[2024-01-24 14:02:51,817] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:02:51,819] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:02:51,819] [INFO] DQC Reference Directory: /var/lib/cwl/stg1b7a81fb-ead5-409e-898f-9f561df96e5f/dqc_reference
[2024-01-24 14:02:53,168] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:02:53,169] [INFO] Task started: Prodigal
[2024-01-24 14:02:53,169] [INFO] Running command: gunzip -c /var/lib/cwl/stgad8f701f-4206-46c5-b526-84d16ed2e213/GCF_000175195.1_ASM17519v1_genomic.fna.gz | prodigal -d GCF_000175195.1_ASM17519v1_genomic.fna/cds.fna -a GCF_000175195.1_ASM17519v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:02:58,378] [INFO] Task succeeded: Prodigal
[2024-01-24 14:02:58,378] [INFO] Task started: HMMsearch
[2024-01-24 14:02:58,378] [INFO] Running command: hmmsearch --tblout GCF_000175195.1_ASM17519v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1b7a81fb-ead5-409e-898f-9f561df96e5f/dqc_reference/reference_markers.hmm GCF_000175195.1_ASM17519v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:02:58,661] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:02:58,663] [INFO] Found 6/6 markers.
[2024-01-24 14:02:58,689] [INFO] Query marker FASTA was written to GCF_000175195.1_ASM17519v1_genomic.fna/markers.fasta
[2024-01-24 14:02:58,690] [INFO] Task started: Blastn
[2024-01-24 14:02:58,690] [INFO] Running command: blastn -query GCF_000175195.1_ASM17519v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1b7a81fb-ead5-409e-898f-9f561df96e5f/dqc_reference/reference_markers.fasta -out GCF_000175195.1_ASM17519v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:02:59,417] [INFO] Task succeeded: Blastn
[2024-01-24 14:02:59,421] [INFO] Selected 23 target genomes.
[2024-01-24 14:02:59,421] [INFO] Target genome list was writen to GCF_000175195.1_ASM17519v1_genomic.fna/target_genomes.txt
[2024-01-24 14:02:59,440] [INFO] Task started: fastANI
[2024-01-24 14:02:59,441] [INFO] Running command: fastANI --query /var/lib/cwl/stgad8f701f-4206-46c5-b526-84d16ed2e213/GCF_000175195.1_ASM17519v1_genomic.fna.gz --refList GCF_000175195.1_ASM17519v1_genomic.fna/target_genomes.txt --output GCF_000175195.1_ASM17519v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:03:10,267] [INFO] Task succeeded: fastANI
[2024-01-24 14:03:10,268] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1b7a81fb-ead5-409e-898f-9f561df96e5f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:03:10,268] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1b7a81fb-ead5-409e-898f-9f561df96e5f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:03:10,288] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:03:10,288] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:03:10,288] [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
Actinobacillus minor	strain=NM305	GCA_000175195.1	51047	51047	type	True	100.0	747	752	95	conclusive
Haemophilus paraphrohaemolyticus	strain=CCUG 3718	GCA_002015045.1	736	736	type	True	79.7501	290	752	95	below_threshold
Haemophilus parahaemolyticus	strain=CCUG 3716	GCA_002015035.1	735	735	type	True	79.7263	291	752	95	below_threshold
Haemophilus parahaemolyticus	strain=FDAARGOS_1199	GCA_016889385.1	735	735	type	True	79.7212	290	752	95	below_threshold
Haemophilus parahaemolyticus	strain=HK385	GCA_000262265.1	735	735	type	True	79.7157	286	752	95	below_threshold
Haemophilus parahaemolyticus	strain=NCTC 8479	GCA_900450675.1	735	735	type	True	79.6674	295	752	95	below_threshold
Actinobacillus equuli	strain=NCTC8529	GCA_900636745.1	718	718	type	True	79.4314	294	752	95	below_threshold
Actinobacillus suis	strain=ATCC 33415	GCA_000739435.1	716	716	type	True	79.4178	312	752	95	below_threshold
Actinobacillus suis	strain=NCTC12996	GCA_900187155.1	716	716	type	True	79.3408	314	752	95	below_threshold
Mannheimia haemolytica	strain=DSM 10531	GCA_004342115.1	75985	75985	type	True	79.3402	266	752	95	below_threshold
Actinobacillus ureae	strain=ATCC 25976	GCA_000188255.1	723	723	type	True	79.3071	287	752	95	below_threshold
Mannheimia haemolytica	strain=NCTC9380	GCA_900452985.1	75985	75985	type	True	79.3057	268	752	95	below_threshold
Actinobacillus lignieresii	strain=NCTC4189	GCA_900444945.1	720	720	type	True	79.2202	257	752	95	below_threshold
Actinobacillus capsulatus	strain=DSM 19761	GCA_000374285.1	717	717	type	True	79.0415	307	752	95	below_threshold
Actinobacillus pleuropneumoniae	strain=4074	GCA_000167095.1	715	715	type	True	78.9503	272	752	95	below_threshold
Mannheimia pernigra	strain=17CN0883	GCA_013377995.1	111844	111844	type	True	78.5706	224	752	95	below_threshold
Mannheimia ovis	strain=ZY170218	GCA_009828705.1	2679994	2679994	type	True	78.4767	227	752	95	below_threshold
Bibersteinia trehalosi	strain=DSM 23101	GCA_004346205.1	47735	47735	type	True	78.4677	196	752	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:03:10,290] [INFO] DFAST Taxonomy check result was written to GCF_000175195.1_ASM17519v1_genomic.fna/tc_result.tsv
