[2024-01-24 11:34:55,800] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:34:55,802] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:34:55,803] [INFO] DQC Reference Directory: /var/lib/cwl/stga8d70802-56ab-4805-9cac-58001071a01f/dqc_reference
[2024-01-24 11:34:57,073] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:34:57,074] [INFO] Task started: Prodigal
[2024-01-24 11:34:57,074] [INFO] Running command: gunzip -c /var/lib/cwl/stgb786c2dd-6763-4d12-8353-040bff25ec63/GCF_014884995.1_ASM1488499v1_genomic.fna.gz | prodigal -d GCF_014884995.1_ASM1488499v1_genomic.fna/cds.fna -a GCF_014884995.1_ASM1488499v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:35:03,364] [INFO] Task succeeded: Prodigal
[2024-01-24 11:35:03,365] [INFO] Task started: HMMsearch
[2024-01-24 11:35:03,365] [INFO] Running command: hmmsearch --tblout GCF_014884995.1_ASM1488499v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga8d70802-56ab-4805-9cac-58001071a01f/dqc_reference/reference_markers.hmm GCF_014884995.1_ASM1488499v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:35:03,633] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:35:03,634] [INFO] Found 6/6 markers.
[2024-01-24 11:35:03,659] [INFO] Query marker FASTA was written to GCF_014884995.1_ASM1488499v1_genomic.fna/markers.fasta
[2024-01-24 11:35:03,660] [INFO] Task started: Blastn
[2024-01-24 11:35:03,660] [INFO] Running command: blastn -query GCF_014884995.1_ASM1488499v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga8d70802-56ab-4805-9cac-58001071a01f/dqc_reference/reference_markers.fasta -out GCF_014884995.1_ASM1488499v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:35:04,358] [INFO] Task succeeded: Blastn
[2024-01-24 11:35:04,362] [INFO] Selected 17 target genomes.
[2024-01-24 11:35:04,363] [INFO] Target genome list was writen to GCF_014884995.1_ASM1488499v1_genomic.fna/target_genomes.txt
[2024-01-24 11:35:04,405] [INFO] Task started: fastANI
[2024-01-24 11:35:04,405] [INFO] Running command: fastANI --query /var/lib/cwl/stgb786c2dd-6763-4d12-8353-040bff25ec63/GCF_014884995.1_ASM1488499v1_genomic.fna.gz --refList GCF_014884995.1_ASM1488499v1_genomic.fna/target_genomes.txt --output GCF_014884995.1_ASM1488499v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:35:12,733] [INFO] Task succeeded: fastANI
[2024-01-24 11:35:12,733] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga8d70802-56ab-4805-9cac-58001071a01f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:35:12,734] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga8d70802-56ab-4805-9cac-58001071a01f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:35:12,756] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:35:12,756] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:35:12,757] [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
Spirabiliibacterium pneumoniae	strain=HPA106	GCA_014884995.1	221400	221400	type	True	100.0	686	686	95	conclusive
Spirabiliibacterium mucosae	strain=20609_3	GCA_014884965.1	28156	28156	type	True	85.0494	547	686	95	below_threshold
Spirabiliibacterium falconis	strain=NCTC 11878	GCA_014885015.1	572023	572023	type	True	80.723	433	686	95	below_threshold
Pasteurella testudinis	strain=NCTC12150	GCA_900454705.1	761	761	type	True	78.0828	157	686	95	below_threshold
Pasteurella testudinis	strain=DSM 23072	GCA_900176075.1	761	761	type	True	77.8538	153	686	95	below_threshold
Pasteurella testudinis	strain=DSM 23072	GCA_019633665.1	761	761	type	True	77.8538	153	686	95	below_threshold
Avibacterium gallinarum	strain=NCTC11188	GCA_900454485.1	755	755	type	True	77.7128	101	686	95	below_threshold
Testudinibacter aquarius	strain=DSM 28140	GCA_004342725.1	1524974	1524974	type	True	77.6176	149	686	95	below_threshold
Testudinibacter aquarius	strain=ELNT2X	GCA_009761355.1	1524974	1524974	type	True	77.5979	145	686	95	below_threshold
Aggregatibacter actinomycetemcomitans	strain=NCTC_9710	GCA_008085305.1	714	714	type	True	77.1228	76	686	95	below_threshold
Aggregatibacter actinomycetemcomitans	strain=DSM 8324	GCA_000372365.1	714	714	type	True	76.9218	76	686	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:35:12,758] [INFO] DFAST Taxonomy check result was written to GCF_014884995.1_ASM1488499v1_genomic.fna/tc_result.tsv
[2024-01-24 11:35:12,759] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:35:12,759] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:35:12,759] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga8d70802-56ab-4805-9cac-58001071a01f/dqc_reference/checkm_data
