[2023-06-13 21:51:08,017] [INFO] DFAST_QC pipeline started.
[2023-06-13 21:51:08,021] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 21:51:08,022] [INFO] DQC Reference Directory: /var/lib/cwl/stg0d7db6f7-c19e-4f23-aa39-e5b3add45151/dqc_reference
[2023-06-13 21:51:09,378] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 21:51:09,379] [INFO] Task started: Prodigal
[2023-06-13 21:51:09,379] [INFO] Running command: gunzip -c /var/lib/cwl/stgfabe0089-7543-4a31-b6d1-cbc4baa232bd/GCA_022784885.1_ASM2278488v1_genomic.fna.gz | prodigal -d GCA_022784885.1_ASM2278488v1_genomic.fna/cds.fna -a GCA_022784885.1_ASM2278488v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 21:51:14,007] [INFO] Task succeeded: Prodigal
[2023-06-13 21:51:14,007] [INFO] Task started: HMMsearch
[2023-06-13 21:51:14,007] [INFO] Running command: hmmsearch --tblout GCA_022784885.1_ASM2278488v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0d7db6f7-c19e-4f23-aa39-e5b3add45151/dqc_reference/reference_markers.hmm GCA_022784885.1_ASM2278488v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 21:51:14,224] [INFO] Task succeeded: HMMsearch
[2023-06-13 21:51:14,225] [INFO] Found 6/6 markers.
[2023-06-13 21:51:14,251] [INFO] Query marker FASTA was written to GCA_022784885.1_ASM2278488v1_genomic.fna/markers.fasta
[2023-06-13 21:51:14,251] [INFO] Task started: Blastn
[2023-06-13 21:51:14,251] [INFO] Running command: blastn -query GCA_022784885.1_ASM2278488v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0d7db6f7-c19e-4f23-aa39-e5b3add45151/dqc_reference/reference_markers.fasta -out GCA_022784885.1_ASM2278488v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 21:51:14,909] [INFO] Task succeeded: Blastn
[2023-06-13 21:51:14,913] [INFO] Selected 22 target genomes.
[2023-06-13 21:51:14,913] [INFO] Target genome list was writen to GCA_022784885.1_ASM2278488v1_genomic.fna/target_genomes.txt
[2023-06-13 21:51:14,916] [INFO] Task started: fastANI
[2023-06-13 21:51:14,916] [INFO] Running command: fastANI --query /var/lib/cwl/stgfabe0089-7543-4a31-b6d1-cbc4baa232bd/GCA_022784885.1_ASM2278488v1_genomic.fna.gz --refList GCA_022784885.1_ASM2278488v1_genomic.fna/target_genomes.txt --output GCA_022784885.1_ASM2278488v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 21:51:26,429] [INFO] Task succeeded: fastANI
[2023-06-13 21:51:26,429] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0d7db6f7-c19e-4f23-aa39-e5b3add45151/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 21:51:26,429] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0d7db6f7-c19e-4f23-aa39-e5b3add45151/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 21:51:26,444] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 21:51:26,444] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 21:51:26,445] [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 seminis	strain=NCTC10851	GCA_900460625.1	722	722	type	True	89.9964	526	644	95	below_threshold
Actinobacillus seminis	strain=ATCC 15768	GCA_002263215.1	722	722	type	True	89.9558	531	644	95	below_threshold
Avibacterium paragallinarum	strain=NCTC11296	GCA_900450705.1	728	728	type	True	78.747	184	644	95	below_threshold
Avibacterium paragallinarum	strain=CCUG 12835	GCA_002921155.1	728	728	type	True	78.5701	178	644	95	below_threshold
Avibacterium gallinarum	strain=NCTC11188	GCA_900454485.1	755	755	type	True	78.393	239	644	95	below_threshold
Avibacterium endocarditidis	strain=20186H4H1	GCA_002921145.1	380674	380674	type	True	78.3467	208	644	95	below_threshold
Avibacterium avium	strain=NCTC 11297	GCA_900454535.1	751	751	type	True	78.3063	224	644	95	below_threshold
Canicola haemoglobinophilus	strain=NCTC1659	GCA_900450725.1	733	733	type	True	78.2674	216	644	95	below_threshold
Avibacterium volantium	strain=NCTC3438	GCA_900635775.1	762	762	type	True	78.2432	234	644	95	below_threshold
Aggregatibacter kilianii	strain=PN_528	GCA_003130255.1	2025884	2025884	type	True	78.0429	194	644	95	below_threshold
Aggregatibacter aphrophilus	strain=ATCC 33389	GCA_000226495.3	732	732	type	True	78.0332	177	644	95	below_threshold
Aggregatibacter aphrophilus	strain=NCTC5906	GCA_900636915.1	732	732	type	True	77.9902	185	644	95	below_threshold
Pasteurella bettyae	strain=CCUG 2042	GCA_000262245.1	752	752	suspected-type	True	77.9777	148	644	95	below_threshold
Rodentibacter myodis	strain=Ac151	GCA_001999305.1	1907939	1907939	type	True	77.9733	191	644	95	below_threshold
Rodentibacter rarus	strain=CCUG 17206	GCA_001998965.1	1908260	1908260	type	True	77.9251	174	644	95	below_threshold
Aggregatibacter actinomycetemcomitans	strain=DSM 8324	GCA_000372365.1	714	714	type	True	77.8795	168	644	95	below_threshold
Aggregatibacter actinomycetemcomitans	strain=NCTC_9710	GCA_008085305.1	714	714	type	True	77.7183	169	644	95	below_threshold
Rodentibacter haemolyticus	strain=DSM 111151	GCA_015356115.1	2778911	2778911	type	True	77.6805	185	644	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 21:51:26,449] [INFO] DFAST Taxonomy check result was written to GCA_022784885.1_ASM2278488v1_genomic.fna/tc_result.tsv