[2024-01-24 14:03:10,291] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:03:10,291] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:03:10,291] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1b7a81fb-ead5-409e-898f-9f561df96e5f/dqc_reference/checkm_data
[2024-01-24 14:03:10,293] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:03:10,320] [INFO] Task started: CheckM
[2024-01-24 14:03:10,321] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000175195.1_ASM17519v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000175195.1_ASM17519v1_genomic.fna/checkm_input GCF_000175195.1_ASM17519v1_genomic.fna/checkm_result
[2024-01-24 14:03:32,801] [INFO] Task succeeded: CheckM
[2024-01-24 14:03:32,802] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:03:32,820] [INFO] ===== Completeness check finished =====
[2024-01-24 14:03:32,820] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:03:32,821] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000175195.1_ASM17519v1_genomic.fna/markers.fasta)
[2024-01-24 14:03:32,821] [INFO] Task started: Blastn
[2024-01-24 14:03:32,821] [INFO] Running command: blastn -query GCF_000175195.1_ASM17519v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1b7a81fb-ead5-409e-898f-9f561df96e5f/dqc_reference/reference_markers_gtdb.fasta -out GCF_000175195.1_ASM17519v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:03:33,967] [INFO] Task succeeded: Blastn
[2024-01-24 14:03:33,971] [INFO] Selected 14 target genomes.
[2024-01-24 14:03:33,971] [INFO] Target genome list was writen to GCF_000175195.1_ASM17519v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:03:33,992] [INFO] Task started: fastANI
[2024-01-24 14:03:33,992] [INFO] Running command: fastANI --query /var/lib/cwl/stgad8f701f-4206-46c5-b526-84d16ed2e213/GCF_000175195.1_ASM17519v1_genomic.fna.gz --refList GCF_000175195.1_ASM17519v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000175195.1_ASM17519v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:03:40,081] [INFO] Task succeeded: fastANI
[2024-01-24 14:03:40,103] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:03:40,104] [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_000175195.1	s__Actinobacillus_A minor	100.0	747	752	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Actinobacillus_A	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003101015.1	s__Actinobacillus_A porcitonsillarum	92.7938	580	752	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Actinobacillus_A	95.0	97.10	97.10	0.92	0.92	2	-
GCF_003260095.1	s__Glaesserella australis	80.2863	270	752	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Glaesserella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002015045.1	s__Haemophilus_A paraphrohaemolyticus	79.7774	288	752	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus_A	95.0	97.72	95.26	0.95	0.91	7	-
GCF_002015035.1	s__Haemophilus_A parahaemolyticus	79.7263	291	752	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus_A	95.0	97.50	95.62	0.95	0.88	11	-
GCF_000739435.1	s__Actinobacillus suis	79.4171	312	752	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Actinobacillus	95.0	99.85	99.75	0.98	0.94	7	-
GCF_900636745.1	s__Actinobacillus equuli	79.3984	296	752	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Actinobacillus	95.0	98.82	97.64	0.96	0.93	3	-
GCA_018373095.1	s__Haemophilus_A parahaemolyticus_A	79.3307	238	752	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000188255.1	s__Actinobacillus ureae	79.3143	286	752	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Actinobacillus	95.0	99.22	99.21	0.97	0.96	3	-
GCF_901687125.1	s__Actinobacillus vicugnae	79.259	292	752	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Actinobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000238795.1	s__Haemophilus_A sputorum	79.2323	249	752	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus_A	95.0	97.57	96.93	0.93	0.88	6	-
GCF_900444945.1	s__Actinobacillus lignieresii	79.229	256	752	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Actinobacillus	95.0	96.69	96.41	0.91	0.89	35	-
GCF_000374285.1	s__Actinobacillus capsulatus	79.0498	308	752	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Actinobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013377995.1	s__Mannheimia pernigra	78.6268	221	752	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Mannheimia	95.0	98.69	97.60	0.91	0.86	5	-
--------------------------------------------------------------------------------
[2024-01-24 14:03:40,106] [INFO] GTDB search result was written to GCF_000175195.1_ASM17519v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:03:40,107] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:03:40,112] [INFO] DFAST_QC result json was written to GCF_000175195.1_ASM17519v1_genomic.fna/dqc_result.json
[2024-01-24 14:03:40,113] [INFO] DFAST_QC completed!
[2024-01-24 14:03:40,113] [INFO] Total running time: 0h0m48s