[2024-01-24 13:40:42,151] [INFO] DFAST_QC pipeline started. [2024-01-24 13:40:42,154] [INFO] DFAST_QC version: 0.5.7 [2024-01-24 13:40:42,154] [INFO] DQC Reference Directory: /var/lib/cwl/stg4443572e-2144-4a43-bb80-2dfe7dd9290a/dqc_reference [2024-01-24 13:40:43,569] [INFO] ===== Start taxonomy check using ANI ===== [2024-01-24 13:40:43,570] [INFO] Task started: Prodigal [2024-01-24 13:40:43,570] [INFO] Running command: gunzip -c /var/lib/cwl/stg8563f9bb-6ee7-41df-a822-bfa0899af1a2/GCF_025770765.1_ASM2577076v1_genomic.fna.gz | prodigal -d GCF_025770765.1_ASM2577076v1_genomic.fna/cds.fna -a GCF_025770765.1_ASM2577076v1_genomic.fna/protein.faa -g 11 -q > /dev/null [2024-01-24 13:40:59,271] [INFO] Task succeeded: Prodigal [2024-01-24 13:40:59,271] [INFO] Task started: HMMsearch [2024-01-24 13:40:59,271] [INFO] Running command: hmmsearch --tblout GCF_025770765.1_ASM2577076v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4443572e-2144-4a43-bb80-2dfe7dd9290a/dqc_reference/reference_markers.hmm GCF_025770765.1_ASM2577076v1_genomic.fna/protein.faa > /dev/null [2024-01-24 13:40:59,617] [INFO] Task succeeded: HMMsearch [2024-01-24 13:40:59,618] [INFO] Found 6/6 markers. [2024-01-24 13:40:59,661] [INFO] Query marker FASTA was written to GCF_025770765.1_ASM2577076v1_genomic.fna/markers.fasta [2024-01-24 13:40:59,662] [INFO] Task started: Blastn [2024-01-24 13:40:59,662] [INFO] Running command: blastn -query GCF_025770765.1_ASM2577076v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4443572e-2144-4a43-bb80-2dfe7dd9290a/dqc_reference/reference_markers.fasta -out GCF_025770765.1_ASM2577076v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5 [2024-01-24 13:41:00,556] [INFO] Task succeeded: Blastn [2024-01-24 13:41:00,563] [INFO] Selected 26 target genomes. [2024-01-24 13:41:00,563] [INFO] Target genome list was writen to GCF_025770765.1_ASM2577076v1_genomic.fna/target_genomes.txt [2024-01-24 13:41:00,572] [INFO] Task started: fastANI [2024-01-24 13:41:00,573] [INFO] Running command: fastANI --query /var/lib/cwl/stg8563f9bb-6ee7-41df-a822-bfa0899af1a2/GCF_025770765.1_ASM2577076v1_genomic.fna.gz --refList GCF_025770765.1_ASM2577076v1_genomic.fna/target_genomes.txt --output GCF_025770765.1_ASM2577076v1_genomic.fna/fastani_result.tsv --threads 1 [2024-01-24 13:41:18,880] [INFO] Task succeeded: fastANI [2024-01-24 13:41:18,881] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4443572e-2144-4a43-bb80-2dfe7dd9290a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt [2024-01-24 13:41:18,881] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4443572e-2144-4a43-bb80-2dfe7dd9290a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt] [2024-01-24 13:41:18,901] [INFO] Found 24 fastANI hits (0 hits with ANI > threshold) [2024-01-24 13:41:18,901] [INFO] The taxonomy check result is classified as 'below_threshold'. [2024-01-24 13:41:18,901] [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 Propionivibrio dicarboxylicus strain=DSM 5885 GCA_900099695.1 83767 83767 type True 78.1301 359 1567 95 below_threshold Propionivibrio limicola strain=GolChi1 GCA_009469695.1 167645 167645 type True 78.1209 281 1567 95 below_threshold Rhodocyclus purpureus strain=DSM 168 GCA_016653115.1 1067 1067 type True 77.8824 222 1567 95 below_threshold Rhodocyclus tenuis strain=2761 GCA_014197755.1 1066 1066 type True 77.6955 258 1567 95 below_threshold Rhodocyclus tenuis strain=2761 GCA_009469755.1 1066 1066 type True 77.6576 258 1567 95 below_threshold Rhodocyclus gracilis strain=DSM 110 GCA_009617575.1 2929842 2929842 type True 77.3926 196 1567 95 below_threshold Azonexus fungiphilus strain=DSM 23841 GCA_003634965.1 146940 146940 type True 77.1949 219 1567 95 below_threshold Georgfuchsia toluolica strain=G5G6 GCA_907163265.1 424218 424218 type True 76.809 88 1567 95 below_threshold Jeongeupia naejangsanensis strain=DSM 24253 GCA_016865585.1 613195 613195 type True 76.7971 106 1567 95 below_threshold Thauera chlorobenzoica strain=3CB1 GCA_001922305.1 96773 96773 type True 76.7675 143 1567 95 below_threshold Thauera chlorobenzoica strain=3CB-1 GCA_900108255.1 96773 96773 type True 76.7088 144 1567 95 below_threshold Thauera aromatica strain=K172 