[2024-01-24 11:52:04,774] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:52:04,776] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:52:04,776] [INFO] DQC Reference Directory: /var/lib/cwl/stg45726a97-cd87-40d7-9114-331316de910c/dqc_reference
[2024-01-24 11:52:06,002] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:52:06,003] [INFO] Task started: Prodigal
[2024-01-24 11:52:06,003] [INFO] Running command: gunzip -c /var/lib/cwl/stg9b743b4d-ac6b-40f9-b064-3ba37849941a/GCF_014885015.1_ASM1488501v1_genomic.fna.gz | prodigal -d GCF_014885015.1_ASM1488501v1_genomic.fna/cds.fna -a GCF_014885015.1_ASM1488501v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:52:11,153] [INFO] Task succeeded: Prodigal
[2024-01-24 11:52:11,153] [INFO] Task started: HMMsearch
[2024-01-24 11:52:11,154] [INFO] Running command: hmmsearch --tblout GCF_014885015.1_ASM1488501v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg45726a97-cd87-40d7-9114-331316de910c/dqc_reference/reference_markers.hmm GCF_014885015.1_ASM1488501v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:52:11,368] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:52:11,369] [INFO] Found 6/6 markers.
[2024-01-24 11:52:11,392] [INFO] Query marker FASTA was written to GCF_014885015.1_ASM1488501v1_genomic.fna/markers.fasta
[2024-01-24 11:52:11,393] [INFO] Task started: Blastn
[2024-01-24 11:52:11,393] [INFO] Running command: blastn -query GCF_014885015.1_ASM1488501v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg45726a97-cd87-40d7-9114-331316de910c/dqc_reference/reference_markers.fasta -out GCF_014885015.1_ASM1488501v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:52:12,006] [INFO] Task succeeded: Blastn
[2024-01-24 11:52:12,009] [INFO] Selected 22 target genomes.
[2024-01-24 11:52:12,009] [INFO] Target genome list was writen to GCF_014885015.1_ASM1488501v1_genomic.fna/target_genomes.txt
[2024-01-24 11:52:12,198] [INFO] Task started: fastANI
[2024-01-24 11:52:12,198] [INFO] Running command: fastANI --query /var/lib/cwl/stg9b743b4d-ac6b-40f9-b064-3ba37849941a/GCF_014885015.1_ASM1488501v1_genomic.fna.gz --refList GCF_014885015.1_ASM1488501v1_genomic.fna/target_genomes.txt --output GCF_014885015.1_ASM1488501v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:52:21,555] [INFO] Task succeeded: fastANI
[2024-01-24 11:52:21,556] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg45726a97-cd87-40d7-9114-331316de910c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:52:21,556] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg45726a97-cd87-40d7-9114-331316de910c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:52:21,572] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:52:21,572] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:52:21,572] [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
Spirabiliibacterium falconis	strain=NCTC 11878	GCA_014885015.1	572023	572023	type	True	100.0	633	633	95	conclusive
Spirabiliibacterium pneumoniae	strain=HPA106	GCA_014884995.1	221400	221400	type	True	80.9193	428	633	95	below_threshold
Spirabiliibacterium mucosae	strain=20609_3	GCA_014884965.1	28156	28156	type	True	80.2333	352	633	95	below_threshold
Vespertiliibacter pulmonis	strain=CCUG 64585	GCA_013377275.1	1443036	1443036	type	True	77.8083	61	633	95	below_threshold
Haemophilus pittmaniae	strain=HK 85	GCA_000223275.2	249188	249188	type	True	77.7017	63	633	95	below_threshold
Haemophilus paraphrohaemolyticus	strain=CCUG 3718	GCA_002015045.1	736	736	type	True	77.665	61	633	95	below_threshold
Bisgaardia hudsonensis	strain=DSM 28231	GCA_004345785.1	109472	109472	type	True	77.4977	76	633	95	below_threshold
Testudinibacter aquarius	strain=DSM 28140	GCA_004342725.1	1524974	1524974	type	True	77.4555	128	633	95	below_threshold
Testudinibacter aquarius	strain=ELNT2X	GCA_009761355.1	1524974	1524974	type	True	77.4471	127	633	95	below_threshold
Mannheimia pernigra	strain=17CN0883	GCA_013377995.1	111844	111844	type	True	77.4236	67	633	95	below_threshold
Bisgaardia hudsonensis	strain=M327/99/2	GCA_013377195.1	109472	109472	type	True	77.3855	79	633	95	below_threshold
Mannheimia ovis	strain=ZY170218	GCA_009828705.1	2679994	2679994	type	True	77.2958	66	633	95	below_threshold
Volucribacter psittacicida	strain=DSM 15534	GCA_004339025.1	203482	203482	type	True	77.2383	94	633	95	below_threshold
Rodentibacter heidelbergensis	strain=Ac69	GCA_002000125.1	1908258	1908258	type	True	76.9728	76	633	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:52:21,575] [INFO] DFAST Taxonomy check result was written to GCF_014885015.1_ASM1488501v1_genomic.fna/tc_result.tsv
[2024-01-24 11:52:21,575] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:52:21,576] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:52:21,576] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg45726a97-cd87-40d7-9114-331316de910c/dqc_reference/checkm_data
