[2023-06-19 11:45:52,123] [INFO] DFAST_QC pipeline started. [2023-06-19 11:45:52,125] [INFO] DFAST_QC version: 0.5.7 [2023-06-19 11:45:52,125] [INFO] DQC Reference Directory: /var/lib/cwl/stg08cdfe16-b971-4fef-b4a7-0a2d7f11edb0/dqc_reference [2023-06-19 11:45:54,611] [INFO] ===== Start taxonomy check using ANI ===== [2023-06-19 11:45:54,612] [INFO] Task started: Prodigal [2023-06-19 11:45:54,612] [INFO] Running command: gunzip -c /var/lib/cwl/stg37a9683f-3ef8-477e-ad4e-0d7384c407cd/GCA_018780705.1_ASM1878070v1_genomic.fna.gz | prodigal -d GCA_018780705.1_ASM1878070v1_genomic.fna/cds.fna -a GCA_018780705.1_ASM1878070v1_genomic.fna/protein.faa -g 11 -q > /dev/null [2023-06-19 11:46:02,617] [INFO] Task succeeded: Prodigal [2023-06-19 11:46:02,618] [INFO] Task started: HMMsearch [2023-06-19 11:46:02,618] [INFO] Running command: hmmsearch --tblout GCA_018780705.1_ASM1878070v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg08cdfe16-b971-4fef-b4a7-0a2d7f11edb0/dqc_reference/reference_markers.hmm GCA_018780705.1_ASM1878070v1_genomic.fna/protein.faa > /dev/null [2023-06-19 11:46:02,805] [INFO] Task succeeded: HMMsearch [2023-06-19 11:46:02,806] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg37a9683f-3ef8-477e-ad4e-0d7384c407cd/GCA_018780705.1_ASM1878070v1_genomic.fna.gz] [2023-06-19 11:46:02,848] [INFO] Query marker FASTA was written to GCA_018780705.1_ASM1878070v1_genomic.fna/markers.fasta [2023-06-19 11:46:02,848] [INFO] Task started: Blastn [2023-06-19 11:46:02,848] [INFO] Running command: blastn -query GCA_018780705.1_ASM1878070v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg08cdfe16-b971-4fef-b4a7-0a2d7f11edb0/dqc_reference/reference_markers.fasta -out GCA_018780705.1_ASM1878070v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5 [2023-06-19 11:46:03,626] [INFO] Task succeeded: Blastn [2023-06-19 11:46:03,630] [INFO] Selected 29 target genomes. [2023-06-19 11:46:03,630] [INFO] Target genome list was writen to GCA_018780705.1_ASM1878070v1_genomic.fna/target_genomes.txt [2023-06-19 11:46:03,633] [INFO] Task started: fastANI [2023-06-19 11:46:03,633] [INFO] Running command: fastANI --query /var/lib/cwl/stg37a9683f-3ef8-477e-ad4e-0d7384c407cd/GCA_018780705.1_ASM1878070v1_genomic.fna.gz --refList GCA_018780705.1_ASM1878070v1_genomic.fna/target_genomes.txt --output GCA_018780705.1_ASM1878070v1_genomic.fna/fastani_result.tsv --threads 1 [2023-06-19 11:46:26,488] [INFO] Task succeeded: fastANI [2023-06-19 11:46:26,489] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg08cdfe16-b971-4fef-b4a7-0a2d7f11edb0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt [2023-06-19 11:46:26,490] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg08cdfe16-b971-4fef-b4a7-0a2d7f11edb0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt] [2023-06-19 11:46:26,510] [INFO] Found 29 fastANI hits (0 hits with ANI > threshold) [2023-06-19 11:46:26,510] [INFO] The taxonomy check result is classified as 'below_threshold'. [2023-06-19 11:46:26,511] [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 Pseudomonas campi strain=S1-A32-2 GCA_013200955.2 2731681 2731681 type True 81.9305 313 471 95 below_threshold Pseudomonas guryensis strain=SR9 GCA_014164785.1 2759165 2759165 type True 81.6559 320 471 95 below_threshold Pseudomonas tumuqii strain=LAMW06 GCA_013184545.1 2715755 2715755 type True 81.6101 291 471 95 below_threshold Pseudomonas ullengensis strain=UL070 