[2024-01-24 12:37:09,446] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:37:09,448] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:37:09,449] [INFO] DQC Reference Directory: /var/lib/cwl/stg1b7e1e98-8a75-4739-b0a8-c1b5703e6f23/dqc_reference
[2024-01-24 12:37:10,770] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:37:10,772] [INFO] Task started: Prodigal
[2024-01-24 12:37:10,772] [INFO] Running command: gunzip -c /var/lib/cwl/stgf2400fab-43ad-4d5f-84a5-75ab8ed53238/GCF_016127115.1_ASM1612711v1_genomic.fna.gz | prodigal -d GCF_016127115.1_ASM1612711v1_genomic.fna/cds.fna -a GCF_016127115.1_ASM1612711v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:37:16,051] [INFO] Task succeeded: Prodigal
[2024-01-24 12:37:16,052] [INFO] Task started: HMMsearch
[2024-01-24 12:37:16,052] [INFO] Running command: hmmsearch --tblout GCF_016127115.1_ASM1612711v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1b7e1e98-8a75-4739-b0a8-c1b5703e6f23/dqc_reference/reference_markers.hmm GCF_016127115.1_ASM1612711v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:37:16,293] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:37:16,295] [INFO] Found 6/6 markers.
[2024-01-24 12:37:16,317] [INFO] Query marker FASTA was written to GCF_016127115.1_ASM1612711v1_genomic.fna/markers.fasta
[2024-01-24 12:37:16,318] [INFO] Task started: Blastn
[2024-01-24 12:37:16,318] [INFO] Running command: blastn -query GCF_016127115.1_ASM1612711v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1b7e1e98-8a75-4739-b0a8-c1b5703e6f23/dqc_reference/reference_markers.fasta -out GCF_016127115.1_ASM1612711v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:37:17,037] [INFO] Task succeeded: Blastn
[2024-01-24 12:37:17,042] [INFO] Selected 13 target genomes.
[2024-01-24 12:37:17,043] [INFO] Target genome list was writen to GCF_016127115.1_ASM1612711v1_genomic.fna/target_genomes.txt
[2024-01-24 12:37:17,081] [INFO] Task started: fastANI
[2024-01-24 12:37:17,081] [INFO] Running command: fastANI --query /var/lib/cwl/stgf2400fab-43ad-4d5f-84a5-75ab8ed53238/GCF_016127115.1_ASM1612711v1_genomic.fna.gz --refList GCF_016127115.1_ASM1612711v1_genomic.fna/target_genomes.txt --output GCF_016127115.1_ASM1612711v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:37:24,000] [INFO] Task succeeded: fastANI
[2024-01-24 12:37:24,001] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1b7e1e98-8a75-4739-b0a8-c1b5703e6f23/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:37:24,001] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1b7e1e98-8a75-4739-b0a8-c1b5703e6f23/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:37:24,012] [INFO] Found 9 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 12:37:24,012] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:37:24,012] [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
Aggregatibacter segnis	strain=FDAARGOS_987	GCA_016127115.1	739	739	type	True	100.0	686	687	95	conclusive
Aggregatibacter segnis	strain=NCTC10977	GCA_900476035.1	739	739	type	True	99.9971	672	687	95	conclusive
Aggregatibacter segnis	strain=ATCC 33393	GCA_000185305.1	739	739	type	True	99.9544	665	687	95	conclusive
Aggregatibacter kilianii	strain=PN_528	GCA_003130255.1	2025884	2025884	type	True	86.6741	525	687	95	below_threshold
Aggregatibacter aphrophilus	strain=NCTC5906	GCA_900636915.1	732	732	type	True	85.9043	499	687	95	below_threshold
Aggregatibacter aphrophilus	strain=ATCC 33389	GCA_000226495.3	732	732	type	True	85.8764	490	687	95	below_threshold
Aggregatibacter actinomycetemcomitans	strain=NCTC_9710	GCA_008085305.1	714	714	type	True	81.6694	432	687	95	below_threshold
Aggregatibacter actinomycetemcomitans	strain=DSM 8324	GCA_000372365.1	714	714	type	True	81.6456	431	687	95	below_threshold
Rodentibacter haemolyticus	strain=DSM 111151	GCA_015356115.1	2778911	2778911	type	True	79.0343	223	687	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:37:24,014] [INFO] DFAST Taxonomy check result was written to GCF_016127115.1_ASM1612711v1_genomic.fna/tc_result.tsv
