[2024-01-25 17:35:35,596] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:35:35,598] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:35:35,598] [INFO] DQC Reference Directory: /var/lib/cwl/stg11786fce-123f-4b93-aae6-4b4d4c2789dd/dqc_reference
[2024-01-25 17:35:36,773] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:35:36,774] [INFO] Task started: Prodigal
[2024-01-25 17:35:36,774] [INFO] Running command: gunzip -c /var/lib/cwl/stgd0076f66-b3c8-4a73-a210-de08a419abe9/GCF_000772265.1_ASM77226v1_genomic.fna.gz | prodigal -d GCF_000772265.1_ASM77226v1_genomic.fna/cds.fna -a GCF_000772265.1_ASM77226v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:35:41,331] [INFO] Task succeeded: Prodigal
[2024-01-25 17:35:41,332] [INFO] Task started: HMMsearch
[2024-01-25 17:35:41,332] [INFO] Running command: hmmsearch --tblout GCF_000772265.1_ASM77226v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg11786fce-123f-4b93-aae6-4b4d4c2789dd/dqc_reference/reference_markers.hmm GCF_000772265.1_ASM77226v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:35:41,525] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:35:41,526] [INFO] Found 6/6 markers.
[2024-01-25 17:35:41,547] [INFO] Query marker FASTA was written to GCF_000772265.1_ASM77226v1_genomic.fna/markers.fasta
[2024-01-25 17:35:41,547] [INFO] Task started: Blastn
[2024-01-25 17:35:41,547] [INFO] Running command: blastn -query GCF_000772265.1_ASM77226v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg11786fce-123f-4b93-aae6-4b4d4c2789dd/dqc_reference/reference_markers.fasta -out GCF_000772265.1_ASM77226v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:35:42,180] [INFO] Task succeeded: Blastn
[2024-01-25 17:35:42,182] [INFO] Selected 17 target genomes.
[2024-01-25 17:35:42,182] [INFO] Target genome list was writen to GCF_000772265.1_ASM77226v1_genomic.fna/target_genomes.txt
[2024-01-25 17:35:42,188] [INFO] Task started: fastANI
[2024-01-25 17:35:42,188] [INFO] Running command: fastANI --query /var/lib/cwl/stgd0076f66-b3c8-4a73-a210-de08a419abe9/GCF_000772265.1_ASM77226v1_genomic.fna.gz --refList GCF_000772265.1_ASM77226v1_genomic.fna/target_genomes.txt --output GCF_000772265.1_ASM77226v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:35:50,935] [INFO] Task succeeded: fastANI
[2024-01-25 17:35:50,936] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg11786fce-123f-4b93-aae6-4b4d4c2789dd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:35:50,936] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg11786fce-123f-4b93-aae6-4b4d4c2789dd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:35:50,944] [INFO] Found 12 fastANI hits (3 hits with ANI > threshold)
[2024-01-25 17:35:50,944] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:35:50,944] [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
Gallibacterium anatis	strain=F149	GCA_000772265.1	750	750	type	True	100.0	738	745	95	conclusive
Gallibacterium anatis	strain=NCTC11413	GCA_900450735.1	750	750	type	True	99.995	745	745	95	conclusive
Gallibacterium anatis	strain=DSM 16844	GCA_000379785.1	750	750	type	True	99.9929	738	745	95	conclusive
Gallibacterium salpingitidis	strain=F150	GCA_001678495.1	505341	505341	type	True	79.9358	365	745	95	below_threshold
Pasteurella canis	strain=NCTC11621	GCA_900454865.1	753	753	type	True	77.9381	86	745	95	below_threshold
Aggregatibacter kilianii	strain=PN_528	GCA_003130255.1	2025884	2025884	type	True	77.6218	96	745	95	below_threshold
Haemophilus aegyptius	strain=NCTC8502	GCA_900475885.1	197575	197575	type	True	77.5937	104	745	95	below_threshold
Rodentibacter haemolyticus	strain=DSM 111151	GCA_015356115.1	2778911	2778911	type	True	77.5698	114	745	95	below_threshold
Mannheimia haemolytica	strain=DSM 10531	GCA_004342115.1	75985	75985	type	True	77.3828	93	745	95	below_threshold
Actinobacillus seminis	strain=ATCC 15768	GCA_002263215.1	722	722	type	True	77.3545	122	745	95	below_threshold
Actinobacillus seminis	strain=NCTC10851	GCA_900460625.1	722	722	type	True	77.2642	125	745	95	below_threshold
Testudinibacter aquarius	strain=DSM 28140	GCA_004342725.1	1524974	1524974	type	True	77.0023	102	745	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:35:50,946] [INFO] DFAST Taxonomy check result was written to GCF_000772265.1_ASM77226v1_genomic.fna/tc_result.tsv
[2024-01-25 17:35:50,947] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:35:50,947] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:35:50,947] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg11786fce-123f-4b93-aae6-4b4d4c2789dd/dqc_reference/checkm_data
[2024-01-25 17:35:50,948] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:35:50,974] [INFO] Task started: CheckM
[2024-01-25 17:35:50,974] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000772265.1_ASM77226v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000772265.1_ASM77226v1_genomic.fna/checkm_input GCF_000772265.1_ASM77226v1_genomic.fna/checkm_result
[2024-01-25 17:36:10,331] [INFO] Task succeeded: CheckM
[2024-01-25 17:36:10,332] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:36:10,365] [INFO] ===== Completeness check finished =====
[2024-01-25 17:36:10,365] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:36:10,366] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000772265.1_ASM77226v1_genomic.fna/markers.fasta)
[2024-01-25 17:36:10,366] [INFO] Task started: Blastn
[2024-01-25 17:36:10,366] [INFO] Running command: blastn -query GCF_000772265.1_ASM77226v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg11786fce-123f-4b93-aae6-4b4d4c2789dd/dqc_reference/reference_markers_gtdb.fasta -out GCF_000772265.1_ASM77226v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:36:11,328] [INFO] Task succeeded: Blastn
[2024-01-25 17:36:11,332] [INFO] Selected 17 target genomes.
