[2024-01-24 13:51:12,458] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:51:12,460] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:51:12,460] [INFO] DQC Reference Directory: /var/lib/cwl/stg6b6e3fab-71bc-4fb2-ac56-5a2958ded366/dqc_reference
[2024-01-24 13:51:13,842] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:51:13,842] [INFO] Task started: Prodigal
[2024-01-24 13:51:13,843] [INFO] Running command: gunzip -c /var/lib/cwl/stga9dffc89-3f04-4c76-90a5-a11ac8051867/GCF_010614725.1_ASM1061472v1_genomic.fna.gz | prodigal -d GCF_010614725.1_ASM1061472v1_genomic.fna/cds.fna -a GCF_010614725.1_ASM1061472v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:51:33,027] [INFO] Task succeeded: Prodigal
[2024-01-24 13:51:33,027] [INFO] Task started: HMMsearch
[2024-01-24 13:51:33,027] [INFO] Running command: hmmsearch --tblout GCF_010614725.1_ASM1061472v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6b6e3fab-71bc-4fb2-ac56-5a2958ded366/dqc_reference/reference_markers.hmm GCF_010614725.1_ASM1061472v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:51:33,362] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:51:33,364] [INFO] Found 6/6 markers.
[2024-01-24 13:51:33,416] [INFO] Query marker FASTA was written to GCF_010614725.1_ASM1061472v1_genomic.fna/markers.fasta
[2024-01-24 13:51:33,417] [INFO] Task started: Blastn
[2024-01-24 13:51:33,417] [INFO] Running command: blastn -query GCF_010614725.1_ASM1061472v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6b6e3fab-71bc-4fb2-ac56-5a2958ded366/dqc_reference/reference_markers.fasta -out GCF_010614725.1_ASM1061472v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:51:34,124] [INFO] Task succeeded: Blastn
[2024-01-24 13:51:34,127] [INFO] Selected 25 target genomes.
[2024-01-24 13:51:34,128] [INFO] Target genome list was writen to GCF_010614725.1_ASM1061472v1_genomic.fna/target_genomes.txt
[2024-01-24 13:51:34,143] [INFO] Task started: fastANI
[2024-01-24 13:51:34,144] [INFO] Running command: fastANI --query /var/lib/cwl/stga9dffc89-3f04-4c76-90a5-a11ac8051867/GCF_010614725.1_ASM1061472v1_genomic.fna.gz --refList GCF_010614725.1_ASM1061472v1_genomic.fna/target_genomes.txt --output GCF_010614725.1_ASM1061472v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:52:01,243] [INFO] Task succeeded: fastANI
[2024-01-24 13:52:01,244] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6b6e3fab-71bc-4fb2-ac56-5a2958ded366/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:52:01,244] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6b6e3fab-71bc-4fb2-ac56-5a2958ded366/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:52:01,274] [INFO] Found 25 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:52:01,275] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:52:01,275] [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 ajazii	strain=SSM4.2	GCA_010614725.1	2692318	2692318	type	True	100.0	1901	1903	95	conclusive
Flavobacterium fluviatile	strain=TAPY14	GCA_010645065.1	1862387	1862387	type	True	85.5242	1054	1903	95	below_threshold
Flavobacterium hydrophilum	strain=IMCC34758	GCA_003202405.1	2211445	2211445	type	True	85.0996	1265	1903	95	below_threshold
Flavobacterium hibisci	strain=THG-HG1.4	GCA_020026925.1	1914462	1914462	type	True	85.0897	1121	1903	95	below_threshold
Flavobacterium salmonis	strain=CIP 111411	GCA_903819435.1	2654844	2654844	type	True	84.6217	1293	1903	95	below_threshold
Flavobacterium resistens	strain=DSM 19382	GCA_009674815.1	443612	443612	type	True	82.522	929	1903	95	below_threshold
Flavobacterium resistens	strain=DSM 19382	GCA_900182645.1	443612	443612	type	True	82.5104	941	1903	95	below_threshold
Flavobacterium soyae	strain=SCIV07	GCA_021245985.1	2903098	2903098	type	True	82.4322	967	1903	95	below_threshold
Flavobacterium cutihirudinis	strain=DSM 25795	GCA_003385895.1	1265740	1265740	type	True	82.3675	915	1903	95	below_threshold
Flavobacterium nitrogenifigens	strain=DSM 29982	GCA_900182675.1	1617283	1617283	type	True	82.3254	892	1903	95	below_threshold
Flavobacterium tistrianum	strain=GB 56.1	GCA_003254545.1	1685414	1685414	type	True	82.2951	860	1903	95	below_threshold
Flavobacterium johnsoniae	strain=UW101; ATCC 17061	GCA_000016645.1	986	986	type	True	82.2724	979	1903	95	below_threshold
Flavobacterium nitrogenifigens	strain=NXU-44	GCA_003254565.1	1617283	1617283	type	True	82.2719	900	1903	95	below_threshold
Flavobacterium johnsoniae	strain=ATCC 17061	GCA_002221975.1	986	986	type	True	82.2682	973	1903	95	below_threshold
Flavobacterium panici		GCA_903819335.1	2654843	2654843	type	True	82.2351	986	1903	95	below_threshold
Flavobacterium tyrosinilyticum	strain=KCTC 42726	GCA_023656565.1	1658740	1658740	type	True	82.2215	914	1903	95	below_threshold
Flavobacterium johnsoniae	strain=DSM 2064	GCA_900142355.1	986	986	type	True	82.2158	989	1903	95	below_threshold
Flavobacterium sharifuzzamanii	strain=A7.6	GCA_003254585.1	2211133	2211133	type	True	82.1668	894	1903	95	below_threshold
Flavobacterium daemonense	strain=JCM 19455	GCA_007341385.1	1393049	1393049	type	True	82.1478	882	1903	95	below_threshold
Flavobacterium endoglycinae	strain=BB8	GCA_017352115.1	2816357	2816357	type	True	82.1269	928	1903	95	below_threshold
Flavobacterium panacis	strain=DCY106	GCA_024649945.1	2962567	2962567	type	True	81.9785	967	1903	95	below_threshold
Flavobacterium quisquiliarum	strain=EA-12	GCA_019308285.1	1834436	1834436	type	True	81.9732	1000	1903	95	below_threshold
