[2024-01-24 13:57:56,286] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:57:56,291] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:57:56,291] [INFO] DQC Reference Directory: /var/lib/cwl/stg6db3cc09-01a2-46f5-97ef-3aa65f87e5ed/dqc_reference
[2024-01-24 13:57:57,580] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:57:57,581] [INFO] Task started: Prodigal
[2024-01-24 13:57:57,581] [INFO] Running command: gunzip -c /var/lib/cwl/stga792bcc6-9317-4401-ae78-d4530c7ff5d4/GCF_900187155.1_51726_C01_genomic.fna.gz | prodigal -d GCF_900187155.1_51726_C01_genomic.fna/cds.fna -a GCF_900187155.1_51726_C01_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:58:03,051] [INFO] Task succeeded: Prodigal
[2024-01-24 13:58:03,051] [INFO] Task started: HMMsearch
[2024-01-24 13:58:03,051] [INFO] Running command: hmmsearch --tblout GCF_900187155.1_51726_C01_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6db3cc09-01a2-46f5-97ef-3aa65f87e5ed/dqc_reference/reference_markers.hmm GCF_900187155.1_51726_C01_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:58:03,348] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:58:03,350] [INFO] Found 6/6 markers.
[2024-01-24 13:58:03,375] [INFO] Query marker FASTA was written to GCF_900187155.1_51726_C01_genomic.fna/markers.fasta
[2024-01-24 13:58:03,375] [INFO] Task started: Blastn
[2024-01-24 13:58:03,375] [INFO] Running command: blastn -query GCF_900187155.1_51726_C01_genomic.fna/markers.fasta -db /var/lib/cwl/stg6db3cc09-01a2-46f5-97ef-3aa65f87e5ed/dqc_reference/reference_markers.fasta -out GCF_900187155.1_51726_C01_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:04,026] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:04,030] [INFO] Selected 16 target genomes.
[2024-01-24 13:58:04,030] [INFO] Target genome list was writen to GCF_900187155.1_51726_C01_genomic.fna/target_genomes.txt
[2024-01-24 13:58:04,036] [INFO] Task started: fastANI
[2024-01-24 13:58:04,036] [INFO] Running command: fastANI --query /var/lib/cwl/stga792bcc6-9317-4401-ae78-d4530c7ff5d4/GCF_900187155.1_51726_C01_genomic.fna.gz --refList GCF_900187155.1_51726_C01_genomic.fna/target_genomes.txt --output GCF_900187155.1_51726_C01_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:58:13,692] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:13,693] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6db3cc09-01a2-46f5-97ef-3aa65f87e5ed/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:58:13,693] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6db3cc09-01a2-46f5-97ef-3aa65f87e5ed/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:58:13,704] [INFO] Found 12 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:58:13,704] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:58:13,705] [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 suis	strain=NCTC12996	GCA_900187155.1	716	716	type	True	100.0	831	833	95	conclusive
Actinobacillus suis	strain=ATCC 33415	GCA_000739435.1	716	716	type	True	99.9989	832	833	95	conclusive
Actinobacillus ureae	strain=ATCC 25976	GCA_000188255.1	723	723	type	True	94.6329	684	833	95	below_threshold
Actinobacillus equuli	strain=NCTC8529	GCA_900636745.1	718	718	type	True	93.792	714	833	95	below_threshold
Actinobacillus capsulatus	strain=DSM 19761	GCA_000374285.1	717	717	type	True	92.3517	700	833	95	below_threshold
Actinobacillus pleuropneumoniae	strain=4074	GCA_000178495.2	715	715	type	True	88.6048	620	833	95	below_threshold
Actinobacillus lignieresii	strain=NCTC4189	GCA_900444945.1	720	720	type	True	88.6013	582	833	95	below_threshold
Actinobacillus pleuropneumoniae	strain=S4074	GCA_003290385.1	715	715	type	True	88.5752	620	833	95	below_threshold
Actinobacillus pleuropneumoniae	strain=4074	GCA_000167095.1	715	715	type	True	88.5226	566	833	95	below_threshold
Otariodibacter oris	strain=Baika1	GCA_009684715.1	1032623	1032623	type	True	79.2306	172	833	95	below_threshold
Rodentibacter haemolyticus	strain=DSM 111151	GCA_015356115.1	2778911	2778911	type	True	79.2264	158	833	95	below_threshold
Otariodibacter oris	strain=DSM 23800	GCA_003634665.1	1032623	1032623	type	True	78.2625	166	833	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:58:13,706] [INFO] DFAST Taxonomy check result was written to GCF_900187155.1_51726_C01_genomic.fna/tc_result.tsv
