c0f1ba/GCF_902833845.1_ASM90283384v1_genomic.fna.gz --refList GCF_902833845.1_ASM90283384v1_genomic.fna/target_genomes.txt --output GCF_902833845.1_ASM90283384v1_genomic.fna/fastani_result.tsv --threads 1 [2024-01-24 14:04:03,646] [INFO] Task succeeded: fastANI [2024-01-24 14:04:03,647] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg62e8049b-4f29-4861-bea9-440439f11885/dqc_reference/prokaryote_ANI_species_specific_threshold.txt [2024-01-24 14:04:03,647] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg62e8049b-4f29-4861-bea9-440439f11885/dqc_reference/prokaryote_ANI_species_specific_threshold.txt] [2024-01-24 14:04:03,665] [INFO] Found 24 fastANI hits (2 hits with ANI > threshold) [2024-01-24 14:04:03,665] [INFO] The taxonomy check result is classified as 'conclusive'. [2024-01-24 14:04:03,666] [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 Robbsia andropogonis strain=LMG 2129 GCA_902833845.1 28092 28092 type True 100.0 2079 2080 95 conclusive Robbsia andropogonis strain=ICMP2807 GCA_000970345.1 28092 28092 type True 99.9473 1936 2080 95 conclusive Paraburkholderia gardini strain=LMG 32171 GCA_907164575.1 2823469 2823469 type True 77.6079 250 2080 95 below_threshold Burkholderia glumae strain=LMG 2196 GCA_902832765.1 337 337 type True 77.5115 305 2080 95 below_threshold Burkholderia ambifaria strain=AMMD GCA_000203915.1 152480 152480 type True 77.4531 298 2080 95 below_threshold Burkholderia pseudomultivorans GCA_902499075.1 1207504 1207504 suspected-type True 77.4032 286 2080 95 below_threshold Paraburkholderia ginsengisoli strain=NBRC 100965 GCA_000739735.1 311231 311231 type True 77.386 274 2080 95 below_threshold Caballeronia concitans GCA_001544615.2 1777133 1777133 type True 77.3835 246 2080 95 below_threshold Burkholderia puraquae strain=CAMPA 1040 GCA_002099195.1 1904757 1904757 type True 77.3732 292 2080 95 below_threshold Paraburkholderia domus strain=LMG 31832 GCA_905220705.1 2793075 2793075 type True 77.3715 265 2080 95 below_threshold Paraburkholderia solitsugae strain=1N GCA_013177695.1 2675748 2675748 type True 77.3526 282 2080 95 below_threshold Burkholderia ubonensis GCA_902499185.1 101571 101571 type True 77.3394 297 2080 95 below_threshold Paraburkholderia flava strain=LD6 GCA_004359985.1 2547393 2547393 type True 77.3387 269 2080 95 below_threshold Burkholderia aenigmatica strain=LMG 13014 GCA_902499175.1 2015348 2015348 suspected-type True 77.3333 284 2080 95 below_threshold Burkholderia puraquae strain=LMG 29660 GCA_902859845.1 1904757 1904757 type True 77.3137 296 2080 95 below_threshold Paraburkholderia madseniana strain=RP11 GCA_009690905.1 2599607 2599607 type True 77.277 278 2080 95 below_threshold Burkholderia anthina GCA_902498995.1 179879 179879 suspected-type True 77.2567 301 2080 95 below_threshold Caballeronia terrestris GCA_001544515.2 1226301 1226301 type True 77.2272 270 2080 95 below_threshold Paraburkholderia hiiakae strain=LMG 27952 GCA_904848665.1 1081782 1081782 type True 77.2266 252 2080 95 below_threshold Caballeronia humi GCA_001544475.2 326474 326474 type True 77.1846 283 2080 95 below_threshold Paraburkholderia podalyriae strain=WC7.3b GCA_014397785.1 1938811 1938811 type True 77.1772 291 2080 95 below_threshold Paraburkholderia heleia strain=NBRC 101817 GCA_000739775.1 634127 634127 type True 77.1598 269 2080 95 below_threshold Paraburkholderia azotifigens strain=NF 2-5-3 GCA_007995085.1 2057004 2057004 type True 77.0176 296 2080 95 below_threshold Caballeronia cordobensis strain=LMG 27620 GCA_001278535.1 1353886 1353886 type True 76.9904 273 2080 95 below_threshold -------------------------------------------------------------------------------- [2024-01-24 14:04:03,667] [INFO] DFAST Taxonomy check result was written to GCF_902833845.1_ASM90283384v1_genomic.fna/tc_result.tsv [2024-01-24 14:04:03,668] [INFO] ===== Taxonomy check completed ===== [2024-01-24 14:04:03,668] [INFO] ===== Start completeness check using CheckM ===== [2024-01-24 14:04:03,668] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg62e8049b-4f29-4861-bea9-440439f11885/dqc_reference/checkm_data [2024-01-24 14:04:03,669] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM [2024-01-24 14:04:03,730] [INFO] Task started: CheckM [2024-01-24 14:04:03,730] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_902833845.1_ASM90283384v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_902833845.1_ASM90283384v1_genomic.fna/checkm_input GCF_902833845.1_ASM90283384v1_genomic.fna/checkm_result [2024-01-24 14:05:03,772] [INFO] Task succeeded: CheckM [2024-01-24 14:05:03,773] [INFO] Completeness check finished. -------------------------------------------------------------------------------- Completeness: 100.00% Contamintation: 0.00% Strain heterogeneity: 0.00% -------------------------------------------------------------------------------- [2024-01-24 14:05:03,798] [INFO] ===== Completeness check finished ===== [2024-01-24 14:05:03,799] [INFO] ===== Start GTDB Search ===== [2024-01-24 14:05:03,799] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_902833845.1_ASM90283384v1_genomic.fna/markers.fasta) [2024-01-24 14:05:03,799] [INFO] Task started: Blastn [2024-01-24 14:05:03,800] [INFO] Running command: blastn -query GCF_902833845.1_ASM90283384v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg62e8049b-4f29-4861-bea9-440439f11885/dqc_reference/reference_markers_gtdb.fasta -out GCF_902833845.1_ASM90283384v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5 [2024-01-24 14:05:04,959] [INFO] Task succeeded: Blastn [2024-01-24 14:05:04,964] [INFO] Selected 32 target genomes. [2024-01-24 14:05:04,964] [INFO] Target genome list was writen to GCF_902833845.1_ASM90283384v1_genomic.fna/target_genomes_gtdb.txt [2024-01-24 14:05:05,020] [INFO] Task started: fastANI [2024-01-24 14:05:05,020] [INFO] Running command: fastANI --query /var/lib/cwl/stg5fa80b45-e0da-4a9b-819a-844df9c0f1ba/GCF_902833845.1_ASM90283384v1_genomic.fna.gz --refList GCF_902833845.1_ASM90283384v1_genomic.fna/target_genomes_gtdb.txt --output GCF_902833845.1_ASM90283384v1_genomic.fna/fastani_result_gtdb.tsv --threads 1 [2024-01-24 14:05:43,363] [INFO] Task succeeded: fastANI [2024-01-24 14:05:43,387] [INFO] Found 28 fastANI hits (1 hits with ANI > circumscription radius) [2024-01-24 14:05:43,387] [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_000970345.1 s__Robbsia andropogonis 99.9473 1936 2080 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Robbsia 95.0 99.73 99.47 0.96 0.92 3 conclusive GCF_013403875.1 s__Burkholderia guangdongensis 77.4369 256 2080 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 N/A N/A N/A N/A 1 - GCF_003253405.1 s__Paraburkholderia sp003253405 77.4149 274 2080 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia 95.0 N/A N/A N/A N/A 1 - GCF_902833145.1 s__Burkholderia sp902833145 77.4131 306 2080 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 99.99 99.99 0.98 0.98 2 - GCF_001718835.1 s__Burkholderia cepacia_F 77.4086 298 2080 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 N/A N/A N/A N/A 1 - GCF_902499075.1 s__Burkholderia pseudomultivorans 77.4014 287 2080 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 96.22 95.54 0.83 0.81 13 - GCF_000739735.1 s__Paraburkholderia ginsengisoli 77.397 273 2080 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia 95.0 100.00 100.00 1.00 1.00 2 - GCF_001544615.1 s__Caballeronia concitans 77.3934 245 2080 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Caballeronia 95.0 99.76 99.76 0.97 0.97 2 - GCF_002099195.1 s__Burkholderia puraquae 77.3637 293 2080 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 97.50 95.00 0.89 0.80 3 - GCF_004359985.1 s__Paraburkholderia sp004359985 77.3457 266 2080 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia 95.0 N/A N/A N/A N/A 1 - GCF_902499175.1 s__Burkholderia aenigmatica 77.3435 283 2080 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 96.89 95.59 0.85 0.80 12 - GCF_000959245.1 s__Burkholderia ubonensis 77.3266 311 2080 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 98.20 95.69 0.89 0.72 308 - GCF_003121405.1 s__Paraburkholderia sp003121405 77.2889 258 2080 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia 95.0 N/A N/A N/A N/A 1 - GCF_001931485.1 s__Paraburkholderia sp001931485 77.2763 303 2080 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia 95.0 N/A N/A N/A N/A 1 - GCF_013426895.1 s__Paraburkholderia sp013426895 77.2709 273 2080 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia 95.0 N/A N/A N/A N/A 1 - GCF_003330765.1 s__Burkholderia pyrrocinia_B 77.2674 297 2080 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 N/A N/A N/A N/A 1 - GCF_009690905.1 s__Paraburkholderia madseniana 77.2668 279 2080 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia 95.0 98.82 98.82 0.85 0.85 2 - GCF_001544515.1 s__Caballeronia terrestris 77.229 267 2080 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Caballeronia 95.0 N/A N/A N/A N/A 1 - GCF_904848665.1 s__Paraburkholderia hiiakae 77.2276 252 2080 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia 95.0 N/A N/A N/A N/A 1 - GCF_902498995.1 s__Burkholderia anthina 77.222 304 2080 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 96.57 95.19 0.86 0.77 22 - GCF_005503145.1 s__Paraburkholderia sp005503145 77.2125 262 2080 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia 95.0 N/A N/A N/A N/A 1 - GCF_003635165.1 s__Burkholderia sp003635165 77.202 290 2080 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 N/A N/A N/A N/A 1 - GCF_001462435.1 s__Burkholderia humptydooensis 77.1868 297 2080 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia 95.0 99.52 99.18 0.95 0.92 12 - GCF_002902925.1 s__Paraburkholderia terrae 77.1557 289 2080 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia 95.2599 98.84 97.67 0.92 0.83 3 - GCF_013409255.1 s__Paraburkholderia sp000745015 77.131 307 2080 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia 95.0 97.63 95.38 0.90 0.84 6 - GCF_017220215.1 s__Caballeronia sp902833455 77.1149 253 2080 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Caballeronia 95.0 98.21 98.21 0.98 0.98 2 - GCF_900142845.1 s__Paraburkholderia phenazinium_A 77.08 288 2080 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia 95.0 N/A N/A N/A N/A 1 - GCF_013426915.1 s__Paraburkholderia sp013426915 77.0223 304 2080 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 14:05:43,389] [INFO] GTDB search result was written to GCF_902833845.1_ASM90283384v1_genomic.fna/result_gtdb.tsv [2024-01-24 14:05:43,389] [INFO] ===== GTDB Search completed ===== [2024-01-24 14:05:43,397] [INFO] DFAST_QC result json was written to GCF_902833845.1_ASM90283384v1_genomic.fna/dqc_result.json [2024-01-24 14:05:43,397] [INFO] DFAST_QC completed! [2024-01-24 14:05:43,398] [INFO] Total running time: 0h2m35s