[2023-03-18 04:16:53,183] [INFO] DFAST_QC pipeline started.
[2023-03-18 04:16:53,183] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 04:16:53,184] [INFO] DQC Reference Directory: /var/lib/cwl/stg1cb52b13-e4bd-4d18-83c2-9cc6f616ae80/dqc_reference
[2023-03-18 04:16:54,279] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 04:16:54,279] [INFO] Task started: Prodigal
[2023-03-18 04:16:54,280] [INFO] Running command: cat /var/lib/cwl/stg6edf00dd-1948-47b0-9fba-3e2e6608cf65/OceanDNA-b20898.fa | prodigal -d OceanDNA-b20898/cds.fna -a OceanDNA-b20898/protein.faa -g 11 -q > /dev/null
[2023-03-18 04:17:22,488] [INFO] Task succeeded: Prodigal
[2023-03-18 04:17:22,488] [INFO] Task started: HMMsearch
[2023-03-18 04:17:22,488] [INFO] Running command: hmmsearch --tblout OceanDNA-b20898/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1cb52b13-e4bd-4d18-83c2-9cc6f616ae80/dqc_reference/reference_markers.hmm OceanDNA-b20898/protein.faa > /dev/null
[2023-03-18 04:17:22,771] [INFO] Task succeeded: HMMsearch
[2023-03-18 04:17:22,772] [INFO] Found 6/6 markers.
[2023-03-18 04:17:22,813] [INFO] Query marker FASTA was written to OceanDNA-b20898/markers.fasta
[2023-03-18 04:17:22,814] [INFO] Task started: Blastn
[2023-03-18 04:17:22,814] [INFO] Running command: blastn -query OceanDNA-b20898/markers.fasta -db /var/lib/cwl/stg1cb52b13-e4bd-4d18-83c2-9cc6f616ae80/dqc_reference/reference_markers.fasta -out OceanDNA-b20898/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 04:17:23,516] [INFO] Task succeeded: Blastn
[2023-03-18 04:17:23,517] [INFO] Selected 39 target genomes.
[2023-03-18 04:17:23,517] [INFO] Target genome list was writen to OceanDNA-b20898/target_genomes.txt
[2023-03-18 04:17:23,586] [INFO] Task started: fastANI
[2023-03-18 04:17:23,586] [INFO] Running command: fastANI --query /var/lib/cwl/stg6edf00dd-1948-47b0-9fba-3e2e6608cf65/OceanDNA-b20898.fa --refList OceanDNA-b20898/target_genomes.txt --output OceanDNA-b20898/fastani_result.tsv --threads 1
[2023-03-18 04:17:57,750] [INFO] Task succeeded: fastANI
[2023-03-18 04:17:57,751] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1cb52b13-e4bd-4d18-83c2-9cc6f616ae80/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 04:17:57,751] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1cb52b13-e4bd-4d18-83c2-9cc6f616ae80/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 04:17:57,767] [INFO] Found 31 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 04:17:57,767] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 04:17:57,767] [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
Stigmatella hybrida	strain=DSM 14722	GCA_020103775.1	394097	394097	type	True	75.2276	152	1447	95	below_threshold
Stigmatella aurantiaca	strain=DSM 17044	GCA_900109545.1	41	41	type	True	75.1978	155	1447	95	below_threshold
Geomonas propionica	strain=Red259	GCA_016458235.1	2798582	2798582	type	True	75.1563	50	1447	95	below_threshold
Geomonas anaerohicana	strain=Red421	GCA_016458305.1	2798583	2798583	type	True	75.1323	60	1447	95	below_threshold
Stigmatella erecta	strain=DSM 16858	GCA_900111745.1	83460	83460	type	True	75.1035	170	1447	95	below_threshold
Anaeromyxobacter dehalogenans	strain=2CP-1	GCA_000022145.1	161493	161493	type	True	75.088	281	1447	95	below_threshold
Myxococcus stipitatus	strain=DSM 14675	GCA_000331735.1	83455	83455	neotype	True	75.0858	185	1447	95	below_threshold
Geomonas paludis	strain=Red736	GCA_014193585.1	2740185	2740185	type	True	75.0844	56	1447	95	below_threshold
Nannocystis exedens	strain=DSM 71	GCA_002343915.1	54	54	type	True	75.0803	450	1447	95	below_threshold
Nannocystis exedens	strain=ATCC 25963	GCA_900112715.1	54	54	type	True	75.0678	434	1447	95	below_threshold
Myxococcus fulvus	strain=DSM 16525	GCA_900111765.1	33	33	type	True	75.027	237	1447	95	below_threshold
