[2024-01-24 15:26:04,584] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:26:04,586] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:26:04,587] [INFO] DQC Reference Directory: /var/lib/cwl/stgf176ee06-98a3-44ed-8543-63a9e06e3fe9/dqc_reference
[2024-01-24 15:26:07,022] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:26:07,023] [INFO] Task started: Prodigal
[2024-01-24 15:26:07,023] [INFO] Running command: gunzip -c /var/lib/cwl/stg3a201b63-9822-4e3b-b4e1-65f5a6549c16/GCF_010645065.1_ASM1064506v1_genomic.fna.gz | prodigal -d GCF_010645065.1_ASM1064506v1_genomic.fna/cds.fna -a GCF_010645065.1_ASM1064506v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:26:24,671] [INFO] Task succeeded: Prodigal
[2024-01-24 15:26:24,671] [INFO] Task started: HMMsearch
[2024-01-24 15:26:24,672] [INFO] Running command: hmmsearch --tblout GCF_010645065.1_ASM1064506v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf176ee06-98a3-44ed-8543-63a9e06e3fe9/dqc_reference/reference_markers.hmm GCF_010645065.1_ASM1064506v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:26:25,008] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:26:25,010] [INFO] Found 6/6 markers.
[2024-01-24 15:26:25,058] [INFO] Query marker FASTA was written to GCF_010645065.1_ASM1064506v1_genomic.fna/markers.fasta
[2024-01-24 15:26:25,059] [INFO] Task started: Blastn
[2024-01-24 15:26:25,059] [INFO] Running command: blastn -query GCF_010645065.1_ASM1064506v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf176ee06-98a3-44ed-8543-63a9e06e3fe9/dqc_reference/reference_markers.fasta -out GCF_010645065.1_ASM1064506v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:26:25,752] [INFO] Task succeeded: Blastn
[2024-01-24 15:26:25,756] [INFO] Selected 13 target genomes.
[2024-01-24 15:26:25,757] [INFO] Target genome list was writen to GCF_010645065.1_ASM1064506v1_genomic.fna/target_genomes.txt
[2024-01-24 15:26:25,763] [INFO] Task started: fastANI
[2024-01-24 15:26:25,763] [INFO] Running command: fastANI --query /var/lib/cwl/stg3a201b63-9822-4e3b-b4e1-65f5a6549c16/GCF_010645065.1_ASM1064506v1_genomic.fna.gz --refList GCF_010645065.1_ASM1064506v1_genomic.fna/target_genomes.txt --output GCF_010645065.1_ASM1064506v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:26:40,339] [INFO] Task succeeded: fastANI
[2024-01-24 15:26:40,340] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf176ee06-98a3-44ed-8543-63a9e06e3fe9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:26:40,340] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf176ee06-98a3-44ed-8543-63a9e06e3fe9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:26:40,351] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:26:40,352] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:26:40,352] [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 fluviatile	strain=TAPY14	GCA_010645065.1	1862387	1862387	type	True	100.0	1646	1655	95	conclusive
Flavobacterium limi	strain=CGMCC 1.16060	GCA_014644395.1	2045105	2045105	type	True	86.4596	1166	1655	95	below_threshold
Flavobacterium limi	strain=THG-AG6.4	GCA_010645075.1	2045105	2045105	type	True	86.3562	1173	1655	95	below_threshold
Flavobacterium hibisci	strain=THG-HG1.4	GCA_020026925.1	1914462	1914462	type	True	86.2376	1099	1655	95	below_threshold
Flavobacterium ajazii	strain=SSM4.2	GCA_010614725.1	2692318	2692318	type	True	85.6207	1056	1655	95	below_threshold
Flavobacterium hydrophilum	strain=IMCC34758	GCA_003202405.1	2211445	2211445	type	True	85.5191	1147	1655	95	below_threshold
Flavobacterium salmonis	strain=CIP 111411	GCA_903819435.1	2654844	2654844	type	True	84.6688	1064	1655	95	below_threshold
Flavobacterium soyae	strain=SCIV07	GCA_021245985.1	2903098	2903098	type	True	81.7207	838	1655	95	below_threshold
Flavobacterium endoglycinae	strain=BB8	GCA_017352115.1	2816357	2816357	type	True	81.4444	814	1655	95	below_threshold
Flavobacterium oncorhynchi	strain=CCUG 59446	GCA_002217355.1	728056	728056	type	True	81.3166	761	1655	95	below_threshold
Flavobacterium panacis	strain=DCY106	GCA_024649945.1	2962567	2962567	type	True	81.2552	848	1655	95	below_threshold
Flavobacterium tyrosinilyticum	strain=KCTC 42726	GCA_023656565.1	1658740	1658740	type	True	81.2128	790	1655	95	below_threshold
Flavobacterium branchiophilum	strain=DSM 24789	GCA_006716585.1	55197	55197	type	True	77.0657	155	1655	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:26:40,353] [INFO] DFAST Taxonomy check result was written to GCF_010645065.1_ASM1064506v1_genomic.fna/tc_result.tsv
