[2024-01-24 13:46:29,588] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:46:29,590] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:46:29,590] [INFO] DQC Reference Directory: /var/lib/cwl/stg766f7b76-4220-4dc3-bb5a-b96099e5b70b/dqc_reference
[2024-01-24 13:46:30,863] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:46:30,864] [INFO] Task started: Prodigal
[2024-01-24 13:46:30,864] [INFO] Running command: gunzip -c /var/lib/cwl/stg5389e514-61b0-422e-aed7-52c49428cac0/GCF_008629655.1_ASM862965v1_genomic.fna.gz | prodigal -d GCF_008629655.1_ASM862965v1_genomic.fna/cds.fna -a GCF_008629655.1_ASM862965v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:46:43,125] [INFO] Task succeeded: Prodigal
[2024-01-24 13:46:43,125] [INFO] Task started: HMMsearch
[2024-01-24 13:46:43,125] [INFO] Running command: hmmsearch --tblout GCF_008629655.1_ASM862965v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg766f7b76-4220-4dc3-bb5a-b96099e5b70b/dqc_reference/reference_markers.hmm GCF_008629655.1_ASM862965v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:46:43,409] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:46:43,411] [INFO] Found 6/6 markers.
[2024-01-24 13:46:43,451] [INFO] Query marker FASTA was written to GCF_008629655.1_ASM862965v1_genomic.fna/markers.fasta
[2024-01-24 13:46:43,451] [INFO] Task started: Blastn
[2024-01-24 13:46:43,451] [INFO] Running command: blastn -query GCF_008629655.1_ASM862965v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg766f7b76-4220-4dc3-bb5a-b96099e5b70b/dqc_reference/reference_markers.fasta -out GCF_008629655.1_ASM862965v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:46:44,166] [INFO] Task succeeded: Blastn
[2024-01-24 13:46:44,176] [INFO] Selected 18 target genomes.
[2024-01-24 13:46:44,177] [INFO] Target genome list was writen to GCF_008629655.1_ASM862965v1_genomic.fna/target_genomes.txt
[2024-01-24 13:46:44,219] [INFO] Task started: fastANI
[2024-01-24 13:46:44,220] [INFO] Running command: fastANI --query /var/lib/cwl/stg5389e514-61b0-422e-aed7-52c49428cac0/GCF_008629655.1_ASM862965v1_genomic.fna.gz --refList GCF_008629655.1_ASM862965v1_genomic.fna/target_genomes.txt --output GCF_008629655.1_ASM862965v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:46:57,906] [INFO] Task succeeded: fastANI
[2024-01-24 13:46:57,907] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg766f7b76-4220-4dc3-bb5a-b96099e5b70b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:46:57,907] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg766f7b76-4220-4dc3-bb5a-b96099e5b70b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:46:57,942] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:46:57,942] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:46:57,943] [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 baculatum	strain=SNL9	GCA_008629655.1	2608000	2608000	type	True	100.0	1094	1099	95	conclusive
Flavobacterium ummariense	strain=DS-12	GCA_900115115.1	913024	913024	type	True	89.5856	799	1099	95	below_threshold
Flavobacterium viscosum	strain=YIM 102796	GCA_003858535.1	2488729	2488729	type	True	87.6812	700	1099	95	below_threshold
Flavobacterium tangerinum	strain=YIM 102701-2	GCA_003865405.1	2488728	2488728	type	True	78.0368	284	1099	95	below_threshold
Flavobacterium inviolabile	strain=P2-65	GCA_013389455.1	2748320	2748320	type	True	77.6278	114	1099	95	below_threshold
Flavobacterium supellecticarium	strain=CC-CTC003	GCA_004801375.1	2565924	2565924	type	True	77.4378	101	1099	95	below_threshold
Flavobacterium oreochromis	strain=Costa Rica 04-02-TN	GCA_019565455.1	2906078	2906078	type	True	77.4366	88	1099	95	below_threshold
Flavobacterium saccharophilum	strain=DSM 1811	GCA_900142735.1	29534	29534	type	True	77.3184	124	1099	95	below_threshold
Flavobacterium johnsoniae	strain=DSM 2064	GCA_900142355.1	986	986	type	True	77.1244	137	1099	95	below_threshold
Flavobacterium johnsoniae	strain=ATCC 17061	GCA_002221975.1	986	986	type	True	77.0486	140	1099	95	below_threshold
Flavobacterium hydrocarbonoxydans	strain=GA093	GCA_009789235.1	2683249	2683249	type	True	77.0447	122	1099	95	below_threshold
Flavobacterium salilacus subsp. salilacus	strain=SaA2.12	GCA_004634195.1	2545633	2898423	type	True	77.0188	60	1099	95	below_threshold
