[2024-01-24 11:12:24,420] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:12:24,423] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:12:24,423] [INFO] DQC Reference Directory: /var/lib/cwl/stga1464114-080c-4339-984d-69cd8b8db052/dqc_reference
[2024-01-24 11:12:27,085] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:12:27,095] [INFO] Task started: Prodigal
[2024-01-24 11:12:27,096] [INFO] Running command: gunzip -c /var/lib/cwl/stg458cf850-ee4b-47e6-b6df-55520119c855/GCF_002263215.1_ASM226321v1_genomic.fna.gz | prodigal -d GCF_002263215.1_ASM226321v1_genomic.fna/cds.fna -a GCF_002263215.1_ASM226321v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:12:32,853] [INFO] Task succeeded: Prodigal
[2024-01-24 11:12:32,854] [INFO] Task started: HMMsearch
[2024-01-24 11:12:32,854] [INFO] Running command: hmmsearch --tblout GCF_002263215.1_ASM226321v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga1464114-080c-4339-984d-69cd8b8db052/dqc_reference/reference_markers.hmm GCF_002263215.1_ASM226321v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:12:33,163] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:12:33,164] [INFO] Found 6/6 markers.
[2024-01-24 11:12:33,194] [INFO] Query marker FASTA was written to GCF_002263215.1_ASM226321v1_genomic.fna/markers.fasta
[2024-01-24 11:12:33,194] [INFO] Task started: Blastn
[2024-01-24 11:12:33,194] [INFO] Running command: blastn -query GCF_002263215.1_ASM226321v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga1464114-080c-4339-984d-69cd8b8db052/dqc_reference/reference_markers.fasta -out GCF_002263215.1_ASM226321v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:12:33,859] [INFO] Task succeeded: Blastn
[2024-01-24 11:12:33,863] [INFO] Selected 27 target genomes.
[2024-01-24 11:12:33,864] [INFO] Target genome list was writen to GCF_002263215.1_ASM226321v1_genomic.fna/target_genomes.txt
[2024-01-24 11:12:33,917] [INFO] Task started: fastANI
[2024-01-24 11:12:33,918] [INFO] Running command: fastANI --query /var/lib/cwl/stg458cf850-ee4b-47e6-b6df-55520119c855/GCF_002263215.1_ASM226321v1_genomic.fna.gz --refList GCF_002263215.1_ASM226321v1_genomic.fna/target_genomes.txt --output GCF_002263215.1_ASM226321v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:12:46,639] [INFO] Task succeeded: fastANI
[2024-01-24 11:12:46,639] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga1464114-080c-4339-984d-69cd8b8db052/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:12:46,640] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga1464114-080c-4339-984d-69cd8b8db052/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:12:46,658] [INFO] Found 17 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:12:46,658] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:12:46,659] [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=ATCC 15768	GCA_002263215.1	722	722	type	True	100.0	774	775	95	conclusive
Actinobacillus seminis	strain=NCTC10851	GCA_900460625.1	722	722	type	True	99.955	773	775	95	conclusive
Avibacterium avium	strain=NCTC 11297	GCA_900454535.1	751	751	type	True	78.314	206	775	95	below_threshold
Avibacterium volantium	strain=NCTC3438	GCA_900635775.1	762	762	type	True	78.2151	241	775	95	below_threshold
Avibacterium gallinarum	strain=NCTC11188	GCA_900454485.1	755	755	type	True	78.1558	231	775	95	below_threshold
Avibacterium gallinarum	strain=DSM 17481	GCA_004362535.1	755	755	type	True	78.149	230	775	95	below_threshold
Aggregatibacter kilianii	strain=PN_528	GCA_003130255.1	2025884	2025884	type	True	78.1256	206	775	95	below_threshold
Avibacterium gallinarum	strain=NCTC 11188	GCA_002921135.1	755	755	type	True	78.0628	224	775	95	below_threshold
Pasteurella dagmatis	strain=NCTC11617	GCA_900186835.1	754	754	type	True	77.861	184	775	95	below_threshold
Pasteurella dagmatis	strain=ATCC 43325	GCA_000163475.1	754	754	type	True	77.8412	182	775	95	below_threshold
Rodentibacter haemolyticus	strain=DSM 111151	GCA_015356115.1	2778911	2778911	type	True	77.8223	173	775	95	below_threshold
Cricetibacter osteomyelitidis	strain=DSM 28404	GCA_004340985.1	1521931	1521931	type	True	77.8031	194	775	95	below_threshold
Aggregatibacter aphrophilus	strain=NCTC5906	GCA_900636915.1	732	732	type	True	77.7644	195	775	95	below_threshold
Vespertiliibacter pulmonis	strain=CCUG 64585	GCA_013377275.1	1443036	1443036	type	True	77.7192	85	775	95	below_threshold
Gallibacterium anatis	strain=NCTC11413	GCA_900450735.1	750	750	type	True	77.5352	128	775	95	below_threshold
Gallibacterium anatis	strain=DSM 16844	GCA_000379785.1	750	750	type	True	77.4572	124	775	95	below_threshold
Gallibacterium anatis	strain=F149	GCA_000772265.1	750	750	type	True	77.4153	121	775	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:12:46,668] [INFO] DFAST Taxonomy check result was written to GCF_002263215.1_ASM226321v1_genomic.fna/tc_result.tsv
[2024-01-24 11:12:46,669] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:12:46,669] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:12:46,669] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga1464114-080c-4339-984d-69cd8b8db052/dqc_reference/checkm_data
[2024-01-24 11:12:46,672] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:12:46,703] [INFO] Task started: CheckM
