[2023-03-16 21:45:13,523] [INFO] DFAST_QC pipeline started.
[2023-03-16 21:45:13,523] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 21:45:13,524] [INFO] DQC Reference Directory: /var/lib/cwl/stg65291ac5-83f1-469c-bce2-69d64f4a4c4e/dqc_reference
[2023-03-16 21:45:15,326] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 21:45:15,327] [INFO] Task started: Prodigal
[2023-03-16 21:45:15,327] [INFO] Running command: cat /var/lib/cwl/stg28223fe3-d051-4ec1-af29-ca951055e756/OceanDNA-b27590.fa | prodigal -d OceanDNA-b27590/cds.fna -a OceanDNA-b27590/protein.faa -g 11 -q > /dev/null
[2023-03-16 21:45:36,460] [INFO] Task succeeded: Prodigal
[2023-03-16 21:45:36,460] [INFO] Task started: HMMsearch
[2023-03-16 21:45:36,460] [INFO] Running command: hmmsearch --tblout OceanDNA-b27590/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg65291ac5-83f1-469c-bce2-69d64f4a4c4e/dqc_reference/reference_markers.hmm OceanDNA-b27590/protein.faa > /dev/null
[2023-03-16 21:45:36,755] [INFO] Task succeeded: HMMsearch
[2023-03-16 21:45:36,755] [INFO] Found 6/6 markers.
[2023-03-16 21:45:36,788] [INFO] Query marker FASTA was written to OceanDNA-b27590/markers.fasta
[2023-03-16 21:45:36,788] [INFO] Task started: Blastn
[2023-03-16 21:45:36,788] [INFO] Running command: blastn -query OceanDNA-b27590/markers.fasta -db /var/lib/cwl/stg65291ac5-83f1-469c-bce2-69d64f4a4c4e/dqc_reference/reference_markers.fasta -out OceanDNA-b27590/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 21:45:37,540] [INFO] Task succeeded: Blastn
[2023-03-16 21:45:37,541] [INFO] Selected 31 target genomes.
[2023-03-16 21:45:37,541] [INFO] Target genome list was writen to OceanDNA-b27590/target_genomes.txt
[2023-03-16 21:45:37,560] [INFO] Task started: fastANI
[2023-03-16 21:45:37,560] [INFO] Running command: fastANI --query /var/lib/cwl/stg28223fe3-d051-4ec1-af29-ca951055e756/OceanDNA-b27590.fa --refList OceanDNA-b27590/target_genomes.txt --output OceanDNA-b27590/fastani_result.tsv --threads 1
[2023-03-16 21:45:57,641] [INFO] Task succeeded: fastANI
[2023-03-16 21:45:57,641] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg65291ac5-83f1-469c-bce2-69d64f4a4c4e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 21:45:57,642] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg65291ac5-83f1-469c-bce2-69d64f4a4c4e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 21:45:57,653] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 21:45:57,653] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 21:45:57,654] [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
Pseudooceanicola nitratireducens	strain=CGMCC 1.7292	GCA_900109195.1	517719	517719	type	True	76.4706	72	1140	95	below_threshold
Pseudooceanicola nitratireducens	strain=DSM 29619	GCA_900112545.1	517719	517719	type	True	76.4427	73	1140	95	below_threshold
Coraliihabitans acroporae	strain=NNCM2	GCA_019891535.1	2834412	2834412	type	True	76.4195	88	1140	95	below_threshold
Sagittula marina	strain=DSM 102235	GCA_014196795.1	943940	943940	type	True	76.3118	69	1140	95	below_threshold
Thalassobius autumnalis	strain=CECT 5118	GCA_001458255.1	2072972	2072972	type	True	76.2921	73	1140	95	below_threshold
Pseudopuniceibacterium antarcticum	strain=HQ09	GCA_014899185.1	2613965	2613965	type	True	76.2907	64	1140	95	below_threshold
Pikeienuella piscinae	strain=RR4-56	GCA_011044155.1	2748098	2748098	type	True	76.245	104	1140	95	below_threshold
Albimonas donghaensis	strain=DSM 17890	GCA_900106695.1	356660	356660	type	True	76.2015	70	1140	95	below_threshold
Roseovarius indicus	strain=DSM 26383	GCA_008728195.1	540747	540747	type	True	76.1763	75	1140	95	below_threshold
Celeribacter neptunius	strain=DSM 26471	GCA_900113955.1	588602	588602	type	True	76.1755	51	1140	95	below_threshold
Tabrizicola alkalilacus	strain=DJC	GCA_003443995.1	2305252	2305252	type	True	76.1534	66	1140	95	below_threshold
Halovulum marinum	strain=2CG4	GCA_009697225.1	2662447	2662447	type	True	76.119	64	1140	95	below_threshold
Mangrovicoccus algicola	strain=HB182678	GCA_014903745.1	2771008	2771008	type	True	76.1148	60	1140	95	below_threshold
Yangia pacifica	strain=DSM 26894	GCA_900116195.1	311180	311180	suspected-type	True	76.0842	61	1140	95	below_threshold
Yangia pacifica	strain=CGMCC 1.3455	GCA_900100725.1	311180	311180	suspected-type	True	76.0589	62	1140	95	below_threshold
Rhodovulum sulfidophilum	strain=DSM 1374	GCA_000520135.2	35806	35806	type	True	75.9561	62	1140	95	below_threshold
Rhodovulum sulfidophilum	strain=DSM 1374	GCA_001633165.1	35806	35806	type	True	75.9561	62	1140	95	below_threshold
Paroceanicella profunda	strain=D4M1	GCA_005887635.2	2579971	2579971	type	True	75.9379	59	1140	95	below_threshold
Rhodovulum steppense	strain=DSM 21153	GCA_004339675.1	540251	540251	type	True	75.8749	63	1140	95	below_threshold
Rubricella aquisinus	strain=DSM 103377	GCA_014199445.1	2028108	2028108	type	True	75.8003	63	1140	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	75.76	73	1140	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 21:45:57,654] [INFO] DFAST Taxonomy check result was written to OceanDNA-b27590/tc_result.tsv
[2023-03-16 21:45:57,654] [INFO] ===== Taxonomy check completed =====
[2023-03-16 21:45:57,654] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 21:45:57,654] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg65291ac5-83f1-469c-bce2-69d64f4a4c4e/dqc_reference/checkm_data
[2023-03-16 21:45:57,655] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 21:45:57,661] [INFO] Task started: CheckM
