[2024-01-24 14:12:02,677] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:12:02,679] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:12:02,679] [INFO] DQC Reference Directory: /var/lib/cwl/stg1dae66a8-4505-4321-a2f6-59cabe28a429/dqc_reference
[2024-01-24 14:12:04,035] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:12:04,036] [INFO] Task started: Prodigal
[2024-01-24 14:12:04,036] [INFO] Running command: gunzip -c /var/lib/cwl/stg378f1156-e389-4fbc-92b3-6a463245c0b4/GCF_900142655.1_IMG-taxon_2671180065_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900142655.1_IMG-taxon_2671180065_annotated_assembly_genomic.fna/cds.fna -a GCF_900142655.1_IMG-taxon_2671180065_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:12:19,346] [INFO] Task succeeded: Prodigal
[2024-01-24 14:12:19,347] [INFO] Task started: HMMsearch
[2024-01-24 14:12:19,347] [INFO] Running command: hmmsearch --tblout GCF_900142655.1_IMG-taxon_2671180065_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1dae66a8-4505-4321-a2f6-59cabe28a429/dqc_reference/reference_markers.hmm GCF_900142655.1_IMG-taxon_2671180065_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:12:19,714] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:12:19,716] [INFO] Found 6/6 markers.
[2024-01-24 14:12:19,757] [INFO] Query marker FASTA was written to GCF_900142655.1_IMG-taxon_2671180065_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 14:12:19,758] [INFO] Task started: Blastn
[2024-01-24 14:12:19,758] [INFO] Running command: blastn -query GCF_900142655.1_IMG-taxon_2671180065_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg1dae66a8-4505-4321-a2f6-59cabe28a429/dqc_reference/reference_markers.fasta -out GCF_900142655.1_IMG-taxon_2671180065_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:12:20,800] [INFO] Task succeeded: Blastn
[2024-01-24 14:12:20,803] [INFO] Selected 10 target genomes.
[2024-01-24 14:12:20,804] [INFO] Target genome list was writen to GCF_900142655.1_IMG-taxon_2671180065_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 14:12:20,806] [INFO] Task started: fastANI
[2024-01-24 14:12:20,806] [INFO] Running command: fastANI --query /var/lib/cwl/stg378f1156-e389-4fbc-92b3-6a463245c0b4/GCF_900142655.1_IMG-taxon_2671180065_annotated_assembly_genomic.fna.gz --refList GCF_900142655.1_IMG-taxon_2671180065_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900142655.1_IMG-taxon_2671180065_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:12:33,263] [INFO] Task succeeded: fastANI
[2024-01-24 14:12:33,264] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1dae66a8-4505-4321-a2f6-59cabe28a429/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:12:33,264] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1dae66a8-4505-4321-a2f6-59cabe28a429/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:12:33,277] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:12:33,277] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:12:33,278] [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 punonensis	strain=CECT 8089	GCA_900142655.1	1220495	1220495	type	True	100.0	1591	1593	95	conclusive
Pseudomonas argentinensis	strain=CCUG 50743	GCA_008801645.1	289370	289370	type	True	88.7805	1374	1593	95	below_threshold
Pseudomonas argentinensis	strain=LMG 22563	GCA_900113905.1	289370	289370	type	True	88.7444	1370	1593	95	below_threshold
Pseudomonas flavescens	strain=NBRC 103044	GCA_002091575.1	29435	29435	type	True	85.7011	1245	1593	95	below_threshold
Pseudomonas flavescens	strain=LMG 18387	GCA_900100535.1	29435	29435	type	True	85.662	1246	1593	95	below_threshold
Pseudomonas insulae	strain=UL073	GCA_016901015.1	2809017	2809017	type	True	80.9412	760	1593	95	below_threshold
Pseudomonas brassicae	strain=MAFF 212427	GCA_010671725.1	2708063	2708063	type	True	80.561	614	1593	95	below_threshold
Pseudomonas pharyngis	strain=BML-PP036	GCA_021602345.1	2892333	2892333	type	True	80.1686	702	1593	95	below_threshold
Pseudomonas sputi	strain=BML-PP014	GCA_021603585.1	2892325	2892325	type	True	80.1408	688	1593	95	below_threshold
