[2024-01-24 13:12:38,930] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:12:38,931] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:12:38,932] [INFO] DQC Reference Directory: /var/lib/cwl/stg7f69ebb0-924f-4bab-b2e3-bf3ce2f666a9/dqc_reference
[2024-01-24 13:12:40,295] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:12:40,296] [INFO] Task started: Prodigal
[2024-01-24 13:12:40,297] [INFO] Running command: gunzip -c /var/lib/cwl/stg76f975f4-0d60-473a-bf9d-9007fa06f777/GCF_902804485.1_CECT7796_genomic.fna.gz | prodigal -d GCF_902804485.1_CECT7796_genomic.fna/cds.fna -a GCF_902804485.1_CECT7796_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:13:00,340] [INFO] Task succeeded: Prodigal
[2024-01-24 13:13:00,341] [INFO] Task started: HMMsearch
[2024-01-24 13:13:00,341] [INFO] Running command: hmmsearch --tblout GCF_902804485.1_CECT7796_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7f69ebb0-924f-4bab-b2e3-bf3ce2f666a9/dqc_reference/reference_markers.hmm GCF_902804485.1_CECT7796_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:13:00,705] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:13:00,707] [INFO] Found 6/6 markers.
[2024-01-24 13:13:00,759] [INFO] Query marker FASTA was written to GCF_902804485.1_CECT7796_genomic.fna/markers.fasta
[2024-01-24 13:13:00,760] [INFO] Task started: Blastn
[2024-01-24 13:13:00,760] [INFO] Running command: blastn -query GCF_902804485.1_CECT7796_genomic.fna/markers.fasta -db /var/lib/cwl/stg7f69ebb0-924f-4bab-b2e3-bf3ce2f666a9/dqc_reference/reference_markers.fasta -out GCF_902804485.1_CECT7796_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:13:01,548] [INFO] Task succeeded: Blastn
[2024-01-24 13:13:01,551] [INFO] Selected 21 target genomes.
[2024-01-24 13:13:01,551] [INFO] Target genome list was writen to GCF_902804485.1_CECT7796_genomic.fna/target_genomes.txt
[2024-01-24 13:13:01,562] [INFO] Task started: fastANI
[2024-01-24 13:13:01,563] [INFO] Running command: fastANI --query /var/lib/cwl/stg76f975f4-0d60-473a-bf9d-9007fa06f777/GCF_902804485.1_CECT7796_genomic.fna.gz --refList GCF_902804485.1_CECT7796_genomic.fna/target_genomes.txt --output GCF_902804485.1_CECT7796_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:13:26,315] [INFO] Task succeeded: fastANI
[2024-01-24 13:13:26,316] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7f69ebb0-924f-4bab-b2e3-bf3ce2f666a9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:13:26,316] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7f69ebb0-924f-4bab-b2e3-bf3ce2f666a9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:13:26,333] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:13:26,333] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:13:26,334] [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 collinsii		GCA_902804485.1	1114861	1114861	type	True	100.0	1825	1830	95	conclusive
Flavobacterium tructae	strain=CCUG 60100	GCA_002217475.1	1114873	1114873	type	True	88.1939	1303	1830	95	below_threshold
Flavobacterium bizetiae	strain=CIP 105534	GCA_904425415.1	2704140	2704140	type	True	83.3946	1056	1830	95	below_threshold
Flavobacterium bizetiae	strain=CIP 105534	GCA_902804475.1	2704140	2704140	type	True	83.3697	1041	1830	95	below_threshold
Flavobacterium aquidurense	strain=DSM 18293	GCA_002217195.1	362413	362413	type	True	83.3665	1034	1830	95	below_threshold
Flavobacterium chilense	strain=DSM 24724	GCA_900142685.1	946677	946677	type	True	83.2963	1107	1830	95	below_threshold
Flavobacterium chilense	strain=LMG 26360	GCA_001602525.1	946677	946677	type	True	83.2311	1106	1830	95	below_threshold
Flavobacterium piscis	strain=CCUG 60099	GCA_001686925.1	1114874	1114874	type	True	83.1858	1019	1830	95	below_threshold
Flavobacterium piscis	strain=CCUG 60099	GCA_002222045.1	1114874	1114874	type	True	83.1635	1015	1830	95	below_threshold
Flavobacterium hibernum	strain=NCTC13514	GCA_900450525.1	37752	37752	type	True	83.1201	1042	1830	95	below_threshold
Flavobacterium hibernum	strain=ATCC 51468	GCA_002217315.1	37752	37752	type	True	83.0928	1027	1830	95	below_threshold
Flavobacterium hibernum	strain=DSM 12611	GCA_000832125.1	37752	37752	type	True	83.0825	1039	1830	95	below_threshold
Flavobacterium araucananum	strain=DSM 24704	GCA_002222055.1	946678	946678	type	True	82.9985	1065	1830	95	below_threshold
Flavobacterium plurextorum	strain=CCUG 60112	GCA_002217395.1	1114867	1114867	type	True	82.1683	943	1830	95	below_threshold
Flavobacterium oncorhynchi	strain=CCUG 59446	GCA_002217355.1	728056	728056	type	True	82.0302	943	1830	95	below_threshold
Flavobacterium soyae	strain=SCIV07	GCA_021245985.1	2903098	2903098	type	True	81.9696	932	1830	95	below_threshold
Flavobacterium hydrocarbonoxydans	strain=GA093	GCA_009789235.1	2683249	2683249	type	True	81.6204	833	1830	95	below_threshold
Flavobacterium endoglycinae	strain=BB8	GCA_017352115.1	2816357	2816357	type	True	81.1503	863	1830	95	below_threshold
Flavobacterium tyrosinilyticum	strain=KCTC 42726	GCA_023656565.1	1658740	1658740	type	True	81.0739	880	1830	95	below_threshold
Flavobacterium panacis	strain=DCY106	GCA_024649945.1	2962567	2962567	type	True	80.9567	877	1830	95	below_threshold