[2024-01-24 15:26:40,354] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:26:40,354] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:26:40,354] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf176ee06-98a3-44ed-8543-63a9e06e3fe9/dqc_reference/checkm_data
[2024-01-24 15:26:40,356] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:26:40,415] [INFO] Task started: CheckM
[2024-01-24 15:26:40,416] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_010645065.1_ASM1064506v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_010645065.1_ASM1064506v1_genomic.fna/checkm_input GCF_010645065.1_ASM1064506v1_genomic.fna/checkm_result
[2024-01-24 15:27:33,553] [INFO] Task succeeded: CheckM
[2024-01-24 15:27:33,555] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:27:33,574] [INFO] ===== Completeness check finished =====
[2024-01-24 15:27:33,575] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:27:33,576] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_010645065.1_ASM1064506v1_genomic.fna/markers.fasta)
[2024-01-24 15:27:33,577] [INFO] Task started: Blastn
[2024-01-24 15:27:33,577] [INFO] Running command: blastn -query GCF_010645065.1_ASM1064506v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf176ee06-98a3-44ed-8543-63a9e06e3fe9/dqc_reference/reference_markers_gtdb.fasta -out GCF_010645065.1_ASM1064506v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:27:34,517] [INFO] Task succeeded: Blastn
[2024-01-24 15:27:34,520] [INFO] Selected 15 target genomes.
[2024-01-24 15:27:34,520] [INFO] Target genome list was writen to GCF_010645065.1_ASM1064506v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:27:34,532] [INFO] Task started: fastANI
[2024-01-24 15:27:34,532] [INFO] Running command: fastANI --query /var/lib/cwl/stg3a201b63-9822-4e3b-b4e1-65f5a6549c16/GCF_010645065.1_ASM1064506v1_genomic.fna.gz --refList GCF_010645065.1_ASM1064506v1_genomic.fna/target_genomes_gtdb.txt --output GCF_010645065.1_ASM1064506v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:27:51,822] [INFO] Task succeeded: fastANI
[2024-01-24 15:27:51,842] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:27:51,842] [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_010645065.1	s__Flavobacterium fluviatile	100.0	1646	1655	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_010645075.1	s__Flavobacterium limi	86.3451	1175	1655	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_010614725.1	s__Flavobacterium ajazii	85.6422	1053	1655	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003202405.1	s__Flavobacterium hydrophilum	85.5157	1147	1655	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000735715.2	s__Flavobacterium chungangense	84.7905	1070	1655	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	96.81	95.16	0.89	0.84	4	-
GCF_003202435.1	s__Flavobacterium cheongpyeongense	83.7994	1035	1655	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003385895.1	s__Flavobacterium cutihirudinis	81.7466	800	1655	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900182645.1	s__Flavobacterium resistens	81.6682	821	1655	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.98	99.98	1.00	1.00	2	-
GCF_017833855.1	s__Flavobacterium sp017833855	81.5956	829	1655	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017744675.1	s__Flavobacterium sp017744675	81.3618	758	1655	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002217355.1	s__Flavobacterium oncorhynchi	81.3075	761	1655	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	96.71	96.71	0.90	0.90	2	-
GCF_016405855.1	s__Flavobacterium sp002399805	81.2843	809	1655	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	96.61	96.61	0.90	0.90	2	-
GCF_003946915.1	s__Flavobacterium sp003946915	81.1897	773	1655	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	81.188	811	1655	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002217285.1	s__Flavobacterium hercynium	80.7616	682	1655	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 15:27:51,844] [INFO] GTDB search result was written to GCF_010645065.1_ASM1064506v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:27:51,845] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:27:51,848] [INFO] DFAST_QC result json was written to GCF_010645065.1_ASM1064506v1_genomic.fna/dqc_result.json
[2024-01-24 15:27:51,849] [INFO] DFAST_QC completed!
[2024-01-24 15:27:51,849] [INFO] Total running time: 0h1m47s