[2024-01-24 13:09:51,512] [INFO] DFAST_QC pipeline started. [2024-01-24 13:09:51,515] [INFO] DFAST_QC version: 0.5.7 [2024-01-24 13:09:51,515] [INFO] DQC Reference Directory: /var/lib/cwl/stg9070b307-6298-407c-b53d-332b2ac19fc4/dqc_reference [2024-01-24 13:09:52,963] [INFO] ===== Start taxonomy check using ANI ===== [2024-01-24 13:09:52,964] [INFO] Task started: Prodigal [2024-01-24 13:09:52,964] [INFO] Running command: gunzip -c /var/lib/cwl/stgb992bef7-d8e4-4741-88aa-2e0ac4436e03/GCF_009296165.1_ASM929616v1_genomic.fna.gz | prodigal -d GCF_009296165.1_ASM929616v1_genomic.fna/cds.fna -a GCF_009296165.1_ASM929616v1_genomic.fna/protein.faa -g 11 -q > /dev/null [2024-01-24 13:10:14,510] [INFO] Task succeeded: Prodigal [2024-01-24 13:10:14,511] [INFO] Task started: HMMsearch [2024-01-24 13:10:14,511] [INFO] Running command: hmmsearch --tblout GCF_009296165.1_ASM929616v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9070b307-6298-407c-b53d-332b2ac19fc4/dqc_reference/reference_markers.hmm GCF_009296165.1_ASM929616v1_genomic.fna/protein.faa > /dev/null [2024-01-24 13:10:14,866] [INFO] Task succeeded: HMMsearch [2024-01-24 13:10:14,867] [INFO] Found 6/6 markers. [2024-01-24 13:10:14,914] [INFO] Query marker FASTA was written to GCF_009296165.1_ASM929616v1_genomic.fna/markers.fasta [2024-01-24 13:10:14,914] [INFO] Task started: Blastn [2024-01-24 13:10:14,914] [INFO] Running command: blastn -query GCF_009296165.1_ASM929616v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9070b307-6298-407c-b53d-332b2ac19fc4/dqc_reference/reference_markers.fasta -out GCF_009296165.1_ASM929616v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5 [2024-01-24 13:10:16,011] [INFO] Task succeeded: Blastn [2024-01-24 13:10:16,014] [INFO] Selected 19 target genomes. [2024-01-24 13:10:16,014] [INFO] Target genome list was writen to GCF_009296165.1_ASM929616v1_genomic.fna/target_genomes.txt [2024-01-24 13:10:16,025] [INFO] Task started: fastANI [2024-01-24 13:10:16,026] [INFO] Running command: fastANI --query /var/lib/cwl/stgb992bef7-d8e4-4741-88aa-2e0ac4436e03/GCF_009296165.1_ASM929616v1_genomic.fna.gz --refList GCF_009296165.1_ASM929616v1_genomic.fna/target_genomes.txt --output GCF_009296165.1_ASM929616v1_genomic.fna/fastani_result.tsv --threads 1 [2024-01-24 13:10:44,635] [INFO] Task succeeded: fastANI [2024-01-24 13:10:44,635] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9070b307-6298-407c-b53d-332b2ac19fc4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt [2024-01-24 13:10:44,635] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9070b307-6298-407c-b53d-332b2ac19fc4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt] [2024-01-24 13:10:44,658] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold) [2024-01-24 13:10:44,658] [INFO] The taxonomy check result is classified as 'conclusive'. [2024-01-24 13:10:44,658] [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 kitaguniensis strain=MAFF 212408 GCA_009296165.1 2607908 2607908 type True 100.0 1829 1839 95 conclusive Pseudomonas antarctica GCA_900624995.1 219572 219572 type True 88.0848 1323 1839 95 below_threshold Pseudomonas antarctica strain=CMS 35 GCA_010634845.1 219572 219572 type True 88.0521 1396 1839 95 below_threshold Pseudomonas fluorescens strain=NBRC 14160 GCA_002091595.1 294 294 suspected-type True 87.968 1403 1839 95 below_threshold Pseudomonas fluorescens strain=DSM 50090 GCA_007858165.1 294 294 suspected-type True 87.9407 1424 1839 95 below_threshold Pseudomonas fluorescens strain=DSM 50090 GCA_001269845.1 294 294 suspected-type True 87.9068 1436 1839 95 below_threshold Pseudomonas fluorescens strain=NCTC10038 GCA_900475215.1 