[2024-01-24 14:20:14,356] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:20:14,358] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:20:14,358] [INFO] DQC Reference Directory: /var/lib/cwl/stgd168666b-94b6-46b2-b7f2-1b175fc0ec67/dqc_reference
[2024-01-24 14:20:15,670] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:20:15,671] [INFO] Task started: Prodigal
[2024-01-24 14:20:15,671] [INFO] Running command: gunzip -c /var/lib/cwl/stg1a861630-c02d-45c7-9a2d-2bf1b635bbbf/GCF_000167095.1_ASM16709v1_genomic.fna.gz | prodigal -d GCF_000167095.1_ASM16709v1_genomic.fna/cds.fna -a GCF_000167095.1_ASM16709v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:20:20,374] [INFO] Task succeeded: Prodigal
[2024-01-24 14:20:20,375] [INFO] Task started: HMMsearch
[2024-01-24 14:20:20,375] [INFO] Running command: hmmsearch --tblout GCF_000167095.1_ASM16709v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd168666b-94b6-46b2-b7f2-1b175fc0ec67/dqc_reference/reference_markers.hmm GCF_000167095.1_ASM16709v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:20:20,601] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:20:20,602] [INFO] Found 6/6 markers.
[2024-01-24 14:20:20,629] [INFO] Query marker FASTA was written to GCF_000167095.1_ASM16709v1_genomic.fna/markers.fasta
[2024-01-24 14:20:20,630] [INFO] Task started: Blastn
[2024-01-24 14:20:20,630] [INFO] Running command: blastn -query GCF_000167095.1_ASM16709v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd168666b-94b6-46b2-b7f2-1b175fc0ec67/dqc_reference/reference_markers.fasta -out GCF_000167095.1_ASM16709v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:20:21,255] [INFO] Task succeeded: Blastn
[2024-01-24 14:20:21,258] [INFO] Selected 12 target genomes.
[2024-01-24 14:20:21,258] [INFO] Target genome list was writen to GCF_000167095.1_ASM16709v1_genomic.fna/target_genomes.txt
[2024-01-24 14:20:21,288] [INFO] Task started: fastANI
[2024-01-24 14:20:21,288] [INFO] Running command: fastANI --query /var/lib/cwl/stg1a861630-c02d-45c7-9a2d-2bf1b635bbbf/GCF_000167095.1_ASM16709v1_genomic.fna.gz --refList GCF_000167095.1_ASM16709v1_genomic.fna/target_genomes.txt --output GCF_000167095.1_ASM16709v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:20:28,725] [INFO] Task succeeded: fastANI
[2024-01-24 14:20:28,726] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd168666b-94b6-46b2-b7f2-1b175fc0ec67/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:20:28,727] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd168666b-94b6-46b2-b7f2-1b175fc0ec67/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:20:28,737] [INFO] Found 8 fastANI hits (4 hits with ANI > threshold)
[2024-01-24 14:20:28,737] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 14:20:28,738] [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 pleuropneumoniae	strain=4074	GCA_000167095.1	715	715	type	True	100.0	704	713	95	inconclusive
Actinobacillus pleuropneumoniae	strain=S4074	GCA_003290385.1	715	715	type	True	98.3377	673	713	95	inconclusive
Actinobacillus pleuropneumoniae	strain=4074	GCA_000178495.2	715	715	type	True	98.3372	673	713	95	inconclusive
Actinobacillus lignieresii	strain=NCTC4189	GCA_900444945.1	720	720	type	True	96.3253	649	713	95	inconclusive
Actinobacillus suis	strain=ATCC 33415	GCA_000739435.1	716	716	type	True	88.8091	561	713	95	below_threshold
Actinobacillus suis	strain=NCTC12996	GCA_900187155.1	716	716	type	True	88.7503	564	713	95	below_threshold
Actinobacillus equuli	strain=NCTC8529	GCA_900636745.1	718	718	type	True	88.0278	553	713	95	below_threshold
Rodentibacter haemolyticus	strain=DSM 111151	GCA_015356115.1	2778911	2778911	type	True	78.1931	150	713	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:20:28,739] [INFO] DFAST Taxonomy check result was written to GCF_000167095.1_ASM16709v1_genomic.fna/tc_result.tsv
[2024-01-24 14:20:28,740] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:20:28,740] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:20:28,740] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd168666b-94b6-46b2-b7f2-1b175fc0ec67/dqc_reference/checkm_data
[2024-01-24 14:20:28,741] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:20:28,767] [INFO] Task started: CheckM
[2024-01-24 14:20:28,767] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000167095.1_ASM16709v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000167095.1_ASM16709v1_genomic.fna/checkm_input GCF_000167095.1_ASM16709v1_genomic.fna/checkm_result
[2024-01-24 14:20:49,592] [INFO] Task succeeded: CheckM
[2024-01-24 14:20:49,593] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:20:49,611] [INFO] ===== Completeness check finished =====
[2024-01-24 14:20:49,612] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:20:49,612] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000167095.1_ASM16709v1_genomic.fna/markers.fasta)
[2024-01-24 14:20:49,612] [INFO] Task started: Blastn
[2024-01-24 14:20:49,613] [INFO] Running command: blastn -query GCF_000167095.1_ASM16709v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd168666b-94b6-46b2-b7f2-1b175fc0ec67/dqc_reference/reference_markers_gtdb.fasta -out GCF_000167095.1_ASM16709v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:20:50,436] [INFO] Task succeeded: Blastn
[2024-01-24 14:20:50,440] [INFO] Selected 7 target genomes.
[2024-01-24 14:20:50,440] [INFO] Target genome list was writen to GCF_000167095.1_ASM16709v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:20:50,455] [INFO] Task started: fastANI
[2024-01-24 14:20:50,455] [INFO] Running command: fastANI --query /var/lib/cwl/stg1a861630-c02d-45c7-9a2d-2bf1b635bbbf/GCF_000167095.1_ASM16709v1_genomic.fna.gz --refList GCF_000167095.1_ASM16709v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000167095.1_ASM16709v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:20:54,616] [INFO] Task succeeded: fastANI
[2024-01-24 14:20:54,648] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:20:54,649] [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_900444945.1	s__Actinobacillus lignieresii	96.3253	649	713	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Actinobacillus	95.0	96.69	96.41	0.91	0.89	35	conclusive
GCF_000739435.1	s__Actinobacillus suis	88.802	562	713	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Actinobacillus	95.0	99.85	99.75	0.98	0.94	7	-
GCF_900636745.1	s__Actinobacillus equuli	88.0278	553	713	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Actinobacillus	95.0	98.82	97.64	0.96	0.93	3	-
GCF_000188255.1	s__Actinobacillus ureae	87.374	540	713	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Actinobacillus	95.0	99.22	99.21	0.97	0.96	3	-
GCF_000374285.1	s__Actinobacillus capsulatus	87.322	554	713	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Actinobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_901687125.1	s__Actinobacillus vicugnae	81.4503	475	713	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Actinobacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:20:54,650] [INFO] GTDB search result was written to GCF_000167095.1_ASM16709v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:20:54,651] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:20:54,654] [INFO] DFAST_QC result json was written to GCF_000167095.1_ASM16709v1_genomic.fna/dqc_result.json
[2024-01-24 14:20:54,655] [INFO] DFAST_QC completed!
[2024-01-24 14:20:54,655] [INFO] Total running time: 0h0m40s