[2023-03-19 02:05:13,342] [INFO] DFAST_QC pipeline started.
[2023-03-19 02:05:13,342] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 02:05:13,342] [INFO] DQC Reference Directory: /var/lib/cwl/stg21825d3f-aaf2-412e-9775-952a9833acd1/dqc_reference
[2023-03-19 02:05:14,494] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 02:05:14,494] [INFO] Task started: Prodigal
[2023-03-19 02:05:14,494] [INFO] Running command: cat /var/lib/cwl/stg90e2bb72-d596-4bf5-bfe3-7eddb4c99372/OceanDNA-b29545.fa | prodigal -d OceanDNA-b29545/cds.fna -a OceanDNA-b29545/protein.faa -g 11 -q > /dev/null
[2023-03-19 02:05:29,489] [INFO] Task succeeded: Prodigal
[2023-03-19 02:05:29,490] [INFO] Task started: HMMsearch
[2023-03-19 02:05:29,490] [INFO] Running command: hmmsearch --tblout OceanDNA-b29545/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg21825d3f-aaf2-412e-9775-952a9833acd1/dqc_reference/reference_markers.hmm OceanDNA-b29545/protein.faa > /dev/null
[2023-03-19 02:05:29,720] [INFO] Task succeeded: HMMsearch
[2023-03-19 02:05:29,720] [INFO] Found 6/6 markers.
[2023-03-19 02:05:29,744] [INFO] Query marker FASTA was written to OceanDNA-b29545/markers.fasta
[2023-03-19 02:05:29,745] [INFO] Task started: Blastn
[2023-03-19 02:05:29,745] [INFO] Running command: blastn -query OceanDNA-b29545/markers.fasta -db /var/lib/cwl/stg21825d3f-aaf2-412e-9775-952a9833acd1/dqc_reference/reference_markers.fasta -out OceanDNA-b29545/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 02:05:30,443] [INFO] Task succeeded: Blastn
[2023-03-19 02:05:30,444] [INFO] Selected 34 target genomes.
[2023-03-19 02:05:30,444] [INFO] Target genome list was writen to OceanDNA-b29545/target_genomes.txt
[2023-03-19 02:05:30,464] [INFO] Task started: fastANI
[2023-03-19 02:05:30,464] [INFO] Running command: fastANI --query /var/lib/cwl/stg90e2bb72-d596-4bf5-bfe3-7eddb4c99372/OceanDNA-b29545.fa --refList OceanDNA-b29545/target_genomes.txt --output OceanDNA-b29545/fastani_result.tsv --threads 1
[2023-03-19 02:05:52,733] [INFO] Task succeeded: fastANI
[2023-03-19 02:05:52,734] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg21825d3f-aaf2-412e-9775-952a9833acd1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 02:05:52,734] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg21825d3f-aaf2-412e-9775-952a9833acd1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 02:05:52,752] [INFO] Found 34 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 02:05:52,752] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-19 02:05:52,752] [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
Pontivivens insulae	strain=CeCT 8812	GCA_900302495.1	1639689	1639689	type	True	77.3471	165	734	95	below_threshold
Pontivivens insulae	strain=DSM 103361	GCA_003385715.1	1639689	1639689	type	True	77.3436	165	734	95	below_threshold
Pontivivens ytuae	strain=MT2928	GCA_015679265.1	2789856	2789856	type	True	77.2014	191	734	95	below_threshold
Nioella sediminis	strain=JS7-11	GCA_001879695.1	1912092	1912092	type	True	76.5207	75	734	95	below_threshold
Rubricella aquisinus	strain=DSM 103377	GCA_014199445.1	2028108	2028108	type	True	76.4473	108	734	95	below_threshold
Halovulum marinum	strain=2CG4	GCA_009697225.1	2662447	2662447	type	True	76.3917	114	734	95	below_threshold
Mameliella sediminis	strain=DP3N28-2	GCA_019218285.1	2836866	2836866	type	True	76.3595	88	734	95	below_threshold
Ruegeria intermedia	strain=DSM 29341	GCA_900129345.1	996115	996115	type	True	76.3581	91	734	95	below_threshold
Roseobacter ponti	strain=DSM 106830	GCA_012932215.1	1891787	1891787	type	True	76.2824	53	734	95	below_threshold
Puniceibacterium sediminis	strain=DSM 29052	GCA_900188035.1	1608407	1608407	type	True	76.2535	97	734	95	below_threshold
Tritonibacter scottomollicae	strain=DSM 25328	GCA_003003215.1	483013	483013	type	True	76.1988	77	734	95	below_threshold
Mangrovicoccus algicola	strain=HB182678	GCA_014903745.1	2771008	2771008	type	True	76.1358	62	734	95	below_threshold
Mameliella alba	strain=DSM 26384	GCA_003051025.1	561184	561184	suspected-type	True	76.1346	99	734	95	below_threshold
