[2023-03-18 00:06:38,078] [INFO] DFAST_QC pipeline started.
[2023-03-18 00:06:38,078] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 00:06:38,078] [INFO] DQC Reference Directory: /var/lib/cwl/stg3835246c-a113-43a6-ab73-da9cd4de9c79/dqc_reference
[2023-03-18 00:06:39,186] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 00:06:39,186] [INFO] Task started: Prodigal
[2023-03-18 00:06:39,186] [INFO] Running command: cat /var/lib/cwl/stg258a9bc1-e78c-415b-889d-ebd4c8e4095c/OceanDNA-b7465.fa | prodigal -d OceanDNA-b7465/cds.fna -a OceanDNA-b7465/protein.faa -g 11 -q > /dev/null
[2023-03-18 00:06:48,918] [INFO] Task succeeded: Prodigal
[2023-03-18 00:06:48,919] [INFO] Task started: HMMsearch
[2023-03-18 00:06:48,919] [INFO] Running command: hmmsearch --tblout OceanDNA-b7465/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3835246c-a113-43a6-ab73-da9cd4de9c79/dqc_reference/reference_markers.hmm OceanDNA-b7465/protein.faa > /dev/null
[2023-03-18 00:06:49,078] [INFO] Task succeeded: HMMsearch
[2023-03-18 00:06:49,079] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg258a9bc1-e78c-415b-889d-ebd4c8e4095c/OceanDNA-b7465.fa]
[2023-03-18 00:06:49,093] [INFO] Query marker FASTA was written to OceanDNA-b7465/markers.fasta
[2023-03-18 00:06:49,095] [INFO] Task started: Blastn
[2023-03-18 00:06:49,095] [INFO] Running command: blastn -query OceanDNA-b7465/markers.fasta -db /var/lib/cwl/stg3835246c-a113-43a6-ab73-da9cd4de9c79/dqc_reference/reference_markers.fasta -out OceanDNA-b7465/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 00:06:49,635] [INFO] Task succeeded: Blastn
[2023-03-18 00:06:49,636] [INFO] Selected 27 target genomes.
[2023-03-18 00:06:49,636] [INFO] Target genome list was writen to OceanDNA-b7465/target_genomes.txt
[2023-03-18 00:06:49,650] [INFO] Task started: fastANI
[2023-03-18 00:06:49,650] [INFO] Running command: fastANI --query /var/lib/cwl/stg258a9bc1-e78c-415b-889d-ebd4c8e4095c/OceanDNA-b7465.fa --refList OceanDNA-b7465/target_genomes.txt --output OceanDNA-b7465/fastani_result.tsv --threads 1
[2023-03-18 00:07:04,752] [INFO] Task succeeded: fastANI
[2023-03-18 00:07:04,753] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3835246c-a113-43a6-ab73-da9cd4de9c79/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 00:07:04,753] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3835246c-a113-43a6-ab73-da9cd4de9c79/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 00:07:04,766] [INFO] Found 26 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 00:07:04,767] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 00:07:04,767] [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
Urechidicola croceus	strain=LPB0138	GCA_001761325.1	1850246	1850246	type	True	77.6954	183	450	95	below_threshold
Lutibacter oceani	strain=JCM30924	GCA_003426875.1	1853311	1853311	type	True	76.9734	122	450	95	below_threshold
Lutibacter agarilyticus	strain=DSM 29150	GCA_900188235.1	1109740	1109740	type	True	76.9273	124	450	95	below_threshold
Polaribacter butkevichii	strain=KCTC 12100	GCA_002954605.1	218490	218490	type	True	76.7769	98	450	95	below_threshold
Polaribacter glomeratus	strain=ACAM 171	GCA_007997115.1	102	102	type	True	76.75	87	450	95	below_threshold
Polaribacter atrinae	strain=KACC 17473	GCA_001640115.1	1333662	1333662	type	True	76.7083	87	450	95	below_threshold
Polaribacter septentrionalilitoris	strain=ANORD1	GCA_009832745.1	2494657	2494657	type	True	76.5939	79	450	95	below_threshold
Polaribacter cellanae	strain=SM13	GCA_017569185.1	2818493	2818493	type	True	76.5524	85	450	95	below_threshold
