[2024-01-24 14:55:27,007] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:55:27,009] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:55:27,009] [INFO] DQC Reference Directory: /var/lib/cwl/stgc0dfeed7-233b-4451-860e-75c13d3663c6/dqc_reference
[2024-01-24 14:55:28,479] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:55:28,480] [INFO] Task started: Prodigal
[2024-01-24 14:55:28,481] [INFO] Running command: gunzip -c /var/lib/cwl/stg168cdd5e-6139-4ab2-a7eb-108a150fa0ab/GCF_000972495.1_ASM97249v1_genomic.fna.gz | prodigal -d GCF_000972495.1_ASM97249v1_genomic.fna/cds.fna -a GCF_000972495.1_ASM97249v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:56:05,839] [INFO] Task succeeded: Prodigal
[2024-01-24 14:56:05,839] [INFO] Task started: HMMsearch
[2024-01-24 14:56:05,839] [INFO] Running command: hmmsearch --tblout GCF_000972495.1_ASM97249v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc0dfeed7-233b-4451-860e-75c13d3663c6/dqc_reference/reference_markers.hmm GCF_000972495.1_ASM97249v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:56:06,089] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:56:06,090] [INFO] Found 6/6 markers.
[2024-01-24 14:56:06,141] [INFO] Query marker FASTA was written to GCF_000972495.1_ASM97249v1_genomic.fna/markers.fasta
[2024-01-24 14:56:06,141] [INFO] Task started: Blastn
[2024-01-24 14:56:06,141] [INFO] Running command: blastn -query GCF_000972495.1_ASM97249v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc0dfeed7-233b-4451-860e-75c13d3663c6/dqc_reference/reference_markers.fasta -out GCF_000972495.1_ASM97249v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:56:06,726] [INFO] Task succeeded: Blastn
[2024-01-24 14:56:06,729] [INFO] Selected 14 target genomes.
[2024-01-24 14:56:06,730] [INFO] Target genome list was writen to GCF_000972495.1_ASM97249v1_genomic.fna/target_genomes.txt
[2024-01-24 14:56:06,738] [INFO] Task started: fastANI
[2024-01-24 14:56:06,738] [INFO] Running command: fastANI --query /var/lib/cwl/stg168cdd5e-6139-4ab2-a7eb-108a150fa0ab/GCF_000972495.1_ASM97249v1_genomic.fna.gz --refList GCF_000972495.1_ASM97249v1_genomic.fna/target_genomes.txt --output GCF_000972495.1_ASM97249v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:56:23,609] [INFO] Task succeeded: fastANI
[2024-01-24 14:56:23,609] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc0dfeed7-233b-4451-860e-75c13d3663c6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:56:23,610] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc0dfeed7-233b-4451-860e-75c13d3663c6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:56:23,621] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:56:23,622] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:56:23,622] [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 terrenus	strain=MIMtkLc17	GCA_000972495.1	1629124	1629124	type	True	100.0	2047	2049	95	conclusive
Hymenobacter terricola	strain=3F2	GCA_017921975.2	2819236	2819236	type	True	82.2471	1099	2049	95	below_threshold
Hymenobacter sedentarius	strain=DG5B	GCA_001507645.1	1411621	1411621	type	True	81.9089	990	2049	95	below_threshold
Hymenobacter armeniacus	strain=BT189	GCA_014699055.1	2771358	2771358	type	True	81.8618	1054	2049	95	below_threshold
Hymenobacter lapidarius	strain=CCM 8643	GCA_001816145.1	1908237	1908237	type	True	81.3932	862	2049	95	below_threshold
Hymenobacter frigidus	strain=CGMCC 1.14966	GCA_014640435.1	1524095	1524095	type	True	81.3736	910	2049	95	below_threshold
Hymenobacter jeongseonensis	strain=BT683	GCA_015694725.1	2791027	2791027	type	True	81.3528	943	2049	95	below_threshold
Hymenobacter glacialis	strain=CCM 8648	GCA_001816165.1	1908236	1908236	type	True	81.2824	848	2049	95	below_threshold
Hymenobacter properus	strain=BT439	GCA_015694735.1	2791026	2791026	type	True	81.2478	996	2049	95	below_threshold
Hymenobacter montanus	strain=BT664	GCA_014699115.1	2771359	2771359	type	True	81.0684	949	2049	95	below_threshold
Hymenobacter metallicola	strain=9PBR-1	GCA_004745645.1	2563114	2563114	type	True	78.3023	523	2049	95	below_threshold
Hymenobacter guriensis	strain=BT594	GCA_015773195.1	2793065	2793065	type	True	78.121	533	2049	95	below_threshold
Frankia canadensis		GCA_900197875.1	1836972	1836972	type	True	74.6652	63	2049	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:56:23,624] [INFO] DFAST Taxonomy check result was written to GCF_000972495.1_ASM97249v1_genomic.fna/tc_result.tsv