Geomonas azotofigens	strain=Red51	GCA_018919395.1	2843196	2843196	type	True	74.9969	65	1447	95	below_threshold
Polyangium aurulentum	strain=SDU3-1	GCA_005144635.2	2567896	2567896	type	True	74.9481	325	1447	95	below_threshold
Corallococcus sicarius	strain=CA040B	GCA_003611735.1	2316726	2316726	type	True	74.9125	199	1447	95	below_threshold
Tistlia consotensis	strain=USBA 355	GCA_900177295.1	1321365	1321365	type	True	74.8854	272	1447	95	below_threshold
Thiohalocapsa marina	strain=DSM 19078	GCA_008632335.1	424902	424902	type	True	74.8846	64	1447	95	below_threshold
Tistlia consotensis	strain=DSM 21585	GCA_900188055.1	1321365	1321365	type	True	74.8807	275	1447	95	below_threshold
Halorhodospira halophila	strain=SL1	GCA_000015585.1	1053	1053	suspected-type	True	74.8718	58	1447	95	below_threshold
Ramlibacter algicola	strain=CrO1	GCA_016641735.1	2795217	2795217	type	True	74.8555	111	1447	95	below_threshold
Cellulomonas rhizosphaerae	strain=NEAU-TCZ24	GCA_003470205.1	2293719	2293719	type	True	74.8411	140	1447	95	below_threshold
Rhodoplanes roseus	strain=DSM 5909	GCA_003258865.1	29409	29409	type	True	74.7953	150	1447	95	below_threshold
Rhodoplanes piscinae	strain=DSM 19946	GCA_003258855.1	444923	444923	type	True	74.7557	144	1447	95	below_threshold
Propionibacterium australiense	strain=NML98A072	GCA_003666605.1	119981	119981	type	True	74.7499	57	1447	95	below_threshold
Pseudonocardia broussonetiae	strain=Gen 01	GCA_013155125.1	2736640	2736640	type	True	74.7377	286	1447	95	below_threshold
Pseudomonas ekonensis	strain=COR58	GCA_019145435.1	2842353	2842353	type	True	74.7344	91	1447	95	below_threshold
Conexibacter arvalis	strain=DSM 23288	GCA_014199525.1	912552	912552	type	True	74.7145	272	1447	95	below_threshold
Jiangella asiatica	strain=5K138	GCA_004349065.1	2530372	2530372	type	True	74.6806	192	1447	95	below_threshold
Pseudomonas sessilinigenes	strain=CMR12a	GCA_003850565.1	658629	658629	type	True	74.6795	53	1447	95	below_threshold
Protaetiibacter intestinalis	strain=2DFWR-13	GCA_003627075.1	2419774	2419774	type	True	74.6785	120	1447	95	below_threshold
Pseudomonas sessilinigenes	strain=CMR12a	GCA_019139855.1	658629	658629	type	True	74.6684	56	1447	95	below_threshold
Agrococcus lahaulensis	strain=DSM 17612	GCA_000425105.1	341722	341722	type	True	74.6672	141	1447	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 04:17:57,768] [INFO] DFAST Taxonomy check result was written to OceanDNA-b20898/tc_result.tsv
[2023-03-18 04:17:57,768] [INFO] ===== Taxonomy check completed =====
[2023-03-18 04:17:57,768] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 04:17:57,768] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1cb52b13-e4bd-4d18-83c2-9cc6f616ae80/dqc_reference/checkm_data
[2023-03-18 04:17:57,769] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 04:17:57,852] [INFO] Task started: CheckM
[2023-03-18 04:17:57,853] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b20898/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b20898/checkm_input OceanDNA-b20898/checkm_result
[2023-03-18 04:19:05,391] [INFO] Task succeeded: CheckM
[2023-03-18 04:19:05,391] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 88.89%
Contamintation: 0.90%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 04:19:05,395] [INFO] ===== Completeness check finished =====
[2023-03-18 04:19:05,395] [INFO] ===== Start GTDB Search =====
[2023-03-18 04:19:05,395] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b20898/markers.fasta)
[2023-03-18 04:19:05,397] [INFO] Task started: Blastn
[2023-03-18 04:19:05,397] [INFO] Running command: blastn -query OceanDNA-b20898/markers.fasta -db /var/lib/cwl/stg1cb52b13-e4bd-4d18-83c2-9cc6f616ae80/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b20898/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 04:19:06,581] [INFO] Task succeeded: Blastn
[2023-03-18 04:19:06,582] [INFO] Selected 39 target genomes.
