[2024-01-24 11:44:23,652] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:44:23,654] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:44:23,654] [INFO] DQC Reference Directory: /var/lib/cwl/stg1858cbc8-86b7-45c6-8c39-af993f8ae75d/dqc_reference
[2024-01-24 11:44:26,339] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:44:26,340] [INFO] Task started: Prodigal
[2024-01-24 11:44:26,341] [INFO] Running command: gunzip -c /var/lib/cwl/stg3333f7d6-8c4b-4356-a215-8ac3ef7916c2/GCF_003202405.1_ASM320240v1_genomic.fna.gz | prodigal -d GCF_003202405.1_ASM320240v1_genomic.fna/cds.fna -a GCF_003202405.1_ASM320240v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:44:45,141] [INFO] Task succeeded: Prodigal
[2024-01-24 11:44:45,142] [INFO] Task started: HMMsearch
[2024-01-24 11:44:45,142] [INFO] Running command: hmmsearch --tblout GCF_003202405.1_ASM320240v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1858cbc8-86b7-45c6-8c39-af993f8ae75d/dqc_reference/reference_markers.hmm GCF_003202405.1_ASM320240v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:44:45,451] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:44:45,452] [INFO] Found 6/6 markers.
[2024-01-24 11:44:45,496] [INFO] Query marker FASTA was written to GCF_003202405.1_ASM320240v1_genomic.fna/markers.fasta
[2024-01-24 11:44:45,496] [INFO] Task started: Blastn
[2024-01-24 11:44:45,496] [INFO] Running command: blastn -query GCF_003202405.1_ASM320240v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1858cbc8-86b7-45c6-8c39-af993f8ae75d/dqc_reference/reference_markers.fasta -out GCF_003202405.1_ASM320240v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:44:46,179] [INFO] Task succeeded: Blastn
[2024-01-24 11:44:46,189] [INFO] Selected 17 target genomes.
[2024-01-24 11:44:46,190] [INFO] Target genome list was writen to GCF_003202405.1_ASM320240v1_genomic.fna/target_genomes.txt
[2024-01-24 11:44:46,197] [INFO] Task started: fastANI
[2024-01-24 11:44:46,197] [INFO] Running command: fastANI --query /var/lib/cwl/stg3333f7d6-8c4b-4356-a215-8ac3ef7916c2/GCF_003202405.1_ASM320240v1_genomic.fna.gz --refList GCF_003202405.1_ASM320240v1_genomic.fna/target_genomes.txt --output GCF_003202405.1_ASM320240v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:45:05,893] [INFO] Task succeeded: fastANI
[2024-01-24 11:45:05,894] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1858cbc8-86b7-45c6-8c39-af993f8ae75d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:45:05,894] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1858cbc8-86b7-45c6-8c39-af993f8ae75d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:45:05,908] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:45:05,908] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:45:05,908] [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 hydrophilum	strain=IMCC34758	GCA_003202405.1	2211445	2211445	type	True	100.0	1843	1845	95	conclusive
Flavobacterium limi	strain=THG-AG6.4	GCA_010645075.1	2045105	2045105	type	True	86.7906	1350	1845	95	below_threshold
Flavobacterium limi	strain=CGMCC 1.16060	GCA_014644395.1	2045105	2045105	type	True	86.7561	1355	1845	95	below_threshold
Flavobacterium salmonis	strain=CIP 111411	GCA_903819435.1	2654844	2654844	type	True	86.4125	1255	1845	95	below_threshold
Flavobacterium hibisci	strain=THG-HG1.4	GCA_020026925.1	1914462	1914462	type	True	86.0323	1264	1845	95	below_threshold
Flavobacterium cheongpyeongense	strain=IMCC34759	GCA_003202435.1	2212651	2212651	type	True	85.8726	1212	1845	95	below_threshold
Flavobacterium fluviatile	strain=TAPY14	GCA_010645065.1	1862387	1862387	type	True	85.4587	1171	1845	95	below_threshold
Flavobacterium pectinovorum	strain=ATCC 19366	GCA_002217365.1	29533	29533	type	True	82.3328	1029	1845	95	below_threshold
Flavobacterium pectinovorum	strain=DSM 6368	GCA_900142715.1	29533	29533	type	True	82.3194	1051	1845	95	below_threshold
Flavobacterium soyae	strain=SCIV07	GCA_021245985.1	2903098	2903098	type	True	82.1844	985	1845	95	below_threshold
Flavobacterium chilense	strain=LMG 26360	GCA_001602525.1	946677	946677	type	True	81.859	949	1845	95	below_threshold
Flavobacterium oncorhynchi	strain=CCUG 59446	GCA_002217355.1	728056	728056	type	True	81.7138	838	1845	95	below_threshold
Flavobacterium tyrosinilyticum	strain=KCTC 42726	GCA_023656565.1	1658740	1658740	type	True	81.5472	893	1845	95	below_threshold
Flavobacterium endoglycinae	strain=BB8	GCA_017352115.1	2816357	2816357	type	True	81.464	924	1845	95	below_threshold
Flavobacterium collinsii		GCA_902804485.1	1114861	1114861	type	True	81.4428	785	1845	95	below_threshold
Flavobacterium panacis	strain=DCY106	GCA_024649945.1	2962567	2962567	type	True	81.239	941	1845	95	below_threshold
