[2024-01-24 14:39:01,521] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:39:01,525] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:39:01,525] [INFO] DQC Reference Directory: /var/lib/cwl/stgc3af27c3-99d1-4397-8973-909b8287b536/dqc_reference
[2024-01-24 14:39:04,243] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:39:04,244] [INFO] Task started: Prodigal
[2024-01-24 14:39:04,244] [INFO] Running command: gunzip -c /var/lib/cwl/stgca6fe6df-ecca-4f2c-96c7-d09c8deac2ea/GCF_003314435.2_ASM331443v2_genomic.fna.gz | prodigal -d GCF_003314435.2_ASM331443v2_genomic.fna/cds.fna -a GCF_003314435.2_ASM331443v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:39:18,481] [INFO] Task succeeded: Prodigal
[2024-01-24 14:39:18,481] [INFO] Task started: HMMsearch
[2024-01-24 14:39:18,481] [INFO] Running command: hmmsearch --tblout GCF_003314435.2_ASM331443v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc3af27c3-99d1-4397-8973-909b8287b536/dqc_reference/reference_markers.hmm GCF_003314435.2_ASM331443v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:39:18,737] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:39:18,739] [INFO] Found 6/6 markers.
[2024-01-24 14:39:18,784] [INFO] Query marker FASTA was written to GCF_003314435.2_ASM331443v2_genomic.fna/markers.fasta
[2024-01-24 14:39:18,786] [INFO] Task started: Blastn
[2024-01-24 14:39:18,789] [INFO] Running command: blastn -query GCF_003314435.2_ASM331443v2_genomic.fna/markers.fasta -db /var/lib/cwl/stgc3af27c3-99d1-4397-8973-909b8287b536/dqc_reference/reference_markers.fasta -out GCF_003314435.2_ASM331443v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:39:19,530] [INFO] Task succeeded: Blastn
[2024-01-24 14:39:19,534] [INFO] Selected 20 target genomes.
[2024-01-24 14:39:19,534] [INFO] Target genome list was writen to GCF_003314435.2_ASM331443v2_genomic.fna/target_genomes.txt
[2024-01-24 14:39:19,541] [INFO] Task started: fastANI
[2024-01-24 14:39:19,541] [INFO] Running command: fastANI --query /var/lib/cwl/stgca6fe6df-ecca-4f2c-96c7-d09c8deac2ea/GCF_003314435.2_ASM331443v2_genomic.fna.gz --refList GCF_003314435.2_ASM331443v2_genomic.fna/target_genomes.txt --output GCF_003314435.2_ASM331443v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:39:36,440] [INFO] Task succeeded: fastANI
[2024-01-24 14:39:36,441] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc3af27c3-99d1-4397-8973-909b8287b536/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:39:36,441] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc3af27c3-99d1-4397-8973-909b8287b536/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:39:36,455] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:39:36,456] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:39:36,456] [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 petrolei	strain=Kopri-42	GCA_003314435.2	2259594	2259594	type	True	100.0	1236	1237	95	conclusive
Flavobacterium psychrolimnae	strain=LMG 22018	GCA_003312425.1	249351	249351	type	True	92.618	973	1237	95	below_threshold
Flavobacterium limicola	strain=DSM 15094	GCA_003634755.1	180441	180441	type	True	90.545	914	1237	95	below_threshold
Flavobacterium sinopsychrotolerans	strain=CGMCC 1.8704	GCA_900110375.1	604089	604089	type	True	90.1653	914	1237	95	below_threshold
Flavobacterium glaciei	strain=DSM 19728	GCA_003350545.1	386300	386300	type	True	86.5524	789	1237	95	below_threshold
Flavobacterium glaciei	strain=CGMCC 1.5380	GCA_007994155.1	386300	386300	type	True	86.5299	800	1237	95	below_threshold
Flavobacterium sandaracinum	strain=LB-D12	GCA_004349135.1	2541733	2541733	type	True	86.0043	866	1237	95	below_threshold
Flavobacterium rhamnosiphilum	strain=LB3P52	GCA_004349195.1	2541724	2541724	type	True	85.3004	794	1237	95	below_threshold
Flavobacterium xinjiangense	strain=CGMCC 1.2749	GCA_900142885.1	178356	178356	type	True	82.5385	708	1237	95	below_threshold
Flavobacterium urumqiense	strain=CGMCC 1.9230	GCA_900108015.1	935224	935224	type	True	82.4609	710	1237	95	below_threshold
Flavobacterium taihuense	strain=NAS39	GCA_019351435.1	2857508	2857508	type	True	79.2299	507	1237	95	below_threshold
Flavobacterium soyae	strain=SCIV07	GCA_021245985.1	2903098	2903098	type	True	78.7611	421	1237	95	below_threshold