[2024-01-24 14:56:23,625] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:56:23,625] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:56:23,625] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc0dfeed7-233b-4451-860e-75c13d3663c6/dqc_reference/checkm_data
[2024-01-24 14:56:23,626] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:56:23,687] [INFO] Task started: CheckM
[2024-01-24 14:56:23,687] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000972495.1_ASM97249v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000972495.1_ASM97249v1_genomic.fna/checkm_input GCF_000972495.1_ASM97249v1_genomic.fna/checkm_result
[2024-01-24 14:57:54,614] [INFO] Task succeeded: CheckM
[2024-01-24 14:57:54,615] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:57:54,634] [INFO] ===== Completeness check finished =====
[2024-01-24 14:57:54,635] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:57:54,635] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000972495.1_ASM97249v1_genomic.fna/markers.fasta)
[2024-01-24 14:57:54,635] [INFO] Task started: Blastn
[2024-01-24 14:57:54,636] [INFO] Running command: blastn -query GCF_000972495.1_ASM97249v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc0dfeed7-233b-4451-860e-75c13d3663c6/dqc_reference/reference_markers_gtdb.fasta -out GCF_000972495.1_ASM97249v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:57:55,495] [INFO] Task succeeded: Blastn
[2024-01-24 14:57:55,498] [INFO] Selected 18 target genomes.
[2024-01-24 14:57:55,499] [INFO] Target genome list was writen to GCF_000972495.1_ASM97249v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:57:55,515] [INFO] Task started: fastANI
[2024-01-24 14:57:55,515] [INFO] Running command: fastANI --query /var/lib/cwl/stg168cdd5e-6139-4ab2-a7eb-108a150fa0ab/GCF_000972495.1_ASM97249v1_genomic.fna.gz --refList GCF_000972495.1_ASM97249v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000972495.1_ASM97249v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:58:16,530] [INFO] Task succeeded: fastANI
[2024-01-24 14:58:16,545] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:58:16,545] [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_000972495.1	s__Hymenobacter terrenus	100.0	2047	2049	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_015694525.1	s__Hymenobacter ruricola	81.9946	1048	2049	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	81.9893	1021	2049	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	95.46	95.46	0.89	0.89	2	-
GCF_001507645.1	s__Hymenobacter sedentarius	81.9131	990	2049	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	81.6483	971	2049	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	81.5612	971	2049	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	97.78	97.78	0.95	0.95	3	-
GCF_012275535.1	s__Hymenobacter artigasi	81.4211	1027	2049	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	81.3907	863	2049	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014640435.1	s__Hymenobacter frigidus	81.3763	910	2049	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	81.3405	945	2049	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	81.277	848	2049	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	81.2769	962	2049	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	99.02	98.98	0.94	0.93	3	-
GCF_015694735.1	s__Hymenobacter properus	81.2459	997	2049	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900115775.1	s__Hymenobacter arizonensis	81.1615	1023	2049	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014699115.1	s__Hymenobacter sp014699115	81.084	946	2049	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	81.0761	933	2049	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018613725.1	s__Hymenobacter sp018613725	78.2078	450	2049	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003583925.1	s__Hymenobacter rubripertinctus	78.19	543	2049	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 14:58:16,547] [INFO] GTDB search result was written to GCF_000972495.1_ASM97249v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:58:16,548] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:58:16,560] [INFO] DFAST_QC result json was written to GCF_000972495.1_ASM97249v1_genomic.fna/dqc_result.json
[2024-01-24 14:58:16,560] [INFO] DFAST_QC completed!
[2024-01-24 14:58:16,561] [INFO] Total running time: 0h2m50s