GCA_003030465.1 59405 59405 type True 76.701 143 1567 95 below_threshold Candidatus Accumulibacter contiguus GCA_012940005.1 2954381 2954381 type True 76.4589 184 1567 95 below_threshold Paraburkholderia podalyriae strain=WC7.3b GCA_014397785.1 1938811 1938811 type True 76.2434 108 1567 95 below_threshold Achromobacter kerstersii strain=LMG 3441 GCA_902859595.1 1353890 1353890 type True 76.165 81 1567 95 below_threshold Vogesella urethralis strain=YM-1 GCA_007644045.2 2592656 2592656 type True 76.1517 63 1567 95 below_threshold Paraburkholderia saeva strain=LMG 31841 GCA_907164555.1 2777537 2777537 type True 76.1516 92 1567 95 below_threshold Chromobacterium piscinae strain=DSM 23278 GCA_021129175.1 686831 686831 type True 76.1128 92 1567 95 below_threshold Massilia agri strain=JCM 31661 GCA_024753255.1 1886785 1886785 type True 76.0157 90 1567 95 below_threshold Achromobacter piechaudii strain=LMG 1873 GCA_902859685.1 72556 72556 type True 75.985 87 1567 95 below_threshold Paludibacterium paludis strain=BCRC 80514 GCA_018802605.1 1225769 1225769 type True 75.9044 72 1567 95 below_threshold Aquitalea magnusonii strain=DSM 25134 GCA_003202035.1 332411 332411 suspected-type True 75.8748 53 1567 95 below_threshold Achromobacter piechaudii strain=NBRC 102461 GCA_001571245.1 72556 72556 type True 75.7721 87 1567 95 below_threshold Paludibacterium paludis strain=KCTC 32182 GCA_014652495.1 1225769 1225769 type True 75.6161 71 1567 95 below_threshold -------------------------------------------------------------------------------- [2024-01-24 13:41:18,903] [INFO] DFAST Taxonomy check result was written to GCF_025770765.1_ASM2577076v1_genomic.fna/tc_result.tsv [2024-01-24 13:41:18,904] [INFO] ===== Taxonomy check completed ===== [2024-01-24 13:41:18,904] [INFO] ===== Start completeness check using CheckM ===== [2024-01-24 13:41:18,904] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4443572e-2144-4a43-bb80-2dfe7dd9290a/dqc_reference/checkm_data [2024-01-24 13:41:18,905] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM [2024-01-24 13:41:18,957] [INFO] Task started: CheckM [2024-01-24 13:41:18,958] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025770765.1_ASM2577076v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025770765.1_ASM2577076v1_genomic.fna/checkm_input GCF_025770765.1_ASM2577076v1_genomic.fna/checkm_result [2024-01-24 13:42:04,270] [INFO] Task succeeded: CheckM [2024-01-24 13:42:04,272] [INFO] Completeness check finished. -------------------------------------------------------------------------------- Completeness: 100.00% Contamintation: 0.00% Strain heterogeneity: 0.00% -------------------------------------------------------------------------------- [2024-01-24 13:42:04,293] [INFO] ===== Completeness check finished ===== [2024-01-24 13:42:04,293] [INFO] ===== Start GTDB Search ===== [2024-01-24 13:42:04,294] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025770765.1_ASM2577076v1_genomic.fna/markers.fasta) [2024-01-24 13:42:04,294] [INFO] Task started: Blastn [2024-01-24 13:42:04,294] [INFO] Running command: blastn -query GCF_025770765.1_ASM2577076v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4443572e-2144-4a43-bb80-2dfe7dd9290a/dqc_reference/reference_markers_gtdb.fasta -out GCF_025770765.1_ASM2577076v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5 [2024-01-24 13:42:05,661] [INFO] Task succeeded: Blastn [2024-01-24 13:42:05,665] [INFO] Selected 25 target genomes. [2024-01-24 13:42:05,665] [INFO] Target genome list was writen to GCF_025770765.1_ASM2577076v1_genomic.fna/target_genomes_gtdb.txt [2024-01-24 13:42:05,698] [INFO] Task started: fastANI [2024-01-24 13:42:05,698] [INFO] Running command: fastANI --query /var/lib/cwl/stg8563f9bb-6ee7-41df-a822-bfa0899af1a2/GCF_025770765.1_ASM2577076v1_genomic.fna.gz --refList GCF_025770765.1_ASM2577076v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025770765.1_ASM2577076v1_genomic.fna/fastani_result_gtdb.tsv --threads 1 [2024-01-24 13:42:22,581] [INFO] Task succeeded: fastANI [2024-01-24 13:42:22,605] [INFO] Found 24 fastANI hits (0 hits with ANI > circumscription radius) [2024-01-24 13:42:22,605] [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 