[2024-01-24 14:30:47,335] [INFO] DFAST_QC pipeline started. [2024-01-24 14:30:47,340] [INFO] DFAST_QC version: 0.5.7 [2024-01-24 14:30:47,341] [INFO] DQC Reference Directory: /var/lib/cwl/stg868adc77-2ab3-4417-990c-0e18ce998af9/dqc_reference [2024-01-24 14:30:48,719] [INFO] ===== Start taxonomy check using ANI ===== [2024-01-24 14:30:48,720] [INFO] Task started: Prodigal [2024-01-24 14:30:48,721] [INFO] Running command: gunzip -c /var/lib/cwl/stgfde063cc-a45a-45fd-921a-d209e869eae5/GCF_017313085.1_ASM1731308v1_genomic.fna.gz | prodigal -d GCF_017313085.1_ASM1731308v1_genomic.fna/cds.fna -a GCF_017313085.1_ASM1731308v1_genomic.fna/protein.faa -g 11 -q > /dev/null [2024-01-24 14:31:04,346] [INFO] Task succeeded: Prodigal [2024-01-24 14:31:04,346] [INFO] Task started: HMMsearch [2024-01-24 14:31:04,346] [INFO] Running command: hmmsearch --tblout GCF_017313085.1_ASM1731308v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg868adc77-2ab3-4417-990c-0e18ce998af9/dqc_reference/reference_markers.hmm GCF_017313085.1_ASM1731308v1_genomic.fna/protein.faa > /dev/null [2024-01-24 14:31:04,733] [INFO] Task succeeded: HMMsearch [2024-01-24 14:31:04,734] [INFO] Found 6/6 markers. [2024-01-24 14:31:04,777] [INFO] Query marker FASTA was written to GCF_017313085.1_ASM1731308v1_genomic.fna/markers.fasta [2024-01-24 14:31:04,777] [INFO] Task started: Blastn [2024-01-24 14:31:04,777] [INFO] Running command: blastn -query GCF_017313085.1_ASM1731308v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg868adc77-2ab3-4417-990c-0e18ce998af9/dqc_reference/reference_markers.fasta -out GCF_017313085.1_ASM1731308v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5 [2024-01-24 14:31:05,745] [INFO] Task succeeded: Blastn [2024-01-24 14:31:05,749] [INFO] Selected 17 target genomes. [2024-01-24 14:31:05,749] [INFO] Target genome list was writen to GCF_017313085.1_ASM1731308v1_genomic.fna/target_genomes.txt [2024-01-24 14:31:05,774] [INFO] Task started: fastANI [2024-01-24 14:31:05,774] [INFO] Running command: fastANI --query /var/lib/cwl/stgfde063cc-a45a-45fd-921a-d209e869eae5/GCF_017313085.1_ASM1731308v1_genomic.fna.gz --refList GCF_017313085.1_ASM1731308v1_genomic.fna/target_genomes.txt --output GCF_017313085.1_ASM1731308v1_genomic.fna/fastani_result.tsv --threads 1 [2024-01-24 14:31:20,606] [INFO] Task succeeded: fastANI [2024-01-24 14:31:20,606] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg868adc77-2ab3-4417-990c-0e18ce998af9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt [2024-01-24 14:31:20,607] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg868adc77-2ab3-4417-990c-0e18ce998af9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt] [2024-01-24 14:31:20,620] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold) [2024-01-24 14:31:20,620] [INFO] The taxonomy check result is classified as 'conclusive'. [2024-01-24 14:31:20,620] [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 Roseibium limicola strain=CAU 1637 GCA_017313085.1 2816037 2816037 type True 100.0 1494 1495 95 conclusive Roseibium aestuarii strain=SYSU M00256-3 GCA_008477545.1 2600299 2600299 type True 79.6221 686 1495 95 below_threshold Roseibium suaedae strain=DSM 22153 GCA_900142725.1 735517 735517 type True 78.6703 432 1495 95 below_threshold Roseibium polysiphoniae strain=KACC 19711 GCA_014842925.1 2571221 2571221 type True 78.5799 371 1495 95 below_threshold Roseibium litorale strain=4C16A GCA_014842915.1 2803841 