Polaribacter sejongensis	strain=KCTC 23670	GCA_002814075.1	985043	985043	type	True	76.5518	88	450	95	below_threshold
Polaribacter pectinis	strain=L12M9	GCA_014352875.1	2738844	2738844	type	True	76.5494	100	450	95	below_threshold
Tenacibaculum todarodis	strain=LPB0136	GCA_001889045.1	1850252	1850252	type	True	76.5468	91	450	95	below_threshold
Polaribacter batillariae	strain=G4M1	GCA_017498485.1	2808900	2808900	type	True	76.4945	86	450	95	below_threshold
Polaribacter undariae	strain=KCTC 42175	GCA_024918935.1	1574269	1574269	type	True	76.4716	96	450	95	below_threshold
Tenacibaculum haliotis	strain=KCTC 52419	GCA_025215075.1	1888914	1888914	type	True	76.4292	92	450	95	below_threshold
Polaribacter aestuariivivens	strain=DBTF-3	GCA_005885675.1	2304626	2304626	type	True	76.4118	106	450	95	below_threshold
Polaribacter haliotis	strain=KCTC 52418	GCA_014784055.1	1888915	1888915	type	True	76.4046	89	450	95	below_threshold
Polaribacter haliotis	strain=RA4-7	GCA_002201315.1	1888915	1888915	type	True	76.3528	88	450	95	below_threshold
Tenacibaculum aquimarinum	strain=K20-16	GCA_022478115.1	2910675	2910675	type	True	76.3078	100	450	95	below_threshold
Polaribacter dokdonensis	strain=KCTC 12392	GCA_024362345.1	326329	326329	type	True	76.2946	94	450	95	below_threshold
Aureivirga marina	strain=LMG 26721	GCA_015767265.1	1182451	1182451	type	True	76.2338	81	450	95	below_threshold
Tenacibaculum gallaicum	strain=DSM 18841	GCA_003387615.1	561505	561505	type	True	76.2062	74	450	95	below_threshold
Aureibaculum algae	strain=10Alg 115	GCA_006065315.1	2584122	2584122	type	True	76.202	68	450	95	below_threshold
Aureibaculum flavum	strain=A20	GCA_016406085.1	2795986	2795986	type	True	76.0751	62	450	95	below_threshold
Winogradskyella wichelsiae	strain=Z738	GCA_013403925.1	2697007	2697007	type	True	76.0352	63	450	95	below_threshold
Aureibaculum luteum	strain=SM1352	GCA_003449015.1	1548456	1548456	type	True	75.9293	63	450	95	below_threshold
Flavivirga rizhaonensis	strain=RZ03	GCA_004791695.1	2559571	2559571	type	True	75.6684	52	450	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 00:07:04,767] [INFO] DFAST Taxonomy check result was written to OceanDNA-b7465/tc_result.tsv
[2023-03-18 00:07:04,767] [INFO] ===== Taxonomy check completed =====
[2023-03-18 00:07:04,767] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 00:07:04,767] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3835246c-a113-43a6-ab73-da9cd4de9c79/dqc_reference/checkm_data
[2023-03-18 00:07:04,768] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 00:07:04,771] [INFO] Task started: CheckM
[2023-03-18 00:07:04,771] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b7465/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b7465/checkm_input OceanDNA-b7465/checkm_result
[2023-03-18 00:07:33,754] [INFO] Task succeeded: CheckM
[2023-03-18 00:07:33,755] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 62.50%
Contamintation: 5.21%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 00:07:33,757] [INFO] ===== Completeness check finished =====
[2023-03-18 00:07:33,757] [INFO] ===== Start GTDB Search =====
[2023-03-18 00:07:33,757] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b7465/markers.fasta)
[2023-03-18 00:07:33,757] [INFO] Task started: Blastn
[2023-03-18 00:07:33,757] [INFO] Running command: blastn -query OceanDNA-b7465/markers.fasta -db /var/lib/cwl/stg3835246c-a113-43a6-ab73-da9cd4de9c79/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b7465/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 00:07:34,531] [INFO] Task succeeded: Blastn
[2023-03-18 00:07:34,531] [INFO] Selected 29 target genomes.
