[2024-01-24 13:01:26,471] [INFO] DFAST_QC pipeline started. [2024-01-24 13:01:26,473] [INFO] DFAST_QC version: 0.5.7 [2024-01-24 13:01:26,473] [INFO] DQC Reference Directory: /var/lib/cwl/stg5a476b96-8353-4a86-bd8c-416fcdd19796/dqc_reference [2024-01-24 13:01:27,909] [INFO] ===== Start taxonomy check using ANI ===== [2024-01-24 13:01:27,910] [INFO] Task started: Prodigal [2024-01-24 13:01:27,910] [INFO] Running command: gunzip -c /var/lib/cwl/stg997c56b3-ad06-4551-832d-581ec2470fa2/GCF_001730605.1_ASM173060v1_genomic.fna.gz | prodigal -d GCF_001730605.1_ASM173060v1_genomic.fna/cds.fna -a GCF_001730605.1_ASM173060v1_genomic.fna/protein.faa -g 11 -q > /dev/null [2024-01-24 13:01:51,365] [INFO] Task succeeded: Prodigal [2024-01-24 13:01:51,366] [INFO] Task started: HMMsearch [2024-01-24 13:01:51,366] [INFO] Running command: hmmsearch --tblout GCF_001730605.1_ASM173060v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5a476b96-8353-4a86-bd8c-416fcdd19796/dqc_reference/reference_markers.hmm GCF_001730605.1_ASM173060v1_genomic.fna/protein.faa > /dev/null [2024-01-24 13:01:51,710] [INFO] Task succeeded: HMMsearch [2024-01-24 13:01:51,711] [INFO] Found 6/6 markers. [2024-01-24 13:01:51,765] [INFO] Query marker FASTA was written to GCF_001730605.1_ASM173060v1_genomic.fna/markers.fasta [2024-01-24 13:01:51,765] [INFO] Task started: Blastn [2024-01-24 13:01:51,766] [INFO] Running command: blastn -query GCF_001730605.1_ASM173060v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5a476b96-8353-4a86-bd8c-416fcdd19796/dqc_reference/reference_markers.fasta -out GCF_001730605.1_ASM173060v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5 [2024-01-24 13:01:52,803] [INFO] Task succeeded: Blastn [2024-01-24 13:01:52,808] [INFO] Selected 15 target genomes. [2024-01-24 13:01:52,808] [INFO] Target genome list was writen to GCF_001730605.1_ASM173060v1_genomic.fna/target_genomes.txt [2024-01-24 13:01:52,814] [INFO] Task started: fastANI [2024-01-24 13:01:52,814] [INFO] Running command: fastANI --query /var/lib/cwl/stg997c56b3-ad06-4551-832d-581ec2470fa2/GCF_001730605.1_ASM173060v1_genomic.fna.gz --refList GCF_001730605.1_ASM173060v1_genomic.fna/target_genomes.txt --output GCF_001730605.1_ASM173060v1_genomic.fna/fastani_result.tsv --threads 1 [2024-01-24 13:02:18,120] [INFO] Task succeeded: fastANI [2024-01-24 13:02:18,121] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5a476b96-8353-4a86-bd8c-416fcdd19796/dqc_reference/prokaryote_ANI_species_specific_threshold.txt [2024-01-24 13:02:18,121] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5a476b96-8353-4a86-bd8c-416fcdd19796/dqc_reference/prokaryote_ANI_species_specific_threshold.txt] [2024-01-24 13:02:18,138] [INFO] Found 15 fastANI hits (2 hits with ANI > threshold) [2024-01-24 13:02:18,138] [INFO] The taxonomy check result is classified as 'conclusive'. [2024-01-24 13:02:18,138] [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 poae strain=LMG 21465 GCA_001730605.1 200451 200451 type True 100.0 1943 1953 95 conclusive Pseudomonas poae strain=DSM 14936 GCA_001439785.1 200451 200451 type True 99.9644 1913 1953 95 conclusive Pseudomonas trivialis strain=LMG 21464 GCA_001730655.1 200450 200450 type True 93.7629 1629 1953 95 below_threshold Pseudomonas trivialis strain=DSM 14937 GCA_001439805.1 200450 200450 type True 93.7465 1623 1953 95 below_threshold Pseudomonas marginalis strain=DSM 13124 GCA_007858155.1 298 298 suspected-type True 87.6331 1441 1953 95 below_threshold Pseudomonas azotoformans