[2024-01-24 12:52:24,923] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:52:24,925] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:52:24,925] [INFO] DQC Reference Directory: /var/lib/cwl/stgf45caec7-0f35-439e-b3d0-d9ecd7e99f58/dqc_reference
[2024-01-24 12:52:26,172] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:52:26,173] [INFO] Task started: Prodigal
[2024-01-24 12:52:26,174] [INFO] Running command: gunzip -c /var/lib/cwl/stg847942f9-dd43-4ccd-9837-2dfea5c4a2c6/GCF_014699115.1_ASM1469911v1_genomic.fna.gz | prodigal -d GCF_014699115.1_ASM1469911v1_genomic.fna/cds.fna -a GCF_014699115.1_ASM1469911v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:52:55,679] [INFO] Task succeeded: Prodigal
[2024-01-24 12:52:55,680] [INFO] Task started: HMMsearch
[2024-01-24 12:52:55,680] [INFO] Running command: hmmsearch --tblout GCF_014699115.1_ASM1469911v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf45caec7-0f35-439e-b3d0-d9ecd7e99f58/dqc_reference/reference_markers.hmm GCF_014699115.1_ASM1469911v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:52:55,980] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:52:55,982] [INFO] Found 6/6 markers.
[2024-01-24 12:52:56,029] [INFO] Query marker FASTA was written to GCF_014699115.1_ASM1469911v1_genomic.fna/markers.fasta
[2024-01-24 12:52:56,030] [INFO] Task started: Blastn
[2024-01-24 12:52:56,030] [INFO] Running command: blastn -query GCF_014699115.1_ASM1469911v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf45caec7-0f35-439e-b3d0-d9ecd7e99f58/dqc_reference/reference_markers.fasta -out GCF_014699115.1_ASM1469911v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:52:56,749] [INFO] Task succeeded: Blastn
[2024-01-24 12:52:56,753] [INFO] Selected 17 target genomes.
[2024-01-24 12:52:56,754] [INFO] Target genome list was writen to GCF_014699115.1_ASM1469911v1_genomic.fna/target_genomes.txt
[2024-01-24 12:52:56,795] [INFO] Task started: fastANI
[2024-01-24 12:52:56,796] [INFO] Running command: fastANI --query /var/lib/cwl/stg847942f9-dd43-4ccd-9837-2dfea5c4a2c6/GCF_014699115.1_ASM1469911v1_genomic.fna.gz --refList GCF_014699115.1_ASM1469911v1_genomic.fna/target_genomes.txt --output GCF_014699115.1_ASM1469911v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:53:15,200] [INFO] Task succeeded: fastANI
[2024-01-24 12:53:15,200] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf45caec7-0f35-439e-b3d0-d9ecd7e99f58/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:53:15,201] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf45caec7-0f35-439e-b3d0-d9ecd7e99f58/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:53:15,218] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:53:15,218] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:53:15,218] [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
Hymenobacter montanus	strain=BT664	GCA_014699115.1	2771359	2771359	type	True	100.0	1762	1765	95	conclusive
Hymenobacter sedentarius	strain=DG5B	GCA_001507645.1	1411621	1411621	type	True	82.135	932	1765	95	below_threshold
Hymenobacter armeniacus	strain=BT189	GCA_014699055.1	2771358	2771358	type	True	81.6911	958	1765	95	below_threshold
Hymenobacter ruricola	strain=BT662	GCA_015694525.1	2791023	2791023	type	True	81.6905	990	1765	95	below_threshold
Hymenobacter terricola	strain=3F2	GCA_017921975.2	2819236	2819236	type	True	81.6082	989	1765	95	below_threshold
Hymenobacter lapidarius	strain=CCM 8643	GCA_001816145.1	1908237	1908237	type	True	81.3717	859	1765	95	below_threshold
Hymenobacter properus	strain=BT439	GCA_015694735.1	2791026	2791026	type	True	81.3712	965	1765	95	below_threshold
Hymenobacter rubidus	strain=DG7B	GCA_016734815.1	1441626	1441626	type	True	81.309	892	1765	95	below_threshold
Hymenobacter glacialis	strain=CCM 8648	GCA_001816165.1	1908236	1908236	type	True	81.2545	840	1765	95	below_threshold
Hymenobacter artigasi	strain=1B	GCA_012275535.1	2719616	2719616	type	True	81.1183	949	1765	95	below_threshold
Hymenobacter jeongseonensis	strain=BT683	GCA_015694725.1	2791027	2791027	type	True	81.1175	883	1765	95	below_threshold
Hymenobacter terrenus	strain=MIMtkLc17	GCA_000972495.1	1629124	1629124	type	True	81.0513	941	1765	95	below_threshold
Hymenobacter polaris	strain=RP-2-7	GCA_012927305.1	2682546	2682546	type	True	78.6732	625	1765	95	below_threshold
Hymenobacter metallicola	strain=9PBR-1	GCA_004745645.1	2563114	2563114	type	True	78.4645	550	1765	95	below_threshold
Hymenobacter guriensis	strain=BT594	GCA_015773195.1	2793065	2793065	type	True	78.346	567	1765	95	below_threshold