[2024-01-24 11:12:46,703] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002263215.1_ASM226321v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002263215.1_ASM226321v1_genomic.fna/checkm_input GCF_002263215.1_ASM226321v1_genomic.fna/checkm_result
[2024-01-24 11:13:11,391] [INFO] Task succeeded: CheckM
[2024-01-24 11:13:11,392] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:13:11,416] [INFO] ===== Completeness check finished =====
[2024-01-24 11:13:11,417] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:13:11,417] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002263215.1_ASM226321v1_genomic.fna/markers.fasta)
[2024-01-24 11:13:11,418] [INFO] Task started: Blastn
[2024-01-24 11:13:11,418] [INFO] Running command: blastn -query GCF_002263215.1_ASM226321v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga1464114-080c-4339-984d-69cd8b8db052/dqc_reference/reference_markers_gtdb.fasta -out GCF_002263215.1_ASM226321v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:13:12,334] [INFO] Task succeeded: Blastn
[2024-01-24 11:13:12,338] [INFO] Selected 18 target genomes.
[2024-01-24 11:13:12,338] [INFO] Target genome list was writen to GCF_002263215.1_ASM226321v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:13:12,388] [INFO] Task started: fastANI
[2024-01-24 11:13:12,388] [INFO] Running command: fastANI --query /var/lib/cwl/stg458cf850-ee4b-47e6-b6df-55520119c855/GCF_002263215.1_ASM226321v1_genomic.fna.gz --refList GCF_002263215.1_ASM226321v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002263215.1_ASM226321v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:13:20,862] [INFO] Task succeeded: fastANI
[2024-01-24 11:13:20,878] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:13:20,878] [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_002263215.1	s__Actinobacillus_B seminis	100.0	774	775	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Actinobacillus_B	95.0	99.95	99.95	1.00	1.00	2	conclusive
GCA_900454475.1	s__Actinobacillus_B mairii	93.1758	657	775	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Actinobacillus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900637275.1	s__Actinobacillus_B aerogenes	89.9463	572	775	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_014202395.1	s__Histophilus somni	79.8871	218	775	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Histophilus	95.0	99.10	98.34	0.94	0.85	61	-
GCF_004345745.1	s__Nicoletella semolina	78.9872	88	775	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Nicoletella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002795405.1	s__Caviibacterium pharyngocola	78.6278	295	775	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Caviibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900454535.1	s__Avibacterium avium	78.3045	207	775	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Avibacterium	95.0	95.69	95.67	0.83	0.83	3	-
GCF_900635775.1	s__Avibacterium volantium	78.1972	241	775	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Avibacterium	95.623	96.13	96.13	0.89	0.89	2	-
GCF_001038205.1	s__Muribacter muris	78.158	96	775	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Muribacter	95.0	96.52	96.51	0.85	0.84	5	-
GCA_000752995.2	s__Necropsobacter massiliensis_B	78.1443	236	775	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Necropsobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003130255.1	s__Aggregatibacter kilianii	78.1204	207	775	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Aggregatibacter	95.0	98.97	97.13	0.96	0.90	14	-
GCA_000751835.1	s__Necropsobacter rosorum	78.0596	200	775	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Necropsobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002921135.1	s__Avibacterium gallinarum	78.0422	226	775	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Avibacterium	95.623	100.00	100.00	1.00	1.00	3	-
GCF_017798005.1	s__Aggregatibacter sp000466335	77.9681	183	775	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Aggregatibacter	95.0	95.63	95.17	0.92	0.88	4	-
GCF_015356115.1	s__Rodentibacter sp015356115	77.8533	172	775	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Rodentibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900186835.1	s__Pasteurella dagmatis	77.844	185	775	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Pasteurella	95.0	99.39	98.82	0.98	0.96	3	-
GCF_004340985.1	s__Cricetibacter osteomyelitidis	77.8397	192	775	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Cricetibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013377275.1	s__Vespertiliibacter pulmonis	77.7538	84	775	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Vespertiliibacter	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 11:13:20,880] [INFO] GTDB search result was written to GCF_002263215.1_ASM226321v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:13:20,880] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:13:20,885] [INFO] DFAST_QC result json was written to GCF_002263215.1_ASM226321v1_genomic.fna/dqc_result.json
[2024-01-24 11:13:20,885] [INFO] DFAST_QC completed!
[2024-01-24 11:13:20,885] [INFO] Total running time: 0h0m56s