[2024-01-24 12:14:49,515] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:14:49,522] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:14:49,523] [INFO] DQC Reference Directory: /var/lib/cwl/stg690c2b52-ba36-4cfd-be51-4635172006c9/dqc_reference
[2024-01-24 12:14:50,868] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:14:50,868] [INFO] Task started: Prodigal
[2024-01-24 12:14:50,869] [INFO] Running command: gunzip -c /var/lib/cwl/stg89e70405-466b-48ca-a62a-4efa0e7357b1/GCF_014305095.1_ASM1430509v1_genomic.fna.gz | prodigal -d GCF_014305095.1_ASM1430509v1_genomic.fna/cds.fna -a GCF_014305095.1_ASM1430509v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:15:03,362] [INFO] Task succeeded: Prodigal
[2024-01-24 12:15:03,362] [INFO] Task started: HMMsearch
[2024-01-24 12:15:03,362] [INFO] Running command: hmmsearch --tblout GCF_014305095.1_ASM1430509v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg690c2b52-ba36-4cfd-be51-4635172006c9/dqc_reference/reference_markers.hmm GCF_014305095.1_ASM1430509v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:15:03,657] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:15:03,659] [INFO] Found 6/6 markers.
[2024-01-24 12:15:03,693] [INFO] Query marker FASTA was written to GCF_014305095.1_ASM1430509v1_genomic.fna/markers.fasta
[2024-01-24 12:15:03,694] [INFO] Task started: Blastn
[2024-01-24 12:15:03,694] [INFO] Running command: blastn -query GCF_014305095.1_ASM1430509v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg690c2b52-ba36-4cfd-be51-4635172006c9/dqc_reference/reference_markers.fasta -out GCF_014305095.1_ASM1430509v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:04,418] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:04,421] [INFO] Selected 22 target genomes.
[2024-01-24 12:15:04,421] [INFO] Target genome list was writen to GCF_014305095.1_ASM1430509v1_genomic.fna/target_genomes.txt
[2024-01-24 12:15:04,431] [INFO] Task started: fastANI
[2024-01-24 12:15:04,431] [INFO] Running command: fastANI --query /var/lib/cwl/stg89e70405-466b-48ca-a62a-4efa0e7357b1/GCF_014305095.1_ASM1430509v1_genomic.fna.gz --refList GCF_014305095.1_ASM1430509v1_genomic.fna/target_genomes.txt --output GCF_014305095.1_ASM1430509v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:15:21,420] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:21,421] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg690c2b52-ba36-4cfd-be51-4635172006c9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:15:21,422] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg690c2b52-ba36-4cfd-be51-4635172006c9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:15:21,444] [INFO] Found 22 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:15:21,444] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:15:21,445] [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 kayseriense	strain=F-47	GCA_014305095.1	2764714	2764714	type	True	100.0	1187	1187	95	conclusive
Flavobacterium turcicum	strain=F-339	GCA_011365745.1	2764718	2764718	type	True	80.9915	367	1187	95	below_threshold
Flavobacterium muglaense	strain=F-60	GCA_014305155.1	2764716	2764716	type	True	80.8517	526	1187	95	below_threshold
Flavobacterium frigidarium	strain=DSM 17623	GCA_000425505.1	99286	99286	type	True	80.7578	455	1187	95	below_threshold
Flavobacterium granuli	strain=DSM 17797	GCA_003003155.1	280093	280093	type	True	80.0203	378	1187	95	below_threshold
Flavobacterium granuli	strain=DSM 19729	GCA_900129705.1	280093	280093	type	True	79.9773	374	1187	95	below_threshold
Flavobacterium gillisiae	strain=DSM 22376	GCA_900107635.1	150146	150146	type	True	79.7746	472	1187	95	below_threshold
Flavobacterium degerlachei	strain=DSM 15718	GCA_900106645.1	229203	229203	type	True	79.7043	446	1187	95	below_threshold
Flavobacterium undicola	strain=BBQ-18	GCA_009909155.2	1932779	1932779	type	True	79.3425	372	1187	95	below_threshold
Flavobacterium hiemivividum	strain=TSA-D2	GCA_004349145.1	2541734	2541734	type	True	79.3034	433	1187	95	below_threshold
Flavobacterium flabelliforme	strain=P4023	GCA_017948675.1	2816119	2816119	type	True	79.1144	394	1187	95	below_threshold
Flavobacterium sinopsychrotolerans	strain=CGMCC 1.8704	GCA_900110375.1	604089	604089	type	True	79.1085	395	1187	95	below_threshold
Flavobacterium taihuense	strain=NAS39	GCA_019351435.1	2857508	2857508	type	True	79.0218	336	1187	95	below_threshold
Flavobacterium faecale	strain=WV33	GCA_003076455.1	1355330	1355330	type	True	78.8837	367	1187	95	below_threshold
Flavobacterium commune	strain=PK15	GCA_001857965.1	1306519	1306519	type	True	78.7988	336	1187	95	below_threshold
Flavobacterium tiangeerense	strain=CGMCC 1.6847	GCA_007830355.1	459471	459471	type	True	78.7078	354	1187	95	below_threshold
Flavobacterium daejeonense	strain=DSM 17708	GCA_000425425.1	350893	350893	type	True	78.6184	306	1187	95	below_threshold
Flavobacterium soyae	strain=SCIV07	GCA_021245985.1	2903098	2903098	type	True	78.399	293	1187	95	below_threshold
Flavobacterium panacis	strain=DCY106	GCA_024649945.1	2962567	2962567	type	True	78.3117	307	1187	95	below_threshold
Flavobacterium channae	strain=KSM-R2A30	GCA_021172165.1	2897181	2897181	type	True	77.4873	168	1187	95	below_threshold
Flavobacterium proteolyticum	strain=1Y8A	GCA_015223105.1	2911683	2911683	type	True	77.1479	168	1187	95	below_threshold
