[2024-01-24 13:01:39,701] [INFO] DFAST_QC pipeline started. [2024-01-24 13:01:39,709] [INFO] DFAST_QC version: 0.5.7 [2024-01-24 13:01:39,709] [INFO] DQC Reference Directory: /var/lib/cwl/stgf6c3afed-a6bb-4fde-a86f-06f819bcd0bd/dqc_reference [2024-01-24 13:01:41,330] [INFO] ===== Start taxonomy check using ANI ===== [2024-01-24 13:01:41,330] [INFO] Task started: Prodigal [2024-01-24 13:01:41,331] [INFO] Running command: gunzip -c /var/lib/cwl/stga3de4800-e980-4230-a3a4-a75518d07395/GCF_002091735.1_ASM209173v1_genomic.fna.gz | prodigal -d GCF_002091735.1_ASM209173v1_genomic.fna/cds.fna -a GCF_002091735.1_ASM209173v1_genomic.fna/protein.faa -g 11 -q > /dev/null [2024-01-24 13:02:03,130] [INFO] Task succeeded: Prodigal [2024-01-24 13:02:03,130] [INFO] Task started: HMMsearch [2024-01-24 13:02:03,130] [INFO] Running command: hmmsearch --tblout GCF_002091735.1_ASM209173v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf6c3afed-a6bb-4fde-a86f-06f819bcd0bd/dqc_reference/reference_markers.hmm GCF_002091735.1_ASM209173v1_genomic.fna/protein.faa > /dev/null [2024-01-24 13:02:03,537] [INFO] Task succeeded: HMMsearch [2024-01-24 13:02:03,538] [INFO] Found 6/6 markers. [2024-01-24 13:02:03,587] [INFO] Query marker FASTA was written to GCF_002091735.1_ASM209173v1_genomic.fna/markers.fasta [2024-01-24 13:02:03,588] [INFO] Task started: Blastn [2024-01-24 13:02:03,588] [INFO] Running command: blastn -query GCF_002091735.1_ASM209173v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf6c3afed-a6bb-4fde-a86f-06f819bcd0bd/dqc_reference/reference_markers.fasta -out GCF_002091735.1_ASM209173v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5 [2024-01-24 13:02:04,666] [INFO] Task succeeded: Blastn [2024-01-24 13:02:04,674] [INFO] Selected 15 target genomes. [2024-01-24 13:02:04,674] [INFO] Target genome list was writen to GCF_002091735.1_ASM209173v1_genomic.fna/target_genomes.txt [2024-01-24 13:02:04,687] [INFO] Task started: fastANI [2024-01-24 13:02:04,687] [INFO] Running command: fastANI --query /var/lib/cwl/stga3de4800-e980-4230-a3a4-a75518d07395/GCF_002091735.1_ASM209173v1_genomic.fna.gz --refList GCF_002091735.1_ASM209173v1_genomic.fna/target_genomes.txt --output GCF_002091735.1_ASM209173v1_genomic.fna/fastani_result.tsv --threads 1 [2024-01-24 13:02:28,142] [INFO] Task succeeded: fastANI [2024-01-24 13:02:28,143] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf6c3afed-a6bb-4fde-a86f-06f819bcd0bd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt [2024-01-24 13:02:28,144] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf6c3afed-a6bb-4fde-a86f-06f819bcd0bd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt] [2024-01-24 13:02:28,163] [INFO] Found 15 fastANI hits (3 hits with ANI > threshold) [2024-01-24 13:02:28,164] [INFO] The taxonomy check result is classified as 'conclusive'. [2024-01-24 13:02:28,164] [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 mucidolens strain=NBRC 103159 GCA_002091735.1 46679 46679 type True 100.0 1895 1900 95 conclusive Pseudomonas mucidolens strain=NCTC8068 GCA_900475945.1 46679 46679 type True 99.9921 1899 1900 95 conclusive Pseudomonas mucidolens strain=LMG 2223 GCA_900106045.1 46679 46679 type True 99.9908 1900 1900 95 conclusive Pseudomonas gessardii GCA_900625085.1 78544 78544 type True 86.2923 1335 1900 95 below_threshold Pseudomonas gessardii strain=DSM 17152 GCA_009671285.1 78544 78544 type True 86.2921 1351 1900 95 below_threshold Pseudomonas proteolytica strain=DSM 15321 GCA_007858275.1 