Paracoccus aestuarii	strain=DSM 19484	GCA_003594815.1	453842	453842	type	True	76.1159	81	734	95	below_threshold
Paracoccus aerius	strain=KCTC 42845	GCA_014656455.1	1915382	1915382	type	True	76.0897	70	734	95	below_threshold
Paracoccus aerius	strain=KCTC 42845	GCA_016757275.1	1915382	1915382	type	True	76.0829	70	734	95	below_threshold
Wenxinia saemankumensis	strain=DSM 100565	GCA_900141735.1	1447782	1447782	type	True	76.0749	65	734	95	below_threshold
Pseudopuniceibacterium antarcticum	strain=HQ09	GCA_014899185.1	2613965	2613965	type	True	76.0552	84	734	95	below_threshold
Paracoccus liaowanqingii	strain=2251	GCA_004683865.2	2560053	2560053	type	True	76.0321	87	734	95	below_threshold
Paracoccus fontiphilus	strain=MVW-1	GCA_017356265.1	1815556	1815556	type	True	76.0235	70	734	95	below_threshold
Thalassorhabdomicrobium marinisediminis	strain=BH-SD16	GCA_003072065.1	2170577	2170577	type	True	75.938	85	734	95	below_threshold
Paracoccus hibiscisoli	strain=CCTCC AB2016182	GCA_005048265.1	2023261	2023261	type	True	75.935	91	734	95	below_threshold
Paracoccus gahaiensis	strain=KCTC 42687	GCA_005048225.1	1706839	1706839	type	True	75.9192	84	734	95	below_threshold
Oceanicella actignis	strain=DSM 22673	GCA_008124525.1	1189325	1189325	type	True	75.8999	70	734	95	below_threshold
Phaeobacter marinintestinus	strain=UB-M7	GCA_007923355.1	1492905	1492905	type	True	75.8923	75	734	95	below_threshold
Defluviimonas aquaemixtae	strain=CECT 8626	GCA_900302475.1	1542388	1542388	type	True	75.8807	55	734	95	below_threshold
Paracoccus laeviglucosivorans	strain=DSM 100094	GCA_900182695.1	1197861	1197861	type	True	75.8781	72	734	95	below_threshold
Paracoccus shandongensis	strain=wg2	GCA_017315735.1	2816048	2816048	type	True	75.8706	76	734	95	below_threshold
Amaricoccus solimangrovi	strain=HB172011	GCA_006385685.1	2589815	2589815	type	True	75.8484	64	734	95	below_threshold
Celeribacter neptunius	strain=DSM 26471	GCA_900113955.1	588602	588602	type	True	75.8319	62	734	95	below_threshold
Tabrizicola sediminis	strain=DRYC-M-16	GCA_004745575.1	2486418	2486418	type	True	75.7926	81	734	95	below_threshold
Albimonas donghaensis	strain=DSM 17890	GCA_900106695.1	356660	356660	type	True	75.6564	92	734	95	below_threshold
Pseudogemmobacter bohemicus	strain=Cd-10	GCA_003290025.1	2250708	2250708	type	True	75.6537	52	734	95	below_threshold
Ruegeria atlantica	strain=CECT 4292	GCA_001458195.1	81569	81569	suspected-type	True	75.6221	59	734	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 02:05:52,753] [INFO] DFAST Taxonomy check result was written to OceanDNA-b29545/tc_result.tsv
[2023-03-19 02:05:52,753] [INFO] ===== Taxonomy check completed =====
[2023-03-19 02:05:52,753] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 02:05:52,753] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg21825d3f-aaf2-412e-9775-952a9833acd1/dqc_reference/checkm_data
[2023-03-19 02:05:52,754] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 02:05:52,758] [INFO] Task started: CheckM
[2023-03-19 02:05:52,758] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b29545/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b29545/checkm_input OceanDNA-b29545/checkm_result
[2023-03-19 02:06:32,668] [INFO] Task succeeded: CheckM
[2023-03-19 02:06:32,668] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 64.58%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 02:06:32,671] [INFO] ===== Completeness check finished =====
[2023-03-19 02:06:32,671] [INFO] ===== Start GTDB Search =====
[2023-03-19 02:06:32,671] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b29545/markers.fasta)
[2023-03-19 02:06:32,672] [INFO] Task started: Blastn
[2023-03-19 02:06:32,672] [INFO] Running command: blastn -query OceanDNA-b29545/markers.fasta -db /var/lib/cwl/stg21825d3f-aaf2-412e-9775-952a9833acd1/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b29545/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 02:06:33,863] [INFO] Task succeeded: Blastn
[2023-03-19 02:06:33,864] [INFO] Selected 24 target genomes.
