[2024-01-24 11:12:58,145] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:12:58,147] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:12:58,147] [INFO] DQC Reference Directory: /var/lib/cwl/stg44799dfd-16be-411e-a9f1-ab134b63d426/dqc_reference
[2024-01-24 11:12:59,624] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:12:59,626] [INFO] Task started: Prodigal
[2024-01-24 11:12:59,627] [INFO] Running command: gunzip -c /var/lib/cwl/stg7f336c09-6752-4b6f-9d17-bd77ab35f909/GCF_003293845.1_ASM329384v1_genomic.fna.gz | prodigal -d GCF_003293845.1_ASM329384v1_genomic.fna/cds.fna -a GCF_003293845.1_ASM329384v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:13:10,122] [INFO] Task succeeded: Prodigal
[2024-01-24 11:13:10,122] [INFO] Task started: HMMsearch
[2024-01-24 11:13:10,122] [INFO] Running command: hmmsearch --tblout GCF_003293845.1_ASM329384v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg44799dfd-16be-411e-a9f1-ab134b63d426/dqc_reference/reference_markers.hmm GCF_003293845.1_ASM329384v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:13:10,405] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:13:10,406] [INFO] Found 6/6 markers.
[2024-01-24 11:13:10,443] [INFO] Query marker FASTA was written to GCF_003293845.1_ASM329384v1_genomic.fna/markers.fasta
[2024-01-24 11:13:10,443] [INFO] Task started: Blastn
[2024-01-24 11:13:10,444] [INFO] Running command: blastn -query GCF_003293845.1_ASM329384v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg44799dfd-16be-411e-a9f1-ab134b63d426/dqc_reference/reference_markers.fasta -out GCF_003293845.1_ASM329384v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:13:11,177] [INFO] Task succeeded: Blastn
[2024-01-24 11:13:11,179] [INFO] Selected 15 target genomes.
[2024-01-24 11:13:11,180] [INFO] Target genome list was writen to GCF_003293845.1_ASM329384v1_genomic.fna/target_genomes.txt
[2024-01-24 11:13:11,186] [INFO] Task started: fastANI
[2024-01-24 11:13:11,186] [INFO] Running command: fastANI --query /var/lib/cwl/stg7f336c09-6752-4b6f-9d17-bd77ab35f909/GCF_003293845.1_ASM329384v1_genomic.fna.gz --refList GCF_003293845.1_ASM329384v1_genomic.fna/target_genomes.txt --output GCF_003293845.1_ASM329384v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:13:22,114] [INFO] Task succeeded: fastANI
[2024-01-24 11:13:22,115] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg44799dfd-16be-411e-a9f1-ab134b63d426/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:13:22,115] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg44799dfd-16be-411e-a9f1-ab134b63d426/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:13:22,128] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:13:22,128] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:13:22,129] [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 tibetense	strain=YH5	GCA_003293845.1	2233533	2233533	type	True	100.0	884	886	95	conclusive
Flavobacterium sasangense	strain=DSM 21067	GCA_000686885.1	503361	503361	type	True	82.0235	502	886	95	below_threshold
Flavobacterium aquaticum	strain=CGMCC 1.12398	GCA_003259835.1	1236486	1236486	type	True	81.9186	526	886	95	below_threshold
Flavobacterium cheniae	strain=CGMCC 1.6844	GCA_007830415.1	295428	295428	type	True	81.8745	519	886	95	below_threshold
Flavobacterium proteolyticum	strain=1Y8A	GCA_015223105.1	2911683	2911683	type	True	81.8495	516	886	95	below_threshold
Flavobacterium cheniae	strain=DSM 22462	GCA_004363695.1	295428	295428	type	True	81.7054	529	886	95	below_threshold
Flavobacterium cyclinae	strain=KSM-R2A25	GCA_021172145.1	2895947	2895947	type	True	81.6496	502	886	95	below_threshold
Flavobacterium celericrescens	strain=TWA-26	GCA_011392075.1	2709780	2709780	type	True	81.3423	454	886	95	below_threshold
Flavobacterium cucumis	strain=DSM 18830	GCA_900148835.1	416016	416016	type	True	81.2207	477	886	95	below_threshold
Flavobacterium channae	strain=KSM-R2A30	GCA_021172165.1	2897181	2897181	type	True	80.8165	485	886	95	below_threshold
Flavobacterium sediminilitoris	strain=YSM-43	GCA_023008245.1	2024526	2024526	type	True	78.7353	335	886	95	below_threshold
Flavobacterium jejuense	strain=EC11	GCA_006491595.2	1544455	1544455	type	True	78.4831	364	886	95	below_threshold
Flavobacterium profundi	strain=TP390	GCA_006491645.1	1774945	1774945	type	True	78.3778	367	886	95	below_threshold
Flavobacterium profundi	strain=TP390	GCA_009753805.1	1774945	1774945	type	True	78.3625	369	886	95	below_threshold
