[2024-01-24 14:46:57,073] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:46:57,075] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:46:57,075] [INFO] DQC Reference Directory: /var/lib/cwl/stgff7e78a0-2842-4dd7-9d53-5ef844443878/dqc_reference
[2024-01-24 14:46:58,558] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:46:58,559] [INFO] Task started: Prodigal
[2024-01-24 14:46:58,559] [INFO] Running command: gunzip -c /var/lib/cwl/stg21a0ef2a-b6fb-4395-81ee-826c4400e496/GCF_012911565.1_ASM1291156v1_genomic.fna.gz | prodigal -d GCF_012911565.1_ASM1291156v1_genomic.fna/cds.fna -a GCF_012911565.1_ASM1291156v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:47:18,517] [INFO] Task succeeded: Prodigal
[2024-01-24 14:47:18,517] [INFO] Task started: HMMsearch
[2024-01-24 14:47:18,517] [INFO] Running command: hmmsearch --tblout GCF_012911565.1_ASM1291156v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgff7e78a0-2842-4dd7-9d53-5ef844443878/dqc_reference/reference_markers.hmm GCF_012911565.1_ASM1291156v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:47:18,814] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:47:18,815] [INFO] Found 6/6 markers.
[2024-01-24 14:47:18,848] [INFO] Query marker FASTA was written to GCF_012911565.1_ASM1291156v1_genomic.fna/markers.fasta
[2024-01-24 14:47:18,849] [INFO] Task started: Blastn
[2024-01-24 14:47:18,849] [INFO] Running command: blastn -query GCF_012911565.1_ASM1291156v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgff7e78a0-2842-4dd7-9d53-5ef844443878/dqc_reference/reference_markers.fasta -out GCF_012911565.1_ASM1291156v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:47:19,477] [INFO] Task succeeded: Blastn
[2024-01-24 14:47:19,484] [INFO] Selected 20 target genomes.
[2024-01-24 14:47:19,485] [INFO] Target genome list was writen to GCF_012911565.1_ASM1291156v1_genomic.fna/target_genomes.txt
[2024-01-24 14:47:19,497] [INFO] Task started: fastANI
[2024-01-24 14:47:19,497] [INFO] Running command: fastANI --query /var/lib/cwl/stg21a0ef2a-b6fb-4395-81ee-826c4400e496/GCF_012911565.1_ASM1291156v1_genomic.fna.gz --refList GCF_012911565.1_ASM1291156v1_genomic.fna/target_genomes.txt --output GCF_012911565.1_ASM1291156v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:47:33,685] [INFO] Task succeeded: fastANI
[2024-01-24 14:47:33,685] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgff7e78a0-2842-4dd7-9d53-5ef844443878/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:47:33,686] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgff7e78a0-2842-4dd7-9d53-5ef844443878/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:47:33,698] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:47:33,698] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:47:33,698] [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
Flavobacterium silvaticum	strain=SE-s28	GCA_012911565.1	1852020	1852020	type	True	100.0	1232	1233	95	conclusive
Flavobacterium agri	strain=MAH-1	GCA_013401995.1	2743471	2743471	type	True	77.9618	336	1233	95	below_threshold
Flavobacterium agri	strain=MAH-1	GCA_013366395.1	2743471	2743471	type	True	77.9603	336	1233	95	below_threshold
Flavobacterium magnum	strain=HYN0048	GCA_003055625.1	2162713	2162713	type	True	77.4507	94	1233	95	below_threshold
Flavobacterium orientale	strain=CGMCC 1.12506	GCA_014638005.1	1756020	1756020	type	True	77.2275	55	1233	95	below_threshold
Flavobacterium pallidum	strain=HYN0049	GCA_003097535.1	2172098	2172098	type	True	77.1068	135	1233	95	below_threshold
Flavobacterium lotistagni	strain=CYK-4	GCA_011392125.1	2709660	2709660	type	True	77.0965	120	1233	95	below_threshold
Flavobacterium microcysteis	strain=MaA-Y11	GCA_006385255.1	2596891	2596891	type	True	76.9788	91	1233	95	below_threshold
Flavobacterium caeni	strain=CGMCC 1.7031	GCA_900101895.1	490189	490189	type	True	76.8067	183	1233	95	below_threshold
Flavobacterium kingsejongi	strain=WV39	GCA_003076475.1	1678728	1678728	type	True	76.7064	80	1233	95	below_threshold
Flavobacterium tructae	strain=CCUG 60100	GCA_002217475.1	1114873	1114873	type	True	76.6485	73	1233	95	below_threshold
Flavobacterium suncheonense	strain=GH29-5	GCA_000769835.1	350894	350894	type	True	76.6309	101	1233	95	below_threshold
Flavobacterium noncentrifugens	strain=CGMCC 1.10076	GCA_900100375.1	1128970	1128970	type	True	76.5986	186	1233	95	below_threshold
Flavobacterium noncentrifugens	strain=NBRC 108844	GCA_007992475.1	1128970	1128970	type	True	76.583	184	1233	95	below_threshold