Flavobacterium jumunjinense	strain=HME7102	GCA_021650975.2	998845	998845	type	True	76.8755	189	1187	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:15:21,446] [INFO] DFAST Taxonomy check result was written to GCF_014305095.1_ASM1430509v1_genomic.fna/tc_result.tsv
[2024-01-24 12:15:21,447] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:15:21,447] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:15:21,447] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg690c2b52-ba36-4cfd-be51-4635172006c9/dqc_reference/checkm_data
[2024-01-24 12:15:21,448] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:15:21,491] [INFO] Task started: CheckM
[2024-01-24 12:15:21,491] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014305095.1_ASM1430509v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014305095.1_ASM1430509v1_genomic.fna/checkm_input GCF_014305095.1_ASM1430509v1_genomic.fna/checkm_result
[2024-01-24 12:16:00,234] [INFO] Task succeeded: CheckM
[2024-01-24 12:16:00,235] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:16:00,257] [INFO] ===== Completeness check finished =====
[2024-01-24 12:16:00,258] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:16:00,258] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014305095.1_ASM1430509v1_genomic.fna/markers.fasta)
[2024-01-24 12:16:00,259] [INFO] Task started: Blastn
[2024-01-24 12:16:00,259] [INFO] Running command: blastn -query GCF_014305095.1_ASM1430509v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg690c2b52-ba36-4cfd-be51-4635172006c9/dqc_reference/reference_markers_gtdb.fasta -out GCF_014305095.1_ASM1430509v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:16:01,158] [INFO] Task succeeded: Blastn
[2024-01-24 12:16:01,162] [INFO] Selected 20 target genomes.
[2024-01-24 12:16:01,163] [INFO] Target genome list was writen to GCF_014305095.1_ASM1430509v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:16:01,229] [INFO] Task started: fastANI
[2024-01-24 12:16:01,230] [INFO] Running command: fastANI --query /var/lib/cwl/stg89e70405-466b-48ca-a62a-4efa0e7357b1/GCF_014305095.1_ASM1430509v1_genomic.fna.gz --refList GCF_014305095.1_ASM1430509v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014305095.1_ASM1430509v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:16:15,317] [INFO] Task succeeded: fastANI
[2024-01-24 12:16:15,340] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:16:15,340] [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_014305095.1	s__Flavobacterium kayseriense	100.0	1187	1187	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.16	98.32	0.96	0.92	3	conclusive
GCF_011365745.1	s__Flavobacterium turcicum	80.9969	366	1187	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014305155.1	s__Flavobacterium sp014305155	80.8726	524	1187	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000425505.1	s__Flavobacterium frigidarium	80.7492	456	1187	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013294005.1	s__Flavobacterium sp013294005	80.4653	514	1187	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	97.41	97.36	0.86	0.85	3	-
GCF_002150205.1	s__Flavobacterium sp002150205	80.4412	339	1187	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013294025.1	s__Flavobacterium sp013294025	80.2363	436	1187	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129705.1	s__Flavobacterium granuli	79.9923	373	1187	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900107635.1	s__Flavobacterium gillisiae	79.7635	473	1187	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900106645.1	s__Flavobacterium degerlachei	79.7059	445	1187	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009909155.2	s__Flavobacterium undicola	79.3425	372	1187	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004349145.1	s__Flavobacterium hiemivividum	79.3311	431	1187	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	95.37	95.37	0.86	0.86	2	-
GCF_014281985.1	s__Flavobacterium sp014281985	79.1709	389	1187	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	98.07	98.07	0.91	0.91	2	-
GCF_900110375.1	s__Flavobacterium sinopsychrotolerans	79.1316	393	1187	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014639535.1	s__Flavobacterium palustre	79.0065	330	1187	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000695795.1	s__Flavobacterium seoulense	78.8598	349	1187	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001857965.1	s__Flavobacterium commune	78.7922	337	1187	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	97.64	97.64	0.89	0.89	2	-
GCF_007830355.1	s__Flavobacterium tiangeerense	78.7078	354	1187	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	95.91	95.91	0.85	0.85	2	-
GCF_002797935.1	s__Flavobacterium sp002797935	78.2081	312	1187	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002382495.1	s__Flavobacterium sp002382495	78.037	222	1187	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 12:16:15,342] [INFO] GTDB search result was written to GCF_014305095.1_ASM1430509v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:16:15,342] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:16:15,346] [INFO] DFAST_QC result json was written to GCF_014305095.1_ASM1430509v1_genomic.fna/dqc_result.json
[2024-01-24 12:16:15,347] [INFO] DFAST_QC completed!
[2024-01-24 12:16:15,347] [INFO] Total running time: 0h1m26s