Flavobacterium branchiophilum	strain=DSM 24789	GCA_006716585.1	55197	55197	type	True	77.4301	123	886	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:13:22,130] [INFO] DFAST Taxonomy check result was written to GCF_003293845.1_ASM329384v1_genomic.fna/tc_result.tsv
[2024-01-24 11:13:22,131] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:13:22,131] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:13:22,131] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg44799dfd-16be-411e-a9f1-ab134b63d426/dqc_reference/checkm_data
[2024-01-24 11:13:22,132] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:13:22,160] [INFO] Task started: CheckM
[2024-01-24 11:13:22,160] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003293845.1_ASM329384v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003293845.1_ASM329384v1_genomic.fna/checkm_input GCF_003293845.1_ASM329384v1_genomic.fna/checkm_result
[2024-01-24 11:13:57,038] [INFO] Task succeeded: CheckM
[2024-01-24 11:13:57,039] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:13:57,054] [INFO] ===== Completeness check finished =====
[2024-01-24 11:13:57,055] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:13:57,056] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003293845.1_ASM329384v1_genomic.fna/markers.fasta)
[2024-01-24 11:13:57,056] [INFO] Task started: Blastn
[2024-01-24 11:13:57,056] [INFO] Running command: blastn -query GCF_003293845.1_ASM329384v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg44799dfd-16be-411e-a9f1-ab134b63d426/dqc_reference/reference_markers_gtdb.fasta -out GCF_003293845.1_ASM329384v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:13:58,026] [INFO] Task succeeded: Blastn
[2024-01-24 11:13:58,030] [INFO] Selected 15 target genomes.
[2024-01-24 11:13:58,030] [INFO] Target genome list was writen to GCF_003293845.1_ASM329384v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:13:58,042] [INFO] Task started: fastANI
[2024-01-24 11:13:58,042] [INFO] Running command: fastANI --query /var/lib/cwl/stg7f336c09-6752-4b6f-9d17-bd77ab35f909/GCF_003293845.1_ASM329384v1_genomic.fna.gz --refList GCF_003293845.1_ASM329384v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003293845.1_ASM329384v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:14:06,768] [INFO] Task succeeded: fastANI
[2024-01-24 11:14:06,785] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:14:06,786] [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_003293845.1	s__Flavobacterium tibetense	100.0	883	886	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_018401995.1	s__Flavobacterium sp018401995	90.9846	575	886	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	82.0334	502	886	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003497625.1	s__Flavobacterium sp003497625	81.9174	510	886	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.98	99.98	0.98	0.98	2	-
GCF_003259835.1	s__Flavobacterium aquaticum	81.9104	526	886	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015223105.1	s__Flavobacterium aquaticum_A	81.856	515	886	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002483315.1	s__Flavobacterium sp002483315	81.8489	490	886	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003963025.1	s__Flavobacterium sp003963025	81.7617	350	886	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004363695.1	s__Flavobacterium cheniae	81.7057	529	886	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCA_004293165.1	s__Flavobacterium sp004293165	81.368	472	886	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	97.30	97.30	0.81	0.81	2	-
GCA_019105125.1	s__Flavobacterium sp019105125	81.3149	275	886	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002715085.1	s__Flavobacterium sp002715085	78.3966	341	886	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006491645.1	s__Flavobacterium sp006491645	78.3729	368	886	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCA_002862755.1	s__Flavobacterium sp002862755	78.331	329	886	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012032075.1	s__Flavobacterium sp012032075	78.2485	286	886	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 11:14:06,787] [INFO] GTDB search result was written to GCF_003293845.1_ASM329384v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:14:06,787] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:14:06,792] [INFO] DFAST_QC result json was written to GCF_003293845.1_ASM329384v1_genomic.fna/dqc_result.json
[2024-01-24 11:14:06,792] [INFO] DFAST_QC completed!
[2024-01-24 11:14:06,793] [INFO] Total running time: 0h1m9s