Flavobacterium fluvii	strain=DSM 19978	GCA_900129545.1	468056	468056	type	True	76.458	76	1233	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:47:33,700] [INFO] DFAST Taxonomy check result was written to GCF_012911565.1_ASM1291156v1_genomic.fna/tc_result.tsv
[2024-01-24 14:47:33,700] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:47:33,700] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:47:33,700] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgff7e78a0-2842-4dd7-9d53-5ef844443878/dqc_reference/checkm_data
[2024-01-24 14:47:33,701] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:47:33,739] [INFO] Task started: CheckM
[2024-01-24 14:47:33,739] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_012911565.1_ASM1291156v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_012911565.1_ASM1291156v1_genomic.fna/checkm_input GCF_012911565.1_ASM1291156v1_genomic.fna/checkm_result
[2024-01-24 14:48:33,496] [INFO] Task succeeded: CheckM
[2024-01-24 14:48:33,497] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:48:33,515] [INFO] ===== Completeness check finished =====
[2024-01-24 14:48:33,516] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:48:33,516] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_012911565.1_ASM1291156v1_genomic.fna/markers.fasta)
[2024-01-24 14:48:33,517] [INFO] Task started: Blastn
[2024-01-24 14:48:33,517] [INFO] Running command: blastn -query GCF_012911565.1_ASM1291156v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgff7e78a0-2842-4dd7-9d53-5ef844443878/dqc_reference/reference_markers_gtdb.fasta -out GCF_012911565.1_ASM1291156v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:48:34,348] [INFO] Task succeeded: Blastn
[2024-01-24 14:48:34,353] [INFO] Selected 19 target genomes.
[2024-01-24 14:48:34,353] [INFO] Target genome list was writen to GCF_012911565.1_ASM1291156v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:48:34,375] [INFO] Task started: fastANI
[2024-01-24 14:48:34,375] [INFO] Running command: fastANI --query /var/lib/cwl/stg21a0ef2a-b6fb-4395-81ee-826c4400e496/GCF_012911565.1_ASM1291156v1_genomic.fna.gz --refList GCF_012911565.1_ASM1291156v1_genomic.fna/target_genomes_gtdb.txt --output GCF_012911565.1_ASM1291156v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:48:46,746] [INFO] Task succeeded: fastANI
[2024-01-24 14:48:46,771] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:48:46,771] [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_012911565.1	s__Flavobacterium sp012911565	100.0	1232	1233	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_013401995.1	s__Flavobacterium agri	77.9516	337	1233	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCA_004295795.1	s__Flavobacterium sp004295795	77.6799	280	1233	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014748335.1	s__Flavobacterium sp014748335	77.6585	238	1233	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003055625.1	s__Flavobacterium magnum	77.4507	94	1233	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004211145.1	s__Flavobacterium sp004211145	77.3781	297	1233	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014638005.1	s__Flavobacterium orientale	77.2788	54	1233	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003097535.1	s__Flavobacterium pallidum	77.1235	134	1233	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006385255.1	s__Flavobacterium microcysteis	76.9831	92	1233	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900101895.1	s__Flavobacterium caeni	76.7985	183	1233	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015234525.1	s__Flavobacterium sp015234525	76.787	82	1233	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003076475.1	s__Flavobacterium kingsejongi	76.7064	80	1233	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003105115.1	s__Flavobacterium sp003105115	76.6344	69	1233	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900100375.1	s__Flavobacterium noncentrifugens	76.5624	186	1233	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_009674775.1	s__Flavobacterium sp009674775	76.4189	66	1233	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017833855.1	s__Flavobacterium sp017833855	76.3029	71	1233	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:48:46,773] [INFO] GTDB search result was written to GCF_012911565.1_ASM1291156v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:48:46,774] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:48:46,778] [INFO] DFAST_QC result json was written to GCF_012911565.1_ASM1291156v1_genomic.fna/dqc_result.json
[2024-01-24 14:48:46,778] [INFO] DFAST_QC completed!
[2024-01-24 14:48:46,778] [INFO] Total running time: 0h1m50s