[2024-01-24 11:09:50,714] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:09:50,716] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:09:50,717] [INFO] DQC Reference Directory: /var/lib/cwl/stg4be61e05-f133-4114-8859-4ee8d567a220/dqc_reference
[2024-01-24 11:09:53,301] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:09:53,302] [INFO] Task started: Prodigal
[2024-01-24 11:09:53,302] [INFO] Running command: gunzip -c /var/lib/cwl/stgdf3c33ac-1753-41cc-98df-8b556633adbb/GCF_001043455.1_ASM104345v1_genomic.fna.gz | prodigal -d GCF_001043455.1_ASM104345v1_genomic.fna/cds.fna -a GCF_001043455.1_ASM104345v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:09:56,390] [INFO] Task succeeded: Prodigal
[2024-01-24 11:09:56,391] [INFO] Task started: HMMsearch
[2024-01-24 11:09:56,391] [INFO] Running command: hmmsearch --tblout GCF_001043455.1_ASM104345v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4be61e05-f133-4114-8859-4ee8d567a220/dqc_reference/reference_markers.hmm GCF_001043455.1_ASM104345v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:09:56,715] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:09:56,717] [INFO] Found 6/6 markers.
[2024-01-24 11:09:56,735] [INFO] Query marker FASTA was written to GCF_001043455.1_ASM104345v1_genomic.fna/markers.fasta
[2024-01-24 11:09:56,739] [INFO] Task started: Blastn
[2024-01-24 11:09:56,739] [INFO] Running command: blastn -query GCF_001043455.1_ASM104345v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4be61e05-f133-4114-8859-4ee8d567a220/dqc_reference/reference_markers.fasta -out GCF_001043455.1_ASM104345v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:10:00,196] [INFO] Task succeeded: Blastn
[2024-01-24 11:10:00,201] [INFO] Selected 16 target genomes.
[2024-01-24 11:10:00,201] [INFO] Target genome list was writen to GCF_001043455.1_ASM104345v1_genomic.fna/target_genomes.txt
[2024-01-24 11:10:00,257] [INFO] Task started: fastANI
[2024-01-24 11:10:00,258] [INFO] Running command: fastANI --query /var/lib/cwl/stgdf3c33ac-1753-41cc-98df-8b556633adbb/GCF_001043455.1_ASM104345v1_genomic.fna.gz --refList GCF_001043455.1_ASM104345v1_genomic.fna/target_genomes.txt --output GCF_001043455.1_ASM104345v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:10:07,528] [INFO] Task succeeded: fastANI
[2024-01-24 11:10:07,529] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4be61e05-f133-4114-8859-4ee8d567a220/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:10:07,529] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4be61e05-f133-4114-8859-4ee8d567a220/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:10:07,545] [INFO] Found 11 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 11:10:07,545] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:10:07,546] [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
[Haemophilus] ducreyi	strain=CIP 54.2	GCA_001043455.1	730	730	type	True	99.9791	508	519	95	conclusive
[Haemophilus] ducreyi	strain=ATCC 33940	GCA_900109315.1	730	730	type	True	99.8791	496	519	95	conclusive
[Haemophilus] ducreyi	strain=CCUG 4438	GCA_002015155.1	730	730	type	True	99.8548	495	519	95	conclusive
Actinobacillus equuli	strain=NCTC8529	GCA_900636745.1	718	718	type	True	79.2747	223	519	95	below_threshold
Actinobacillus capsulatus	strain=DSM 19761	GCA_000374285.1	717	717	type	True	78.9701	239	519	95	below_threshold
Actinobacillus suis	strain=ATCC 33415	GCA_000739435.1	716	716	type	True	78.7442	241	519	95	below_threshold
Actinobacillus pleuropneumoniae	strain=4074	GCA_000167095.1	715	715	type	True	78.6646	182	519	95	below_threshold
Actinobacillus ureae	strain=ATCC 25976	GCA_000188255.1	723	723	type	True	78.5894	228	519	95	below_threshold
Mannheimia granulomatis	strain=DSM 19156	GCA_000621105.1	85402	85402	type	True	78.1851	155	519	95	below_threshold
Mannheimia bovis	strain=ZY190616	GCA_014541205.1	2770636	2770636	type	True	78.1305	151	519	95	below_threshold
Ursidibacter maritimus	strain=Pb43106	GCA_009761395.1	1331689	1331689	type	True	77.7553	145	519	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:10:07,547] [INFO] DFAST Taxonomy check result was written to GCF_001043455.1_ASM104345v1_genomic.fna/tc_result.tsv
[2024-01-24 11:10:07,548] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:10:07,548] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:10:07,548] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4be61e05-f133-4114-8859-4ee8d567a220/dqc_reference/checkm_data
[2024-01-24 11:10:07,549] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:10:07,566] [INFO] Task started: CheckM
[2024-01-24 11:10:07,567] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001043455.1_ASM104345v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001043455.1_ASM104345v1_genomic.fna/checkm_input GCF_001043455.1_ASM104345v1_genomic.fna/checkm_result
[2024-01-24 11:10:25,714] [INFO] Task succeeded: CheckM
[2024-01-24 11:10:25,715] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:10:25,733] [INFO] ===== Completeness check finished =====
[2024-01-24 11:10:25,733] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:10:25,733] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001043455.1_ASM104345v1_genomic.fna/markers.fasta)
[2024-01-24 11:10:25,735] [INFO] Task started: Blastn
[2024-01-24 11:10:25,735] [INFO] Running command: blastn -query GCF_001043455.1_ASM104345v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4be61e05-f133-4114-8859-4ee8d567a220/dqc_reference/reference_markers_gtdb.fasta -out GCF_001043455.1_ASM104345v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:10:27,156] [INFO] Task succeeded: Blastn
[2024-01-24 11:10:27,158] [INFO] Selected 17 target genomes.