219574 219574 type True 86.1067 1347 1900 95 below_threshold Pseudomonas proteolytica strain=CCUG 51515T GCA_008692865.1 219574 219574 type True 86.0814 1332 1900 95 below_threshold Pseudomonas spelaei strain=CCM 7893 GCA_009724245.1 1055469 1055469 type True 85.4826 1306 1900 95 below_threshold Pseudomonas karstica strain=CCM 7891 GCA_009707515.1 1055468 1055468 type True 85.409 1302 1900 95 below_threshold Pseudomonas marginalis strain=DSM 13124 GCA_007858155.1 298 298 suspected-type True 85.1888 1317 1900 95 below_threshold Pseudomonas pergaminensis strain=1008 GCA_024112395.1 2853159 2853159 type True 84.9423 1331 1900 95 below_threshold Pseudomonas lurida strain=LMG 21995 GCA_002563895.1 244566 244566 type True 84.7852 1290 1900 95 below_threshold Pseudomonas fluorescens strain=NCTC10038 GCA_900475215.1 294 294 suspected-type True 84.7292 1286 1900 95 below_threshold Pseudomonas fluorescens strain=DSM 50090 GCA_007858165.1 294 294 suspected-type True 84.7228 1290 1900 95 below_threshold Pseudomonas pisciculturae strain=P115 GCA_015461805.1 2730413 2730413 type True 84.6599 1238 1900 95 below_threshold -------------------------------------------------------------------------------- [2024-01-24 13:02:28,166] [INFO] DFAST Taxonomy check result was written to GCF_002091735.1_ASM209173v1_genomic.fna/tc_result.tsv [2024-01-24 13:02:28,166] [INFO] ===== Taxonomy check completed ===== [2024-01-24 13:02:28,167] [INFO] ===== Start completeness check using CheckM ===== [2024-01-24 13:02:28,167] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf6c3afed-a6bb-4fde-a86f-06f819bcd0bd/dqc_reference/checkm_data [2024-01-24 13:02:28,168] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM [2024-01-24 13:02:28,226] [INFO] Task started: CheckM [2024-01-24 13:02:28,227] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002091735.1_ASM209173v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002091735.1_ASM209173v1_genomic.fna/checkm_input GCF_002091735.1_ASM209173v1_genomic.fna/checkm_result [2024-01-24 13:03:27,391] [INFO] Task succeeded: CheckM [2024-01-24 13:03:27,393] [INFO] Completeness check finished. -------------------------------------------------------------------------------- Completeness: 100.00% Contamintation: 0.00% Strain heterogeneity: 0.00% -------------------------------------------------------------------------------- [2024-01-24 13:03:27,418] [INFO] ===== Completeness check finished ===== [2024-01-24 13:03:27,419] [INFO] ===== Start GTDB Search ===== [2024-01-24 13:03:27,419] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002091735.1_ASM209173v1_genomic.fna/markers.fasta) [2024-01-24 13:03:27,420] [INFO] Task started: Blastn [2024-01-24 13:03:27,420] [INFO] Running command: blastn -query GCF_002091735.1_ASM209173v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf6c3afed-a6bb-4fde-a86f-06f819bcd0bd/dqc_reference/reference_markers_gtdb.fasta -out GCF_002091735.1_ASM209173v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5 [2024-01-24 13:03:29,122] [INFO] Task succeeded: Blastn [2024-01-24 13:03:29,126] [INFO] Selected 19 target genomes. [2024-01-24 13:03:29,126] [INFO] Target genome list was writen to GCF_002091735.1_ASM209173v1_genomic.fna/target_genomes_gtdb.txt [2024-01-24 13:03:29,140] [INFO] Task started: fastANI [2024-01-24 13:03:29,140] [INFO] Running command: fastANI --query /var/lib/cwl/stga3de4800-e980-4230-a3a4-a75518d07395/GCF_002091735.1_ASM209173v1_genomic.fna.gz --refList