[2024-01-24 13:12:34,528] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:12:34,530] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:12:34,530] [INFO] DQC Reference Directory: /var/lib/cwl/stg3fc45b46-6da4-4458-9128-f9f0e73128a5/dqc_reference
[2024-01-24 13:12:35,757] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:12:35,758] [INFO] Task started: Prodigal
[2024-01-24 13:12:35,758] [INFO] Running command: gunzip -c /var/lib/cwl/stg352911d6-193a-40d8-af5d-abcfe9a9e004/GCF_900445655.1_51184_H02_genomic.fna.gz | prodigal -d GCF_900445655.1_51184_H02_genomic.fna/cds.fna -a GCF_900445655.1_51184_H02_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:12:45,065] [INFO] Task succeeded: Prodigal
[2024-01-24 13:12:45,066] [INFO] Task started: HMMsearch
[2024-01-24 13:12:45,066] [INFO] Running command: hmmsearch --tblout GCF_900445655.1_51184_H02_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3fc45b46-6da4-4458-9128-f9f0e73128a5/dqc_reference/reference_markers.hmm GCF_900445655.1_51184_H02_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:12:45,338] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:12:45,339] [INFO] Found 6/6 markers.
[2024-01-24 13:12:45,362] [INFO] Query marker FASTA was written to GCF_900445655.1_51184_H02_genomic.fna/markers.fasta
[2024-01-24 13:12:45,362] [INFO] Task started: Blastn
[2024-01-24 13:12:45,362] [INFO] Running command: blastn -query GCF_900445655.1_51184_H02_genomic.fna/markers.fasta -db /var/lib/cwl/stg3fc45b46-6da4-4458-9128-f9f0e73128a5/dqc_reference/reference_markers.fasta -out GCF_900445655.1_51184_H02_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:12:46,044] [INFO] Task succeeded: Blastn
[2024-01-24 13:12:46,047] [INFO] Selected 20 target genomes.
[2024-01-24 13:12:46,048] [INFO] Target genome list was writen to GCF_900445655.1_51184_H02_genomic.fna/target_genomes.txt
[2024-01-24 13:12:46,082] [INFO] Task started: fastANI
[2024-01-24 13:12:46,082] [INFO] Running command: fastANI --query /var/lib/cwl/stg352911d6-193a-40d8-af5d-abcfe9a9e004/GCF_900445655.1_51184_H02_genomic.fna.gz --refList GCF_900445655.1_51184_H02_genomic.fna/target_genomes.txt --output GCF_900445655.1_51184_H02_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:12:59,110] [INFO] Task succeeded: fastANI
[2024-01-24 13:12:59,111] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3fc45b46-6da4-4458-9128-f9f0e73128a5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:12:59,111] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3fc45b46-6da4-4458-9128-f9f0e73128a5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:12:59,126] [INFO] Found 18 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:12:59,127] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:12:59,127] [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
Bergeyella zoohelcum	strain=NCTC11660	GCA_900445655.1	1015	1015	type	True	100.0	775	776	95	conclusive
Bergeyella zoohelcum	strain=ATCC 43767	GCA_000301075.1	1015	1015	type	True	99.9515	766	776	95	conclusive
Epilithonimonas vandammei	strain=F5649	GCA_003860525.1	2487072	2487072	type	True	78.4186	59	776	95	below_threshold
Chryseobacterium ginsenosidimutans	strain=THG 15	GCA_024807225.1	687846	687846	type	True	78.3015	78	776	95	below_threshold
Chryseobacterium gleum	strain=FDAARGOS_1103	GCA_016766875.1	250	250	type	True	78.2233	81	776	95	below_threshold
Kaistella carnis	strain=G0081	GCA_003860585.1	1241979	1241979	type	True	77.9119	62	776	95	below_threshold
Amniculibacterium aquaticum	strain=KYPW7	GCA_003852705.1	2479858	2479858	type	True	77.377	89	776	95	below_threshold
Chryseobacterium gleum	strain=ATCC 35910	GCA_000143785.1	250	250	type	True	77.3617	77	776	95	below_threshold
Cloacibacterium rupense	strain=CGMCC 1.7656	GCA_014645495.1	517423	517423	type	True	77.2049	85	776	95	below_threshold
Chryseobacterium tagetis	strain=RG1	GCA_016735585.2	2801334	2801334	type	True	77.1317	74	776	95	below_threshold
Chryseobacterium binzhouense	strain=LM2	GCA_007474545.1	2593646	2593646	type	True	77.106	76	776	95	below_threshold
Chryseobacterium indologenes	strain=NBRC 14944	GCA_000520835.1	253	253	type	True	77.0827	75	776	95	below_threshold
Chryseobacterium piscicola	strain=DSM 21068	GCA_002943675.1	551459	551459	type	True	77.0246	80	776	95	below_threshold
Chryseobacterium gwangjuense	strain=THG-A18	GCA_021311115.1	1069980	1069980	type	True	76.9893	85	776	95	below_threshold
Chryseobacterium piscicola	strain=DSM 21068	GCA_900156685.1	551459	551459	type	True	76.9858	78	776	95	below_threshold
Chryseobacterium aquaticum subsp. greenlandense	strain=UMB34	GCA_001507325.1	345663	452084	type	True	76.9	78	776	95	below_threshold
Chryseobacterium aquaticum	strain=KCTC 12483	GCA_001420285.1	452084	452084	type	True	76.6366	83	776	95	below_threshold
Chryseobacterium piscium	strain=CCUG 51923	GCA_003385415.1	333702	333702	type	True	76.6268	84	776	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:12:59,136] [INFO] DFAST Taxonomy check result was written to GCF_900445655.1_51184_H02_genomic.fna/tc_result.tsv
[2024-01-24 13:12:59,137] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:12:59,138] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:12:59,138] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3fc45b46-6da4-4458-9128-f9f0e73128a5/dqc_reference/checkm_data
[2024-01-24 13:12:59,139] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:12:59,169] [INFO] Task started: CheckM
[2024-01-24 13:12:59,170] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900445655.1_51184_H02_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900445655.1_51184_H02_genomic.fna/checkm_input GCF_900445655.1_51184_H02_genomic.fna/checkm_result
[2024-01-24 13:13:32,667] [INFO] Task succeeded: CheckM
[2024-01-24 13:13:32,668] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:13:32,689] [INFO] ===== Completeness check finished =====
[2024-01-24 13:13:32,689] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:13:32,689] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900445655.1_51184_H02_genomic.fna/markers.fasta)
[2024-01-24 13:13:32,690] [INFO] Task started: Blastn
[2024-01-24 13:13:32,690] [INFO] Running command: blastn -query GCF_900445655.1_51184_H02_genomic.fna/markers.fasta -db /var/lib/cwl/stg3fc45b46-6da4-4458-9128-f9f0e73128a5/dqc_reference/reference_markers_gtdb.fasta -out GCF_900445655.1_51184_H02_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:13:33,522] [INFO] Task succeeded: Blastn
[2024-01-24 13:13:33,526] [INFO] Selected 28 target genomes.