[2024-01-24 11:10:27,158] [INFO] Target genome list was writen to GCF_001043455.1_ASM104345v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:10:27,237] [INFO] Task started: fastANI
[2024-01-24 11:10:27,238] [INFO] Running command: fastANI --query /var/lib/cwl/stgdf3c33ac-1753-41cc-98df-8b556633adbb/GCF_001043455.1_ASM104345v1_genomic.fna.gz --refList GCF_001043455.1_ASM104345v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001043455.1_ASM104345v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:10:34,430] [INFO] Task succeeded: fastANI
[2024-01-24 11:10:34,453] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:10:34,453] [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_900109315.1	s__Haemophilus_B ducreyi	99.8791	496	519	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus_B	95.0	98.41	97.61	0.95	0.91	31	conclusive
GCF_901687125.1	s__Actinobacillus vicugnae	79.3756	267	519	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Actinobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900636745.1	s__Actinobacillus equuli	79.2284	223	519	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	78.9951	238	519	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	78.7858	200	519	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Actinobacillus	95.0	96.69	96.41	0.91	0.89	35	-
GCF_000739435.1	s__Actinobacillus suis	78.7004	240	519	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Actinobacillus	95.0	99.85	99.75	0.98	0.94	7	-
GCF_000188255.1	s__Actinobacillus ureae	78.5894	228	519	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Actinobacillus	95.0	99.22	99.21	0.97	0.96	3	-
GCF_003101015.1	s__Actinobacillus_A porcitonsillarum	78.4054	165	519	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Actinobacillus_A	95.0	97.10	97.10	0.92	0.92	2	-
GCF_000521605.1	s__Mannheimia sp000521605	78.314	149	519	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	78.3029	156	519	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Mannheimia	95.0	97.47	97.09	0.96	0.94	7	-
GCF_013377255.1	s__Mannheimia granulomatis	78.227	160	519	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Mannheimia	95.0	97.35	95.73	0.92	0.88	5	-
GCF_004342115.1	s__Mannheimia haemolytica	78.1853	142	519	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Mannheimia	95.0	99.19	95.33	0.93	0.85	196	-
GCF_014541205.1	s__Mannheimia bovis	78.1296	150	519	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Mannheimia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009761395.1	s__Ursidibacter maritimus	77.7352	146	519	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Ursidibacter	95.0	99.92	99.03	0.98	0.97	15	-
GCA_900637275.1	s__Actinobacillus_B aerogenes	77.6784	89	519	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_013377295.1	s__Phocoenobacter skyensis	77.6669	101	519	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Phocoenobacter	95.0	99.99	99.99	0.99	0.99	2	-
GCF_013377195.1	s__Bisgaardia hudsonensis	77.5454	115	519	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Bisgaardia	95.0	99.99	99.99	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-24 11:10:34,455] [INFO] GTDB search result was written to GCF_001043455.1_ASM104345v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:10:34,455] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:10:34,459] [INFO] DFAST_QC result json was written to GCF_001043455.1_ASM104345v1_genomic.fna/dqc_result.json
[2024-01-24 11:10:34,460] [INFO] DFAST_QC completed!
[2024-01-24 11:10:34,460] [INFO] Total running time: 0h0m44s