[2024-01-24 11:51:24,968] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:51:24,971] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:51:24,972] [INFO] DQC Reference Directory: /var/lib/cwl/stgb05c289c-bb02-48a6-a477-3f834258b68a/dqc_reference
[2024-01-24 11:51:26,291] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:51:26,292] [INFO] Task started: Prodigal
[2024-01-24 11:51:26,292] [INFO] Running command: gunzip -c /var/lib/cwl/stgf5d8391b-e47e-4091-a0a7-f98fa2120f24/GCF_006381105.1_ASM638110v1_genomic.fna.gz | prodigal -d GCF_006381105.1_ASM638110v1_genomic.fna/cds.fna -a GCF_006381105.1_ASM638110v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:51:42,897] [INFO] Task succeeded: Prodigal
[2024-01-24 11:51:42,897] [INFO] Task started: HMMsearch
[2024-01-24 11:51:42,897] [INFO] Running command: hmmsearch --tblout GCF_006381105.1_ASM638110v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb05c289c-bb02-48a6-a477-3f834258b68a/dqc_reference/reference_markers.hmm GCF_006381105.1_ASM638110v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:51:43,186] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:51:43,188] [INFO] Found 6/6 markers.
[2024-01-24 11:51:43,226] [INFO] Query marker FASTA was written to GCF_006381105.1_ASM638110v1_genomic.fna/markers.fasta
[2024-01-24 11:51:43,226] [INFO] Task started: Blastn
[2024-01-24 11:51:43,227] [INFO] Running command: blastn -query GCF_006381105.1_ASM638110v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb05c289c-bb02-48a6-a477-3f834258b68a/dqc_reference/reference_markers.fasta -out GCF_006381105.1_ASM638110v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:51:43,892] [INFO] Task succeeded: Blastn
[2024-01-24 11:51:43,896] [INFO] Selected 25 target genomes.
[2024-01-24 11:51:43,896] [INFO] Target genome list was writen to GCF_006381105.1_ASM638110v1_genomic.fna/target_genomes.txt
[2024-01-24 11:51:43,907] [INFO] Task started: fastANI
[2024-01-24 11:51:43,907] [INFO] Running command: fastANI --query /var/lib/cwl/stgf5d8391b-e47e-4091-a0a7-f98fa2120f24/GCF_006381105.1_ASM638110v1_genomic.fna.gz --refList GCF_006381105.1_ASM638110v1_genomic.fna/target_genomes.txt --output GCF_006381105.1_ASM638110v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:52:00,135] [INFO] Task succeeded: fastANI
[2024-01-24 11:52:00,136] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb05c289c-bb02-48a6-a477-3f834258b68a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:52:00,136] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb05c289c-bb02-48a6-a477-3f834258b68a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:52:00,154] [INFO] Found 23 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:52:00,154] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:52:00,155] [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
Flavicella sediminum	strain=ALS 84	GCA_006381105.1	2585141	2585141	type	True	100.0	1487	1490	95	conclusive
Wenyingzhuangia aestuarii	strain=DSM 105044	GCA_011927765.1	1647582	1647582	type	True	78.7398	318	1490	95	below_threshold
Flavicella marina	strain=2A-7	GCA_009193215.1	1475951	1475951	type	True	78.7345	342	1490	95	below_threshold
Wenyingzhuangia fucanilytica	strain=CZ1127	GCA_001697185.1	1790137	1790137	type	True	77.8207	300	1490	95	below_threshold
Polaribacter butkevichii	strain=KCTC 12100	GCA_002954605.1	218490	218490	type	True	77.6853	266	1490	95	below_threshold
Wenyingzhuangia marina	strain=CGMCC 1.12162	GCA_014636515.1	1195760	1195760	type	True	77.5004	267	1490	95	below_threshold
Tenacibaculum todarodis	strain=LPB0136	GCA_001889045.1	1850252	1850252	type	True	77.4532	177	1490	95	below_threshold
Polaribacter atrinae	strain=KACC 17473	GCA_001640115.1	1333662	1333662	type	True	77.291	230	1490	95	below_threshold
Tenacibaculum aquimarinum	strain=K20-16	GCA_022478115.1	2910675	2910675	type	True	77.2874	182	1490	95	below_threshold
Polaribacter pectinis	strain=L12M9	GCA_014352875.1	2738844	2738844	type	True	77.1982	231	1490	95	below_threshold
Polaribacter sejongensis	strain=KCTC 23670	GCA_002814075.1	985043	985043	type	True	77.1425	270	1490	95	below_threshold
Polaribacter undariae	strain=KCTC 42175	GCA_024918935.1	1574269	1574269	type	True	77.1032	273	1490	95	below_threshold
Tenacibaculum finnmarkense	strain=TNO010	GCA_900239495.1	2781243	2781243	type	True	77.0613	152	1490	95	below_threshold
Polaribacter haliotis	strain=RA4-7	GCA_002201315.1	1888915	1888915	type	True	77.0422	208	1490	95	below_threshold
Polaribacter septentrionalilitoris	strain=ANORD1	GCA_009832745.1	2494657	2494657	type	True	77.0148	203	1490	95	below_threshold
Tenacibaculum haliotis	strain=KCTC 52419	GCA_025215075.1	1888914	1888914	type	True	76.8199	181	1490	95	below_threshold
Lutibacter maritimus	strain=DSM 24450	GCA_900116115.1	593133	593133	type	True	76.8104	182	1490	95	below_threshold
Tenacibaculum aiptasiae	strain=a4	GCA_008806755.1	426481	426481	type	True	76.5047	158	1490	95	below_threshold
Aureibaculum flavum	strain=A20	GCA_016406085.1	2795986	2795986	type	True	76.4499	154	1490	95	below_threshold
Aureibaculum luteum	strain=SM1352	GCA_003449015.1	1548456	1548456	type	True	76.3482	150	1490	95	below_threshold
Flavobacterium faecale	strain=WV33	GCA_003076455.1	1355330	1355330	type	True	75.8912	116	1490	95	below_threshold
Cellulophaga tyrosinoxydans	strain=DSM 21164	GCA_900176415.1	504486	504486	type	True	75.8872	107	1490	95	below_threshold
Mesonia oceanica	strain=ISS653	GCA_902499555.1	2687242	2687242	type	True	75.7775	79	1490	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:52:00,157] [INFO] DFAST Taxonomy check result was written to GCF_006381105.1_ASM638110v1_genomic.fna/tc_result.tsv