Pseudomonas germanica	strain=FIT28	GCA_019614655.1	2815720	2815720	type	True	79.7959	639	1593	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:12:33,279] [INFO] DFAST Taxonomy check result was written to GCF_900142655.1_IMG-taxon_2671180065_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 14:12:33,280] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:12:33,280] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:12:33,280] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1dae66a8-4505-4321-a2f6-59cabe28a429/dqc_reference/checkm_data
[2024-01-24 14:12:33,281] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:12:33,326] [INFO] Task started: CheckM
[2024-01-24 14:12:33,327] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900142655.1_IMG-taxon_2671180065_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900142655.1_IMG-taxon_2671180065_annotated_assembly_genomic.fna/checkm_input GCF_900142655.1_IMG-taxon_2671180065_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 14:13:17,421] [INFO] Task succeeded: CheckM
[2024-01-24 14:13:17,422] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:13:17,440] [INFO] ===== Completeness check finished =====
[2024-01-24 14:13:17,440] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:13:17,441] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900142655.1_IMG-taxon_2671180065_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 14:13:17,441] [INFO] Task started: Blastn
[2024-01-24 14:13:17,441] [INFO] Running command: blastn -query GCF_900142655.1_IMG-taxon_2671180065_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg1dae66a8-4505-4321-a2f6-59cabe28a429/dqc_reference/reference_markers_gtdb.fasta -out GCF_900142655.1_IMG-taxon_2671180065_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:13:19,254] [INFO] Task succeeded: Blastn
[2024-01-24 14:13:19,258] [INFO] Selected 11 target genomes.
[2024-01-24 14:13:19,258] [INFO] Target genome list was writen to GCF_900142655.1_IMG-taxon_2671180065_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:13:19,272] [INFO] Task started: fastANI
[2024-01-24 14:13:19,272] [INFO] Running command: fastANI --query /var/lib/cwl/stg378f1156-e389-4fbc-92b3-6a463245c0b4/GCF_900142655.1_IMG-taxon_2671180065_annotated_assembly_genomic.fna.gz --refList GCF_900142655.1_IMG-taxon_2671180065_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900142655.1_IMG-taxon_2671180065_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:13:33,833] [INFO] Task succeeded: fastANI
[2024-01-24 14:13:33,843] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:13:33,843] [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_900142655.1	s__Pseudomonas_E punonensis	100.0	1591	1593	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003253735.1	s__Pseudomonas_E sp003253735	90.1638	1387	1593	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.17	98.17	0.95	0.95	2	-
GCF_900113905.1	s__Pseudomonas_E argentinensis	88.7379	1370	1593	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_001839655.1	s__Pseudomonas_E argentinensis_B	88.6157	1340	1593	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_000213805.1	s__Pseudomonas_E fulva_B	88.4432	1371	1593	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.53	96.12	0.92	0.90	6	-
GCF_900112645.1	s__Pseudomonas_E straminea	88.3522	1392	1593	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.06	98.06	0.94	0.94	2	-
GCF_001945445.1	s__Pseudomonas_E sp001945445	88.2014	1380	1593	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.66	98.66	0.91	0.91	2	-
GCF_001945395.1	s__Pseudomonas_E sp001945395	87.8355	1351	1593	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_013408425.1	s__Pseudomonas_E fulva_A	86.3787	1365	1593	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.00	99.00	0.95	0.95	2	-
GCF_900100535.1	s__Pseudomonas_E flavescens	85.6497	1247	1593	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_900102335.1	s__Pseudomonas_E seleniipraecipitans	85.2049	1214	1593	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.06	98.05	0.91	0.90	3	-
--------------------------------------------------------------------------------
[2024-01-24 14:13:33,844] [INFO] GTDB search result was written to GCF_900142655.1_IMG-taxon_2671180065_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 14:13:33,845] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:13:33,849] [INFO] DFAST_QC result json was written to GCF_900142655.1_IMG-taxon_2671180065_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 14:13:33,849] [INFO] DFAST_QC completed!
[2024-01-24 14:13:33,849] [INFO] Total running time: 0h1m31s