[2023-03-18 00:07:34,532] [INFO] Target genome list was writen to OceanDNA-b7465/target_genomes_gtdb.txt
[2023-03-18 00:07:34,556] [INFO] Task started: fastANI
[2023-03-18 00:07:34,556] [INFO] Running command: fastANI --query /var/lib/cwl/stg258a9bc1-e78c-415b-889d-ebd4c8e4095c/OceanDNA-b7465.fa --refList OceanDNA-b7465/target_genomes_gtdb.txt --output OceanDNA-b7465/fastani_result_gtdb.tsv --threads 1
[2023-03-18 00:07:49,680] [INFO] Task succeeded: fastANI
[2023-03-18 00:07:49,696] [INFO] Found 29 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 00:07:49,697] [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_016744415.1	s__Urechidicola sp016744415	77.886	168	450	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Urechidicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002401215.1	s__Urechidicola sp002401215	77.7454	102	450	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Urechidicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001761325.1	s__Urechidicola croceus	77.7135	182	450	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Urechidicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001874265.1	s__Urechidicola sp001874265	77.7024	156	450	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Urechidicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002733665.1	s__Urechidicola sp002733665	77.6854	158	450	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Urechidicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905181865.1	s__Urechidicola croceus_A	77.5882	165	450	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Urechidicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905479835.1	s__Urechidicola sp905479835	77.2683	104	450	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Urechidicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013139515.1	s__Lutibacter sp013139515	77.1012	105	450	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013041805.1	s__Lutibacter sp013041805	77.0877	83	450	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	100.00	100.00	0.99	0.99	2	-
GCF_012524075.1	s__Lutibacter sp012524075	77.0494	108	450	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004195315.1	s__Lutibacter sp004195315	76.9889	74	450	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900188235.1	s__Lutibacter agarilyticus	76.9273	124	450	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019263805.1	s__Polaribacter sp011379025	76.7614	89	450	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	98.52	98.52	0.95	0.95	2	-
GCF_007827455.1	s__VISM01 sp007827455	76.7177	95	450	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__VISM01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001640115.1	s__Polaribacter atrinae	76.7083	87	450	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002163835.1	s__Polaribacter sp002163835	76.6529	106	450	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009796785.1	s__Polaribacter sp009796785	76.6327	92	450	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002163675.1	s__Polaribacter sp002163675	76.5862	108	450	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002814075.1	s__Polaribacter sejongensis	76.5518	88	450	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	97.48	97.48	0.89	0.89	2	-
GCF_014352875.1	s__Polaribacter sp014352875	76.5494	100	450	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000766795.1	s__Polaribacter sp000766795	76.5265	111	450	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017498485.1	s__Polaribacter sp017498485	76.4945	86	450	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002836595.1	s__Tenacibaculum sp002836595	76.449	105	450	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005885675.1	s__Polaribacter aestuariivivens	76.4118	106	450	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900105985.1	s__Tenacibaculum sp900105985	76.262	88	450	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	98.69	98.69	0.93	0.93	2	-
GCF_015767265.1	s__Aureivirga marina	76.2338	81	450	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aureivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_006065315.1	s__Aureibaculum sp006065315	76.202	68	450	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aureibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013403925.1	s__Winogradskyella wichelsiae	76.0352	63	450	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003516285.1	s__Lutibacter sp003516285	75.7403	50	450	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	97.80	97.80	0.83	0.83	2	-
--------------------------------------------------------------------------------
[2023-03-18 00:07:49,697] [INFO] GTDB search result was written to OceanDNA-b7465/result_gtdb.tsv
[2023-03-18 00:07:49,697] [INFO] ===== GTDB Search completed =====
[2023-03-18 00:07:49,700] [INFO] DFAST_QC result json was written to OceanDNA-b7465/dqc_result.json
[2023-03-18 00:07:49,700] [INFO] DFAST_QC completed!
[2023-03-18 00:07:49,700] [INFO] Total running time: 0h1m12s