[2024-01-24 13:01:04,152] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:01:04,154] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:01:04,154] [INFO] DQC Reference Directory: /var/lib/cwl/stg0f87ad88-2736-4242-87a5-2c83e2923744/dqc_reference
[2024-01-24 13:01:06,816] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:01:06,817] [INFO] Task started: Prodigal
[2024-01-24 13:01:06,818] [INFO] Running command: gunzip -c /var/lib/cwl/stg4c4e6f2e-c453-43d4-904e-ca57b98ddbe1/GCF_000621105.1_ASM62110v1_genomic.fna.gz | prodigal -d GCF_000621105.1_ASM62110v1_genomic.fna/cds.fna -a GCF_000621105.1_ASM62110v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:01:11,793] [INFO] Task succeeded: Prodigal
[2024-01-24 13:01:11,794] [INFO] Task started: HMMsearch
[2024-01-24 13:01:11,794] [INFO] Running command: hmmsearch --tblout GCF_000621105.1_ASM62110v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0f87ad88-2736-4242-87a5-2c83e2923744/dqc_reference/reference_markers.hmm GCF_000621105.1_ASM62110v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:01:12,039] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:01:12,040] [INFO] Found 6/6 markers.
[2024-01-24 13:01:12,066] [INFO] Query marker FASTA was written to GCF_000621105.1_ASM62110v1_genomic.fna/markers.fasta
[2024-01-24 13:01:12,066] [INFO] Task started: Blastn
[2024-01-24 13:01:12,066] [INFO] Running command: blastn -query GCF_000621105.1_ASM62110v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0f87ad88-2736-4242-87a5-2c83e2923744/dqc_reference/reference_markers.fasta -out GCF_000621105.1_ASM62110v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:01:14,151] [INFO] Task succeeded: Blastn
[2024-01-24 13:01:14,157] [INFO] Selected 19 target genomes.
[2024-01-24 13:01:14,158] [INFO] Target genome list was writen to GCF_000621105.1_ASM62110v1_genomic.fna/target_genomes.txt
[2024-01-24 13:01:14,601] [INFO] Task started: fastANI
[2024-01-24 13:01:14,602] [INFO] Running command: fastANI --query /var/lib/cwl/stg4c4e6f2e-c453-43d4-904e-ca57b98ddbe1/GCF_000621105.1_ASM62110v1_genomic.fna.gz --refList GCF_000621105.1_ASM62110v1_genomic.fna/target_genomes.txt --output GCF_000621105.1_ASM62110v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:01:23,510] [INFO] Task succeeded: fastANI
[2024-01-24 13:01:23,511] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0f87ad88-2736-4242-87a5-2c83e2923744/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:01:23,511] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0f87ad88-2736-4242-87a5-2c83e2923744/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:01:23,527] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:01:23,527] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:01:23,527] [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
Mannheimia granulomatis	strain=DSM 19156	GCA_000621105.1	85402	85402	type	True	100.0	753	753	95	conclusive
Mannheimia bovis	strain=ZY190616	GCA_014541205.1	2770636	2770636	type	True	82.417	509	753	95	below_threshold
Mannheimia varigena	strain=177	GCA_013377235.1	85404	85404	type	True	81.938	512	753	95	below_threshold
Mannheimia haemolytica	strain=DSM 10531	GCA_004342115.1	75985	75985	type	True	81.6326	508	753	95	below_threshold
Mannheimia haemolytica	strain=NCTC9380	GCA_900452985.1	75985	75985	type	True	81.6314	535	753	95	below_threshold
Mannheimia pernigra	strain=17CN0883	GCA_013377995.1	111844	111844	type	True	80.7225	459	753	95	below_threshold
Mannheimia ovis	strain=ZY170218	GCA_009828705.1	2679994	2679994	type	True	80.6068	461	753	95	below_threshold
Actinobacillus equuli	strain=NCTC8529	GCA_900636745.1	718	718	type	True	78.8614	303	753	95	below_threshold
Haemophilus paraphrohaemolyticus	strain=CCUG 3718	GCA_002015045.1	736	736	type	True	78.6528	221	753	95	below_threshold
Haemophilus parahaemolyticus	strain=CCUG 3716	GCA_002015035.1	735	735	type	True	78.6327	222	753	95	below_threshold
Haemophilus sputorum	strain=CCUG 13788	GCA_000238795.2	1078480	1078480	type	True	78.5815	214	753	95	below_threshold
[Haemophilus] ducreyi	strain=CIP 54.2	GCA_001043455.1	730	730	type	True	78.2777	144	753	95	below_threshold
[Haemophilus] ducreyi	strain=ATCC 33940	GCA_900109315.1	730	730	type	True	78.2301	145	753	95	below_threshold