[2024-01-24 11:52:21,577] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:52:21,597] [INFO] Task started: CheckM
[2024-01-24 11:52:21,598] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014885015.1_ASM1488501v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014885015.1_ASM1488501v1_genomic.fna/checkm_input GCF_014885015.1_ASM1488501v1_genomic.fna/checkm_result
[2024-01-24 11:52:43,887] [INFO] Task succeeded: CheckM
[2024-01-24 11:52:43,888] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:52:43,909] [INFO] ===== Completeness check finished =====
[2024-01-24 11:52:43,909] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:52:43,910] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014885015.1_ASM1488501v1_genomic.fna/markers.fasta)
[2024-01-24 11:52:43,910] [INFO] Task started: Blastn
[2024-01-24 11:52:43,910] [INFO] Running command: blastn -query GCF_014885015.1_ASM1488501v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg45726a97-cd87-40d7-9114-331316de910c/dqc_reference/reference_markers_gtdb.fasta -out GCF_014885015.1_ASM1488501v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:52:44,681] [INFO] Task succeeded: Blastn
[2024-01-24 11:52:44,686] [INFO] Selected 19 target genomes.
[2024-01-24 11:52:44,686] [INFO] Target genome list was writen to GCF_014885015.1_ASM1488501v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:52:44,717] [INFO] Task started: fastANI
[2024-01-24 11:52:44,717] [INFO] Running command: fastANI --query /var/lib/cwl/stg9b743b4d-ac6b-40f9-b064-3ba37849941a/GCF_014885015.1_ASM1488501v1_genomic.fna.gz --refList GCF_014885015.1_ASM1488501v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014885015.1_ASM1488501v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:52:52,279] [INFO] Task succeeded: fastANI
[2024-01-24 11:52:52,295] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:52:52,295] [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_014885015.1	s__Spirabiliibacterium falconis	100.0	633	633	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Spirabiliibacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014884995.1	s__Spirabiliibacterium pneumoniae	80.9185	428	633	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Spirabiliibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014884965.1	s__Spirabiliibacterium mucosae	80.2822	349	633	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Spirabiliibacterium	95.0	96.18	96.18	0.92	0.92	2	-
GCA_006228005.1	s__Chelonobacter sp006228005	77.8173	106	633	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Chelonobacter	95.0	99.89	99.87	0.94	0.93	5	-
GCF_002015045.1	s__Haemophilus_A paraphrohaemolyticus	77.665	61	633	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus_A	95.0	97.72	95.26	0.95	0.91	7	-
GCA_901420285.1	s__Rodentibacter sp901420285	77.6184	57	633	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Rodentibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000772535.1	s__Chelonobacter oris	77.5632	114	633	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Chelonobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004342725.1	s__Chelonobacter aquarius	77.4797	127	633	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Chelonobacter	95.0	97.20	95.17	0.92	0.86	10	-
GCF_014202395.1	s__Histophilus somni	77.4522	75	633	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Histophilus	95.0	99.10	98.34	0.94	0.85	61	-
GCF_004340985.1	s__Cricetibacter osteomyelitidis	77.409	78	633	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Cricetibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013377995.1	s__Mannheimia pernigra	77.3789	68	633	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Mannheimia	95.0	98.69	97.60	0.91	0.86	5	-
GCF_003101015.1	s__Actinobacillus_A porcitonsillarum	77.3288	69	633	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_006384255.1	s__Haemophilus seminalis	77.2389	77	633	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus	95.0	96.02	95.40	0.91	0.84	26	-
GCF_001276515.1	s__Haemophilus sp001276515	77.1261	78	633	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus	95.0	95.49	95.48	0.91	0.90	3	-
GCF_002000125.1	s__Rodentibacter heidelbergensis	76.9728	76	633	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Rodentibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:52:52,296] [INFO] GTDB search result was written to GCF_014885015.1_ASM1488501v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:52:52,297] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:52:52,301] [INFO] DFAST_QC result json was written to GCF_014885015.1_ASM1488501v1_genomic.fna/dqc_result.json
[2024-01-24 11:52:52,301] [INFO] DFAST_QC completed!
[2024-01-24 11:52:52,301] [INFO] Total running time: 0h0m48s