Flavobacterium branchiophilum	strain=DSM 24789	GCA_006716585.1	55197	55197	type	True	77.2552	155	1830	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:13:26,335] [INFO] DFAST Taxonomy check result was written to GCF_902804485.1_CECT7796_genomic.fna/tc_result.tsv
[2024-01-24 13:13:26,336] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:13:26,336] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:13:26,336] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7f69ebb0-924f-4bab-b2e3-bf3ce2f666a9/dqc_reference/checkm_data
[2024-01-24 13:13:26,338] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:13:26,394] [INFO] Task started: CheckM
[2024-01-24 13:13:26,394] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_902804485.1_CECT7796_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_902804485.1_CECT7796_genomic.fna/checkm_input GCF_902804485.1_CECT7796_genomic.fna/checkm_result
[2024-01-24 13:14:22,960] [INFO] Task succeeded: CheckM
[2024-01-24 13:14:22,962] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:14:22,985] [INFO] ===== Completeness check finished =====
[2024-01-24 13:14:22,985] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:14:22,986] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_902804485.1_CECT7796_genomic.fna/markers.fasta)
[2024-01-24 13:14:22,986] [INFO] Task started: Blastn
[2024-01-24 13:14:22,986] [INFO] Running command: blastn -query GCF_902804485.1_CECT7796_genomic.fna/markers.fasta -db /var/lib/cwl/stg7f69ebb0-924f-4bab-b2e3-bf3ce2f666a9/dqc_reference/reference_markers_gtdb.fasta -out GCF_902804485.1_CECT7796_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:14:23,959] [INFO] Task succeeded: Blastn
[2024-01-24 13:14:23,962] [INFO] Selected 18 target genomes.
[2024-01-24 13:14:23,962] [INFO] Target genome list was writen to GCF_902804485.1_CECT7796_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:14:23,979] [INFO] Task started: fastANI
[2024-01-24 13:14:23,979] [INFO] Running command: fastANI --query /var/lib/cwl/stg76f975f4-0d60-473a-bf9d-9007fa06f777/GCF_902804485.1_CECT7796_genomic.fna.gz --refList GCF_902804485.1_CECT7796_genomic.fna/target_genomes_gtdb.txt --output GCF_902804485.1_CECT7796_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:14:46,909] [INFO] Task succeeded: fastANI
[2024-01-24 13:14:46,928] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:14:46,929] [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_902804485.1	s__Flavobacterium collinsii	100.0	1825	1830	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_903469665.1	s__Flavobacterium sp903469665	88.2186	1289	1830	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002217475.1	s__Flavobacterium tructae	88.1886	1304	1830	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	97.59	96.94	0.94	0.93	4	-
GCF_902804475.1	s__Flavobacterium bizetiae	83.3977	1038	1830	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.96	99.94	0.99	0.99	3	-
GCA_900129595.1	s__Flavobacterium frigidimaris	83.3836	1052	1830	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.99	99.99	1.00	1.00	2	-
GCF_001404985.1	s__Flavobacterium aquidurense_B	83.374	1036	1830	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009664855.1	s__Flavobacterium sp009664855	83.2766	1049	1830	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	98.90	98.90	0.89	0.89	2	-
GCF_001975985.1	s__Flavobacterium sp001975985	83.2573	1052	1830	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001602525.1	s__Flavobacterium chilense	83.2098	1108	1830	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	98.30	96.61	0.93	0.86	3	-
GCF_001686925.1	s__Flavobacterium piscis	83.1988	1017	1830	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	98.33	97.30	0.93	0.88	4	-
GCF_002754195.1	s__Flavobacterium sp002754195	83.1355	1105	1830	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004339525.1	s__Flavobacterium sp004339525	83.0367	1114	1830	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.99	99.99	1.00	1.00	2	-
GCF_006438875.1	s__Flavobacterium pectinovorum_A	82.9037	1094	1830	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004362015.1	s__Flavobacterium sp004362015	82.5233	910	1830	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009711135.1	s__Flavobacterium sp009711135	82.0166	916	1830	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004368785.1	s__Flavobacterium sp004368785	81.86	926	1830	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	81.8282	821	1830	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018383905.1	s__Flavobacterium branchiicola	81.7912	988	1830	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 13:14:46,931] [INFO] GTDB search result was written to GCF_902804485.1_CECT7796_genomic.fna/result_gtdb.tsv
[2024-01-24 13:14:46,931] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:14:46,939] [INFO] DFAST_QC result json was written to GCF_902804485.1_CECT7796_genomic.fna/dqc_result.json
[2024-01-24 13:14:46,939] [INFO] DFAST_QC completed!
[2024-01-24 13:14:46,940] [INFO] Total running time: 0h2m8s