[Haemophilus] ducreyi	strain=CCUG 4438	GCA_002015155.1	730	730	type	True	77.9556	147	753	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:01:23,530] [INFO] DFAST Taxonomy check result was written to GCF_000621105.1_ASM62110v1_genomic.fna/tc_result.tsv
[2024-01-24 13:01:23,531] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:01:23,531] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:01:23,531] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0f87ad88-2736-4242-87a5-2c83e2923744/dqc_reference/checkm_data
[2024-01-24 13:01:23,532] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:01:23,564] [INFO] Task started: CheckM
[2024-01-24 13:01:23,564] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000621105.1_ASM62110v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000621105.1_ASM62110v1_genomic.fna/checkm_input GCF_000621105.1_ASM62110v1_genomic.fna/checkm_result
[2024-01-24 13:01:46,146] [INFO] Task succeeded: CheckM
[2024-01-24 13:01:46,148] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:01:46,169] [INFO] ===== Completeness check finished =====
[2024-01-24 13:01:46,169] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:01:46,170] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000621105.1_ASM62110v1_genomic.fna/markers.fasta)
[2024-01-24 13:01:46,170] [INFO] Task started: Blastn
[2024-01-24 13:01:46,170] [INFO] Running command: blastn -query GCF_000621105.1_ASM62110v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0f87ad88-2736-4242-87a5-2c83e2923744/dqc_reference/reference_markers_gtdb.fasta -out GCF_000621105.1_ASM62110v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:01:47,261] [INFO] Task succeeded: Blastn
[2024-01-24 13:01:47,278] [INFO] Selected 9 target genomes.
[2024-01-24 13:01:47,278] [INFO] Target genome list was writen to GCF_000621105.1_ASM62110v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:01:47,286] [INFO] Task started: fastANI
[2024-01-24 13:01:47,286] [INFO] Running command: fastANI --query /var/lib/cwl/stg4c4e6f2e-c453-43d4-904e-ca57b98ddbe1/GCF_000621105.1_ASM62110v1_genomic.fna.gz --refList GCF_000621105.1_ASM62110v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000621105.1_ASM62110v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:01:51,999] [INFO] Task succeeded: fastANI
[2024-01-24 13:01:52,015] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:01:52,015] [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_013377255.1	s__Mannheimia granulomatis	99.9959	753	753	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Mannheimia	95.0	97.35	95.73	0.92	0.88	5	conclusive
GCF_011455695.1	s__Mannheimia granulomatis_A	94.6194	684	753	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Mannheimia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000521605.1	s__Mannheimia sp000521605	82.8805	530	753	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Mannheimia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014541205.1	s__Mannheimia bovis	82.4103	510	753	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Mannheimia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013377235.1	s__Mannheimia varigena	81.9103	514	753	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Mannheimia	95.0	97.47	97.09	0.96	0.94	7	-
GCF_004342115.1	s__Mannheimia haemolytica	81.6144	510	753	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Mannheimia	95.0	99.19	95.33	0.93	0.85	196	-
GCF_013377995.1	s__Mannheimia pernigra	80.7378	457	753	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Mannheimia	95.0	98.69	97.60	0.91	0.86	5	-
GCF_900636745.1	s__Actinobacillus equuli	78.8688	304	753	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Actinobacillus	95.0	98.82	97.64	0.96	0.93	3	-
GCF_900109315.1	s__Haemophilus_B ducreyi	78.2032	146	753	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus_B	95.0	98.41	97.61	0.95	0.91	31	-
--------------------------------------------------------------------------------
[2024-01-24 13:01:52,017] [INFO] GTDB search result was written to GCF_000621105.1_ASM62110v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:01:52,018] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:01:52,043] [INFO] DFAST_QC result json was written to GCF_000621105.1_ASM62110v1_genomic.fna/dqc_result.json
[2024-01-24 13:01:52,044] [INFO] DFAST_QC completed!
[2024-01-24 13:01:52,044] [INFO] Total running time: 0h0m48s