[2024-01-24 13:17:34,581] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:17:34,588] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:17:34,589] [INFO] DQC Reference Directory: /var/lib/cwl/stg597f8db9-028d-4d94-8724-43001d0d2763/dqc_reference
[2024-01-24 13:17:36,020] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:17:36,021] [INFO] Task started: Prodigal
[2024-01-24 13:17:36,021] [INFO] Running command: gunzip -c /var/lib/cwl/stgb355ae66-6525-40ff-bfa5-9622726da551/GCF_900142035.1_IMG-taxon_2695421047_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900142035.1_IMG-taxon_2695421047_annotated_assembly_genomic.fna/cds.fna -a GCF_900142035.1_IMG-taxon_2695421047_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:17:46,715] [INFO] Task succeeded: Prodigal
[2024-01-24 13:17:46,716] [INFO] Task started: HMMsearch
[2024-01-24 13:17:46,716] [INFO] Running command: hmmsearch --tblout GCF_900142035.1_IMG-taxon_2695421047_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg597f8db9-028d-4d94-8724-43001d0d2763/dqc_reference/reference_markers.hmm GCF_900142035.1_IMG-taxon_2695421047_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:17:46,981] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:17:46,982] [INFO] Found 6/6 markers.
[2024-01-24 13:17:47,010] [INFO] Query marker FASTA was written to GCF_900142035.1_IMG-taxon_2695421047_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 13:17:47,010] [INFO] Task started: Blastn
[2024-01-24 13:17:47,010] [INFO] Running command: blastn -query GCF_900142035.1_IMG-taxon_2695421047_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg597f8db9-028d-4d94-8724-43001d0d2763/dqc_reference/reference_markers.fasta -out GCF_900142035.1_IMG-taxon_2695421047_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:17:47,823] [INFO] Task succeeded: Blastn
[2024-01-24 13:17:47,826] [INFO] Selected 19 target genomes.
[2024-01-24 13:17:47,826] [INFO] Target genome list was writen to GCF_900142035.1_IMG-taxon_2695421047_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 13:17:47,857] [INFO] Task started: fastANI
[2024-01-24 13:17:47,857] [INFO] Running command: fastANI --query /var/lib/cwl/stgb355ae66-6525-40ff-bfa5-9622726da551/GCF_900142035.1_IMG-taxon_2695421047_annotated_assembly_genomic.fna.gz --refList GCF_900142035.1_IMG-taxon_2695421047_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900142035.1_IMG-taxon_2695421047_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:17:59,283] [INFO] Task succeeded: fastANI
[2024-01-24 13:17:59,283] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg597f8db9-028d-4d94-8724-43001d0d2763/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:17:59,284] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg597f8db9-028d-4d94-8724-43001d0d2763/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:17:59,299] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:17:59,300] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:17:59,300] [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 terrae	strain=DSM 18829	GCA_900142035.1	415425	415425	type	True	100.0	1042	1043	95	conclusive
Flavobacterium amniphilum	strain=KYPY10	GCA_023634845.1	1834035	1834035	type	True	79.4148	403	1043	95	below_threshold
Flavobacterium amnicola	strain=LLJ-11	GCA_004122165.1	2506422	2506422	type	True	79.3704	376	1043	95	below_threshold
Flavobacterium channae	strain=KSM-R2A30	GCA_021172165.1	2897181	2897181	type	True	78.9654	277	1043	95	below_threshold
Flavobacterium oreochromis	strain=Costa Rica 04-02-TN	GCA_019565455.1	2906078	2906078	type	True	78.6755	320	1043	95	below_threshold
Flavobacterium proteolyticum	strain=1Y8A	GCA_015223105.1	2911683	2911683	type	True	78.5706	253	1043	95	below_threshold
Flavobacterium davisii	strain=90-106	GCA_019565505.1	2906077	2906077	type	True	78.4469	298	1043	95	below_threshold
Flavobacterium sasangense	strain=DSM 21067	GCA_000686885.1	503361	503361	type	True	78.4413	263	1043	95	below_threshold
Flavobacterium celericrescens	strain=TWA-26	GCA_011392075.1	2709780	2709780	type	True	78.1691	271	1043	95	below_threshold
Flavobacterium humi	strain=DS2-A	GCA_004745595.1	2562683	2562683	type	True	78.1546	201	1043	95	below_threshold
Flavobacterium saliperosum	strain=CGMCC 1.3801	GCA_900100625.1	329186	329186	type	True	78.1494	165	1043	95	below_threshold
Flavobacterium macrobrachii	strain=LMG 25203	GCA_014385475.2	591204	591204	type	True	77.8253	239	1043	95	below_threshold
Flavobacterium macrobrachii	strain=an-8	GCA_014486675.1	591204	591204	type	True	77.7502	244	1043	95	below_threshold
Flavobacterium soyae	strain=SCIV07	GCA_021245985.1	2903098	2903098	type	True	77.6827	219	1043	95	below_threshold
Flavobacterium saccharophilum	strain=DSM 1811	GCA_900142735.1	29534	29534	type	True	77.5933	222	1043	95	below_threshold
Flavobacterium xinjiangense	strain=CGMCC 1.2749	GCA_900142885.1	178356	178356	type	True	77.5909	186	1043	95	below_threshold
Flavobacterium sediminilitoris	strain=YSM-43	GCA_023008245.1	2024526	2024526	type	True	77.3926	273	1043	95	below_threshold
Flavobacterium jumunjinense	strain=HME7102	GCA_021650975.2	998845	998845	type	True	77.2952	243	1043	95	below_threshold