[2024-01-24 13:58:13,707] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:58:13,707] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:58:13,707] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6db3cc09-01a2-46f5-97ef-3aa65f87e5ed/dqc_reference/checkm_data
[2024-01-24 13:58:13,709] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:58:13,737] [INFO] Task started: CheckM
[2024-01-24 13:58:13,737] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900187155.1_51726_C01_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900187155.1_51726_C01_genomic.fna/checkm_input GCF_900187155.1_51726_C01_genomic.fna/checkm_result
[2024-01-24 13:58:37,781] [INFO] Task succeeded: CheckM
[2024-01-24 13:58:37,782] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:58:37,801] [INFO] ===== Completeness check finished =====
[2024-01-24 13:58:37,802] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:58:37,802] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900187155.1_51726_C01_genomic.fna/markers.fasta)
[2024-01-24 13:58:37,803] [INFO] Task started: Blastn
[2024-01-24 13:58:37,803] [INFO] Running command: blastn -query GCF_900187155.1_51726_C01_genomic.fna/markers.fasta -db /var/lib/cwl/stg6db3cc09-01a2-46f5-97ef-3aa65f87e5ed/dqc_reference/reference_markers_gtdb.fasta -out GCF_900187155.1_51726_C01_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:38,732] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:38,735] [INFO] Selected 9 target genomes.
[2024-01-24 13:58:38,735] [INFO] Target genome list was writen to GCF_900187155.1_51726_C01_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:58:38,742] [INFO] Task started: fastANI
[2024-01-24 13:58:38,743] [INFO] Running command: fastANI --query /var/lib/cwl/stga792bcc6-9317-4401-ae78-d4530c7ff5d4/GCF_900187155.1_51726_C01_genomic.fna.gz --refList GCF_900187155.1_51726_C01_genomic.fna/target_genomes_gtdb.txt --output GCF_900187155.1_51726_C01_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:58:43,939] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:43,949] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:58:43,949] [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_000739435.1	s__Actinobacillus suis	99.9989	832	833	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Actinobacillus	95.0	99.85	99.75	0.98	0.94	7	conclusive
GCF_000188255.1	s__Actinobacillus ureae	94.6329	684	833	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Actinobacillus	95.0	99.22	99.21	0.97	0.96	3	-
GCF_900636745.1	s__Actinobacillus equuli	93.7846	713	833	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Actinobacillus	95.0	98.82	97.64	0.96	0.93	3	-
GCF_000374285.1	s__Actinobacillus capsulatus	92.3517	700	833	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Actinobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900444945.1	s__Actinobacillus lignieresii	88.6457	585	833	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Actinobacillus	95.0	96.69	96.41	0.91	0.89	35	-
GCF_901687125.1	s__Actinobacillus vicugnae	83.6029	614	833	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Actinobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900444965.1	s__Basfia_A rossii	80.1397	173	833	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_013377195.1	s__Bisgaardia hudsonensis	79.2052	115	833	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Bisgaardia	95.0	99.99	99.99	0.99	0.99	2	-
GCF_000262245.1	s__Basfia bettyae	78.1107	144	833	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Basfia	95.0	98.65	97.30	0.95	0.89	3	-
--------------------------------------------------------------------------------
[2024-01-24 13:58:43,951] [INFO] GTDB search result was written to GCF_900187155.1_51726_C01_genomic.fna/result_gtdb.tsv
[2024-01-24 13:58:43,952] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:58:43,956] [INFO] DFAST_QC result json was written to GCF_900187155.1_51726_C01_genomic.fna/dqc_result.json
[2024-01-24 13:58:43,956] [INFO] DFAST_QC completed!
[2024-01-24 13:58:43,956] [INFO] Total running time: 0h0m48s