[2024-01-24 10:47:40,969] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:47:40,974] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:47:40,975] [INFO] DQC Reference Directory: /var/lib/cwl/stg1f1060cd-21b6-42e8-818b-ebd1c0c24973/dqc_reference
[2024-01-24 10:47:44,786] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:47:44,789] [INFO] Task started: Prodigal
[2024-01-24 10:47:44,789] [INFO] Running command: gunzip -c /var/lib/cwl/stga1525a42-144e-4bbc-99f8-8bd3214f49a8/GCF_017565765.1_ASM1756576v1_genomic.fna.gz | prodigal -d GCF_017565765.1_ASM1756576v1_genomic.fna/cds.fna -a GCF_017565765.1_ASM1756576v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:47:56,043] [INFO] Task succeeded: Prodigal
[2024-01-24 10:47:56,043] [INFO] Task started: HMMsearch
[2024-01-24 10:47:56,044] [INFO] Running command: hmmsearch --tblout GCF_017565765.1_ASM1756576v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1f1060cd-21b6-42e8-818b-ebd1c0c24973/dqc_reference/reference_markers.hmm GCF_017565765.1_ASM1756576v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:47:56,318] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:47:56,320] [INFO] Found 6/6 markers.
[2024-01-24 10:47:56,349] [INFO] Query marker FASTA was written to GCF_017565765.1_ASM1756576v1_genomic.fna/markers.fasta
[2024-01-24 10:47:56,349] [INFO] Task started: Blastn
[2024-01-24 10:47:56,350] [INFO] Running command: blastn -query GCF_017565765.1_ASM1756576v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1f1060cd-21b6-42e8-818b-ebd1c0c24973/dqc_reference/reference_markers.fasta -out GCF_017565765.1_ASM1756576v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:47:56,935] [INFO] Task succeeded: Blastn
[2024-01-24 10:47:56,945] [INFO] Selected 19 target genomes.
[2024-01-24 10:47:56,946] [INFO] Target genome list was writen to GCF_017565765.1_ASM1756576v1_genomic.fna/target_genomes.txt
[2024-01-24 10:47:56,953] [INFO] Task started: fastANI
[2024-01-24 10:47:56,954] [INFO] Running command: fastANI --query /var/lib/cwl/stga1525a42-144e-4bbc-99f8-8bd3214f49a8/GCF_017565765.1_ASM1756576v1_genomic.fna.gz --refList GCF_017565765.1_ASM1756576v1_genomic.fna/target_genomes.txt --output GCF_017565765.1_ASM1756576v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:48:08,189] [INFO] Task succeeded: fastANI
[2024-01-24 10:48:08,190] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1f1060cd-21b6-42e8-818b-ebd1c0c24973/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:48:08,190] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1f1060cd-21b6-42e8-818b-ebd1c0c24973/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:48:08,198] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 10:48:08,198] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:48:08,199] [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
Capnocytophaga bilenii	strain=Marseille-Q4570	GCA_017565765.1	2819369	2819369	type	True	99.9999	898	900	95	conclusive
Capnocytophaga leadbetteri	strain=DSM 22902	GCA_003054025.1	327575	327575	type	True	81.3233	341	900	95	below_threshold
Capnocytophaga endodontalis	strain=ChDC OS43	GCA_002209445.1	2708117	2708117	type	True	79.9756	342	900	95	below_threshold
Capnocytophaga sputigena	strain=NCTC11653	GCA_900446695.1	1019	1019	type	True	79.7873	327	900	95	below_threshold
Capnocytophaga periodontitidis	strain=p1a2	GCA_016126015.1	2795027	2795027	type	True	79.6935	333	900	95	below_threshold
Capnocytophaga ochracea	strain=FDAARGOS_1468	GCA_019930725.1	1018	1018	type	True	79.2812	252	900	95	below_threshold
Capnocytophaga ochracea	strain=DSM 7271	GCA_000023285.1	1018	1018	type	True	79.2087	264	900	95	below_threshold
Capnocytophaga canimorsus	strain=NCTC12242	GCA_900460905.1	28188	28188	type	True	77.2342	72	900	95	below_threshold
Capnocytophaga canimorsus	strain=DSM 19204	GCA_002797785.1	28188	28188	type	True	76.4994	71	900	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:48:08,200] [INFO] DFAST Taxonomy check result was written to GCF_017565765.1_ASM1756576v1_genomic.fna/tc_result.tsv