Flavobacterium urumqiense	strain=CGMCC 1.9230	GCA_900108015.1	935224	935224	type	True	77.0631	174	1043	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:17:59,302] [INFO] DFAST Taxonomy check result was written to GCF_900142035.1_IMG-taxon_2695421047_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 13:17:59,302] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:17:59,302] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:17:59,303] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg597f8db9-028d-4d94-8724-43001d0d2763/dqc_reference/checkm_data
[2024-01-24 13:17:59,304] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:17:59,338] [INFO] Task started: CheckM
[2024-01-24 13:17:59,338] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900142035.1_IMG-taxon_2695421047_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900142035.1_IMG-taxon_2695421047_annotated_assembly_genomic.fna/checkm_input GCF_900142035.1_IMG-taxon_2695421047_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 13:18:34,077] [INFO] Task succeeded: CheckM
[2024-01-24 13:18:34,078] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:18:34,094] [INFO] ===== Completeness check finished =====
[2024-01-24 13:18:34,094] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:18:34,095] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900142035.1_IMG-taxon_2695421047_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 13:18:34,095] [INFO] Task started: Blastn
[2024-01-24 13:18:34,095] [INFO] Running command: blastn -query GCF_900142035.1_IMG-taxon_2695421047_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg597f8db9-028d-4d94-8724-43001d0d2763/dqc_reference/reference_markers_gtdb.fasta -out GCF_900142035.1_IMG-taxon_2695421047_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:18:35,126] [INFO] Task succeeded: Blastn
[2024-01-24 13:18:35,130] [INFO] Selected 22 target genomes.
[2024-01-24 13:18:35,130] [INFO] Target genome list was writen to GCF_900142035.1_IMG-taxon_2695421047_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:18:35,175] [INFO] Task started: fastANI
[2024-01-24 13:18:35,175] [INFO] Running command: fastANI --query /var/lib/cwl/stgb355ae66-6525-40ff-bfa5-9622726da551/GCF_900142035.1_IMG-taxon_2695421047_annotated_assembly_genomic.fna.gz --refList GCF_900142035.1_IMG-taxon_2695421047_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900142035.1_IMG-taxon_2695421047_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:18:48,851] [INFO] Task succeeded: fastANI
[2024-01-24 13:18:48,875] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:18:48,876] [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_900142035.1	s__Flavobacterium terrae	100.0	1042	1043	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_004959765.1	s__Flavobacterium sp004959765	79.8958	451	1043	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004122165.1	s__Flavobacterium sp004122165	79.3834	375	1043	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900290975.1	s__Flavobacterium columnare_D	78.5649	288	1043	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	98.86	98.55	0.90	0.88	3	-
GCF_015223105.1	s__Flavobacterium aquaticum_A	78.5629	254	1043	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018062725.1	s__Flavobacterium sp018062725	78.5304	255	1043	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000686885.1	s__Flavobacterium sasangense	78.4413	263	1043	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011392075.1	s__Flavobacterium celericrescens	78.1691	271	1043	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004745595.1	s__Flavobacterium humi	78.1546	201	1043	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017983975.1	s__Flavobacterium sp017983975	77.9848	169	1043	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000757385.1	s__Flavobacterium aquatile	77.8574	238	1043	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	99.99	1.00	1.00	3	-
GCF_014486675.1	s__Flavobacterium macrobrachii	77.7642	243	1043	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	98.85	97.73	0.92	0.87	3	-
GCA_001464475.1	s__Flavobacterium sp001464475	77.7489	275	1043	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903889745.1	s__Flavobacterium sp903889745	77.695	164	1043	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	77.6663	241	1043	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	98.80	96.54	0.96	0.91	4	-
GCF_004362015.1	s__Flavobacterium sp004362015	77.5899	216	1043	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	77.5707	235	1043	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013298525.1	s__Flavobacterium sp013298525	77.4645	233	1043	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009707955.1	s__Flavobacterium sp009707955	77.3803	247	1043	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.99	99.99	0.99	0.99	2	-
GCF_000282055.1	s__Flavobacterium sp000282055	77.3132	206	1043	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002813295.1	s__Flavobacterium sp002813295	77.2442	227	1043	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900108015.1	s__Flavobacterium urumqiense	77.0351	175	1043	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 13:18:48,877] [INFO] GTDB search result was written to GCF_900142035.1_IMG-taxon_2695421047_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 13:18:48,878] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:18:48,883] [INFO] DFAST_QC result json was written to GCF_900142035.1_IMG-taxon_2695421047_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 13:18:48,883] [INFO] DFAST_QC completed!
[2024-01-24 13:18:48,883] [INFO] Total running time: 0h1m14s