[2024-01-24 13:13:33,526] [INFO] Target genome list was writen to GCF_900445655.1_51184_H02_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:13:33,584] [INFO] Task started: fastANI
[2024-01-24 13:13:33,584] [INFO] Running command: fastANI --query /var/lib/cwl/stg352911d6-193a-40d8-af5d-abcfe9a9e004/GCF_900445655.1_51184_H02_genomic.fna.gz --refList GCF_900445655.1_51184_H02_genomic.fna/target_genomes_gtdb.txt --output GCF_900445655.1_51184_H02_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:13:48,400] [INFO] Task succeeded: fastANI
[2024-01-24 13:13:48,418] [INFO] Found 24 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:13:48,419] [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_000301075.1	s__Bergeyella zoohelcum	99.9515	766	776	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Bergeyella	95.0	97.89	97.05	0.90	0.85	5	conclusive
GCF_003860525.1	s__Epilithonimonas vandammei	78.5642	60	776	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Epilithonimonas	95.0	96.28	95.86	0.86	0.84	4	-
GCF_006088815.1	s__Elizabethkingia sp006088815	78.1786	78	776	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Elizabethkingia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001403755.1	s__Kaistella senegalense	78.1436	67	776	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Kaistella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016025055.1	s__Chryseobacterium indologenes	78.0956	82	776	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	99.10	98.65	0.93	0.89	60	-
GCF_003669035.1	s__Chryseobacterium sp003669035	77.8426	71	776	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003614945.1	s__Bergeyella_A cardium	77.7179	85	776	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Bergeyella_A	95.0	98.84	98.84	0.96	0.96	2	-
GCF_003709475.1	s__Chryseobacterium nematophagum_A	77.6902	100	776	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	95.82	95.82	0.85	0.85	2	-
GCF_003730015.1	s__Epilithonimonas hominis	77.6857	63	776	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Epilithonimonas	95.0	96.55	96.42	0.86	0.85	3	-
GCF_003852705.1	s__Amniculibacterium aquaticum	77.377	89	776	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Amniculibacterium	95.0	98.89	98.89	0.92	0.92	2	-
GCF_009663465.1	s__Riemerella anatipestifer_C	77.3202	83	776	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Riemerella	95.0	96.04	95.95	0.82	0.80	3	-
GCF_001425355.1	s__Chryseobacterium sp001425355	77.234	77	776	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009670965.1	s__Riemerella anatipestifer_B	77.1469	88	776	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Riemerella	95.0	95.18	95.18	0.86	0.86	2	-
GCA_001898255.1	s__Kaistella sp001898255	77.0071	58	776	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Kaistella	95.0	99.97	99.97	0.99	0.99	2	-
GCF_900156685.1	s__Chryseobacterium piscicola	76.9858	78	776	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	99.99	99.99	1.00	1.00	2	-
GCF_002979455.1	s__Chryseobacterium sp002979455	76.9752	74	776	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000813825.1	s__Chryseobacterium taiwanense	76.9642	76	776	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011752975.1	s__Chryseobacterium sp011752975	76.9578	73	776	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000799455.1	s__Chryseobacterium sp000799455	76.957	86	776	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001507325.1	s__Chryseobacterium greenlandense	76.9	78	776	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	96.6446	N/A	N/A	N/A	N/A	1	-
GCF_012952015.1	s__Chryseobacterium aquaticum_A	76.6618	80	776	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	96.4843	100.00	100.00	1.00	1.00	2	-
GCF_001420285.1	s__Chryseobacterium aquaticum	76.6366	83	776	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	96.6446	96.87	96.87	0.89	0.89	2	-
GCF_003385415.1	s__Chryseobacterium piscium	76.6268	84	776	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	96.69	96.60	0.88	0.87	3	-
GCA_002439165.1	s__Chryseobacterium indologenes_E	76.3189	74	776	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:13:48,421] [INFO] GTDB search result was written to GCF_900445655.1_51184_H02_genomic.fna/result_gtdb.tsv
[2024-01-24 13:13:48,422] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:13:48,429] [INFO] DFAST_QC result json was written to GCF_900445655.1_51184_H02_genomic.fna/dqc_result.json
[2024-01-24 13:13:48,430] [INFO] DFAST_QC completed!
[2024-01-24 13:13:48,430] [INFO] Total running time: 0h1m14s