2803841 type True 78.4029 419 1495 95 below_threshold Roseibium aggregatum strain=IAM 12614 GCA_000168975.1 187304 187304 suspected-type True 78.2223 422 1495 95 below_threshold Pannonibacter phragmitetus strain=NCTC13350 GCA_900454465.1 121719 121719 suspected-type True 77.7601 334 1495 95 below_threshold Pannonibacter indicus strain=DSM 23407 GCA_001517385.1 466044 466044 type True 77.664 338 1495 95 below_threshold Pannonibacter indicus strain=DSM 23407 GCA_001418225.1 466044 466044 type True 77.656 339 1495 95 below_threshold Rhizobium taibaishanense strain=14971 GCA_001938985.1 887144 887144 type True 76.4725 128 1495 95 below_threshold Rhizobium taibaishanense strain=DSM 100021 GCA_014196735.1 887144 887144 type True 76.4604 132 1495 95 below_threshold Rhizobium tumorigenes strain=1078 GCA_003240565.1 2041385 2041385 type True 76.3516 113 1495 95 below_threshold Novispirillum itersonii subsp. itersonii strain=ATCC 12639 GCA_000381985.1 180199 189 type True 75.9811 55 1495 95 below_threshold Pseudochrobactrum algeriensis GCA_907164595.1 2834768 2834768 type True 75.859 66 1495 95 below_threshold Pseudochrobactrum algeriensis GCA_018436245.1 2834768 2834768 type True 75.859 66 1495 95 below_threshold -------------------------------------------------------------------------------- [2024-01-24 14:31:20,630] [INFO] DFAST Taxonomy check result was written to GCF_017313085.1_ASM1731308v1_genomic.fna/tc_result.tsv [2024-01-24 14:31:20,631] [INFO] ===== Taxonomy check completed ===== [2024-01-24 14:31:20,631] [INFO] ===== Start completeness check using CheckM ===== [2024-01-24 14:31:20,632] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg868adc77-2ab3-4417-990c-0e18ce998af9/dqc_reference/checkm_data [2024-01-24 14:31:20,634] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM [2024-01-24 14:31:20,683] [INFO] Task started: CheckM [2024-01-24 14:31:20,684] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017313085.1_ASM1731308v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017313085.1_ASM1731308v1_genomic.fna/checkm_input GCF_017313085.1_ASM1731308v1_genomic.fna/checkm_result [2024-01-24 14:32:08,458] [INFO] Task succeeded: CheckM [2024-01-24 14:32:08,459] [INFO] Completeness check finished. -------------------------------------------------------------------------------- Completeness: 100.00% Contamintation: 0.00% Strain heterogeneity: 0.00% -------------------------------------------------------------------------------- [2024-01-24 14:32:08,491] [INFO] ===== Completeness check finished ===== [2024-01-24 14:32:08,492] [INFO] ===== Start GTDB Search ===== [2024-01-24 14:32:08,492] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017313085.1_ASM1731308v1_genomic.fna/markers.fasta) [2024-01-24 14:32:08,493] [INFO] Task started: Blastn [2024-01-24 14:32:08,493] [INFO] Running command: blastn -query GCF_017313085.1_ASM1731308v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg868adc77-2ab3-4417-990c-0e18ce998af9/dqc_reference/reference_markers_gtdb.fasta -out GCF_017313085.1_ASM1731308v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5 [2024-01-24 14:32:10,232] [INFO] Task succeeded: Blastn [2024-01-24 14:32:10,235] [INFO] Selected 16 target genomes. [2024-01-24 14:32:10,236] [INFO] Target genome list was writen to GCF_017313085.1_ASM1731308v1_genomic.fna/target_genomes_gtdb.txt [2024-01-24 14:32:10,257] [INFO] Task started: fastANI [2024-01-24 14:32:10,258] [INFO] Running