[2024-01-24 12:44:08,068] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:44:08,070] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:44:08,071] [INFO] DQC Reference Directory: /var/lib/cwl/stg76610c96-f8b8-4110-b920-fe717cd6524c/dqc_reference
[2024-01-24 12:44:09,334] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:44:09,335] [INFO] Task started: Prodigal
[2024-01-24 12:44:09,335] [INFO] Running command: gunzip -c /var/lib/cwl/stg3fe6889a-e5a8-4750-8b06-f3004990f8cd/GCF_900141795.1_IMG-taxon_2695421043_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900141795.1_IMG-taxon_2695421043_annotated_assembly_genomic.fna/cds.fna -a GCF_900141795.1_IMG-taxon_2695421043_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:44:14,762] [INFO] Task succeeded: Prodigal
[2024-01-24 12:44:14,762] [INFO] Task started: HMMsearch
[2024-01-24 12:44:14,762] [INFO] Running command: hmmsearch --tblout GCF_900141795.1_IMG-taxon_2695421043_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg76610c96-f8b8-4110-b920-fe717cd6524c/dqc_reference/reference_markers.hmm GCF_900141795.1_IMG-taxon_2695421043_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:44:15,054] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:44:15,056] [INFO] Found 6/6 markers.
[2024-01-24 12:44:15,080] [INFO] Query marker FASTA was written to GCF_900141795.1_IMG-taxon_2695421043_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 12:44:15,081] [INFO] Task started: Blastn
[2024-01-24 12:44:15,081] [INFO] Running command: blastn -query GCF_900141795.1_IMG-taxon_2695421043_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg76610c96-f8b8-4110-b920-fe717cd6524c/dqc_reference/reference_markers.fasta -out GCF_900141795.1_IMG-taxon_2695421043_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:44:15,895] [INFO] Task succeeded: Blastn
[2024-01-24 12:44:15,898] [INFO] Selected 30 target genomes.
[2024-01-24 12:44:15,899] [INFO] Target genome list was writen to GCF_900141795.1_IMG-taxon_2695421043_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 12:44:16,029] [INFO] Task started: fastANI
[2024-01-24 12:44:16,029] [INFO] Running command: fastANI --query /var/lib/cwl/stg3fe6889a-e5a8-4750-8b06-f3004990f8cd/GCF_900141795.1_IMG-taxon_2695421043_annotated_assembly_genomic.fna.gz --refList GCF_900141795.1_IMG-taxon_2695421043_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900141795.1_IMG-taxon_2695421043_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:44:33,346] [INFO] Task succeeded: fastANI
[2024-01-24 12:44:33,347] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg76610c96-f8b8-4110-b920-fe717cd6524c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:44:33,347] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg76610c96-f8b8-4110-b920-fe717cd6524c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:44:33,355] [INFO] Found 6 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:44:33,355] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:44:33,355] [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
Sulfurivirga caldicuralii	strain=DSM 17737	GCA_900141795.1	364032	364032	type	True	100.0	555	555	95	conclusive
Thioalkalivibrio sulfidiphilus	strain=HL-EbGR7	GCA_000021985.1	1033854	1033854	type	True	76.5248	66	555	95	below_threshold
Sulfurivermis fontis	strain=JG42	GCA_004001245.1	1972068	1972068	type	True	76.522	68	555	95	below_threshold
Pseudomonas aromaticivorans	strain=MAP12	GCA_019097855.1	2849492	2849492	type	True	76.3437	61	555	95	below_threshold
Alcanivorax indicus	strain=SW127	GCA_003259185.1	2202653	2202653	type	True	75.9952	54	555	95	below_threshold
Alcanivorax hongdengensis	strain=A-11-3	GCA_000300995.1	519051	519051	type	True	75.8534	53	555	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:44:33,358] [INFO] DFAST Taxonomy check result was written to GCF_900141795.1_IMG-taxon_2695421043_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 12:44:33,358] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:44:33,359] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:44:33,359] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg76610c96-f8b8-4110-b920-fe717cd6524c/dqc_reference/checkm_data
[2024-01-24 12:44:33,361] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:44:33,383] [INFO] Task started: CheckM
[2024-01-24 12:44:33,383] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900141795.1_IMG-taxon_2695421043_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900141795.1_IMG-taxon_2695421043_annotated_assembly_genomic.fna/checkm_input GCF_900141795.1_IMG-taxon_2695421043_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 12:44:56,858] [INFO] Task succeeded: CheckM
[2024-01-24 12:44:56,860] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:44:56,878] [INFO] ===== Completeness check finished =====
[2024-01-24 12:44:56,879] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:44:56,879] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900141795.1_IMG-taxon_2695421043_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 12:44:56,879] [INFO] Task started: Blastn
[2024-01-24 12:44:56,879] [INFO] Running command: blastn -query GCF_900141795.1_IMG-taxon_2695421043_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg76610c96-f8b8-4110-b920-fe717cd6524c/dqc_reference/reference_markers_gtdb.fasta -out GCF_900141795.1_IMG-taxon_2695421043_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:44:58,402] [INFO] Task succeeded: Blastn
[2024-01-24 12:44:58,406] [INFO] Selected 22 target genomes.
[2024-01-24 12:44:58,406] [INFO] Target genome list was writen to GCF_900141795.1_IMG-taxon_2695421043_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:44:58,455] [INFO] Task started: fastANI
[2024-01-24 12:44:58,456] [INFO] Running command: fastANI --query /var/lib/cwl/stg3fe6889a-e5a8-4750-8b06-f3004990f8cd/GCF_900141795.1_IMG-taxon_2695421043_annotated_assembly_genomic.fna.gz --refList GCF_900141795.1_IMG-taxon_2695421043_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900141795.1_IMG-taxon_2695421043_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:45:09,879] [INFO] Task succeeded: fastANI
[2024-01-24 12:45:09,893] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:45:09,893] [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_900141795.1	s__Sulfurivirga caldicuralii	100.0	555	555	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiomicrospirales;f__Thiomicrospiraceae;g__Sulfurivirga	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_015490265.1	s__Sulfurivirga sp015490265	79.9189	293	555	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiomicrospirales;f__Thiomicrospiraceae;g__Sulfurivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015661715.1	s__Sulfurivirga caldicuralii_A	77.5319	167	555	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiomicrospirales;f__Thiomicrospiraceae;g__Sulfurivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000021985.1	s__Thioalkalivibrio_A sulfidiphilus	76.5248	66	555	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Ectothiorhodospiraceae;g__Thioalkalivibrio_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004001245.1	s__Sulfurivermis fontis	76.522	68	555	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiohalomonadales;f__Thiohalomonadaceae;g__Sulfurivermis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000225005.1	s__Ectothiorhodospira sp000225005	76.2791	57	555	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Ectothiorhodospiraceae;g__Ectothiorhodospira	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001507535.1	s__Hydrogenovibrio sp001507535	76.2151	59	555	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiomicrospirales;f__Thiomicrospiraceae;g__Hydrogenovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003259185.1	s__Alcanivorax_A indicus	75.9952	54	555	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:45:09,895] [INFO] GTDB search result was written to GCF_900141795.1_IMG-taxon_2695421043_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 12:45:09,895] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:45:09,898] [INFO] DFAST_QC result json was written to GCF_900141795.1_IMG-taxon_2695421043_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 12:45:09,898] [INFO] DFAST_QC completed!
[2024-01-24 12:45:09,898] [INFO] Total running time: 0h1m2s