[2024-01-24 12:37:24,014] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:37:24,014] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:37:24,015] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1b7e1e98-8a75-4739-b0a8-c1b5703e6f23/dqc_reference/checkm_data
[2024-01-24 12:37:24,016] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:37:24,037] [INFO] Task started: CheckM
[2024-01-24 12:37:24,037] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016127115.1_ASM1612711v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016127115.1_ASM1612711v1_genomic.fna/checkm_input GCF_016127115.1_ASM1612711v1_genomic.fna/checkm_result
[2024-01-24 12:37:46,412] [INFO] Task succeeded: CheckM
[2024-01-24 12:37:46,413] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:37:46,434] [INFO] ===== Completeness check finished =====
[2024-01-24 12:37:46,434] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:37:46,434] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016127115.1_ASM1612711v1_genomic.fna/markers.fasta)
[2024-01-24 12:37:46,435] [INFO] Task started: Blastn
[2024-01-24 12:37:46,435] [INFO] Running command: blastn -query GCF_016127115.1_ASM1612711v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1b7e1e98-8a75-4739-b0a8-c1b5703e6f23/dqc_reference/reference_markers_gtdb.fasta -out GCF_016127115.1_ASM1612711v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:37:47,560] [INFO] Task succeeded: Blastn
[2024-01-24 12:37:47,565] [INFO] Selected 7 target genomes.
[2024-01-24 12:37:47,565] [INFO] Target genome list was writen to GCF_016127115.1_ASM1612711v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:37:47,571] [INFO] Task started: fastANI
[2024-01-24 12:37:47,572] [INFO] Running command: fastANI --query /var/lib/cwl/stgf2400fab-43ad-4d5f-84a5-75ab8ed53238/GCF_016127115.1_ASM1612711v1_genomic.fna.gz --refList GCF_016127115.1_ASM1612711v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016127115.1_ASM1612711v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:37:51,594] [INFO] Task succeeded: fastANI
[2024-01-24 12:37:51,601] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:37:51,601] [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_000185305.1	s__Aggregatibacter segnis	99.9544	665	687	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Aggregatibacter	95.0	97.84	95.38	0.95	0.88	6	conclusive
GCF_003130075.1	s__Aggregatibacter segnis_A	94.9798	582	687	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Aggregatibacter	95.0	95.43	95.32	0.90	0.88	6	-
GCF_017798005.1	s__Aggregatibacter sp000466335	90.3761	484	687	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Aggregatibacter	95.0	95.63	95.17	0.92	0.88	4	-
GCF_003130255.1	s__Aggregatibacter kilianii	86.6724	524	687	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Aggregatibacter	95.0	98.97	97.13	0.96	0.90	14	-
GCF_900636915.1	s__Aggregatibacter aphrophilus	85.8424	498	687	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Aggregatibacter	95.0	97.58	96.00	0.94	0.87	19	-
GCF_003129965.1	s__Aggregatibacter kilianii_A	82.5678	489	687	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Aggregatibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000372365.1	s__Aggregatibacter actinomycetemcomitans	81.6352	432	687	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Aggregatibacter	95.0	98.51	97.12	0.94	0.88	80	-
--------------------------------------------------------------------------------
[2024-01-24 12:37:51,604] [INFO] GTDB search result was written to GCF_016127115.1_ASM1612711v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:37:51,604] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:37:51,607] [INFO] DFAST_QC result json was written to GCF_016127115.1_ASM1612711v1_genomic.fna/dqc_result.json
[2024-01-24 12:37:51,608] [INFO] DFAST_QC completed!
[2024-01-24 12:37:51,608] [INFO] Total running time: 0h0m42s