294 294 suspected-type True 87.8577 1430 1839 95 below_threshold Pseudomonas salomonii strain=ICMP 14252 GCA_900107155.1 191391 191391 type True 87.747 1438 1839 95 below_threshold Pseudomonas salomonii strain=LMG 22120 GCA_001730645.1 191391 191391 type True 87.6665 1446 1839 95 below_threshold Pseudomonas marginalis strain=DSM 13124 GCA_007858155.1 298 298 suspected-type True 87.3761 1364 1839 95 below_threshold Pseudomonas marginalis strain=ICMP 3553 GCA_003700725.1 298 298 suspected-type True 87.3531 1311 1839 95 below_threshold Pseudomonas pergaminensis strain=1008 GCA_024112395.1 2853159 2853159 type True 87.2025 1362 1839 95 below_threshold Pseudomonas lurida strain=LMG 21995 GCA_002563895.1 244566 244566 type True 86.9733 1350 1839 95 below_threshold Pseudomonas simiae strain=CCUG 50988 GCA_001730615.1 321846 321846 type True 86.8528 1333 1839 95 below_threshold Pseudomonas simiae strain=CCUG 50988 GCA_900111895.1 321846 321846 type True 86.779 1341 1839 95 below_threshold Pseudomonas pisciculturae strain=P115 GCA_015461805.1 2730413 2730413 type True 86.6976 1323 1839 95 below_threshold Pseudomonas spelaei strain=CCM 7893 GCA_009724245.1 1055469 1055469 type True 85.2808 1240 1839 95 below_threshold Pseudomonas brenneri strain=JCM 13307 GCA_014646715.1 129817 129817 type True 85.2659 1196 1839 95 below_threshold Pseudomonas karstica strain=CCM 7891 GCA_009707515.1 1055468 1055468 type True 84.4874 1143 1839 95 below_threshold -------------------------------------------------------------------------------- [2024-01-24 13:10:44,660] [INFO] DFAST Taxonomy check result was written to GCF_009296165.1_ASM929616v1_genomic.fna/tc_result.tsv [2024-01-24 13:10:44,660] [INFO] ===== Taxonomy check completed ===== [2024-01-24 13:10:44,660] [INFO] ===== Start completeness check using CheckM ===== [2024-01-24 13:10:44,661] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9070b307-6298-407c-b53d-332b2ac19fc4/dqc_reference/checkm_data [2024-01-24 13:10:44,662] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM [2024-01-24 13:10:44,717] [INFO] Task started: CheckM [2024-01-24 13:10:44,718] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009296165.1_ASM929616v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009296165.1_ASM929616v1_genomic.fna/checkm_input GCF_009296165.1_ASM929616v1_genomic.fna/checkm_result [2024-01-24 13:11:46,689] [INFO] Task succeeded: CheckM [2024-01-24 13:11:46,690] [INFO] Completeness check finished. -------------------------------------------------------------------------------- Completeness: 100.00% Contamintation: 0.00% Strain heterogeneity: 0.00% -------------------------------------------------------------------------------- [2024-01-24 13:11:46,712] [INFO] ===== Completeness check finished ===== [2024-01-24 13:11:46,712] [INFO] ===== Start GTDB Search ===== [2024-01-24 13:11:46,713] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009296165.1_ASM929616v1_genomic.fna/markers.fasta) [2024-01-24 13:11:46,713] [INFO] Task started: Blastn [2024-01-24 13:11:46,713] [INFO] Running command: blastn -query GCF_009296165.1_ASM929616v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9070b307-6298-407c-b53d-332b2ac19fc4/dqc_reference/reference_markers_gtdb.fasta -out GCF_009296165.1_ASM929616v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5 [2024-01-24 13:11:48,599] [INFO] Task succeeded: Blastn [2024-01-24 13:11:48,603] [INFO] Selected 21 target genomes. [2024-01-24 13:11:48,603] [INFO] Target genome list was writen to GCF_009296165.1_ASM929616v1_genomic.fna/target_genomes_gtdb.txt [2024-01-24 13:11:48,618] [INFO] Task started: fastANI [2024-01-24 