GCA_014174475.1 2759166 2759166 type True 81.3827 315 471 95 below_threshold Pseudomonas lalucatii strain=R1b54 GCA_018398425.1 1424203 1424203 type True 81.3675 294 471 95 below_threshold Pseudomonas borbori strain=DSM 17834 GCA_900115555.1 289003 289003 type True 81.3179 292 471 95 below_threshold Pseudomonas tohonis strain=TUM18999 GCA_012767755.2 2725477 2725477 type True 81.2399 314 471 95 below_threshold Pseudomonas cavernae strain=K2W31S-8 GCA_003595175.1 2320867 2320867 type True 81.1581 308 471 95 below_threshold Pseudomonas peli strain=DSM 17833 GCA_012986145.1 592361 592361 type True 81.0687 292 471 95 below_threshold Pseudomonas peli strain=DSM 17833 GCA_900099645.1 592361 592361 type True 81.0466 292 471 95 below_threshold Pseudomonas cuatrocienegasensis strain=CIP 109853 GCA_900110925.1 543360 543360 type True 80.9138 275 471 95 below_threshold Pseudomonas insulae strain=UL073 GCA_016901015.1 2809017 2809017 type True 80.9057 297 471 95 below_threshold Pseudomonas otitidis strain=DSM 17224 GCA_900111835.1 319939 319939 suspected-type True 80.7256 309 471 95 below_threshold Pseudomonas cavernicola strain=K1S02-6 GCA_003596405.1 2320866 2320866 type True 80.5545 282 471 95 below_threshold Pseudomonas kuykendallii strain=NRRL B-59562 GCA_900106975.1 1007099 1007099 type True 80.4867 262 471 95 below_threshold Pseudomonas mosselii strain=DSM 17497 GCA_019823065.1 78327 78327 type True 80.1235 228 471 95 below_threshold Pseudomonas mosselii strain=DSM 17497 GCA_000621225.1 78327 78327 type True 80.1129 228 471 95 below_threshold Pseudomonas faucium strain=BML-PP048 GCA_013373935.1 2740518 2740518 type True 80.0346 233 471 95 below_threshold Pseudomonas iranensis strain=SWRI54 GCA_014268585.2 2745503 2745503 type True 80.015 211 471 95 below_threshold Pseudomonas siliginis strain=SWRI31 GCA_019145195.1 2842346 2842346 type True 79.9385 213 471 95 below_threshold Pseudomonas yamanorum strain=LMG 27247 GCA_900105735.1 515393 515393 suspected-type True 79.9031 229 471 95 below_threshold Pseudomonas paralactis strain=DSM 29164 GCA_001439735.1 1615673 1615673 type True 79.8087 197 471 95 below_threshold Pseudomonas guineae strain=LMG 24016 GCA_900113745.1 425504 425504 type True 79.7016 256 471 95 below_threshold Pseudomonas extremorientalis strain=CCUG 51517 GCA_008801565.1 169669 169669 type True 79.5759 216 471 95 below_threshold Pseudomonas extremorientalis GCA_900625005.1 169669 169669 type True 79.5444 219 471 95 below_threshold Pseudomonas extremorientalis strain=LMG 19695 GCA_001870465.1 169669 169669 type True 79.5239 218 471 95 below_threshold [Pseudomonas] nosocomialis strain=A31/70 GCA_005876855.1 1056496 1056496 type True 79.4955 204 471 95 below_threshold Stutzerimonas azotifigens strain=DSM 17556 GCA_000425625.1 291995 291995 type True 79.4642 217 471 95 below_threshold Pseudomonas azotoformans strain=NBRC 12693 GCA_002091515.1 47878 47878 suspected-type True 79.4242 232 471 95 below_threshold -------------------------------------------------------------------------------- [2023-06-19 11:46:26,513] [INFO] DFAST Taxonomy check result was written to GCA_018780705.1_ASM1878070v1_genomic.fna/tc_result.tsv [2023-06-19 11:46:26,514] [INFO] ===== Taxonomy check completed ===== [2023-06-19 11:46:26,514] [INFO] ===== Start completeness check using CheckM ===== [2023-06-19 11:46:26,514] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg08cdfe16-b971-4fef-b4a7-0a2d7f11edb0/dqc_reference/checkm_data [2023-06-19 11:46:26,515] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM [2023-06-19 11:46:26,549] [INFO] Task started: CheckM [2023-06-19 11:46:26,549] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018780705.1_ASM1878070v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018780705.1_ASM1878070v1_genomic.fna/checkm_input GCA_018780705.1_ASM1878070v1_genomic.fna/checkm_result [2023-06-19 11:46:53,903] [INFO] Task succeeded: CheckM [2023-06-19 11:46:53,905] [INFO] Completeness check finished. -------------------------------------------------------------------------------- Completeness: 65.66% Contamintation: 0.00% Strain heterogeneity: 0.00% -------------------------------------------------------------------------------- [2023-06-19 11:46:53,925] [INFO] ===== Completeness check finished ===== [2023-06-19 11:46:53,925] [INFO] ===== Start GTDB Search ===== [2023-06-19 11:46:53,926] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018780705.1_ASM1878070v1_genomic.fna/markers.fasta) [2023-06-19 11:46:53,926] [INFO] Task started: Blastn [2023-06-19 11:46:53,926] [INFO] Running command: blastn -query GCA_018780705.1_ASM1878070v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg08cdfe16-b971-4fef-b4a7-0a2d7f11edb0/dqc_reference/reference_markers_gtdb.fasta -out GCA_018780705.1_ASM1878070v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5 [2023-06-19 11:46:55,257] [INFO] Task succeeded: Blastn [2023-06-19 11:46:55,261] [INFO] Selected 29 target genomes. [2023-06-19 11:46:55,261] [INFO] Target genome list was writen to GCA_018780705.1_ASM1878070v1_genomic.fna/target_genomes_gtdb.txt [2023-06-19 11:46:55,271] [INFO] Task started: fastANI [2023-06-19 11:46:55,272] [INFO] Running command: fastANI --query /var/lib/cwl/stg37a9683f-3ef8-477e-ad4e-0d7384c407cd/GCA_018780705.1_ASM1878070v1_genomic.fna.gz --refList GCA_018780705.1_ASM1878070v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018780705.1_ASM1878070v1_genomic.fna/fastani_result_gtdb.tsv --threads 1 [2023-06-19 11:47:16,587] [INFO] Task succeeded: fastANI [2023-06-19 11:47:16,610] [INFO] Found 29 fastANI hits (0 hits with ANI > circumscription radius) [2023-06-19 11:47:16,610] [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_009799925.1 s__Pseudomonas_E sp009799925 82.435 316 471 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 N/A N/A N/A N/A 1 - GCF_902506505.1 s__Pseudomonas_E sp902506505 82.2284 311 471 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 95.45 95.45 0.88 0.88 2 - GCF_013200955.2 s__Pseudomonas_E campi 81.9535 312 471 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 N/A N/A N/A N/A 1 - GCF_014164785.1 s__Pseudomonas_E sp014164785 81.6559 320 471 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 N/A N/A N/A N/A 1 - GCA_002840155.1 s__Pseudomonas_E sp002840155 81.6071 292 471 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 N/A N/A N/A N/A 1 - GCA_002354655.1 s__Pseudomonas_E sp002354655 81.5967 302 471 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 99.84 99.84 0.95 0.95 2 - GCF_013184545.1 s__Pseudomonas_E sp013184545 81.5861 292 471 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 N/A N/A N/A N/A 1 - GCF_014174475.1 s__Pseudomonas_E sp014174475 81.4266 313 471 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 N/A N/A N/A N/A 1 - GCF_018398425.1 s__Pseudomonas_E