strain=NBRC 12693 GCA_002091515.1 47878 47878 suspected-type True 87.4972 1415 1953 95 below_threshold Pseudomonas marginalis strain=ICMP 3553 GCA_003700725.1 298 298 suspected-type True 87.4078 1373 1953 95 below_threshold Pseudomonas pergaminensis strain=1008 GCA_024112395.1 2853159 2853159 type True 87.3473 1463 1953 95 below_threshold Pseudomonas salomonii strain=ICMP 14252 GCA_900107155.1 191391 191391 type True 87.2852 1444 1953 95 below_threshold Pseudomonas cedrina subsp. cedrina GCA_900625035.1 76762 651740 type True 87.2212 1428 1953 95 below_threshold Pseudomonas extremaustralis strain=DSM 17835 GCA_007858235.1 359110 359110 type True 87.19 1308 1953 95 below_threshold Pseudomonas lurida strain=LMG 21995 GCA_002563895.1 244566 244566 type True 87.1741 1414 1953 95 below_threshold Pseudomonas kairouanensis strain=KC12 GCA_004682055.1 2293832 2293832 type True 87.1138 1354 1953 95 below_threshold Pseudomonas spelaei strain=CCM 7893 GCA_009724245.1 1055469 1055469 type True 85.2768 1263 1953 95 below_threshold Pseudomonas karstica strain=CCM 7891 GCA_009707515.1 1055468 1055468 type True 84.6313 1183 1953 95 below_threshold -------------------------------------------------------------------------------- [2024-01-24 13:02:18,140] [INFO] DFAST Taxonomy check result was written to GCF_001730605.1_ASM173060v1_genomic.fna/tc_result.tsv [2024-01-24 13:02:18,140] [INFO] ===== Taxonomy check completed ===== [2024-01-24 13:02:18,141] [INFO] ===== Start completeness check using CheckM ===== [2024-01-24 13:02:18,141] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5a476b96-8353-4a86-bd8c-416fcdd19796/dqc_reference/checkm_data [2024-01-24 13:02:18,142] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM [2024-01-24 13:02:18,202] [INFO] Task started: CheckM [2024-01-24 13:02:18,202] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001730605.1_ASM173060v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001730605.1_ASM173060v1_genomic.fna/checkm_input GCF_001730605.1_ASM173060v1_genomic.fna/checkm_result [2024-01-24 13:03:29,055] [INFO] Task succeeded: CheckM [2024-01-24 13:03:29,057] [INFO] Completeness check finished. -------------------------------------------------------------------------------- Completeness: 100.00% Contamintation: 0.00% Strain heterogeneity: 0.00% -------------------------------------------------------------------------------- [2024-01-24 13:03:29,082] [INFO] ===== Completeness check finished ===== [2024-01-24 13:03:29,082] [INFO] ===== Start GTDB Search ===== [2024-01-24 13:03:29,082] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001730605.1_ASM173060v1_genomic.fna/markers.fasta) [2024-01-24 13:03:29,083] [INFO] Task started: Blastn [2024-01-24 13:03:29,083] [INFO] Running command: blastn -query GCF_001730605.1_ASM173060v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5a476b96-8353-4a86-bd8c-416fcdd19796/dqc_reference/reference_markers_gtdb.fasta -out GCF_001730605.1_ASM173060v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5 [2024-01-24 13:03:30,968] [INFO] Task succeeded: Blastn [2024-01-24 13:03:30,973] [INFO] Selected 21 target genomes. [2024-01-24 13:03:30,973] [INFO] Target genome list was writen to GCF_001730605.1_ASM173060v1_genomic.fna/target_genomes_gtdb.txt [2024-01-24 13:03:30,997] [INFO] Task started: fastANI [2024-01-24 13:03:30,997] [INFO] Running command: fastANI --query /var/lib/cwl/stg997c56b3-ad06-4551-832d-581ec2470fa2/GCF_001730605.1_ASM173060v1_genomic.fna.gz --refList