Flavobacterium fluviale	strain=HYN0086	GCA_003312915.1	2249356	2249356	type	True	81.9444	893	1903	95	below_threshold
Flavobacterium hercynium	strain=DSM 18292	GCA_002217285.1	387094	387094	type	True	80.7842	796	1903	95	below_threshold
Flavobacterium sediminilitoris	strain=YSM-43	GCA_023008245.1	2024526	2024526	type	True	76.9139	200	1903	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:52:01,277] [INFO] DFAST Taxonomy check result was written to GCF_010614725.1_ASM1061472v1_genomic.fna/tc_result.tsv
[2024-01-24 13:52:01,277] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:52:01,278] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:52:01,278] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6b6e3fab-71bc-4fb2-ac56-5a2958ded366/dqc_reference/checkm_data
[2024-01-24 13:52:01,280] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:52:01,336] [INFO] Task started: CheckM
[2024-01-24 13:52:01,336] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_010614725.1_ASM1061472v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_010614725.1_ASM1061472v1_genomic.fna/checkm_input GCF_010614725.1_ASM1061472v1_genomic.fna/checkm_result
[2024-01-24 13:52:58,558] [INFO] Task succeeded: CheckM
[2024-01-24 13:52:58,559] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:52:58,583] [INFO] ===== Completeness check finished =====
[2024-01-24 13:52:58,583] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:52:58,584] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_010614725.1_ASM1061472v1_genomic.fna/markers.fasta)
[2024-01-24 13:52:58,584] [INFO] Task started: Blastn
[2024-01-24 13:52:58,584] [INFO] Running command: blastn -query GCF_010614725.1_ASM1061472v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6b6e3fab-71bc-4fb2-ac56-5a2958ded366/dqc_reference/reference_markers_gtdb.fasta -out GCF_010614725.1_ASM1061472v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:52:59,551] [INFO] Task succeeded: Blastn
[2024-01-24 13:52:59,556] [INFO] Selected 20 target genomes.
[2024-01-24 13:52:59,557] [INFO] Target genome list was writen to GCF_010614725.1_ASM1061472v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:52:59,573] [INFO] Task started: fastANI
[2024-01-24 13:52:59,573] [INFO] Running command: fastANI --query /var/lib/cwl/stga9dffc89-3f04-4c76-90a5-a11ac8051867/GCF_010614725.1_ASM1061472v1_genomic.fna.gz --refList GCF_010614725.1_ASM1061472v1_genomic.fna/target_genomes_gtdb.txt --output GCF_010614725.1_ASM1061472v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:53:24,397] [INFO] Task succeeded: fastANI
[2024-01-24 13:53:24,418] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:53:24,418] [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_010614725.1	s__Flavobacterium ajazii	100.0	1901	1903	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_010645065.1	s__Flavobacterium fluviatile	85.5324	1053	1903	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	85.3519	1319	1903	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	96.81	95.16	0.89	0.84	4	-
GCF_003202405.1	s__Flavobacterium hydrophilum	85.0942	1267	1903	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010645075.1	s__Flavobacterium limi	84.6669	1233	1903	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_013388355.1	s__Flavobacterium sp013388355	82.7312	685	1903	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	82.5335	938	1903	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.98	99.98	1.00	1.00	2	-
GCF_003385895.1	s__Flavobacterium cutihirudinis	82.3673	915	1903	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000745775.1	s__Flavobacterium sp000745775	82.3574	936	1903	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016735615.1	s__Flavobacterium sp016735615	82.3319	908	1903	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014207905.1	s__Flavobacterium notoginsengisoli	82.3179	952	1903	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002210235.1	s__Flavobacterium sp002210235	82.3172	972	1903	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	98.80	96.54	0.96	0.91	4	-
GCF_003254545.1	s__Flavobacterium tistrianum	82.2951	860	1903	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000016645.1	s__Flavobacterium johnsoniae	82.2794	977	1903	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	98.23	96.72	0.94	0.86	7	-
GCF_003254585.1	s__Flavobacterium sharifuzzamanii	82.1441	897	1903	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001879205.1	s__Flavobacterium johnsoniae_A	82.0202	962	1903	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902167265.1	s__Flavobacterium anhuiense_B	82.0153	982	1903	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.99	99.99	1.00	1.00	4	-
GCA_017744675.1	s__Flavobacterium sp017744675	82.0144	905	1903	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002482975.1	s__Flavobacterium sp002482975	81.8831	998	1903	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	80.7999	794	1903	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 13:53:24,421] [INFO] GTDB search result was written to GCF_010614725.1_ASM1061472v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:53:24,421] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:53:24,426] [INFO] DFAST_QC result json was written to GCF_010614725.1_ASM1061472v1_genomic.fna/dqc_result.json
[2024-01-24 13:53:24,426] [INFO] DFAST_QC completed!
[2024-01-24 13:53:24,426] [INFO] Total running time: 0h2m12s