Flavobacterium panacis	strain=DCY106	GCA_024649945.1	2962567	2962567	type	True	78.6855	403	1237	95	below_threshold
Flavobacterium endoglycinae	strain=BB8	GCA_017352115.1	2816357	2816357	type	True	78.3545	410	1237	95	below_threshold
Flavobacterium tyrosinilyticum	strain=KCTC 42726	GCA_023656565.1	1658740	1658740	type	True	78.3229	391	1237	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:39:36,458] [INFO] DFAST Taxonomy check result was written to GCF_003314435.2_ASM331443v2_genomic.fna/tc_result.tsv
[2024-01-24 14:39:36,458] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:39:36,458] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:39:36,459] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc3af27c3-99d1-4397-8973-909b8287b536/dqc_reference/checkm_data
[2024-01-24 14:39:36,460] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:39:36,511] [INFO] Task started: CheckM
[2024-01-24 14:39:36,512] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003314435.2_ASM331443v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003314435.2_ASM331443v2_genomic.fna/checkm_input GCF_003314435.2_ASM331443v2_genomic.fna/checkm_result
[2024-01-24 14:40:21,569] [INFO] Task succeeded: CheckM
[2024-01-24 14:40:21,570] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.38%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:40:21,588] [INFO] ===== Completeness check finished =====
[2024-01-24 14:40:21,589] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:40:21,589] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003314435.2_ASM331443v2_genomic.fna/markers.fasta)
[2024-01-24 14:40:21,589] [INFO] Task started: Blastn
[2024-01-24 14:40:21,589] [INFO] Running command: blastn -query GCF_003314435.2_ASM331443v2_genomic.fna/markers.fasta -db /var/lib/cwl/stgc3af27c3-99d1-4397-8973-909b8287b536/dqc_reference/reference_markers_gtdb.fasta -out GCF_003314435.2_ASM331443v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:40:22,526] [INFO] Task succeeded: Blastn
[2024-01-24 14:40:22,530] [INFO] Selected 13 target genomes.
[2024-01-24 14:40:22,530] [INFO] Target genome list was writen to GCF_003314435.2_ASM331443v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:40:22,539] [INFO] Task started: fastANI
[2024-01-24 14:40:22,539] [INFO] Running command: fastANI --query /var/lib/cwl/stgca6fe6df-ecca-4f2c-96c7-d09c8deac2ea/GCF_003314435.2_ASM331443v2_genomic.fna.gz --refList GCF_003314435.2_ASM331443v2_genomic.fna/target_genomes_gtdb.txt --output GCF_003314435.2_ASM331443v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:40:32,843] [INFO] Task succeeded: fastANI
[2024-01-24 14:40:32,851] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:40:32,852] [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_003314435.2	s__Flavobacterium petrolei	100.0	1236	1237	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	97.35	97.35	0.87	0.87	2	conclusive
GCF_003312425.1	s__Flavobacterium psychrolimnae	92.6326	972	1237	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015752255.1	s__Flavobacterium sp015752255	92.2415	970	1237	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003634755.1	s__Flavobacterium limicola	90.5626	913	1237	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110375.1	s__Flavobacterium sinopsychrotolerans	90.1499	916	1237	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004349085.1	s__Flavobacterium caseinilyticum	86.9776	843	1237	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003350545.1	s__Flavobacterium glaciei	86.5293	791	1237	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.99	99.99	0.99	0.99	2	-
GCF_004349135.1	s__Flavobacterium sandaracinum	86.0125	865	1237	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142885.1	s__Flavobacterium xinjiangense	82.5155	710	1237	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 14:40:32,853] [INFO] GTDB search result was written to GCF_003314435.2_ASM331443v2_genomic.fna/result_gtdb.tsv
[2024-01-24 14:40:32,854] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:40:32,857] [INFO] DFAST_QC result json was written to GCF_003314435.2_ASM331443v2_genomic.fna/dqc_result.json
[2024-01-24 14:40:32,858] [INFO] DFAST_QC completed!
[2024-01-24 14:40:32,858] [INFO] Total running time: 0h1m31s