[2024-01-25 20:23:05,653] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:23:05,655] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:23:05,655] [INFO] DQC Reference Directory: /var/lib/cwl/stgc83b747c-5f29-4963-8764-7baf470662cf/dqc_reference
[2024-01-25 20:23:06,853] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:23:06,854] [INFO] Task started: Prodigal
[2024-01-25 20:23:06,854] [INFO] Running command: gunzip -c /var/lib/cwl/stg7edf2d6b-a83e-4634-b7dd-9c4fad88a121/GCF_015476115.1_ASM1547611v1_genomic.fna.gz | prodigal -d GCF_015476115.1_ASM1547611v1_genomic.fna/cds.fna -a GCF_015476115.1_ASM1547611v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:23:19,689] [INFO] Task succeeded: Prodigal
[2024-01-25 20:23:19,689] [INFO] Task started: HMMsearch
[2024-01-25 20:23:19,689] [INFO] Running command: hmmsearch --tblout GCF_015476115.1_ASM1547611v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc83b747c-5f29-4963-8764-7baf470662cf/dqc_reference/reference_markers.hmm GCF_015476115.1_ASM1547611v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:23:19,965] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:23:19,966] [INFO] Found 6/6 markers.
[2024-01-25 20:23:20,011] [INFO] Query marker FASTA was written to GCF_015476115.1_ASM1547611v1_genomic.fna/markers.fasta
[2024-01-25 20:23:20,012] [INFO] Task started: Blastn
[2024-01-25 20:23:20,012] [INFO] Running command: blastn -query GCF_015476115.1_ASM1547611v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc83b747c-5f29-4963-8764-7baf470662cf/dqc_reference/reference_markers.fasta -out GCF_015476115.1_ASM1547611v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:23:20,620] [INFO] Task succeeded: Blastn
[2024-01-25 20:23:20,623] [INFO] Selected 28 target genomes.
[2024-01-25 20:23:20,623] [INFO] Target genome list was writen to GCF_015476115.1_ASM1547611v1_genomic.fna/target_genomes.txt
[2024-01-25 20:23:20,657] [INFO] Task started: fastANI
[2024-01-25 20:23:20,657] [INFO] Running command: fastANI --query /var/lib/cwl/stg7edf2d6b-a83e-4634-b7dd-9c4fad88a121/GCF_015476115.1_ASM1547611v1_genomic.fna.gz --refList GCF_015476115.1_ASM1547611v1_genomic.fna/target_genomes.txt --output GCF_015476115.1_ASM1547611v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:23:37,318] [INFO] Task succeeded: fastANI
[2024-01-25 20:23:37,318] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc83b747c-5f29-4963-8764-7baf470662cf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:23:37,318] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc83b747c-5f29-4963-8764-7baf470662cf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:23:37,333] [INFO] Found 27 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:23:37,334] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:23:37,334] [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
Aegicerativicinus sediminis	strain=SM2-F	GCA_015476115.1	2893202	2893202	type	True	100.0	1362	1364	95	conclusive
Hanstruepera flava	strain=NBU2984	GCA_023634025.1	2930218	2930218	type	True	77.0625	104	1364	95	below_threshold
Mangrovimonas xylaniphaga	strain=ST2L12	GCA_001280435.1	1645915	1645915	type	True	76.9728	99	1364	95	below_threshold
Tenacibaculum jejuense	strain=type strain: KCTC 22618	GCA_900198195.1	584609	584609	type	True	76.8722	64	1364	95	below_threshold
Winogradskyella sediminis	strain=DSM 28134	GCA_003387355.1	1382466	1382466	type	True	76.8698	96	1364	95	below_threshold
Hanstruepera marina	strain=NBU2968	GCA_019880635.1	2873265	2873265	type	True	76.8044	114	1364	95	below_threshold
Gelidibacter sediminis	strain=DSM 28135	GCA_004364975.1	1608710	1608710	type	True	76.7784	82	1364	95	below_threshold
Winogradskyella forsetii	strain=HL857	GCA_013394595.1	2686077	2686077	type	True	76.7267	112	1364	95	below_threshold