[2024-01-25 17:36:11,332] [INFO] Target genome list was writen to GCF_000772265.1_ASM77226v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:36:11,339] [INFO] Task started: fastANI
[2024-01-25 17:36:11,340] [INFO] Running command: fastANI --query /var/lib/cwl/stgd0076f66-b3c8-4a73-a210-de08a419abe9/GCF_000772265.1_ASM77226v1_genomic.fna.gz --refList GCF_000772265.1_ASM77226v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000772265.1_ASM77226v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:36:18,751] [INFO] Task succeeded: fastANI
[2024-01-25 17:36:18,761] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:36:18,761] [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_000379785.1	s__Gallibacterium anatis	99.9929	738	745	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Gallibacterium	95.0	97.46	96.89	0.84	0.80	28	conclusive
GCF_000771875.1	s__Gallibacterium sp000771875	92.6229	593	745	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Gallibacterium	95.0	96.90	96.47	0.87	0.86	4	-
GCF_001678495.1	s__Gallibacterium salpingitidis	79.9424	365	745	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Gallibacterium	95.0	97.50	97.42	0.85	0.85	3	-
GCF_001678475.1	s__Gallibacterium sp001678475	79.8832	340	745	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Gallibacterium	95.0	96.69	96.63	0.86	0.84	3	-
GCF_002850605.1	s__Pasteurella oralis	78.0184	89	745	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Pasteurella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900454865.1	s__Pasteurella canis	77.9861	87	745	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Pasteurella	95.0	98.76	98.68	0.94	0.91	4	-
GCF_000973525.1	s__Pasteurella multocida_A	77.9483	100	745	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Pasteurella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004339025.1	s__Volucribacter psittacicida	77.6594	114	745	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Volucribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003130255.1	s__Aggregatibacter kilianii	77.6366	96	745	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Aggregatibacter	95.0	98.97	97.13	0.96	0.90	14	-
GCA_000752995.2	s__Necropsobacter massiliensis_B	77.6125	97	745	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Necropsobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_015356115.1	s__Rodentibacter sp015356115	77.5715	113	745	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Rodentibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018343795.1	s__Phocoenobacter atlantica	77.5548	74	745	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Phocoenobacter	95.0	99.99	99.99	1.00	1.00	2	-
GCF_000222025.1	s__Haemophilus haemolyticus_G	77.5201	95	745	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900444945.1	s__Actinobacillus lignieresii	77.5193	109	745	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Actinobacillus	95.0	96.69	96.41	0.91	0.89	35	-
GCF_004342115.1	s__Mannheimia haemolytica	77.36	93	745	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Mannheimia	95.0	99.19	95.33	0.93	0.85	196	-
GCF_002263215.1	s__Actinobacillus_B seminis	77.3549	123	745	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Actinobacillus_B	95.0	99.95	99.95	1.00	1.00	2	-
GCF_004342725.1	s__Chelonobacter aquarius	77.0057	101	745	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Chelonobacter	95.0	97.20	95.17	0.92	0.86	10	-
--------------------------------------------------------------------------------
[2024-01-25 17:36:18,763] [INFO] GTDB search result was written to GCF_000772265.1_ASM77226v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:36:18,763] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:36:18,766] [INFO] DFAST_QC result json was written to GCF_000772265.1_ASM77226v1_genomic.fna/dqc_result.json
[2024-01-25 17:36:18,767] [INFO] DFAST_QC completed!
[2024-01-25 17:36:18,767] [INFO] Total running time: 0h0m43s