[2024-01-24 13:28:12,498] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:28:12,500] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:28:12,500] [INFO] DQC Reference Directory: /var/lib/cwl/stg1e5a3ab0-bb20-4a1f-98c1-ad63cfef1a15/dqc_reference
[2024-01-24 13:28:13,824] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:28:13,825] [INFO] Task started: Prodigal
[2024-01-24 13:28:13,826] [INFO] Running command: gunzip -c /var/lib/cwl/stg9305ec7e-c5b9-47f0-a483-6f8ede2229b2/GCF_019565505.1_ASM1956550v1_genomic.fna.gz | prodigal -d GCF_019565505.1_ASM1956550v1_genomic.fna/cds.fna -a GCF_019565505.1_ASM1956550v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:28:23,448] [INFO] Task succeeded: Prodigal
[2024-01-24 13:28:23,448] [INFO] Task started: HMMsearch
[2024-01-24 13:28:23,449] [INFO] Running command: hmmsearch --tblout GCF_019565505.1_ASM1956550v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1e5a3ab0-bb20-4a1f-98c1-ad63cfef1a15/dqc_reference/reference_markers.hmm GCF_019565505.1_ASM1956550v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:28:23,720] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:28:23,721] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg9305ec7e-c5b9-47f0-a483-6f8ede2229b2/GCF_019565505.1_ASM1956550v1_genomic.fna.gz]
[2024-01-24 13:28:23,754] [INFO] Query marker FASTA was written to GCF_019565505.1_ASM1956550v1_genomic.fna/markers.fasta
[2024-01-24 13:28:23,755] [INFO] Task started: Blastn
[2024-01-24 13:28:23,755] [INFO] Running command: blastn -query GCF_019565505.1_ASM1956550v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1e5a3ab0-bb20-4a1f-98c1-ad63cfef1a15/dqc_reference/reference_markers.fasta -out GCF_019565505.1_ASM1956550v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:28:24,506] [INFO] Task succeeded: Blastn
[2024-01-24 13:28:24,512] [INFO] Selected 11 target genomes.
[2024-01-24 13:28:24,512] [INFO] Target genome list was writen to GCF_019565505.1_ASM1956550v1_genomic.fna/target_genomes.txt
[2024-01-24 13:28:24,525] [INFO] Task started: fastANI
[2024-01-24 13:28:24,525] [INFO] Running command: fastANI --query /var/lib/cwl/stg9305ec7e-c5b9-47f0-a483-6f8ede2229b2/GCF_019565505.1_ASM1956550v1_genomic.fna.gz --refList GCF_019565505.1_ASM1956550v1_genomic.fna/target_genomes.txt --output GCF_019565505.1_ASM1956550v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:28:33,167] [INFO] Task succeeded: fastANI
[2024-01-24 13:28:33,168] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1e5a3ab0-bb20-4a1f-98c1-ad63cfef1a15/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:28:33,168] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1e5a3ab0-bb20-4a1f-98c1-ad63cfef1a15/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:28:33,178] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:28:33,179] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:28:33,179] [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 davisii	strain=90-106	GCA_019565505.1	2906077	2906077	type	True	100.0	1134	1134	95	conclusive
Flavobacterium columnare	strain=ATCC 23463	GCA_002530675.1	996	996	type	True	85.0193	792	1134	95	below_threshold
Flavobacterium columnare	strain=NBRC 100251	GCA_007990835.1	996	996	type	True	84.9821	791	1134	95	below_threshold
Flavobacterium oreochromis	strain=Costa Rica 04-02-TN	GCA_019565455.1	2906078	2906078	type	True	83.7142	804	1134	95	below_threshold
Flavobacterium terrae	strain=DSM 18829	GCA_900142035.1	415425	415425	type	True	78.1244	318	1134	95	below_threshold
Flavobacterium haoranii	strain=DSM 22807	GCA_900142055.1	683124	683124	type	True	77.6618	207	1134	95	below_threshold
Flavobacterium supellecticarium	strain=CC-CTC003	GCA_004801375.1	2565924	2565924	type	True	77.4541	104	1134	95	below_threshold
Flavobacterium soyae	strain=SCIV07	GCA_021245985.1	2903098	2903098	type	True	77.4032	141	1134	95	below_threshold
Flavobacterium sediminilitoris	strain=YSM-43	GCA_023008245.1	2024526	2024526	type	True	77.3776	242	1134	95	below_threshold
Flavobacterium celericrescens	strain=TWA-26	GCA_011392075.1	2709780	2709780	type	True	77.2626	199	1134	95	below_threshold