Rhodocaloribacter litoris	strain=ISCAR-4553	GCA_011682235.2	2558931	2558931	type	True	75.4217	50	1765	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:53:15,220] [INFO] DFAST Taxonomy check result was written to GCF_014699115.1_ASM1469911v1_genomic.fna/tc_result.tsv
[2024-01-24 12:53:15,220] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:53:15,221] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:53:15,221] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf45caec7-0f35-439e-b3d0-d9ecd7e99f58/dqc_reference/checkm_data
[2024-01-24 12:53:15,222] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:53:15,274] [INFO] Task started: CheckM
[2024-01-24 12:53:15,274] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014699115.1_ASM1469911v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014699115.1_ASM1469911v1_genomic.fna/checkm_input GCF_014699115.1_ASM1469911v1_genomic.fna/checkm_result
[2024-01-24 12:54:30,253] [INFO] Task succeeded: CheckM
[2024-01-24 12:54:30,254] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:54:30,279] [INFO] ===== Completeness check finished =====
[2024-01-24 12:54:30,279] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:54:30,280] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014699115.1_ASM1469911v1_genomic.fna/markers.fasta)
[2024-01-24 12:54:30,280] [INFO] Task started: Blastn
[2024-01-24 12:54:30,281] [INFO] Running command: blastn -query GCF_014699115.1_ASM1469911v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf45caec7-0f35-439e-b3d0-d9ecd7e99f58/dqc_reference/reference_markers_gtdb.fasta -out GCF_014699115.1_ASM1469911v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:54:31,161] [INFO] Task succeeded: Blastn
[2024-01-24 12:54:31,165] [INFO] Selected 16 target genomes.
[2024-01-24 12:54:31,165] [INFO] Target genome list was writen to GCF_014699115.1_ASM1469911v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:54:31,209] [INFO] Task started: fastANI
[2024-01-24 12:54:31,210] [INFO] Running command: fastANI --query /var/lib/cwl/stg847942f9-dd43-4ccd-9837-2dfea5c4a2c6/GCF_014699115.1_ASM1469911v1_genomic.fna.gz --refList GCF_014699115.1_ASM1469911v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014699115.1_ASM1469911v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:54:49,609] [INFO] Task succeeded: fastANI
[2024-01-24 12:54:49,622] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:54:49,623] [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_014699115.1	s__Hymenobacter sp014699115	100.0	1762	1765	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001507645.1	s__Hymenobacter sedentarius	82.1405	931	1765	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016427455.1	s__Hymenobacter sp016427455	81.6958	964	1765	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	95.46	95.46	0.89	0.89	2	-
GCF_015694525.1	s__Hymenobacter ruricola	81.6905	990	1765	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001816145.1	s__Hymenobacter lapidarius	81.3717	859	1765	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016734815.1	s__Hymenobacter rubidus	81.2864	895	1765	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001816165.1	s__Hymenobacter glacialis	81.2809	837	1765	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015694725.1	s__Hymenobacter jeongseonensis	81.1076	884	1765	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012275535.1	s__Hymenobacter artigasi	81.1064	952	1765	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016056375.1	s__Hymenobacter negativus_A	81.0699	883	1765	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	97.78	97.78	0.95	0.95	3	-
GCF_000972495.1	s__Hymenobacter terrenus	81.0537	941	1765	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000715495.1	s__Hymenobacter sp000715495	81.0359	867	1765	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900115775.1	s__Hymenobacter arizonensis	80.988	960	1765	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018967845.1	s__Hymenobacter sp018967845	80.907	898	1765	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	99.02	98.98	0.94	0.93	3	-
GCF_900141805.1	s__Hymenobacter daecheongensis	78.5945	598	1765	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004745955.1	s__Hymenobacter elongatus	78.3576	487	1765	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:54:49,625] [INFO] GTDB search result was written to GCF_014699115.1_ASM1469911v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:54:49,626] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:54:49,631] [INFO] DFAST_QC result json was written to GCF_014699115.1_ASM1469911v1_genomic.fna/dqc_result.json
[2024-01-24 12:54:49,632] [INFO] DFAST_QC completed!
[2024-01-24 12:54:49,632] [INFO] Total running time: 0h2m25s