13:11:48,618] [INFO] Running command: fastANI --query /var/lib/cwl/stgb992bef7-d8e4-4741-88aa-2e0ac4436e03/GCF_009296165.1_ASM929616v1_genomic.fna.gz --refList GCF_009296165.1_ASM929616v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009296165.1_ASM929616v1_genomic.fna/fastani_result_gtdb.tsv --threads 1 [2024-01-24 13:12:17,810] [INFO] Task succeeded: fastANI [2024-01-24 13:12:17,838] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius) [2024-01-24 13:12:17,838] [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_009296165.1 s__Pseudomonas_E kitaguniensis 100.0 1829 1839 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 98.01 96.76 0.90 0.88 5 conclusive GCF_009707325.1 s__Pseudomonas_E sp002263605 88.7649 1365 1839 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 99.58 99.58 0.94 0.94 2 - GCF_009834565.1 s__Pseudomonas_E sp009834565 88.4796 1427 1839 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 97.71 97.35 0.93 0.93 3 - GCF_001647715.1 s__Pseudomonas_E antarctica_A 88.2063 1422 1839 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 97.45 97.45 0.91 0.91 2 - GCF_003852315.1 s__Pseudomonas_E sp003014915 88.1708 1426 1839 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 98.48 96.20 0.95 0.91 10 - GCF_900624995.1 s__Pseudomonas_E antarctica 88.078 1324 1839 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 99.98 99.98 1.00 1.00 3 - GCF_900215245.1 s__Pseudomonas_E fluorescens 87.8536 1438 1839 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 87.7753 1435 1839 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_013385965.1 s__Pseudomonas_E edaphica 87.7401 1400 1839 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_002022275.1 s__Pseudomonas_E fluorescens_AJ 87.7172 1383 1839 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_900580675.1 s__Pseudomonas_E sp900580675 87.703 1333 1839 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_900591205.1 s__Pseudomonas_E sp900591205 87.5962 1410 1839 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_001050345.1 s__Pseudomonas_E fildesensis 87.5793 1371 1839 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_003208475.1 s__Pseudomonas_E sp003208475 87.3504 1371 1839 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_007858185.1 s__Pseudomonas_E grimontii 87.3467 1381 1839 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 100.00 100.00 1.00 1.00 2 - GCF_003852405.1 s__Pseudomonas_E sp003852405 87.3036 1338 1839 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 95.89 95.89 0.88 0.88 2 - GCF_001439695.1 s__Pseudomonas_E veronii 87.2393 1313 1839 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 86.8255 1284 1839 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_015461805.1 s__Pseudomonas_E pisciculturae 86.7144 1321 1839 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 99.09 99.09 0.95 0.95 2 - GCF_900583165.1 s__Pseudomonas_E sp900583165 86.4786 1307 1839 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 99.99 99.99 1.00 0.99 4 - GCF_013386765.1 s__Pseudomonas_E yamanorum_A 86.2271 1340 1839 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 98.70 98.16 0.94 0.91 5 - -------------------------------------------------------------------------------- [2024-01-24 13:12:17,840] [INFO] GTDB search result was written to GCF_009296165.1_ASM929616v1_genomic.fna/result_gtdb.tsv [2024-01-24 13:12:17,840] [INFO] ===== GTDB Search completed ===== [2024-01-24 13:12:17,844] [INFO] DFAST_QC result json was written to GCF_009296165.1_ASM929616v1_genomic.fna/dqc_result.json [2024-01-24 13:12:17,845] [INFO] DFAST_QC completed! [2024-01-24 13:12:17,845] [INFO] Total running time: 0h2m26s