[2024-01-24 10:48:08,201] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:48:08,201] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:48:08,202] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1f1060cd-21b6-42e8-818b-ebd1c0c24973/dqc_reference/checkm_data
[2024-01-24 10:48:08,204] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:48:08,237] [INFO] Task started: CheckM
[2024-01-24 10:48:08,237] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017565765.1_ASM1756576v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017565765.1_ASM1756576v1_genomic.fna/checkm_input GCF_017565765.1_ASM1756576v1_genomic.fna/checkm_result
[2024-01-24 10:48:43,744] [INFO] Task succeeded: CheckM
[2024-01-24 10:48:43,745] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:48:43,761] [INFO] ===== Completeness check finished =====
[2024-01-24 10:48:43,761] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:48:43,762] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017565765.1_ASM1756576v1_genomic.fna/markers.fasta)
[2024-01-24 10:48:43,762] [INFO] Task started: Blastn
[2024-01-24 10:48:43,762] [INFO] Running command: blastn -query GCF_017565765.1_ASM1756576v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1f1060cd-21b6-42e8-818b-ebd1c0c24973/dqc_reference/reference_markers_gtdb.fasta -out GCF_017565765.1_ASM1756576v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:48:44,579] [INFO] Task succeeded: Blastn
[2024-01-24 10:48:44,583] [INFO] Selected 23 target genomes.
[2024-01-24 10:48:44,583] [INFO] Target genome list was writen to GCF_017565765.1_ASM1756576v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:48:44,648] [INFO] Task started: fastANI
[2024-01-24 10:48:44,648] [INFO] Running command: fastANI --query /var/lib/cwl/stga1525a42-144e-4bbc-99f8-8bd3214f49a8/GCF_017565765.1_ASM1756576v1_genomic.fna.gz --refList GCF_017565765.1_ASM1756576v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017565765.1_ASM1756576v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:48:58,230] [INFO] Task succeeded: fastANI
[2024-01-24 10:48:58,243] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:48:58,244] [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_017565765.1	s__Capnocytophaga bilenii	99.9999	898	900	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Capnocytophaga	95.0	97.25	97.25	0.91	0.91	2	conclusive
GCF_003054025.1	s__Capnocytophaga leadbetteri	81.2522	345	900	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Capnocytophaga	95.0	95.46	95.36	0.86	0.85	6	-
GCF_000192225.1	s__Capnocytophaga sp000192225	80.6534	96	900	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Capnocytophaga	95.0	99.03	99.03	0.97	0.97	2	-
GCF_002999135.1	s__Capnocytophaga sp002999135	80.3914	303	900	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Capnocytophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002209445.1	s__Capnocytophaga endodontalis	79.9431	347	900	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Capnocytophaga	95.0	96.66	96.51	0.90	0.87	9	-
GCF_900446695.1	s__Capnocytophaga sputigena	79.8099	328	900	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Capnocytophaga	95.0	97.52	96.32	0.92	0.88	8	-
GCF_000023285.1	s__Capnocytophaga ochracea	79.1557	262	900	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Capnocytophaga	95.0	96.34	96.09	0.90	0.87	17	-
GCF_000379185.1	s__Capnocytophaga cynodegmi	77.1992	72	900	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Capnocytophaga	95.0	97.53	96.05	0.91	0.86	7	-
GCF_002302565.1	s__Capnocytophaga canimorsus	77.0582	71	900	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Capnocytophaga	95.0	98.20	97.29	0.93	0.87	15	-
--------------------------------------------------------------------------------
[2024-01-24 10:48:58,246] [INFO] GTDB search result was written to GCF_017565765.1_ASM1756576v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:48:58,246] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:48:58,249] [INFO] DFAST_QC result json was written to GCF_017565765.1_ASM1756576v1_genomic.fna/dqc_result.json
[2024-01-24 10:48:58,249] [INFO] DFAST_QC completed!
[2024-01-24 10:48:58,249] [INFO] Total running time: 0h1m17s