[2024-01-25 20:26:35,929] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:26:35,930] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:26:35,931] [INFO] DQC Reference Directory: /var/lib/cwl/stged014558-c1e9-46ef-8dfe-af964b748b24/dqc_reference
[2024-01-25 20:26:37,091] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:26:37,093] [INFO] Task started: Prodigal
[2024-01-25 20:26:37,093] [INFO] Running command: gunzip -c /var/lib/cwl/stg3e65ff61-682e-42af-9eec-236705be15cd/GCF_002795405.1_ASM279540v1_genomic.fna.gz | prodigal -d GCF_002795405.1_ASM279540v1_genomic.fna/cds.fna -a GCF_002795405.1_ASM279540v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:26:42,292] [INFO] Task succeeded: Prodigal
[2024-01-25 20:26:42,293] [INFO] Task started: HMMsearch
[2024-01-25 20:26:42,293] [INFO] Running command: hmmsearch --tblout GCF_002795405.1_ASM279540v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stged014558-c1e9-46ef-8dfe-af964b748b24/dqc_reference/reference_markers.hmm GCF_002795405.1_ASM279540v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:26:42,513] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:26:42,515] [INFO] Found 6/6 markers.
[2024-01-25 20:26:42,535] [INFO] Query marker FASTA was written to GCF_002795405.1_ASM279540v1_genomic.fna/markers.fasta
[2024-01-25 20:26:42,535] [INFO] Task started: Blastn
[2024-01-25 20:26:42,535] [INFO] Running command: blastn -query GCF_002795405.1_ASM279540v1_genomic.fna/markers.fasta -db /var/lib/cwl/stged014558-c1e9-46ef-8dfe-af964b748b24/dqc_reference/reference_markers.fasta -out GCF_002795405.1_ASM279540v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:26:43,135] [INFO] Task succeeded: Blastn
[2024-01-25 20:26:43,138] [INFO] Selected 25 target genomes.
[2024-01-25 20:26:43,138] [INFO] Target genome list was writen to GCF_002795405.1_ASM279540v1_genomic.fna/target_genomes.txt
[2024-01-25 20:26:43,186] [INFO] Task started: fastANI
[2024-01-25 20:26:43,187] [INFO] Running command: fastANI --query /var/lib/cwl/stg3e65ff61-682e-42af-9eec-236705be15cd/GCF_002795405.1_ASM279540v1_genomic.fna.gz --refList GCF_002795405.1_ASM279540v1_genomic.fna/target_genomes.txt --output GCF_002795405.1_ASM279540v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:26:53,481] [INFO] Task succeeded: fastANI
[2024-01-25 20:26:53,481] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stged014558-c1e9-46ef-8dfe-af964b748b24/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:26:53,481] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stged014558-c1e9-46ef-8dfe-af964b748b24/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:26:53,492] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 20:26:53,493] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 20:26:53,493] [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
Avibacterium gallinarum	strain=DSM 17481	GCA_004362535.1	755	755	type	True	78.8292	299	806	95	below_threshold
Avibacterium gallinarum	strain=NCTC 11188	GCA_002921135.1	755	755	type	True	78.8174	292	806	95	below_threshold
Avibacterium gallinarum	strain=NCTC11188	GCA_900454485.1	755	755	type	True	78.742	304	806	95	below_threshold
Actinobacillus seminis	strain=ATCC 15768	GCA_002263215.1	722	722	type	True	78.7114	301	806	95	below_threshold
Actinobacillus seminis	strain=NCTC10851	GCA_900460625.1	722	722	type	True	78.629	309	806	95	below_threshold
Avibacterium volantium	strain=NCTC3438	GCA_900635775.1	762	762	type	True	78.5146	304	806	95	below_threshold
Avibacterium endocarditidis	strain=20186H4H1	GCA_002921145.1	380674	380674	type	True	78.4529	279	806	95	below_threshold
Avibacterium avium	strain=NCTC 11297	GCA_900454535.1	751	751	type	True	78.4402	276	806	95	below_threshold
Actinobacillus porcinus	strain=NM319	GCA_901764995.1	51048	51048	type	True	78.397	209	806	95	below_threshold
Aggregatibacter segnis	strain=ATCC 33393	GCA_000185305.1	739	739	type	True	78.3882	219	806	95	below_threshold
Actinobacillus porcinus	strain=NM319	GCA_900773985.1	51048	51048	type	True	78.3614	211	806	95	below_threshold
Aggregatibacter kilianii	strain=PN_528	GCA_003130255.1	2025884	2025884	type	True	78.284	251	806	95	below_threshold
Aggregatibacter actinomycetemcomitans	strain=NCTC_9710	GCA_008085305.1	714	714	type	True	78.2606	262	806	95	below_threshold
Basfia succiniciproducens	strain=JF4016	GCA_011455875.1	653940	653940	suspected-type	True	78.1011	278	806	95	below_threshold
Aggregatibacter actinomycetemcomitans	strain=DSM 8324	GCA_000372365.1	714	714	type	True	78.0891	272	806	95	below_threshold
Rodentibacter haemolyticus	strain=DSM 111151	GCA_015356115.1	2778911	2778911	type	True	78.0476	221	806	95	below_threshold
Aggregatibacter aphrophilus	strain=NCTC5906	GCA_900636915.1	732	732	type	True	78.0202	245	806	95	below_threshold
Aggregatibacter aphrophilus	strain=ATCC 33389	GCA_000226495.3	732	732	type	True	77.9783	244	806	95	below_threshold
Actinobacillus lignieresii	strain=NCTC4189	GCA_900444945.1	720	720	type	True	77.8929	189	806	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:26:53,494] [INFO] DFAST Taxonomy check result was written to GCF_002795405.1_ASM279540v1_genomic.fna/tc_result.tsv
[2024-01-25 20:26:53,494] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:26:53,495] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:26:53,495] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stged014558-c1e9-46ef-8dfe-af964b748b24/dqc_reference/checkm_data
