[2024-01-24 12:14:35,891] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:14:35,893] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:14:35,893] [INFO] DQC Reference Directory: /var/lib/cwl/stg350a0fba-cc07-48cb-befc-7b523883ef20/dqc_reference
[2024-01-24 12:14:37,211] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:14:37,211] [INFO] Task started: Prodigal
[2024-01-24 12:14:37,212] [INFO] Running command: gunzip -c /var/lib/cwl/stgc6b26e3b-3715-4760-9101-dc0872feedfc/GCF_002072105.2_ASM207210v2_genomic.fna.gz | prodigal -d GCF_002072105.2_ASM207210v2_genomic.fna/cds.fna -a GCF_002072105.2_ASM207210v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:14:50,850] [INFO] Task succeeded: Prodigal
[2024-01-24 12:14:50,850] [INFO] Task started: HMMsearch
[2024-01-24 12:14:50,850] [INFO] Running command: hmmsearch --tblout GCF_002072105.2_ASM207210v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg350a0fba-cc07-48cb-befc-7b523883ef20/dqc_reference/reference_markers.hmm GCF_002072105.2_ASM207210v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:14:51,085] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:14:51,087] [INFO] Found 6/6 markers.
[2024-01-24 12:14:51,115] [INFO] Query marker FASTA was written to GCF_002072105.2_ASM207210v2_genomic.fna/markers.fasta
[2024-01-24 12:14:51,116] [INFO] Task started: Blastn
[2024-01-24 12:14:51,116] [INFO] Running command: blastn -query GCF_002072105.2_ASM207210v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg350a0fba-cc07-48cb-befc-7b523883ef20/dqc_reference/reference_markers.fasta -out GCF_002072105.2_ASM207210v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:14:51,777] [INFO] Task succeeded: Blastn
[2024-01-24 12:14:51,784] [INFO] Selected 28 target genomes.
[2024-01-24 12:14:51,784] [INFO] Target genome list was writen to GCF_002072105.2_ASM207210v2_genomic.fna/target_genomes.txt
[2024-01-24 12:14:51,794] [INFO] Task started: fastANI
[2024-01-24 12:14:51,794] [INFO] Running command: fastANI --query /var/lib/cwl/stgc6b26e3b-3715-4760-9101-dc0872feedfc/GCF_002072105.2_ASM207210v2_genomic.fna.gz --refList GCF_002072105.2_ASM207210v2_genomic.fna/target_genomes.txt --output GCF_002072105.2_ASM207210v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:15:08,480] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:08,481] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg350a0fba-cc07-48cb-befc-7b523883ef20/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:15:08,481] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg350a0fba-cc07-48cb-befc-7b523883ef20/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:15:08,500] [INFO] Found 23 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:15:08,500] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:15:08,501] [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
Croceivirga radicis	strain=HSG9	GCA_002072105.2	1929488	1929488	type	True	100.0	1188	1190	95	conclusive
Croceivirga lutea	strain=CSW06	GCA_014235875.1	1775167	1775167	type	True	77.9156	244	1190	95	below_threshold
Croceivirga lutea	strain=CGMCC 1.15761	GCA_014643615.1	1775167	1775167	type	True	77.8701	243	1190	95	below_threshold
Muricauda parva	strain=DSM 25885	GCA_900215465.1	1247520	1247520	type	True	76.9011	146	1190	95	below_threshold
Cellulophaga omnivescoria	strain=W5C	GCA_001999725.1	1888890	1888890	type	True	76.7123	173	1190	95	below_threshold
Muricauda onchidii	strain=XY-359	GCA_004804315.1	2562684	2562684	type	True	76.7058	127	1190	95	below_threshold
Muricauda zhangzhouensis	strain=DSM 25030	GCA_900106825.1	1073328	1073328	type	True	76.692	163	1190	95	below_threshold
Maribacter hydrothermalis	strain=T28	GCA_001673755.1	1836467	1836467	type	True	76.6539	163	1190	95	below_threshold
Maribacter vaceletii	strain=DSM 25230	GCA_003634105.1	1206816	1206816	type	True	76.6111	176	1190	95	below_threshold
Maribacter hydrothermalis	strain=T28	GCA_001913155.1	1836467	1836467	type	True	76.6063	161	1190	95	below_threshold
Cellulophaga lytica	strain=DSM 7489	GCA_000190595.1	979	979	type	True	76.4678	163	1190	95	below_threshold
Muricauda aurantiaca	strain=HME9304	GCA_003269425.1	1383885	1383885	type	True	76.4383	126	1190	95	below_threshold
Winogradskyella wandonensis	strain=CECT 8445	GCA_004346845.1	1442586	1442586	type	True	76.4102	65	1190	95	below_threshold
Joostella marina	strain=DSM 19592	GCA_000260115.1	453852	453852	type	True	76.3922	104	1190	95	below_threshold
Cellulophaga fucicola	strain=DSM 24786	GCA_900119145.1	76595	76595	type	True	76.36	170	1190	95	below_threshold
Aestuariivivens insulae	strain=AH-MY3	GCA_022662195.1	1621988	1621988	type	True	76.2924	74	1190	95	below_threshold
Cellulophaga tyrosinoxydans	strain=DSM 21164	GCA_900176415.1	504486	504486	type	True	76.2155	138	1190	95	below_threshold
Hanstruepera flava	strain=NBU2984	GCA_023634025.1	2930218	2930218	type	True	76.1934	64	1190	95	below_threshold
Aquimarina longa	strain=SW024	GCA_001401755.1	1080221	1080221	type	True	76.1016	72	1190	95	below_threshold
Flavobacterium filum	strain=DSM 17961	GCA_000425465.1	370974	370974	type	True	76.0715	52	1190	95	below_threshold
Haloflavibacter putidus	strain=PLHSN227	GCA_006546625.1	2576776	2576776	type	True	76.0207	61	1190	95	below_threshold
Seonamhaeicola maritimus	strain=1505	GCA_008056315.1	2591822	2591822	type	True	76.0187	83	1190	95	below_threshold