[2024-01-24 11:52:00,158] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:52:00,158] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:52:00,158] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb05c289c-bb02-48a6-a477-3f834258b68a/dqc_reference/checkm_data
[2024-01-24 11:52:00,160] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:52:00,209] [INFO] Task started: CheckM
[2024-01-24 11:52:00,209] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_006381105.1_ASM638110v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_006381105.1_ASM638110v1_genomic.fna/checkm_input GCF_006381105.1_ASM638110v1_genomic.fna/checkm_result
[2024-01-24 11:52:49,681] [INFO] Task succeeded: CheckM
[2024-01-24 11:52:49,683] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:52:49,706] [INFO] ===== Completeness check finished =====
[2024-01-24 11:52:49,707] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:52:49,707] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_006381105.1_ASM638110v1_genomic.fna/markers.fasta)
[2024-01-24 11:52:49,708] [INFO] Task started: Blastn
[2024-01-24 11:52:49,708] [INFO] Running command: blastn -query GCF_006381105.1_ASM638110v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb05c289c-bb02-48a6-a477-3f834258b68a/dqc_reference/reference_markers_gtdb.fasta -out GCF_006381105.1_ASM638110v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:52:50,605] [INFO] Task succeeded: Blastn
[2024-01-24 11:52:50,610] [INFO] Selected 23 target genomes.
[2024-01-24 11:52:50,610] [INFO] Target genome list was writen to GCF_006381105.1_ASM638110v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:52:50,650] [INFO] Task started: fastANI
[2024-01-24 11:52:50,650] [INFO] Running command: fastANI --query /var/lib/cwl/stgf5d8391b-e47e-4091-a0a7-f98fa2120f24/GCF_006381105.1_ASM638110v1_genomic.fna.gz --refList GCF_006381105.1_ASM638110v1_genomic.fna/target_genomes_gtdb.txt --output GCF_006381105.1_ASM638110v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:53:04,167] [INFO] Task succeeded: fastANI
[2024-01-24 11:53:04,185] [INFO] Found 23 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:53:04,185] [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_006381105.1	s__Flavicella sediminum	100.0	1487	1490	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavicella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_009193215.1	s__Flavicella marina	78.729	343	1490	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavicella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011927765.1	s__Wenyingzhuangia aestuarii	78.7087	317	1490	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Wenyingzhuangia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905479475.1	s__Flavicella sp905479475	78.2675	228	1490	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavicella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002954605.1	s__Polaribacter butkevichii	77.6836	266	1490	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002477565.1	s__Flavicella sp002477565	77.4365	133	1490	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavicella	95.0	98.32	98.32	0.91	0.91	2	-
GCF_001889045.1	s__Tenacibaculum_A todarodis	77.4298	180	1490	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019263805.1	s__Polaribacter sp011379025	77.3487	235	1490	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	98.52	98.52	0.95	0.95	2	-
GCF_001640115.1	s__Polaribacter atrinae	77.291	230	1490	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001761365.1	s__Polaribacter vadi	77.278	219	1490	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002814075.1	s__Polaribacter sejongensis	77.1519	270	1490	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	97.48	97.48	0.89	0.89	2	-
GCF_016858305.2	s__Polaribacter sp016858305	77.1474	274	1490	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009796825.1	s__Algibacter sp009796825	76.9656	184	1490	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900239505.1	s__Tenacibaculum piscium	76.9448	171	1490	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	99.64	99.33	0.97	0.95	5	-
GCF_900239345.1	s__Tenacibaculum dicentrarchi	76.9098	165	1490	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	98.61	97.94	0.93	0.91	10	-
GCF_900106075.1	s__Polaribacter sp900106075	76.7858	186	1490	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	98.66	98.45	0.96	0.92	5	-
GCA_002162765.1	s__MAAR01 sp002162765	76.6267	67	1490	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAAR01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016342705.1	s__Lutibacter sp016342705	76.6223	186	1490	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000981625.1	s__Polaribacter sp000981625	76.5242	134	1490	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008806755.1	s__Tenacibaculum aiptasiae	76.5053	158	1490	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002954685.1	s__Polaribacter porphyrae	76.4998	172	1490	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015665265.1	s__SCGC-AAA160-P02 sp015665265	76.3009	106	1490	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__SCGC-AAA160-P02	95.0	96.43	96.43	0.88	0.88	2	-
GCA_015488935.1	s__S010-17 sp015488935	75.7646	58	1490	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__S010-17	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:53:04,188] [INFO] GTDB search result was written to GCF_006381105.1_ASM638110v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:53:04,189] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:53:04,193] [INFO] DFAST_QC result json was written to GCF_006381105.1_ASM638110v1_genomic.fna/dqc_result.json
[2024-01-24 11:53:04,194] [INFO] DFAST_QC completed!
[2024-01-24 11:53:04,194] [INFO] Total running time: 0h1m39s