[2023-06-13 21:51:26,450] [INFO] ===== Taxonomy check completed =====
[2023-06-13 21:51:26,450] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 21:51:26,451] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0d7db6f7-c19e-4f23-aa39-e5b3add45151/dqc_reference/checkm_data
[2023-06-13 21:51:26,452] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 21:51:26,477] [INFO] Task started: CheckM
[2023-06-13 21:51:26,477] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022784885.1_ASM2278488v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022784885.1_ASM2278488v1_genomic.fna/checkm_input GCA_022784885.1_ASM2278488v1_genomic.fna/checkm_result
[2023-06-13 21:51:47,718] [INFO] Task succeeded: CheckM
[2023-06-13 21:51:47,720] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 97.73%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 21:51:47,739] [INFO] ===== Completeness check finished =====
[2023-06-13 21:51:47,740] [INFO] ===== Start GTDB Search =====
[2023-06-13 21:51:47,740] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022784885.1_ASM2278488v1_genomic.fna/markers.fasta)
[2023-06-13 21:51:47,740] [INFO] Task started: Blastn
[2023-06-13 21:51:47,740] [INFO] Running command: blastn -query GCA_022784885.1_ASM2278488v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0d7db6f7-c19e-4f23-aa39-e5b3add45151/dqc_reference/reference_markers_gtdb.fasta -out GCA_022784885.1_ASM2278488v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 21:51:48,781] [INFO] Task succeeded: Blastn
[2023-06-13 21:51:48,787] [INFO] Selected 13 target genomes.
[2023-06-13 21:51:48,788] [INFO] Target genome list was writen to GCA_022784885.1_ASM2278488v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 21:51:48,794] [INFO] Task started: fastANI
[2023-06-13 21:51:48,794] [INFO] Running command: fastANI --query /var/lib/cwl/stgfabe0089-7543-4a31-b6d1-cbc4baa232bd/GCA_022784885.1_ASM2278488v1_genomic.fna.gz --refList GCA_022784885.1_ASM2278488v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022784885.1_ASM2278488v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 21:51:54,603] [INFO] Task succeeded: fastANI
[2023-06-13 21:51:54,614] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 21:51:54,614] [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
GCA_900637275.1	s__Actinobacillus_B aerogenes	98.9303	605	644	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Actinobacillus_B	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_900454475.1	s__Actinobacillus_B mairii	91.0581	556	644	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Actinobacillus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002263215.1	s__Actinobacillus_B seminis	89.9558	531	644	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_900450705.1	s__Avibacterium paragallinarum	78.6371	189	644	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Avibacterium	95.0	97.58	96.82	0.90	0.82	41	-
GCF_002795405.1	s__Caviibacterium pharyngocola	78.6237	310	644	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Caviibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002921145.1	s__Avibacterium endocarditidis	78.328	209	644	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Avibacterium	95.5151	N/A	N/A	N/A	N/A	1	-
GCF_900635775.1	s__Avibacterium volantium	78.2436	235	644	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Avibacterium	95.623	96.13	96.13	0.89	0.89	2	-
GCA_000751835.1	s__Necropsobacter rosorum	78.095	198	644	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Necropsobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017798005.1	s__Aggregatibacter sp000466335	78.0406	183	644	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Aggregatibacter	95.0	95.63	95.17	0.92	0.88	4	-
GCF_003130255.1	s__Aggregatibacter kilianii	78.0225	194	644	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Aggregatibacter	95.0	98.97	97.13	0.96	0.90	14	-
GCF_001999305.1	s__Rodentibacter myodis	77.9707	191	644	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Rodentibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001998965.1	s__Rodentibacter rarus	77.9422	173	644	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Rodentibacter	95.0	99.19	99.19	0.90	0.90	2	-
GCA_900756875.1	s__Haemophilus_D sp900756875	77.9076	143	644	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus_D	95.0	95.91	95.91	0.89	0.89	2	-
--------------------------------------------------------------------------------
[2023-06-13 21:51:54,616] [INFO] GTDB search result was written to GCA_022784885.1_ASM2278488v1_genomic.fna/result_gtdb.tsv
[2023-06-13 21:51:54,618] [INFO] ===== GTDB Search completed =====
[2023-06-13 21:51:54,622] [INFO] DFAST_QC result json was written to GCA_022784885.1_ASM2278488v1_genomic.fna/dqc_result.json
[2023-06-13 21:51:54,622] [INFO] DFAST_QC completed!
[2023-06-13 21:51:54,622] [INFO] Total running time: 0h0m47s