[2024-01-24 13:18:40,969] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:18:40,970] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:18:40,971] [INFO] DQC Reference Directory: /var/lib/cwl/stg5c2d49d4-02fe-4d76-843e-04903c08b0d1/dqc_reference
[2024-01-24 13:18:42,348] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:18:42,349] [INFO] Task started: Prodigal
[2024-01-24 13:18:42,349] [INFO] Running command: gunzip -c /var/lib/cwl/stga8b1e862-1b97-479b-945b-e8e4e876cfd9/GCF_028743515.2_ASM2874351v2_genomic.fna.gz | prodigal -d GCF_028743515.2_ASM2874351v2_genomic.fna/cds.fna -a GCF_028743515.2_ASM2874351v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:18:53,868] [INFO] Task succeeded: Prodigal
[2024-01-24 13:18:53,868] [INFO] Task started: HMMsearch
[2024-01-24 13:18:53,868] [INFO] Running command: hmmsearch --tblout GCF_028743515.2_ASM2874351v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5c2d49d4-02fe-4d76-843e-04903c08b0d1/dqc_reference/reference_markers.hmm GCF_028743515.2_ASM2874351v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:18:54,164] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:18:54,165] [INFO] Found 6/6 markers.
[2024-01-24 13:18:54,192] [INFO] Query marker FASTA was written to GCF_028743515.2_ASM2874351v2_genomic.fna/markers.fasta
[2024-01-24 13:18:54,192] [INFO] Task started: Blastn
[2024-01-24 13:18:54,193] [INFO] Running command: blastn -query GCF_028743515.2_ASM2874351v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg5c2d49d4-02fe-4d76-843e-04903c08b0d1/dqc_reference/reference_markers.fasta -out GCF_028743515.2_ASM2874351v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:18:54,865] [INFO] Task succeeded: Blastn
[2024-01-24 13:18:54,869] [INFO] Selected 26 target genomes.
[2024-01-24 13:18:54,870] [INFO] Target genome list was writen to GCF_028743515.2_ASM2874351v2_genomic.fna/target_genomes.txt
[2024-01-24 13:18:54,904] [INFO] Task started: fastANI
[2024-01-24 13:18:54,905] [INFO] Running command: fastANI --query /var/lib/cwl/stga8b1e862-1b97-479b-945b-e8e4e876cfd9/GCF_028743515.2_ASM2874351v2_genomic.fna.gz --refList GCF_028743515.2_ASM2874351v2_genomic.fna/target_genomes.txt --output GCF_028743515.2_ASM2874351v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:19:09,721] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:09,721] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5c2d49d4-02fe-4d76-843e-04903c08b0d1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:19:09,722] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5c2d49d4-02fe-4d76-843e-04903c08b0d1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:19:09,742] [INFO] Found 24 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:19:09,742] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:19:09,743] [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
Imtechella halotolerans	strain=K1	GCA_000260835.1	1165090	1165090	type	True	99.9765	1004	1037	95	conclusive
Hanstruepera marina	strain=NBU2968	GCA_019880635.1	2873265	2873265	type	True	77.8188	56	1037	95	below_threshold
Abyssalbus ytuae	strain=MT3330	GCA_022807975.1	2926907	2926907	type	True	77.5733	85	1037	95	below_threshold
Joostella marina	strain=DSM 19592	GCA_000260115.1	453852	453852	type	True	77.4474	102	1037	95	below_threshold
Flavobacterium haoranii	strain=KCTC 23008	GCA_009363055.1	683124	683124	type	True	77.2429	83	1037	95	below_threshold
Aurantibacter crassamenti	strain=HG732	GCA_016811105.1	1837375	1837375	type	True	77.1779	77	1037	95	below_threshold
Zhouia amylolytica	strain=CGMCC 1.6114	GCA_900116365.1	376730	376730	type	True	77.147	83	1037	95	below_threshold
Algibacter alginicilyticus	strain=HZ22	GCA_001310225.1	1736674	1736674	type	True	77.1041	70	1037	95	below_threshold
Algibacter pacificus	strain=H164	GCA_008033385.1	2599389	2599389	type	True	76.9485	57	1037	95	below_threshold
Pontimicrobium aquaticum	strain=CAU 1491	GCA_005047595.1	2565367	2565367	type	True	76.9396	59	1037	95	below_threshold
Pustulibacterium marinum	strain=CGMCC 1.12333	GCA_900116665.1	1224947	1224947	type	True	76.8726	94	1037	95	below_threshold
Flavobacterium oreochromis	strain=Costa Rica 04-02-TN	GCA_019565455.1	2906078	2906078	type	True	76.8358	81	1037	95	below_threshold
Joostella atrarenae	strain=M1-2	GCA_021764745.1	679257	679257	type	True	76.8308	96	1037	95	below_threshold
Winogradskyella psychrotolerans	strain=RS-3	GCA_000427335.1	1344585	1344585	type	True	76.7754	53	1037	95	below_threshold
Flavobacterium haoranii	strain=DSM 22807	GCA_900142055.1	683124	683124	type	True	76.7479	81	1037	95	below_threshold
Tamlana haliotis	strain=B1N29	GCA_008806375.1	2614804	2614804	type	True	76.6131	62	1037	95	below_threshold
Flavobacterium jejuense	strain=EC11	GCA_006491595.2	1544455	1544455	type	True	76.5498	78	1037	95	below_threshold
Psychroserpens luteolus	strain=XSD401	GCA_021032705.1	2855840	2855840	type	True	76.4825	70	1037	95	below_threshold
Flavobacterium hiemivividum	strain=TSA-D2	GCA_004349145.1	2541734	2541734	type	True	76.4695	61	1037	95	below_threshold
Psychroserpens jangbogonensis	strain=PAMC 27130	GCA_000797465.1	1484460	1484460	type	True	76.3528	64	1037	95	below_threshold
Flavobacterium dankookense	strain=DSM 25687	GCA_004362665.1	706186	706186	type	True	76.3388	60	1037	95	below_threshold
Winogradskyella epiphytica	strain=KCTC 12220	GCA_014651315.1	262005	262005	type	True	76.1049	59	1037	95	below_threshold
Aquimarina muelleri	strain=KCTC 12285	GCA_014651355.1	279356	279356	type	True	76.0996	85	1037	95	below_threshold
Aquimarina muelleri	strain=DSM 19832	GCA_000430665.1	279356	279356	type	True	76.0527	84	1037	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:19:09,744] [INFO] DFAST Taxonomy check result was written to GCF_028743515.2_ASM2874351v2_genomic.fna/tc_result.tsv
