[2024-01-24 14:39:34,340] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:39:34,347] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:39:34,347] [INFO] DQC Reference Directory: /var/lib/cwl/stgf552e950-211a-443d-955a-857965fe8bab/dqc_reference
[2024-01-24 14:39:36,895] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:39:36,896] [INFO] Task started: Prodigal
[2024-01-24 14:39:36,896] [INFO] Running command: gunzip -c /var/lib/cwl/stg9ea90e5e-f757-4447-8263-76b71c9452f0/GCF_002015155.1_ASM201515v1_genomic.fna.gz | prodigal -d GCF_002015155.1_ASM201515v1_genomic.fna/cds.fna -a GCF_002015155.1_ASM201515v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:39:40,108] [INFO] Task succeeded: Prodigal
[2024-01-24 14:39:40,108] [INFO] Task started: HMMsearch
[2024-01-24 14:39:40,108] [INFO] Running command: hmmsearch --tblout GCF_002015155.1_ASM201515v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf552e950-211a-443d-955a-857965fe8bab/dqc_reference/reference_markers.hmm GCF_002015155.1_ASM201515v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:39:40,371] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:39:40,373] [INFO] Found 6/6 markers.
[2024-01-24 14:39:40,392] [INFO] Query marker FASTA was written to GCF_002015155.1_ASM201515v1_genomic.fna/markers.fasta
[2024-01-24 14:39:40,392] [INFO] Task started: Blastn
[2024-01-24 14:39:40,392] [INFO] Running command: blastn -query GCF_002015155.1_ASM201515v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf552e950-211a-443d-955a-857965fe8bab/dqc_reference/reference_markers.fasta -out GCF_002015155.1_ASM201515v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:39:42,603] [INFO] Task succeeded: Blastn
[2024-01-24 14:39:42,607] [INFO] Selected 16 target genomes.
[2024-01-24 14:39:42,607] [INFO] Target genome list was writen to GCF_002015155.1_ASM201515v1_genomic.fna/target_genomes.txt
[2024-01-24 14:39:42,697] [INFO] Task started: fastANI
[2024-01-24 14:39:42,697] [INFO] Running command: fastANI --query /var/lib/cwl/stg9ea90e5e-f757-4447-8263-76b71c9452f0/GCF_002015155.1_ASM201515v1_genomic.fna.gz --refList GCF_002015155.1_ASM201515v1_genomic.fna/target_genomes.txt --output GCF_002015155.1_ASM201515v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:39:50,512] [INFO] Task succeeded: fastANI
[2024-01-24 14:39:50,513] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf552e950-211a-443d-955a-857965fe8bab/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:39:50,513] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf552e950-211a-443d-955a-857965fe8bab/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:39:50,523] [INFO] Found 11 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 14:39:50,524] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:39:50,524] [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=CCUG 4438	GCA_002015155.1	730	730	type	True	100.0	500	500	95	conclusive
[Haemophilus] ducreyi	strain=ATCC 33940	GCA_900109315.1	730	730	type	True	99.9795	498	500	95	conclusive
[Haemophilus] ducreyi	strain=CIP 54.2	GCA_001043455.1	730	730	type	True	99.8895	495	500	95	conclusive
Actinobacillus equuli	strain=NCTC8529	GCA_900636745.1	718	718	type	True	79.2019	213	500	95	below_threshold
Actinobacillus capsulatus	strain=DSM 19761	GCA_000374285.1	717	717	type	True	78.9876	224	500	95	below_threshold
Actinobacillus suis	strain=ATCC 33415	GCA_000739435.1	716	716	type	True	78.8978	228	500	95	below_threshold
Actinobacillus ureae	strain=ATCC 25976	GCA_000188255.1	723	723	type	True	78.8134	207	500	95	below_threshold
Actinobacillus pleuropneumoniae	strain=4074	GCA_000167095.1	715	715	type	True	78.4817	181	500	95	below_threshold
Mannheimia granulomatis	strain=DSM 19156	GCA_000621105.1	85402	85402	type	True	78.0991	141	500	95	below_threshold
Mannheimia bovis	strain=ZY190616	GCA_014541205.1	2770636	2770636	type	True	77.9887	140	500	95	below_threshold
Ursidibacter maritimus	strain=Pb43106	GCA_009761395.1	1331689	1331689	type	True	77.833	141	500	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:39:50,525] [INFO] DFAST Taxonomy check result was written to GCF_002015155.1_ASM201515v1_genomic.fna/tc_result.tsv
[2024-01-24 14:39:50,526] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:39:50,526] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:39:50,527] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf552e950-211a-443d-955a-857965fe8bab/dqc_reference/checkm_data
[2024-01-24 14:39:50,528] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:39:50,560] [INFO] Task started: CheckM