GCF_001730605.1_ASM173060v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001730605.1_ASM173060v1_genomic.fna/fastani_result_gtdb.tsv --threads 1 [2024-01-24 13:04:06,839] [INFO] Task succeeded: fastANI [2024-01-24 13:04:06,859] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius) [2024-01-24 13:04:06,859] [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_001439785.1 s__Pseudomonas_E poae 99.9644 1913 1953 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 99.09 98.80 0.95 0.92 10 conclusive GCF_001439805.1 s__Pseudomonas_E trivialis 93.7514 1623 1953 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_003097075.1 s__Pseudomonas_E sp003097075 88.0547 1399 1953 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 98.77 98.77 0.94 0.94 2 - GCF_900580675.1 s__Pseudomonas_E sp900580675 87.6265 1361 1953 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_900103345.1 s__Pseudomonas_E azotoformans 87.5336 1423 1953 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_003612935.1 s__Pseudomonas_E sp003013355 87.5315 1431 1953 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 98.87 98.56 0.95 0.92 7 - GCF_015163715.1 s__Pseudomonas_E cyclaminis 87.5186 1303 1953 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 96.88 95.83 0.83 0.80 14 - GCF_001439695.1 s__Pseudomonas_E veronii 87.4277 1394 1953 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_009834565.1 s__Pseudomonas_E sp009834565 87.4011 1457 1953 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_009707325.1 s__Pseudomonas_E sp002263605 87.4 1369 1953 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_001645105.1 s__Pseudomonas_E marginalis_B 87.3659 1449 1953 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 98.70 98.28 0.91 0.87 10 - GCF_013385985.1 s__Pseudomonas_E sp013385985 87.3313 1385 1953 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_013386585.1 s__Pseudomonas_E sp013386585 87.2951 1370 1953 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_900107155.1 s__Pseudomonas_E salomonii 87.2845 1444 1953 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_001579805.1 s__Pseudomonas_E azotoformans_A 87.2824 1433 1953 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 96.75 96.24 0.87 0.84 8 - GCF_900102035.1 s__Pseudomonas_E extremaustralis 87.1932 1345 1953 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_001983175.1 s__Pseudomonas_E cedrina 87.1822 1440 1953 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 99.10 97.30 0.97 0.92 4 - GCF_001708445.1 s__Pseudomonas_E fluorescens_AN 87.181 1417 1953 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 99.17 98.56 0.90 0.82 34 - GCF_001186335.1 s__Pseudomonas_E trivialis_B 87.1379 1429 1953 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_012844475.1 s__Pseudomonas_E sp012844475 87.1051 1351 1953 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_003851685.1 s__Pseudomonas_E sp003851685 87.0085 1432 1953 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 N/A N/A N/A N/A 1 - -------------------------------------------------------------------------------- [2024-01-24 13:04:06,861] [INFO] GTDB search result was written to GCF_001730605.1_ASM173060v1_genomic.fna/result_gtdb.tsv [2024-01-24 13:04:06,861] [INFO] ===== GTDB Search completed ===== [2024-01-24 13:04:06,866] [INFO] DFAST_QC result json was written to GCF_001730605.1_ASM173060v1_genomic.fna/dqc_result.json [2024-01-24 13:04:06,866] [INFO] DFAST_QC completed! [2024-01-24 13:04:06,866] [INFO] Total running time: 0h2m40s