[2023-03-16 21:45:57,661] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b27590/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b27590/checkm_input OceanDNA-b27590/checkm_result
[2023-03-16 21:46:51,768] [INFO] Task succeeded: CheckM
[2023-03-16 21:46:51,768] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.12%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 21:46:51,771] [INFO] ===== Completeness check finished =====
[2023-03-16 21:46:51,771] [INFO] ===== Start GTDB Search =====
[2023-03-16 21:46:51,771] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b27590/markers.fasta)
[2023-03-16 21:46:51,772] [INFO] Task started: Blastn
[2023-03-16 21:46:51,772] [INFO] Running command: blastn -query OceanDNA-b27590/markers.fasta -db /var/lib/cwl/stg65291ac5-83f1-469c-bce2-69d64f4a4c4e/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b27590/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 21:46:53,008] [INFO] Task succeeded: Blastn
[2023-03-16 21:46:53,009] [INFO] Selected 36 target genomes.
[2023-03-16 21:46:53,009] [INFO] Target genome list was writen to OceanDNA-b27590/target_genomes_gtdb.txt
[2023-03-16 21:46:53,124] [INFO] Task started: fastANI
[2023-03-16 21:46:53,124] [INFO] Running command: fastANI --query /var/lib/cwl/stg28223fe3-d051-4ec1-af29-ca951055e756/OceanDNA-b27590.fa --refList OceanDNA-b27590/target_genomes_gtdb.txt --output OceanDNA-b27590/fastani_result_gtdb.tsv --threads 1
[2023-03-16 21:47:15,773] [INFO] Task succeeded: fastANI
[2023-03-16 21:47:15,786] [INFO] Found 24 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 21:47:15,787] [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_003318255.1	s__Ruegeria sp003318255	76.3524	61	1140	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014196795.1	s__Sagittula marina	76.3118	69	1140	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sagittula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001458255.1	s__Thalassobius autumnalis	76.2921	73	1140	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	99.93	99.93	0.99	0.99	2	-
GCF_011044155.1	s__Pikeienuella piscinae	76.245	104	1140	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pikeienuella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001205715.1	s__Pseudaestuariivita atlantica	76.2439	94	1140	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudaestuariivita	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003337565.1	s__Paracoccus lutimaris	76.2412	56	1140	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900106695.1	s__Albimonas donghaensis	76.2015	70	1140	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Albimonas	95.0	97.11	97.08	0.90	0.88	3	-
GCF_002210165.1	s__CAU-1492 sp002210165	76.1629	77	1140	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__CAU-1492	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013031405.1	s__Ruegeria sp013031405	76.1493	88	1140	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018200035.1	s__Sulfitobacter sp018200035	76.1403	86	1140	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009697225.1	s__Halovulum marinum	76.119	64	1140	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Halovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014903745.1	s__Mangrovicoccus sp014903745	76.1148	60	1140	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Mangrovicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900116195.1	s__Salipiger pacificus	76.1112	60	1140	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	99.99	99.99	1.00	1.00	2	-
GCF_009363715.1	s__Roseovarius sp009363715	76.1034	65	1140	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002119405.1	s__Fluviibacterium sp002119405	76.056	50	1140	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Fluviibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900302495.1	s__Pontivivens insulae	76.031	57	1140	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pontivivens	95.0	100.00	100.00	1.00	1.00	2	-
GCA_014762635.1	s__JABURR01 sp014762635	76.0025	71	1140	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JABURR01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013030985.1	s__Ruegeria arenilitoris_B	75.9934	84	1140	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	99.15	99.15	0.92	0.92	2	-
GCF_005887635.2	s__Paroceanicella profunda	75.9379	59	1140	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paroceanicella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004339675.1	s__Rhodovulum steppense	75.8749	63	1140	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001874255.1	s__Epibacterium sp001874255	75.8524	64	1140	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Epibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003053725.1	s__Rhodovulum kholense	75.8514	62	1140	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	98.27	98.27	0.96	0.96	2	-
GCF_000169415.1	s__Sagittula stellata	75.8201	76	1140	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sagittula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014199445.1	s__Rubricella aquisinus	75.8003	63	1140	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rubricella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 21:47:15,787] [INFO] GTDB search result was written to OceanDNA-b27590/result_gtdb.tsv
[2023-03-16 21:47:15,787] [INFO] ===== GTDB Search completed =====
[2023-03-16 21:47:15,789] [INFO] DFAST_QC result json was written to OceanDNA-b27590/dqc_result.json
[2023-03-16 21:47:15,789] [INFO] DFAST_QC completed!
[2023-03-16 21:47:15,789] [INFO] Total running time: 0h2m2s