GCA_017995515.1 s__Propionivibrio sp017995515 78.3664 384 1567 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Propionivibrio 95.0 N/A N/A N/A N/A 1 - GCA_002304785.1 s__Propionivibrio sp002304785 78.305 371 1567 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Propionivibrio 95.0 N/A N/A N/A N/A 1 - GCF_900099695.1 s__Propionivibrio dicarboxylicus 78.144 354 1567 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Propionivibrio 95.0 N/A N/A N/A N/A 1 - GCA_018262095.1 s__Propionivibrio sp018262095 78.1329 436 1567 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Propionivibrio 95.0 N/A N/A N/A N/A 1 - GCF_009469695.1 s__Propionivibrio limicola 78.1301 281 1567 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Propionivibrio 95.0 N/A N/A N/A N/A 1 - GCA_003249625.1 s__Propionivibrio sp003249625 78.0475 237 1567 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Propionivibrio 95.0 N/A N/A N/A N/A 1 - GCA_903886975.1 s__Propionivibrio sp903886975 77.9938 321 1567 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Propionivibrio 95.0 N/A N/A N/A N/A 1 - GCA_001897745.1 s__66-26 sp001897745 77.9903 347 1567 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__66-26 95.0 97.97 95.98 0.93 0.89 3 - GCA_017990155.1 s__Propionivibrio sp017990155 77.9662 258 1567 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Propionivibrio 95.0 98.81 98.47 0.75 0.75 3 - GCA_907163075.1 s__Propionivibrio sp907163075 77.9658 402 1567 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Propionivibrio 95.0 N/A N/A N/A N/A 1 - GCF_014197755.1 s__Rhodocyclus tenuis 77.7076 257 1567 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Rhodocyclus 95.0 98.79 97.58 0.96 0.93 3 - GCA_016710885.1 s__Azospira_A sp016710885 77.4209 183 1567 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azospira_A 95.0 98.08 98.08 0.87 0.87 2 - GCA_016208425.1 s__JACQYA01 sp016208425 77.2318 224 1567 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__JACQYA01 95.0 N/A N/A N/A N/A 1 - GCA_017592775.1 s__Accumulibacter sp017592775 77.1414 226 1567 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Accumulibacter 95.0 99.29 99.29 0.85 0.85 2 - GCF_900089955.1 s__Accumulibacter aalborgensis 77.0907 188 1567 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Accumulibacter 95.0 N/A N/A N/A N/A 1 - GCA_013347225.1 s__Accumulibacter sp005524045 76.9046 198 1567 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Accumulibacter 95.0 98.94 98.94 0.93 0.93 2 - GCF_001682385.1 s__Azoarcus olearius 76.9024 166 1567 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azoarcus 95.0 98.77 98.77 0.96 0.96 2 - GCA_002337055.1 s__UBA1934 sp002337055 76.6689 112 1567 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__UBA1934 95.0 N/A N/A N/A N/A 1 - GCF_002028455.1 s__Zoogloea sp002028455 76.6675 149 1567 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Zoogloea 95.0 N/A N/A N/A N/A 1 - GCA_000987445.1 s__Accumulibacter phosphatis_A 76.6319 136 1567 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Accumulibacter 95.0 N/A N/A N/A N/A 1 - GCA_018261935.1 s__JAGTRP01 sp018261935 76.4118 128 1567 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__JAGTRP01 95.0 N/A N/A N/A N/A 1 - GCF_018802605.1 s__Paludibacterium paludis 75.919 73 1567 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Paludibacterium 95.0 100.00 100.00 1.00 1.00 2 - GCF_003202035.1 s__Aquitalea magnusonii 75.8748 53 1567 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Aquitalea 95.0 99.21 98.53 0.95 0.91 3 - GCF_009856625.1 s__Aquitalea denitrificans 75.5666 56 1567 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Aquitalea 95.0 N/A N/A N/A N/A 1 - -------------------------------------------------------------------------------- [2024-01-24 13:42:22,607] [INFO] GTDB search result was written to GCF_025770765.1_ASM2577076v1_genomic.fna/result_gtdb.tsv [2024-01-24 13:42:22,608] [INFO] ===== GTDB Search completed ===== [2024-01-24 13:42:22,618] [INFO] DFAST_QC result json was written to GCF_025770765.1_ASM2577076v1_genomic.fna/dqc_result.json [2024-01-24 13:42:22,618] [INFO] DFAST_QC completed! [2024-01-24 13:42:22,618] [INFO] Total running time: 0h1m40s