[2023-03-18 04:19:06,582] [INFO] Target genome list was writen to OceanDNA-b20898/target_genomes_gtdb.txt
[2023-03-18 04:19:06,703] [INFO] Task started: fastANI
[2023-03-18 04:19:06,704] [INFO] Running command: fastANI --query /var/lib/cwl/stg6edf00dd-1948-47b0-9fba-3e2e6608cf65/OceanDNA-b20898.fa --refList OceanDNA-b20898/target_genomes_gtdb.txt --output OceanDNA-b20898/fastani_result_gtdb.tsv --threads 1
[2023-03-18 04:19:43,357] [INFO] Task succeeded: fastANI
[2023-03-18 04:19:43,374] [INFO] Found 32 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 04:19:43,375] [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_009692505.1	s__SHZC01 sp009692505	76.2722	197	1447	d__Bacteria;p__Myxococcota;c__Bradymonadia;o__UBA7976;f__UBA1532;g__SHZC01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903847385.1	s__CAINDO01 sp903847385	76.2639	463	1447	d__Bacteria;p__Myxococcota;c__Bradymonadia;o__UBA7976;f__UBA1532;g__CAINDO01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018813065.1	s__JAHJCH01 sp018813065	75.7571	206	1447	d__Bacteria;p__Myxococcota;c__Bradymonadia;o__UBA7976;f__UBA1532;g__JAHJCH01	95.0	99.74	99.61	0.91	0.89	3	-
GCA_017644045.1	s__UBA1660 sp017644045	75.1672	250	1447	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__SG8-38;g__UBA1660	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016458235.1	s__Geomonas propionica	75.1563	50	1447	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Geobacteraceae;g__Geomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016719945.1	s__CAITIQ01 sp016719945	75.1298	294	1447	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__CAITIQ01	95.0	99.43	99.43	0.95	0.95	2	-
GCF_000022145.1	s__Anaeromyxobacter dehalogenans	75.1106	270	1447	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Anaeromyxobacteraceae;g__Anaeromyxobacter	95.0	97.16	97.16	0.92	0.92	2	-
GCF_016458305.1	s__Geomonas anaerohicana	75.1033	59	1447	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Geobacteraceae;g__Geomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002716585.1	s__GCA-2716585 sp002716585	75.0759	130	1447	d__Bacteria;p__Myxococcota;c__Bradymonadia;o__Bradymonadales;f__GCA-2716585;g__GCA-2716585	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900696455.1	s__UBA2376 sp900696455	75.0706	444	1447	d__Bacteria;p__Myxococcota;c__Polyangia;o__Haliangiales;f__Haliangiaceae;g__UBA2376	95.0	98.40	97.29	0.91	0.90	3	-
GCF_012933655.1	s__Myxococcus fallax	75.0659	272	1447	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Myxococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005888115.1	s__40CM-4-68-19 sp005888115	75.0336	121	1447	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__40CM-4-68-19;g__40CM-4-68-19	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000964525.1	s__Anaeromyxobacter sp000964525	75.0322	241	1447	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Anaeromyxobacteraceae;g__Anaeromyxobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010894405.1	s__Myxococcus caerfyrddinensis	75.0076	257	1447	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Myxococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017301735.1	s__Myxococcus sp017301735	74.9854	226	1447	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Myxococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005144635.1	s__Polyangium sp005144635	74.9435	326	1447	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__Polyangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009649845.1	s__Polyangium spumosum	74.9124	303	1447	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__Polyangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014842975.1	s__Rhodanobacter sp014842975	74.8532	95	1447	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Rhodanobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016793325.1	s__Ga0077539 sp016793325	74.845	227	1447	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Ga0077539;g__Ga0077539	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014843005.1	s__Rhodanobacter sp014843005	74.8402	77	1447	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Rhodanobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005779305.1	s__UBA2376 sp005779305	74.8204	304	1447	d__Bacteria;p__Myxococcota;c__Polyangia;o__Haliangiales;f__Haliangiaceae;g__UBA2376	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018240325.1	s__Rubrivivax sp018240325	74.8029	172	1447	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rubrivivax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002283555.1	s__Rubrivirga sp002283555	74.7761	145	1447	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Rhodothermales;f__Rubricoccaceae;g__Rubrivirga	95.0	98.32	98.29	0.93	0.92	3	-
GCF_005144585.1	s__Polyangium fumosum	74.768	277	1447	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__Polyangium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003243275.1	s__Protaetiibacter sp003243275	74.7488	102	1447	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Protaetiibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000263855.1	s__Pseudomonas_E sp000263855	74.7474	61	1447	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002283365.1	s__Rubrivirga marina	74.7342	155	1447	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Rhodothermales;f__Rubricoccaceae;g__Rubrivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002428705.1	s__UBA6079 sp002428705	74.7302	100	1447	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__UBA6079	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007679035.1	s__Agrococcus jejuensis_A	74.7047	175	1447	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agrococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004357765.1	s__Pseudomonas_E putida_U	74.7041	51	1447	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.43	99.43	0.90	0.90	2	-
GCF_003627075.1	s__Protaetiibacter intestinalis	74.6778	120	1447	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Protaetiibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001547895.1	s__Pseudomonas_E sp001547895	74.6091	84	1447	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.12	98.88	0.95	0.94	4	-
--------------------------------------------------------------------------------
[2023-03-18 04:19:43,375] [INFO] GTDB search result was written to OceanDNA-b20898/result_gtdb.tsv
[2023-03-18 04:19:43,375] [INFO] ===== GTDB Search completed =====
[2023-03-18 04:19:43,378] [INFO] DFAST_QC result json was written to OceanDNA-b20898/dqc_result.json
[2023-03-18 04:19:43,378] [INFO] DFAST_QC completed!
[2023-03-18 04:19:43,378] [INFO] Total running time: 0h2m50s