[2024-01-24 11:35:12,760] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:35:12,788] [INFO] Task started: CheckM
[2024-01-24 11:35:12,788] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014884995.1_ASM1488499v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014884995.1_ASM1488499v1_genomic.fna/checkm_input GCF_014884995.1_ASM1488499v1_genomic.fna/checkm_result
[2024-01-24 11:35:37,673] [INFO] Task succeeded: CheckM
[2024-01-24 11:35:37,674] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:35:37,692] [INFO] ===== Completeness check finished =====
[2024-01-24 11:35:37,692] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:35:37,693] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014884995.1_ASM1488499v1_genomic.fna/markers.fasta)
[2024-01-24 11:35:37,693] [INFO] Task started: Blastn
[2024-01-24 11:35:37,693] [INFO] Running command: blastn -query GCF_014884995.1_ASM1488499v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga8d70802-56ab-4805-9cac-58001071a01f/dqc_reference/reference_markers_gtdb.fasta -out GCF_014884995.1_ASM1488499v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:35:38,830] [INFO] Task succeeded: Blastn
[2024-01-24 11:35:38,834] [INFO] Selected 17 target genomes.
[2024-01-24 11:35:38,834] [INFO] Target genome list was writen to GCF_014884995.1_ASM1488499v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:35:38,848] [INFO] Task started: fastANI
[2024-01-24 11:35:38,849] [INFO] Running command: fastANI --query /var/lib/cwl/stgb786c2dd-6763-4d12-8353-040bff25ec63/GCF_014884995.1_ASM1488499v1_genomic.fna.gz --refList GCF_014884995.1_ASM1488499v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014884995.1_ASM1488499v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:35:47,297] [INFO] Task succeeded: fastANI
[2024-01-24 11:35:47,312] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:35:47,312] [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_014884995.1	s__Spirabiliibacterium pneumoniae	100.0	686	686	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Spirabiliibacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014884965.1	s__Spirabiliibacterium mucosae	85.0494	547	686	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Spirabiliibacterium	95.0	96.18	96.18	0.92	0.92	2	-
GCF_014885015.1	s__Spirabiliibacterium falconis	80.752	431	686	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Spirabiliibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900176075.1	s__Chelonobacter testudinis	77.8751	152	686	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Chelonobacter	95.0	99.99	99.99	1.00	1.00	2	-
GCF_001678495.1	s__Gallibacterium salpingitidis	77.8409	70	686	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Gallibacterium	95.0	97.50	97.42	0.85	0.85	3	-
GCF_000772535.1	s__Chelonobacter oris	77.7398	128	686	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Chelonobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004342725.1	s__Chelonobacter aquarius	77.658	147	686	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Chelonobacter	95.0	97.20	95.17	0.92	0.86	10	-
GCA_006228005.1	s__Chelonobacter sp006228005	77.4905	151	686	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Chelonobacter	95.0	99.89	99.87	0.94	0.93	5	-
GCF_011455695.1	s__Mannheimia granulomatis_A	77.3524	60	686	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Mannheimia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002000545.1	s__Rodentibacter trehalosifermentans	77.1423	65	686	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Rodentibacter	95.0	98.00	97.91	0.88	0.88	3	-
GCF_000372365.1	s__Aggregatibacter actinomycetemcomitans	76.956	75	686	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Aggregatibacter	95.0	98.51	97.12	0.94	0.88	80	-
--------------------------------------------------------------------------------
[2024-01-24 11:35:47,314] [INFO] GTDB search result was written to GCF_014884995.1_ASM1488499v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:35:47,314] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:35:47,318] [INFO] DFAST_QC result json was written to GCF_014884995.1_ASM1488499v1_genomic.fna/dqc_result.json
[2024-01-24 11:35:47,318] [INFO] DFAST_QC completed!
[2024-01-24 11:35:47,318] [INFO] Total running time: 0h0m52s