Hyunsoonleella ulvae	strain=HU1-3	GCA_016827605.1	2799948	2799948	type	True	76.013	75	1190	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:15:08,503] [INFO] DFAST Taxonomy check result was written to GCF_002072105.2_ASM207210v2_genomic.fna/tc_result.tsv
[2024-01-24 12:15:08,503] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:15:08,503] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:15:08,504] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg350a0fba-cc07-48cb-befc-7b523883ef20/dqc_reference/checkm_data
[2024-01-24 12:15:08,505] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:15:08,542] [INFO] Task started: CheckM
[2024-01-24 12:15:08,543] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002072105.2_ASM207210v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002072105.2_ASM207210v2_genomic.fna/checkm_input GCF_002072105.2_ASM207210v2_genomic.fna/checkm_result
[2024-01-24 12:15:49,541] [INFO] Task succeeded: CheckM
[2024-01-24 12:15:49,542] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:15:49,566] [INFO] ===== Completeness check finished =====
[2024-01-24 12:15:49,566] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:15:49,566] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002072105.2_ASM207210v2_genomic.fna/markers.fasta)
[2024-01-24 12:15:49,567] [INFO] Task started: Blastn
[2024-01-24 12:15:49,567] [INFO] Running command: blastn -query GCF_002072105.2_ASM207210v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg350a0fba-cc07-48cb-befc-7b523883ef20/dqc_reference/reference_markers_gtdb.fasta -out GCF_002072105.2_ASM207210v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:50,430] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:50,434] [INFO] Selected 21 target genomes.
[2024-01-24 12:15:50,434] [INFO] Target genome list was writen to GCF_002072105.2_ASM207210v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:15:50,458] [INFO] Task started: fastANI
[2024-01-24 12:15:50,458] [INFO] Running command: fastANI --query /var/lib/cwl/stgc6b26e3b-3715-4760-9101-dc0872feedfc/GCF_002072105.2_ASM207210v2_genomic.fna.gz --refList GCF_002072105.2_ASM207210v2_genomic.fna/target_genomes_gtdb.txt --output GCF_002072105.2_ASM207210v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:16:02,634] [INFO] Task succeeded: fastANI
[2024-01-24 12:16:02,649] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:16:02,649] [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_002072105.2	s__Croceivirga radicis	100.0	1187	1190	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Croceivirga	95.0	97.98	97.98	0.93	0.93	2	conclusive
GCF_005144745.1	s__Croceivirga sp005144745	84.7333	579	1190	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Croceivirga	95.0	97.80	97.80	0.93	0.93	2	-
GCF_014235875.1	s__Croceivirga lutea	77.9302	243	1190	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Croceivirga	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003149745.1	s__Muricauda koreensis	76.9132	140	1190	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102925.1	s__Muricauda zhangzhouensis	76.7417	160	1190	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001999725.1	s__Cellulophaga omnivescoria	76.7258	172	1190	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Cellulophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003634105.1	s__Maribacter_B vaceletii	76.6111	176	1190	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001913155.1	s__Maribacter hydrothermalis	76.5928	162	1190	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002813425.1	s__Cellulophaga sp002813425	76.5492	173	1190	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Cellulophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008040165.1	s__Muricauda hymeniacidonis	76.4902	150	1190	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000190595.1	s__Cellulophaga lytica	76.4894	161	1190	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Cellulophaga	95.0	99.01	98.71	0.94	0.93	6	-
GCA_013001145.1	s__Croceitalea sp013001145	76.4875	113	1190	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Croceitalea	95.0	99.20	99.17	0.87	0.85	5	-
GCF_004346845.1	s__Winogradskyella wandonensis	76.3807	66	1190	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900119145.1	s__Cellulophaga fucicola	76.36	170	1190	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Cellulophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009797025.1	s__Cellulophaga sp009797025	76.2166	158	1190	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Cellulophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018860745.1	s__Zobellia uliginosa_B	76.1875	134	1190	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Zobellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000425465.1	s__Flavobacterium filum	76.0715	52	1190	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008056315.1	s__Seonamhaeicola maritimus	76.0187	83	1190	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Seonamhaeicola	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:16:02,652] [INFO] GTDB search result was written to GCF_002072105.2_ASM207210v2_genomic.fna/result_gtdb.tsv
[2024-01-24 12:16:02,653] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:16:02,658] [INFO] DFAST_QC result json was written to GCF_002072105.2_ASM207210v2_genomic.fna/dqc_result.json
[2024-01-24 12:16:02,658] [INFO] DFAST_QC completed!
[2024-01-24 12:16:02,659] [INFO] Total running time: 0h1m27s