[2024-01-24 13:57:14,408] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:57:14,410] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:57:14,410] [INFO] DQC Reference Directory: /var/lib/cwl/stg49426704-10f4-43e8-9da0-cdf01ba4e235/dqc_reference
[2024-01-24 13:57:15,866] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:57:15,867] [INFO] Task started: Prodigal
[2024-01-24 13:57:15,867] [INFO] Running command: gunzip -c /var/lib/cwl/stga4cc8966-4bda-4999-b655-4012bbbb8eaa/GCF_000262245.1_ASM26224v1_genomic.fna.gz | prodigal -d GCF_000262245.1_ASM26224v1_genomic.fna/cds.fna -a GCF_000262245.1_ASM26224v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:57:20,431] [INFO] Task succeeded: Prodigal
[2024-01-24 13:57:20,431] [INFO] Task started: HMMsearch
[2024-01-24 13:57:20,431] [INFO] Running command: hmmsearch --tblout GCF_000262245.1_ASM26224v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg49426704-10f4-43e8-9da0-cdf01ba4e235/dqc_reference/reference_markers.hmm GCF_000262245.1_ASM26224v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:57:20,674] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:57:20,675] [INFO] Found 6/6 markers.
[2024-01-24 13:57:20,697] [INFO] Query marker FASTA was written to GCF_000262245.1_ASM26224v1_genomic.fna/markers.fasta
[2024-01-24 13:57:20,698] [INFO] Task started: Blastn
[2024-01-24 13:57:20,698] [INFO] Running command: blastn -query GCF_000262245.1_ASM26224v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg49426704-10f4-43e8-9da0-cdf01ba4e235/dqc_reference/reference_markers.fasta -out GCF_000262245.1_ASM26224v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:57:21,395] [INFO] Task succeeded: Blastn
[2024-01-24 13:57:21,398] [INFO] Selected 20 target genomes.
[2024-01-24 13:57:21,398] [INFO] Target genome list was writen to GCF_000262245.1_ASM26224v1_genomic.fna/target_genomes.txt
[2024-01-24 13:57:21,407] [INFO] Task started: fastANI
[2024-01-24 13:57:21,407] [INFO] Running command: fastANI --query /var/lib/cwl/stga4cc8966-4bda-4999-b655-4012bbbb8eaa/GCF_000262245.1_ASM26224v1_genomic.fna.gz --refList GCF_000262245.1_ASM26224v1_genomic.fna/target_genomes.txt --output GCF_000262245.1_ASM26224v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:57:31,474] [INFO] Task succeeded: fastANI
[2024-01-24 13:57:31,474] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg49426704-10f4-43e8-9da0-cdf01ba4e235/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:57:31,475] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg49426704-10f4-43e8-9da0-cdf01ba4e235/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:57:31,486] [INFO] Found 13 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:57:31,486] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:57:31,486] [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
Pasteurella bettyae	strain=CCUG 2042	GCA_000262245.1	752	752	suspected-type	True	100.0	729	729	95	conclusive
Pasteurella bettyae	strain=NCTC10535	GCA_900454515.1	752	752	suspected-type	True	99.9939	729	729	95	conclusive
Basfia succiniciproducens	strain=JF4016	GCA_011455875.1	653940	653940	suspected-type	True	78.7292	247	729	95	below_threshold
Basfia succiniciproducens	strain=DSM 22022	GCA_900101275.1	653940	653940	suspected-type	True	78.6986	245	729	95	below_threshold
Aggregatibacter kilianii	strain=PN_528	GCA_003130255.1	2025884	2025884	type	True	78.5301	134	729	95	below_threshold
Haemophilus parainfluenzae	strain=NCTC 7857	GCA_900450845.1	729	729	suspected-type	True	78.4536	190	729	95	below_threshold
Actinobacillus porcinus	strain=NM319	GCA_901764995.1	51048	51048	type	True	78.356	203	729	95	below_threshold
Haemophilus seminalis	strain=SZY H1	GCA_006384255.1	2582921	2582921	type	True	78.3428	192	729	95	below_threshold
Pasteurella canis	strain=NCTC11621	GCA_900454865.1	753	753	type	True	78.1909	215	729	95	below_threshold
Pasteurella dagmatis	strain=NCTC11617	GCA_900186835.1	754	754	type	True	78.0541	210	729	95	below_threshold
Lonepinella koalarum	strain=ATCC 700131	GCA_004565475.1	53417	53417	type	True	77.6994	202	729	95	below_threshold
Lonepinella koalarum	strain=DSM 10053	GCA_004339625.1	53417	53417	type	True	77.6932	202	729	95	below_threshold
Rodentibacter haemolyticus	strain=DSM 111151	GCA_015356115.1	2778911	2778911	type	True	77.655	155	729	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:57:31,489] [INFO] DFAST Taxonomy check result was written to GCF_000262245.1_ASM26224v1_genomic.fna/tc_result.tsv
[2024-01-24 13:57:31,489] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:57:31,490] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:57:31,490] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg49426704-10f4-43e8-9da0-cdf01ba4e235/dqc_reference/checkm_data
[2024-01-24 13:57:31,492] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:57:31,531] [INFO] Task started: CheckM
[2024-01-24 13:57:31,531] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000262245.1_ASM26224v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000262245.1_ASM26224v1_genomic.fna/checkm_input GCF_000262245.1_ASM26224v1_genomic.fna/checkm_result
[2024-01-24 13:57:52,658] [INFO] Task succeeded: CheckM
[2024-01-24 13:57:52,659] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:57:52,684] [INFO] ===== Completeness check finished =====
[2024-01-24 13:57:52,685] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:57:52,685] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000262245.1_ASM26224v1_genomic.fna/markers.fasta)
[2024-01-24 13:57:52,686] [INFO] Task started: Blastn
[2024-01-24 13:57:52,686] [INFO] Running command: blastn -query GCF_000262245.1_ASM26224v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg49426704-10f4-43e8-9da0-cdf01ba4e235/dqc_reference/reference_markers_gtdb.fasta -out GCF_000262245.1_ASM26224v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:57:53,698] [INFO] Task succeeded: Blastn
[2024-01-24 13:57:53,701] [INFO] Selected 23 target genomes.