Flavobacterium amniphilum	strain=KYPY10	GCA_023634845.1	1834035	1834035	type	True	77.3801	172	1845	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:45:05,910] [INFO] DFAST Taxonomy check result was written to GCF_003202405.1_ASM320240v1_genomic.fna/tc_result.tsv
[2024-01-24 11:45:05,910] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:45:05,910] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:45:05,910] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1858cbc8-86b7-45c6-8c39-af993f8ae75d/dqc_reference/checkm_data
[2024-01-24 11:45:05,911] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:45:05,966] [INFO] Task started: CheckM
[2024-01-24 11:45:05,966] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003202405.1_ASM320240v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003202405.1_ASM320240v1_genomic.fna/checkm_input GCF_003202405.1_ASM320240v1_genomic.fna/checkm_result
[2024-01-24 11:46:00,550] [INFO] Task succeeded: CheckM
[2024-01-24 11:46:00,551] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:46:00,577] [INFO] ===== Completeness check finished =====
[2024-01-24 11:46:00,578] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:46:00,578] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003202405.1_ASM320240v1_genomic.fna/markers.fasta)
[2024-01-24 11:46:00,579] [INFO] Task started: Blastn
[2024-01-24 11:46:00,579] [INFO] Running command: blastn -query GCF_003202405.1_ASM320240v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1858cbc8-86b7-45c6-8c39-af993f8ae75d/dqc_reference/reference_markers_gtdb.fasta -out GCF_003202405.1_ASM320240v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:46:01,546] [INFO] Task succeeded: Blastn
[2024-01-24 11:46:01,550] [INFO] Selected 16 target genomes.
[2024-01-24 11:46:01,550] [INFO] Target genome list was writen to GCF_003202405.1_ASM320240v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:46:01,562] [INFO] Task started: fastANI
[2024-01-24 11:46:01,562] [INFO] Running command: fastANI --query /var/lib/cwl/stg3333f7d6-8c4b-4356-a215-8ac3ef7916c2/GCF_003202405.1_ASM320240v1_genomic.fna.gz --refList GCF_003202405.1_ASM320240v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003202405.1_ASM320240v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:46:21,959] [INFO] Task succeeded: fastANI
[2024-01-24 11:46:21,976] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:46:21,976] [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_003202405.1	s__Flavobacterium hydrophilum	100.0	1843	1845	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_000735715.2	s__Flavobacterium chungangense	87.4188	1265	1845	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	96.81	95.16	0.89	0.84	4	-
GCF_010645075.1	s__Flavobacterium limi	86.7754	1352	1845	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003202435.1	s__Flavobacterium cheongpyeongense	85.8604	1213	1845	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010645065.1	s__Flavobacterium fluviatile	85.4423	1173	1845	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002210235.1	s__Flavobacterium sp002210235	82.2796	1014	1845	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	98.80	96.54	0.96	0.91	4	-
GCF_009707955.1	s__Flavobacterium sp009707955	82.2736	1009	1845	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.99	99.99	0.99	0.99	2	-
GCF_900129795.1	s__Flavobacterium sp900129795	82.2008	1011	1845	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.99	99.99	0.98	0.98	2	-
GCF_018383905.1	s__Flavobacterium branchiicola	82.0807	876	1845	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	82.0652	907	1845	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000708595.2	s__Flavobacterium sp000708595	81.9961	928	1845	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	98.30	98.27	0.95	0.93	3	-
GCA_002482975.1	s__Flavobacterium sp002482975	81.9359	1006	1845	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	81.7881	990	1845	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	81.7361	835	1845	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	96.71	96.71	0.90	0.90	2	-
GCF_009789235.1	s__Flavobacterium sp009789235	81.6272	939	1845	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002303885.1	s__Flavobacterium sp002303885	81.3732	895	1845	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 11:46:21,978] [INFO] GTDB search result was written to GCF_003202405.1_ASM320240v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:46:21,978] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:46:21,982] [INFO] DFAST_QC result json was written to GCF_003202405.1_ASM320240v1_genomic.fna/dqc_result.json
[2024-01-24 11:46:21,983] [INFO] DFAST_QC completed!
[2024-01-24 11:46:21,983] [INFO] Total running time: 0h1m58s