Flavobacterium cyclinae	strain=KSM-R2A25	GCA_021172145.1	2895947	2895947	type	True	77.0076	138	1099	95	below_threshold
Flavobacterium salilacus subsp. altitudinum	strain=LaA7.5	GCA_010078225.1	2691899	2898423	type	True	77.0069	67	1099	95	below_threshold
Flavobacterium endoglycinae	strain=BB8	GCA_017352115.1	2816357	2816357	type	True	76.7655	162	1099	95	below_threshold
Faecalibacter bovis	strain=ZY171143	GCA_017948305.1	2898187	2898187	type	True	76.5388	54	1099	95	below_threshold
Flavivirga algicola	strain=Y03	GCA_012910715.1	2729136	2729136	type	True	76.3639	54	1099	95	below_threshold
Polaribacter septentrionalilitoris	strain=ANORD1	GCA_009832745.1	2494657	2494657	type	True	76.0503	85	1099	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:46:57,944] [INFO] DFAST Taxonomy check result was written to GCF_008629655.1_ASM862965v1_genomic.fna/tc_result.tsv
[2024-01-24 13:46:57,945] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:46:57,945] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:46:57,945] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg766f7b76-4220-4dc3-bb5a-b96099e5b70b/dqc_reference/checkm_data
[2024-01-24 13:46:57,947] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:46:57,984] [INFO] Task started: CheckM
[2024-01-24 13:46:57,985] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008629655.1_ASM862965v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008629655.1_ASM862965v1_genomic.fna/checkm_input GCF_008629655.1_ASM862965v1_genomic.fna/checkm_result
[2024-01-24 13:47:36,326] [INFO] Task succeeded: CheckM
[2024-01-24 13:47:36,327] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:47:36,346] [INFO] ===== Completeness check finished =====
[2024-01-24 13:47:36,347] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:47:36,347] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008629655.1_ASM862965v1_genomic.fna/markers.fasta)
[2024-01-24 13:47:36,348] [INFO] Task started: Blastn
[2024-01-24 13:47:36,348] [INFO] Running command: blastn -query GCF_008629655.1_ASM862965v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg766f7b76-4220-4dc3-bb5a-b96099e5b70b/dqc_reference/reference_markers_gtdb.fasta -out GCF_008629655.1_ASM862965v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:47:37,218] [INFO] Task succeeded: Blastn
[2024-01-24 13:47:37,221] [INFO] Selected 7 target genomes.
[2024-01-24 13:47:37,221] [INFO] Target genome list was writen to GCF_008629655.1_ASM862965v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:47:37,231] [INFO] Task started: fastANI
[2024-01-24 13:47:37,231] [INFO] Running command: fastANI --query /var/lib/cwl/stg5389e514-61b0-422e-aed7-52c49428cac0/GCF_008629655.1_ASM862965v1_genomic.fna.gz --refList GCF_008629655.1_ASM862965v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008629655.1_ASM862965v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:47:42,498] [INFO] Task succeeded: fastANI
[2024-01-24 13:47:42,510] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:47:42,510] [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_008629655.1	s__Flavobacterium baculatum	100.0	1094	1099	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_900115115.1	s__Flavobacterium ummariense	89.5856	799	1099	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003858535.1	s__Flavobacterium viscosum	87.6845	700	1099	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004151275.1	s__Flavobacterium sp004151275	85.6643	615	1099	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900108395.1	s__Flavobacterium marinum	81.6339	559	1099	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013874595.1	s__Flavobacterium sp013874595	80.5115	493	1099	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	100.00	0.97	0.97	3	-
GCA_018384465.1	s__Flavobacterium sp018384465	80.4699	304	1099	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 13:47:42,512] [INFO] GTDB search result was written to GCF_008629655.1_ASM862965v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:47:42,512] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:47:42,516] [INFO] DFAST_QC result json was written to GCF_008629655.1_ASM862965v1_genomic.fna/dqc_result.json
[2024-01-24 13:47:42,517] [INFO] DFAST_QC completed!
[2024-01-24 13:47:42,517] [INFO] Total running time: 0h1m13s