Confluentibacter flavum	strain=3B	GCA_002843175.1	1909700	1909700	type	True	76.7191	102	1364	95	below_threshold
Flavobacterium indicum	strain=GPTSA100-9	GCA_000455605.1	312277	312277	type	True	76.7038	65	1364	95	below_threshold
Algibacter pacificus	strain=H164	GCA_008033385.1	2599389	2599389	type	True	76.6477	74	1364	95	below_threshold
Algibacter marinivivus	strain=ZY111	GCA_003143755.1	2100723	2100723	type	True	76.6423	108	1364	95	below_threshold
Tenacibaculum todarodis	strain=LPB0136	GCA_001889045.1	1850252	1850252	type	True	76.6251	54	1364	95	below_threshold
Winogradskyella flava	strain=KCTC 52348	GCA_014243395.1	1884876	1884876	type	True	76.6196	99	1364	95	below_threshold
Winogradskyella echinorum	strain=KCTC 22026	GCA_014284085.1	538189	538189	type	True	76.5991	115	1364	95	below_threshold
Winogradskyella echinorum	strain=KCTC 22026	GCA_014297365.1	538189	538189	type	True	76.5991	115	1364	95	below_threshold
Hyunsoonleella pacifica	strain=SW033	GCA_004310335.1	1080224	1080224	type	True	76.5893	90	1364	95	below_threshold
Hyunsoonleella pacifica	strain=CGMCC 1.11009	GCA_014636335.1	1080224	1080224	type	True	76.5893	90	1364	95	below_threshold
Seonamhaeicola maritimus	strain=1505	GCA_008056315.1	2591822	2591822	type	True	76.5754	113	1364	95	below_threshold
Hanstruepera neustonica	strain=JCM19743	GCA_002895005.1	1445657	1445657	type	True	76.5245	102	1364	95	below_threshold
Winogradskyella litoriviva	strain=KMM6491	GCA_013249065.1	1220182	1220182	type	True	76.509	113	1364	95	below_threshold
Algibacter mikhailovii	strain=KCTC 12710	GCA_014651495.1	425498	425498	type	True	76.4854	100	1364	95	below_threshold
Winogradskyella costae	strain=Z3138	GCA_013403865.1	2697008	2697008	type	True	76.3359	95	1364	95	below_threshold
Bizionia algoritergicola	strain=APA-1	GCA_008086165.1	291187	291187	type	True	76.2639	97	1364	95	below_threshold
Cellulophaga omnivescoria	strain=W5C	GCA_001999725.1	1888890	1888890	type	True	76.1756	75	1364	95	below_threshold
Winogradskyella vidalii	strain=HL634	GCA_013403955.1	2615024	2615024	type	True	76.1384	102	1364	95	below_threshold
Hyunsoonleella ulvae	strain=HU1-3	GCA_016827605.1	2799948	2799948	type	True	76.0631	101	1364	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:23:37,335] [INFO] DFAST Taxonomy check result was written to GCF_015476115.1_ASM1547611v1_genomic.fna/tc_result.tsv
[2024-01-25 20:23:37,336] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:23:37,336] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:23:37,336] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc83b747c-5f29-4963-8764-7baf470662cf/dqc_reference/checkm_data
[2024-01-25 20:23:37,337] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:23:37,378] [INFO] Task started: CheckM
[2024-01-25 20:23:37,378] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_015476115.1_ASM1547611v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_015476115.1_ASM1547611v1_genomic.fna/checkm_input GCF_015476115.1_ASM1547611v1_genomic.fna/checkm_result
[2024-01-25 20:24:16,126] [INFO] Task succeeded: CheckM
[2024-01-25 20:24:16,127] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:24:16,143] [INFO] ===== Completeness check finished =====
[2024-01-25 20:24:16,143] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:24:16,144] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_015476115.1_ASM1547611v1_genomic.fna/markers.fasta)
[2024-01-25 20:24:16,144] [INFO] Task started: Blastn
[2024-01-25 20:24:16,144] [INFO] Running command: blastn -query GCF_015476115.1_ASM1547611v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc83b747c-5f29-4963-8764-7baf470662cf/dqc_reference/reference_markers_gtdb.fasta -out GCF_015476115.1_ASM1547611v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:24:16,993] [INFO] Task succeeded: Blastn
[2024-01-25 20:24:16,995] [INFO] Selected 25 target genomes.