[2024-01-24 13:19:09,745] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:19:09,745] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:19:09,745] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5c2d49d4-02fe-4d76-843e-04903c08b0d1/dqc_reference/checkm_data
[2024-01-24 13:19:09,747] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:19:09,788] [INFO] Task started: CheckM
[2024-01-24 13:19:09,788] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_028743515.2_ASM2874351v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_028743515.2_ASM2874351v2_genomic.fna/checkm_input GCF_028743515.2_ASM2874351v2_genomic.fna/checkm_result
[2024-01-24 13:19:49,855] [INFO] Task succeeded: CheckM
[2024-01-24 13:19:49,856] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:19:49,872] [INFO] ===== Completeness check finished =====
[2024-01-24 13:19:49,873] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:19:49,873] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_028743515.2_ASM2874351v2_genomic.fna/markers.fasta)
[2024-01-24 13:19:49,873] [INFO] Task started: Blastn
[2024-01-24 13:19:49,873] [INFO] Running command: blastn -query GCF_028743515.2_ASM2874351v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg5c2d49d4-02fe-4d76-843e-04903c08b0d1/dqc_reference/reference_markers_gtdb.fasta -out GCF_028743515.2_ASM2874351v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:50,831] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:50,836] [INFO] Selected 26 target genomes.
[2024-01-24 13:19:50,837] [INFO] Target genome list was writen to GCF_028743515.2_ASM2874351v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:19:50,958] [INFO] Task started: fastANI
[2024-01-24 13:19:50,958] [INFO] Running command: fastANI --query /var/lib/cwl/stga8b1e862-1b97-479b-945b-e8e4e876cfd9/GCF_028743515.2_ASM2874351v2_genomic.fna.gz --refList GCF_028743515.2_ASM2874351v2_genomic.fna/target_genomes_gtdb.txt --output GCF_028743515.2_ASM2874351v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:20:06,185] [INFO] Task succeeded: fastANI
[2024-01-24 13:20:06,207] [INFO] Found 23 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:20:06,207] [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_000260835.1	s__Imtechella halotolerans	99.9765	1004	1037	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Imtechella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_013391805.1	s__Galbibacter_A sp013391805	77.9476	71	1037	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Galbibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000941055.1	s__Siansivirga zeaxanthinifaciens	77.6251	63	1037	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Siansivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000260115.1	s__Joostella marina	77.2702	102	1037	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Joostella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009363055.1	s__Flavobacterium haoranii	77.2429	83	1037	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.98	99.98	1.00	1.00	2	-
GCF_900116365.1	s__Zhouia amylolytica	77.1425	84	1037	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Zhouia	95.0	98.62	98.62	0.95	0.95	2	-
GCF_001310225.1	s__Algibacter_A alginicilyticus	77.0518	69	1037	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019021925.1	s__Cellulophaga sp019021925	77.0306	77	1037	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Cellulophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016811105.1	s__Aurantibacter_A crassamenti	76.9913	76	1037	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aurantibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900116665.1	s__Pustulibacterium marinum	76.9277	96	1037	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Pustulibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000967805.1	s__Flavobacterium sp000967805	76.8382	99	1037	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016734785.1	s__Galbibacter_A mesophilus	76.7945	78	1037	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Galbibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114085.1	s__Flavobacterium guanonis	76.613	50	1037	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006491595.2	s__Flavobacterium jejuense	76.5209	77	1037	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011762485.1	s__Yeosuana marina	76.4702	65	1037	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Yeosuana	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000797465.1	s__Psychroserpens jangbogonensis	76.3528	64	1037	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroserpens	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004362665.1	s__Flavobacterium dankookense	76.3288	58	1037	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900176415.1	s__Cellulophaga tyrosinoxydans	76.2949	66	1037	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Cellulophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002120225.1	s__Tenacibaculum holothuriorum	76.2758	52	1037	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002204895.1	s__Flavobacterium columnare_C	76.109	77	1037	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.67	99.21	0.94	0.90	7	-
GCA_002746415.1	s__Saonia sp002746415	76.0821	68	1037	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Saonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000430665.1	s__Aquimarina muelleri	76.0527	84	1037	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquimarina	95.0	99.98	99.98	0.99	0.99	2	-
GCA_002364335.1	s__Winogradskyella sp002364335	75.7836	54	1037	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:20:06,209] [INFO] GTDB search result was written to GCF_028743515.2_ASM2874351v2_genomic.fna/result_gtdb.tsv
[2024-01-24 13:20:06,210] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:20:06,214] [INFO] DFAST_QC result json was written to GCF_028743515.2_ASM2874351v2_genomic.fna/dqc_result.json
[2024-01-24 13:20:06,215] [INFO] DFAST_QC completed!
[2024-01-24 13:20:06,215] [INFO] Total running time: 0h1m25s