GCF_002091735.1_ASM209173v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002091735.1_ASM209173v1_genomic.fna/fastani_result_gtdb.tsv --threads 1 [2024-01-24 13:03:56,847] [INFO] Task succeeded: fastANI [2024-01-24 13:03:56,868] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius) [2024-01-24 13:03:56,868] [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_900106045.1 s__Pseudomonas_E mucidolens 99.9908 1900 1900 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 99.99 99.99 1.00 1.00 4 conclusive GCF_012985465.1 s__Pseudomonas_E sp012985465 86.3385 1347 1900 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 99.03 98.94 0.91 0.90 5 - GCF_001983165.1 s__Pseudomonas_E gessardii 86.2921 1351 1900 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 98.96 98.08 0.94 0.88 9 - GCF_003626995.1 s__Pseudomonas_E fluorescens_BA 86.2477 1386 1900 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 98.95 98.57 0.93 0.88 19 - GCF_016925675.1 s__Pseudomonas_E sp012985665 86.1987 1330 1900 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 98.30 97.44 0.92 0.88 4 - GCF_007858275.1 s__Pseudomonas_E proteolytica 86.1194 1345 1900 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 98.69 98.38 0.90 0.86 19 - GCF_013386765.1 s__Pseudomonas_E yamanorum_A 85.6948 1345 1900 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 98.70 98.16 0.94 0.91 5 - GCF_012935715.1 s__Pseudomonas_E sp000242655 85.557 1359 1900 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 98.42 98.02 0.94 0.92 3 - GCF_013403585.1 s__Pseudomonas_E yamanorum_B 85.5359 1296 1900 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 98.31 98.31 0.89 0.89 2 - GCF_018614655.1 s__Pseudomonas_E fluorescens_BX 85.4437 1272 1900 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_012935695.1 s__Pseudomonas_E sp012935695 85.4311 1351 1900 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_000346755.1 s__Pseudomonas_E sp000346755 85.1596 1246 1900 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_001439695.1 s__Pseudomonas_E veronii 85.1136 1316 1900 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 98.79 98.13 0.89 0.82 43 - GCF_900102035.1 s__Pseudomonas_E extremaustralis 84.9083 1261 1900 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 99.74 98.99 0.98 0.92 5 - GCF_013385965.1 s__Pseudomonas_E edaphica 84.757 1301 1900 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 99.04 98.93 0.94 0.92 9 - GCF_900215245.1 s__Pseudomonas_E fluorescens 84.7517 1281 1900 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 99.68 99.25 0.98 0.92 14 - GCF_900107155.1 s__Pseudomonas_E salomonii 84.7444 1283 1900 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 98.30 96.43 0.92 0.87 14 - GCF_001439805.1 s__Pseudomonas_E trivialis 84.5441 1190 1900 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 98.47 95.41 0.96 0.87 4 - GCF_009296165.1 s__Pseudomonas_E kitaguniensis 84.0787 1138 1900 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 98.01 96.76 0.90 0.88 5 - -------------------------------------------------------------------------------- [2024-01-24 13:03:56,871] [INFO] GTDB search result was written to GCF_002091735.1_ASM209173v1_genomic.fna/result_gtdb.tsv [2024-01-24 13:03:56,872] [INFO] ===== GTDB Search completed ===== [2024-01-24 13:03:56,876] [INFO] DFAST_QC result json was written to GCF_002091735.1_ASM209173v1_genomic.fna/dqc_result.json [2024-01-24 13:03:56,876] [INFO] DFAST_QC completed! [2024-01-24 13:03:56,876] [INFO] Total running time: 0h2m17s