command: fastANI --query /var/lib/cwl/stgfde063cc-a45a-45fd-921a-d209e869eae5/GCF_017313085.1_ASM1731308v1_genomic.fna.gz --refList GCF_017313085.1_ASM1731308v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017313085.1_ASM1731308v1_genomic.fna/fastani_result_gtdb.tsv --threads 1 [2024-01-24 14:32:25,533] [INFO] Task succeeded: fastANI [2024-01-24 14:32:25,554] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius) [2024-01-24 14:32:25,555] [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_017313085.1 s__Roseibium sp017313085 100.0 1494 1495 d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Roseibium 95.0 N/A N/A N/A N/A 1 conclusive GCF_008477545.1 s__Roseibium aestuarii 79.6221 686 1495 d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Roseibium 95.0 N/A N/A N/A N/A 1 - GCF_900142725.1 s__Roseibium suaedae 78.6745 431 1495 d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Roseibium 95.0 N/A N/A N/A N/A 1 - GCF_009650605.1 s__Roseibium sp009650605 78.6225 381 1495 d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Roseibium 95.0 N/A N/A N/A N/A 1 - GCF_014842925.1 s__Roseibium polysiphoniae 78.5799 371 1495 d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Roseibium 95.0 96.20 96.20 0.93 0.93 2 - GCF_014842915.1 s__Roseibium litorale 78.4118 418 1495 d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Roseibium 95.0 N/A N/A N/A N/A 1 - GCF_014692675.1 s__Roseibium aggregatum_C 78.2911 440 1495 d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Roseibium 95.0 N/A N/A N/A N/A 1 - GCF_000168975.1 s__Roseibium aggregatum 78.2246 421 1495 d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Roseibium 95.0 N/A N/A N/A N/A 1 - GCF_001999245.1 s__Roseibium aggregatum_A 78.1932 393 1495 d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Roseibium 95.0 97.61 96.85 0.93 0.89 16 - GCF_008107695.1 s__Roseibium sp008107695 77.9969 386 1495 d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Roseibium 95.0 N/A N/A N/A N/A 1 - GCF_003075075.1 s__Roseibium sp003075075 77.9046 391 1495 d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Roseibium 95.0 N/A N/A N/A N/A 1 - GCF_009915765.1 s__Pannonibacter sp009915765 77.7914 322 1495 d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Pannonibacter 95.0 98.76 98.76 0.96 0.96 2 - GCF_000382365.1 s__Pannonibacter phragmitetus 77.6841 339 1495 d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Pannonibacter 95.0 99.99 99.99 1.00 1.00 2 - GCF_001418225.1 s__Pannonibacter indicus 77.6699 336 1495 d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Pannonibacter 95.0 96.01 95.55 0.94 0.89 12 - GCF_001938985.1 s__Allorhizobium taibaishanense 76.4692 127 1495 d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium 95.0 100.00 100.00 1.00 1.00 2 - GCA_900473205.1 s__Agrobacterium sp900473205 76.0977 121 1495 d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Agrobacterium 95.0 99.99 99.99 0.99 0.99 2 - -------------------------------------------------------------------------------- [2024-01-24 14:32:25,557] [INFO] GTDB search result was written to GCF_017313085.1_ASM1731308v1_genomic.fna/result_gtdb.tsv [2024-01-24 14:32:25,557] [INFO] ===== GTDB Search completed ===== [2024-01-24 14:32:25,562] [INFO] DFAST_QC result json was written to GCF_017313085.1_ASM1731308v1_genomic.fna/dqc_result.json [2024-01-24 14:32:25,562] [INFO] DFAST_QC completed! [2024-01-24 14:32:25,562] [INFO] Total running time: 0h1m38s