Flavobacterium tyrosinilyticum	strain=KCTC 42726	GCA_023656565.1	1658740	1658740	type	True	76.9403	154	1134	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:28:33,181] [INFO] DFAST Taxonomy check result was written to GCF_019565505.1_ASM1956550v1_genomic.fna/tc_result.tsv
[2024-01-24 13:28:33,182] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:28:33,182] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:28:33,182] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1e5a3ab0-bb20-4a1f-98c1-ad63cfef1a15/dqc_reference/checkm_data
[2024-01-24 13:28:33,184] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:28:33,222] [INFO] Task started: CheckM
[2024-01-24 13:28:33,222] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019565505.1_ASM1956550v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019565505.1_ASM1956550v1_genomic.fna/checkm_input GCF_019565505.1_ASM1956550v1_genomic.fna/checkm_result
[2024-01-24 13:29:06,953] [INFO] Task succeeded: CheckM
[2024-01-24 13:29:06,954] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:29:06,969] [INFO] ===== Completeness check finished =====
[2024-01-24 13:29:06,970] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:29:06,970] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019565505.1_ASM1956550v1_genomic.fna/markers.fasta)
[2024-01-24 13:29:06,971] [INFO] Task started: Blastn
[2024-01-24 13:29:06,971] [INFO] Running command: blastn -query GCF_019565505.1_ASM1956550v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1e5a3ab0-bb20-4a1f-98c1-ad63cfef1a15/dqc_reference/reference_markers_gtdb.fasta -out GCF_019565505.1_ASM1956550v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:29:07,967] [INFO] Task succeeded: Blastn
[2024-01-24 13:29:07,971] [INFO] Selected 10 target genomes.
[2024-01-24 13:29:07,971] [INFO] Target genome list was writen to GCF_019565505.1_ASM1956550v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:29:07,982] [INFO] Task started: fastANI
[2024-01-24 13:29:07,983] [INFO] Running command: fastANI --query /var/lib/cwl/stg9305ec7e-c5b9-47f0-a483-6f8ede2229b2/GCF_019565505.1_ASM1956550v1_genomic.fna.gz --refList GCF_019565505.1_ASM1956550v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019565505.1_ASM1956550v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:29:14,897] [INFO] Task succeeded: fastANI
[2024-01-24 13:29:14,907] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:29:14,907] [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_900290975.1	s__Flavobacterium columnare_D	99.0642	951	1134	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	98.86	98.55	0.90	0.88	3	conclusive
GCA_002217245.1	s__Flavobacterium columnare_A	85.3971	785	1134	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.08	98.79	0.92	0.89	11	-
GCF_002530675.1	s__Flavobacterium columnare	85.024	791	1134	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.33	99.02	0.96	0.93	39	-
GCF_002204895.1	s__Flavobacterium columnare_C	83.5968	776	1134	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.67	99.21	0.94	0.90	7	-
GCF_004959765.1	s__Flavobacterium sp004959765	78.65	305	1134	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000169355.1	s__Flavobacterium sp000169355	77.9941	197	1134	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	96.75	96.74	0.84	0.84	3	-
GCF_004801375.1	s__Flavobacterium sp004801375	77.4795	103	1134	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	77.2896	196	1134	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	77.2321	186	1134	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009764685.1	s__Flavobacterium sp009764685	76.7009	135	1134	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.83	99.83	0.96	0.96	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:29:14,911] [INFO] GTDB search result was written to GCF_019565505.1_ASM1956550v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:29:14,912] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:29:14,915] [INFO] DFAST_QC result json was written to GCF_019565505.1_ASM1956550v1_genomic.fna/dqc_result.json
[2024-01-24 13:29:14,915] [INFO] DFAST_QC completed!
[2024-01-24 13:29:14,915] [INFO] Total running time: 0h1m2s