[2024-01-25 20:24:16,996] [INFO] Target genome list was writen to GCF_015476115.1_ASM1547611v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:24:17,027] [INFO] Task started: fastANI
[2024-01-25 20:24:17,027] [INFO] Running command: fastANI --query /var/lib/cwl/stg7edf2d6b-a83e-4634-b7dd-9c4fad88a121/GCF_015476115.1_ASM1547611v1_genomic.fna.gz --refList GCF_015476115.1_ASM1547611v1_genomic.fna/target_genomes_gtdb.txt --output GCF_015476115.1_ASM1547611v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:24:31,937] [INFO] Task succeeded: fastANI
[2024-01-25 20:24:31,953] [INFO] Found 25 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:24:31,953] [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
GCA_015476115.1	s__MAR-2010-188 sp015476115	100.0	1362	1364	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAR-2010-188	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001280435.1	s__Mangrovimonas_A xylaniphaga	76.9728	99	1364	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mangrovimonas_A	95.0	96.35	96.35	0.93	0.93	2	-
GCF_000455605.1	s__Flavobacterium indicum	76.8506	66	1364	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002163855.1	s__Winogradskyella sp002163855	76.8063	96	1364	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	99.88	99.82	0.99	0.99	3	-
GCF_003335675.1	s__Winogradskyella sp003335675	76.7531	100	1364	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013394595.1	s__Winogradskyella forsetii	76.7282	112	1364	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	97.73	96.59	0.91	0.86	4	-
GCA_002162765.1	s__MAAR01 sp002162765	76.7071	107	1364	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAAR01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003610635.1	s__Ichthyenterobacterium magnum	76.681	117	1364	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Ichthyenterobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013042245.1	s__Winogradskyella sp013042245	76.6742	76	1364	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	99.97	99.97	0.95	0.95	2	-
GCF_014651495.1	s__Algibacter_E mikhailovii	76.6498	100	1364	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013403915.1	s__Winogradskyella pacifica	76.6358	103	1364	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	97.90	97.90	0.94	0.94	2	-
GCF_003143755.1	s__Algibacter_B sp003143755	76.6201	109	1364	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014297365.1	s__Winogradskyella echinorum	76.6162	114	1364	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004310335.1	s__Jejuia pacifica	76.6117	89	1364	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Jejuia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_013249065.1	s__Winogradskyella litoriviva	76.5435	111	1364	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002895005.1	s__Hanstruepera neustonica	76.5431	101	1364	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Hanstruepera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008084905.1	s__Xanthomarina maritima	76.523	118	1364	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Xanthomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018860565.1	s__Winogradskyella psychrotolerans_B	76.382	124	1364	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011777505.1	s__CAU-1491 sp011777505	76.375	115	1364	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__CAU-1491	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001874335.1	s__MedPE-SWsnd-G2 sp001874335	76.3132	108	1364	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MedPE-SWsnd-G2	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018860245.1	s__Tamlana_A agarivorans_A	76.286	85	1364	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tamlana_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001874145.1	s__Lacinutrix sp001874145	76.2024	86	1364	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lacinutrix	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013151975.1	s__PRS1 sp013151975	76.1623	85	1364	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__PRS1	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004791695.1	s__Flavivirga rizhaonensis	76.0227	111	1364	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002414705.1	s__Algorimicrobium sp002414705	75.5688	99	1364	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algorimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:24:31,955] [INFO] GTDB search result was written to GCF_015476115.1_ASM1547611v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:24:31,956] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:24:31,978] [INFO] DFAST_QC result json was written to GCF_015476115.1_ASM1547611v1_genomic.fna/dqc_result.json
[2024-01-25 20:24:31,979] [INFO] DFAST_QC completed!
[2024-01-25 20:24:31,979] [INFO] Total running time: 0h1m26s