lalucatii 81.3909 293 471 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 99.68 99.28 0.97 0.92 4 - GCF_014851905.1 s__Pseudomonas_E sp014851905 81.3782 312 471 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 N/A N/A N/A N/A 1 - GCF_900115555.1 s__Pseudomonas_E borbori 81.3084 293 471 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 N/A N/A N/A N/A 1 - GCF_009763245.1 s__Pseudomonas_E sp009763245 81.0632 293 471 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 N/A N/A N/A N/A 1 - GCF_900099645.1 s__Pseudomonas_E peli 81.0466 292 471 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 96.85 96.04 0.90 0.85 7 - GCA_001830395.1 s__Pseudomonas_E sp001830395 81.0114 236 471 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 N/A N/A N/A N/A 1 - GCF_900105355.1 s__Pseudomonas_E anguilliseptica 80.936 277 471 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 96.12 96.12 0.88 0.88 2 - GCF_005502935.1 s__Pseudomonas_E sp005502935 80.9303 276 471 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 95.95 95.95 0.83 0.83 2 - GCF_016901015.1 s__Pseudomonas_E sp016901015 80.9057 297 471 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 N/A N/A N/A N/A 1 - GCF_002025205.1 s__Pseudomonas_E sp002025205 80.8545 274 471 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 N/A N/A N/A N/A 1 - GCF_000412695.1 s__Pseudomonas_F resinovorans_A 80.7619 306 471 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_F 95.0 N/A N/A N/A N/A 1 - GCA_002418465.1 s__Pseudomonas_O sp002418465 80.5371 238 471 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_O 95.0 N/A N/A N/A N/A 1 - GCF_003050835.1 s__Pseudomonas_E sp003050835 80.4983 294 471 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 100.00 100.00 1.00 1.00 3 - GCF_007993865.1 s__Pseudomonas_E sp007993865 80.4826 279 471 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 N/A N/A N/A N/A 1 - GCF_016861355.1 s__Pseudomonas_E sp001259595 80.1028 238 471 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.3017 95.65 95.59 0.90 0.88 5 - GCF_013393345.1 s__Pseudomonas_F resinovorans_C 79.9972 280 471 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_F 95.0 95.04 95.04 0.90 0.90 2 - GCF_001439735.1 s__Pseudomonas_E paralactis 79.8087 197 471 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 98.61 98.52 0.94 0.92 4 - GCF_001186335.1 s__Pseudomonas_E trivialis_B 79.5625 205 471 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 95.34 95.31 0.86 0.86 8 - GCF_001870465.1 s__Pseudomonas_E extremorientalis 79.5591 216 471 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 98.37 98.13 0.91 0.89 29 - GCF_900103345.1 s__Pseudomonas_E azotoformans 79.4832 232 471 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 97.97 95.87 0.94 0.87 9 - GCF_002563895.1 s__Pseudomonas_E lurida 79.433 205 471 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 99.19 99.03 0.94 0.91 25 - -------------------------------------------------------------------------------- [2023-06-19 11:47:16,612] [INFO] GTDB search result was written to GCA_018780705.1_ASM1878070v1_genomic.fna/result_gtdb.tsv [2023-06-19 11:47:16,612] [INFO] ===== GTDB Search completed ===== [2023-06-19 11:47:16,618] [INFO] DFAST_QC result json was written to GCA_018780705.1_ASM1878070v1_genomic.fna/dqc_result.json [2023-06-19 11:47:16,618] [INFO] DFAST_QC completed! [2023-06-19 11:47:16,619] [INFO] Total running time: 0h1m24s