[2024-01-24 13:57:53,701] [INFO] Target genome list was writen to GCF_000262245.1_ASM26224v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:57:53,720] [INFO] Task started: fastANI
[2024-01-24 13:57:53,721] [INFO] Running command: fastANI --query /var/lib/cwl/stga4cc8966-4bda-4999-b655-4012bbbb8eaa/GCF_000262245.1_ASM26224v1_genomic.fna.gz --refList GCF_000262245.1_ASM26224v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000262245.1_ASM26224v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:58:04,790] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:04,809] [INFO] Found 23 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:58:04,809] [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_000262245.1	s__Basfia bettyae	100.0	729	729	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Basfia	95.0	98.65	97.30	0.95	0.89	3	conclusive
GCF_014931395.1	s__Haemophilus_D sp900764435	78.9244	187	729	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus_D	95.0	95.55	95.23	0.94	0.91	6	-
GCF_003096995.1	s__Basfia_A langaaensis	78.8684	196	729	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_011455875.1	s__Basfia succiniciproducens	78.7641	245	729	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Basfia	95.0	99.17	98.70	0.95	0.93	4	-
GCA_905215245.1	s__Haemophilus_D sp905215245	78.7304	141	729	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus_D	95.0	95.18	95.12	0.97	0.97	5	-
GCF_001679045.1	s__Haemophilus haemolyticus	78.6444	193	729	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus	95.0	95.67	95.07	0.90	0.84	29	-
GCF_003130255.1	s__Aggregatibacter kilianii	78.5301	134	729	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Aggregatibacter	95.0	98.97	97.13	0.96	0.90	14	-
GCF_003493605.1	s__Haemophilus haemolyticus_J	78.4649	181	729	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905205995.1	s__Haemophilus_D sp905205995	78.4322	195	729	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014931275.1	s__Haemophilus_D sp900755445	78.3773	204	729	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus_D	95.096	96.11	95.22	0.94	0.92	6	-
GCF_006384255.1	s__Haemophilus seminalis	78.3621	191	729	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus	95.0	96.02	95.40	0.91	0.84	26	-
GCF_900454865.1	s__Pasteurella canis	78.1987	214	729	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Pasteurella	95.0	98.76	98.68	0.94	0.91	4	-
GCF_000739435.1	s__Actinobacillus suis	78.1857	134	729	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Actinobacillus	95.0	99.85	99.75	0.98	0.94	7	-
GCF_002850605.1	s__Pasteurella oralis	78.1669	204	729	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Pasteurella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000973525.1	s__Pasteurella multocida_A	78.1617	190	729	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Pasteurella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900444965.1	s__Basfia_A rossii	78.1617	247	729	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_900636745.1	s__Actinobacillus equuli	78.138	130	729	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Actinobacillus	95.0	98.82	97.64	0.96	0.93	3	-
GCF_013377195.1	s__Bisgaardia hudsonensis	78.0424	207	729	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Bisgaardia	95.0	99.99	99.99	0.99	0.99	2	-
GCF_900186835.1	s__Pasteurella dagmatis	78.022	212	729	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Pasteurella	95.0	99.39	98.82	0.98	0.96	3	-
GCF_900635775.1	s__Avibacterium volantium	77.9391	164	729	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Avibacterium	95.623	96.13	96.13	0.89	0.89	2	-
GCA_905207935.1	s__Haemophilus_D sp905207935	77.8527	157	729	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015356115.1	s__Rodentibacter sp015356115	77.7036	152	729	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Rodentibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004565475.1	s__Lonepinella koalarum	77.6986	202	729	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Lonepinella	95.0	99.41	98.83	0.96	0.92	3	-
--------------------------------------------------------------------------------
[2024-01-24 13:58:04,811] [INFO] GTDB search result was written to GCF_000262245.1_ASM26224v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:58:04,812] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:58:04,819] [INFO] DFAST_QC result json was written to GCF_000262245.1_ASM26224v1_genomic.fna/dqc_result.json
[2024-01-24 13:58:04,819] [INFO] DFAST_QC completed!
[2024-01-24 13:58:04,819] [INFO] Total running time: 0h0m50s