[2023-03-19 02:06:33,864] [INFO] Target genome list was writen to OceanDNA-b29545/target_genomes_gtdb.txt
[2023-03-19 02:06:34,517] [INFO] Task started: fastANI
[2023-03-19 02:06:34,517] [INFO] Running command: fastANI --query /var/lib/cwl/stg90e2bb72-d596-4bf5-bfe3-7eddb4c99372/OceanDNA-b29545.fa --refList OceanDNA-b29545/target_genomes_gtdb.txt --output OceanDNA-b29545/fastani_result_gtdb.tsv --threads 1
[2023-03-19 02:06:49,387] [INFO] Task succeeded: fastANI
[2023-03-19 02:06:49,400] [INFO] Found 24 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 02:06:49,400] [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_900231835.1	s__Monaibacterium marinum	80.9922	499	734	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Monaibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011290545.1	s__Monaibacterium sp011290545	80.635	451	734	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Monaibacterium	95.0	96.75	96.75	0.88	0.88	2	-
GCF_900302495.1	s__Pontivivens insulae	77.3471	165	734	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pontivivens	95.0	100.00	100.00	1.00	1.00	2	-
GCF_015679265.1	s__MT2928 sp015679265	77.2014	191	734	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__MT2928	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001879695.1	s__Nioella sediminis	76.5207	75	734	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Nioella	95.0	100.00	100.00	0.99	0.99	2	-
GCF_900129345.1	s__Ruegeria intermedia	76.3581	91	734	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009833495.1	s__Oceanomicrobium pacificus	76.302	87	734	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Oceanomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003667315.2	s__Tropicibacter sp003667315	76.1749	108	734	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tropicibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014656455.1	s__Paracoccus aerius	76.0897	70	734	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	99.01	98.03	0.91	0.84	3	-
GCF_009789075.1	s__Pseudooceanicola pacificus	76.082	69	734	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004683865.2	s__Paracoccus liaowanqingii	76.0321	87	734	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	96.54	96.54	0.86	0.86	2	-
GCF_015644665.1	s__Roseobacter sp015644665	76.0272	69	734	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017356265.1	s__Paracoccus fontiphilus	76.0004	71	734	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017743885.1	s__Sulfitobacter sp001635605	75.9955	91	734	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	98.54	95.97	0.90	0.86	4	-
GCF_000622145.1	s__Paracoccus yeei	75.9451	66	734	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	96.0533	98.39	97.89	0.87	0.83	7	-
GCF_000153305.1	s__Oceanicola granulosus	75.9432	69	734	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Oceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003255745.1	s__Paracoccus saliphilus_A	75.9029	69	734	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008124525.1	s__Oceanicella actignis	75.8999	70	734	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Oceanicella	95.0	98.87	98.87	0.96	0.96	3	-
GCF_900182695.1	s__Paracoccus laeviglucosivorans	75.8781	72	734	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006385685.1	s__Amaricoccus solimangrovi	75.8484	64	734	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Amaricoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007830335.1	s__Paracoccus sulfuroxidans	75.7909	72	734	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004145845.1	s__Marivivens sp004145845	75.7799	82	734	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marivivens	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013031245.1	s__Ruegeria lacuscaerulensis_C	75.7778	59	734	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900106695.1	s__Albimonas donghaensis	75.6563	92	734	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Albimonas	95.0	97.11	97.08	0.90	0.88	3	-
--------------------------------------------------------------------------------
[2023-03-19 02:06:49,401] [INFO] GTDB search result was written to OceanDNA-b29545/result_gtdb.tsv
[2023-03-19 02:06:49,401] [INFO] ===== GTDB Search completed =====
[2023-03-19 02:06:49,403] [INFO] DFAST_QC result json was written to OceanDNA-b29545/dqc_result.json
[2023-03-19 02:06:49,404] [INFO] DFAST_QC completed!
[2023-03-19 02:06:49,404] [INFO] Total running time: 0h1m36s