[2024-01-25 20:26:53,495] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:26:53,521] [INFO] Task started: CheckM
[2024-01-25 20:26:53,521] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002795405.1_ASM279540v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002795405.1_ASM279540v1_genomic.fna/checkm_input GCF_002795405.1_ASM279540v1_genomic.fna/checkm_result
[2024-01-25 20:27:13,562] [INFO] Task succeeded: CheckM
[2024-01-25 20:27:13,563] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:27:13,581] [INFO] ===== Completeness check finished =====
[2024-01-25 20:27:13,581] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:27:13,581] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002795405.1_ASM279540v1_genomic.fna/markers.fasta)
[2024-01-25 20:27:13,582] [INFO] Task started: Blastn
[2024-01-25 20:27:13,582] [INFO] Running command: blastn -query GCF_002795405.1_ASM279540v1_genomic.fna/markers.fasta -db /var/lib/cwl/stged014558-c1e9-46ef-8dfe-af964b748b24/dqc_reference/reference_markers_gtdb.fasta -out GCF_002795405.1_ASM279540v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:27:14,458] [INFO] Task succeeded: Blastn
[2024-01-25 20:27:14,460] [INFO] Selected 19 target genomes.
[2024-01-25 20:27:14,461] [INFO] Target genome list was writen to GCF_002795405.1_ASM279540v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:27:14,487] [INFO] Task started: fastANI
[2024-01-25 20:27:14,487] [INFO] Running command: fastANI --query /var/lib/cwl/stg3e65ff61-682e-42af-9eec-236705be15cd/GCF_002795405.1_ASM279540v1_genomic.fna.gz --refList GCF_002795405.1_ASM279540v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002795405.1_ASM279540v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:27:23,135] [INFO] Task succeeded: fastANI
[2024-01-25 20:27:23,146] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:27:23,146] [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_002795405.1	s__Caviibacterium pharyngocola	100.0	805	806	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Caviibacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_000751835.1	s__Necropsobacter rosorum	79.336	392	806	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Necropsobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000827595.2	s__Necropsobacter massiliensis	79.1844	377	806	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Necropsobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900637275.1	s__Actinobacillus_B aerogenes	78.8595	340	806	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Actinobacillus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000752995.2	s__Necropsobacter massiliensis_B	78.849	403	806	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Necropsobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002921135.1	s__Avibacterium gallinarum	78.8026	293	806	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Avibacterium	95.623	100.00	100.00	1.00	1.00	3	-
GCF_003129965.1	s__Aggregatibacter kilianii_A	78.676	311	806	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Aggregatibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017160915.1	s__Aggregatibacter actinomycetemcomitans_B	78.673	316	806	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Aggregatibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002921145.1	s__Avibacterium endocarditidis	78.4671	278	806	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Avibacterium	95.5151	N/A	N/A	N/A	N/A	1	-
GCF_900454535.1	s__Avibacterium avium	78.4124	278	806	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Avibacterium	95.0	95.69	95.67	0.83	0.83	3	-
GCF_901764995.1	s__Basfia_A porcinus	78.3796	210	806	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Basfia_A	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003130075.1	s__Aggregatibacter segnis_A	78.3127	238	806	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Aggregatibacter	95.0	95.43	95.32	0.90	0.88	6	-
GCA_900444965.1	s__Basfia_A rossii	78.2281	183	806	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Basfia_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003130205.1	s__Aggregatibacter actinomycetemcomitans_A	78.2111	268	806	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Aggregatibacter	95.0	97.99	96.75	0.93	0.87	15	-
GCA_901420285.1	s__Rodentibacter sp901420285	78.148	248	806	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Rodentibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011455875.1	s__Basfia succiniciproducens	78.1273	276	806	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Basfia	95.0	99.17	98.70	0.95	0.93	4	-
GCF_000372365.1	s__Aggregatibacter actinomycetemcomitans	78.0906	273	806	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Aggregatibacter	95.0	98.51	97.12	0.94	0.88	80	-
--------------------------------------------------------------------------------
[2024-01-25 20:27:23,149] [INFO] GTDB search result was written to GCF_002795405.1_ASM279540v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:27:23,150] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:27:23,154] [INFO] DFAST_QC result json was written to GCF_002795405.1_ASM279540v1_genomic.fna/dqc_result.json
[2024-01-25 20:27:23,155] [INFO] DFAST_QC completed!
[2024-01-25 20:27:23,155] [INFO] Total running time: 0h0m47s