[2024-01-24 14:39:50,560] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002015155.1_ASM201515v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002015155.1_ASM201515v1_genomic.fna/checkm_input GCF_002015155.1_ASM201515v1_genomic.fna/checkm_result
[2024-01-24 14:40:09,078] [INFO] Task succeeded: CheckM
[2024-01-24 14:40:09,080] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:40:09,101] [INFO] ===== Completeness check finished =====
[2024-01-24 14:40:09,102] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:40:09,103] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002015155.1_ASM201515v1_genomic.fna/markers.fasta)
[2024-01-24 14:40:09,104] [INFO] Task started: Blastn
[2024-01-24 14:40:09,104] [INFO] Running command: blastn -query GCF_002015155.1_ASM201515v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf552e950-211a-443d-955a-857965fe8bab/dqc_reference/reference_markers_gtdb.fasta -out GCF_002015155.1_ASM201515v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:40:10,189] [INFO] Task succeeded: Blastn
[2024-01-24 14:40:10,194] [INFO] Selected 17 target genomes.
[2024-01-24 14:40:10,195] [INFO] Target genome list was writen to GCF_002015155.1_ASM201515v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:40:10,231] [INFO] Task started: fastANI
[2024-01-24 14:40:10,232] [INFO] Running command: fastANI --query /var/lib/cwl/stg9ea90e5e-f757-4447-8263-76b71c9452f0/GCF_002015155.1_ASM201515v1_genomic.fna.gz --refList GCF_002015155.1_ASM201515v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002015155.1_ASM201515v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:40:16,999] [INFO] Task succeeded: fastANI
[2024-01-24 14:40:17,016] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:40:17,016] [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	99.9795	498	500	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_900636745.1	s__Actinobacillus equuli	79.2224	212	500	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Actinobacillus	95.0	98.82	97.64	0.96	0.93	3	-
GCF_901687125.1	s__Actinobacillus vicugnae	79.1071	264	500	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Actinobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000374285.1	s__Actinobacillus capsulatus	78.9876	224	500	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Actinobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000739435.1	s__Actinobacillus suis	78.8978	228	500	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	78.7922	208	500	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Actinobacillus	95.0	99.22	99.21	0.97	0.96	3	-
GCF_900444945.1	s__Actinobacillus lignieresii	78.6563	200	500	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Actinobacillus	95.0	96.69	96.41	0.91	0.89	35	-
GCF_003101015.1	s__Actinobacillus_A porcitonsillarum	78.3887	158	500	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_013377255.1	s__Mannheimia granulomatis	78.3089	143	500	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Mannheimia	95.0	97.35	95.73	0.92	0.88	5	-
GCF_000521605.1	s__Mannheimia sp000521605	78.1483	147	500	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	78.1081	148	500	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Mannheimia	95.0	97.47	97.09	0.96	0.94	7	-
GCF_004342115.1	s__Mannheimia haemolytica	78.0277	142	500	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Mannheimia	95.0	99.19	95.33	0.93	0.85	196	-
GCA_900637275.1	s__Actinobacillus_B aerogenes	78.0157	79	500	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_014541205.1	s__Mannheimia bovis	77.9887	140	500	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	77.7855	143	500	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Ursidibacter	95.0	99.92	99.03	0.98	0.97	15	-
GCF_013377195.1	s__Bisgaardia hudsonensis	77.6291	107	500	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Bisgaardia	95.0	99.99	99.99	0.99	0.99	2	-
GCF_013377295.1	s__Phocoenobacter skyensis	77.4452	96	500	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Phocoenobacter	95.0	99.99	99.99	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:40:17,018] [INFO] GTDB search result was written to GCF_002015155.1_ASM201515v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:40:17,019] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:40:17,023] [INFO] DFAST_QC result json was written to GCF_002015155.1_ASM201515v1_genomic.fna/dqc_result.json
[2024-01-24 14:40:17,023] [INFO] DFAST_QC completed!
[2024-01-24 14:40:17,023] [INFO] Total running time: 0h0m43s