[2023-03-18 02:27:37,204] [INFO] DFAST_QC pipeline started.
[2023-03-18 02:27:37,204] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 02:27:37,204] [INFO] DQC Reference Directory: /var/lib/cwl/stg05f809fb-8831-42a8-8ce7-87f8f869f90e/dqc_reference
[2023-03-18 02:27:38,463] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 02:27:38,463] [INFO] Task started: Prodigal
[2023-03-18 02:27:38,463] [INFO] Running command: cat /var/lib/cwl/stg449936d8-241e-4b2a-b6f2-88a26415a30a/OceanDNA-b30559.fa | prodigal -d OceanDNA-b30559/cds.fna -a OceanDNA-b30559/protein.faa -g 11 -q > /dev/null
[2023-03-18 02:27:51,415] [INFO] Task succeeded: Prodigal
[2023-03-18 02:27:51,415] [INFO] Task started: HMMsearch
[2023-03-18 02:27:51,415] [INFO] Running command: hmmsearch --tblout OceanDNA-b30559/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg05f809fb-8831-42a8-8ce7-87f8f869f90e/dqc_reference/reference_markers.hmm OceanDNA-b30559/protein.faa > /dev/null
[2023-03-18 02:27:51,601] [INFO] Task succeeded: HMMsearch
[2023-03-18 02:27:51,602] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg449936d8-241e-4b2a-b6f2-88a26415a30a/OceanDNA-b30559.fa]
[2023-03-18 02:27:51,632] [INFO] Query marker FASTA was written to OceanDNA-b30559/markers.fasta
[2023-03-18 02:27:51,632] [INFO] Task started: Blastn
[2023-03-18 02:27:51,632] [INFO] Running command: blastn -query OceanDNA-b30559/markers.fasta -db /var/lib/cwl/stg05f809fb-8831-42a8-8ce7-87f8f869f90e/dqc_reference/reference_markers.fasta -out OceanDNA-b30559/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 02:27:52,258] [INFO] Task succeeded: Blastn
[2023-03-18 02:27:52,258] [INFO] Selected 21 target genomes.
[2023-03-18 02:27:52,259] [INFO] Target genome list was writen to OceanDNA-b30559/target_genomes.txt
[2023-03-18 02:27:52,267] [INFO] Task started: fastANI
[2023-03-18 02:27:52,267] [INFO] Running command: fastANI --query /var/lib/cwl/stg449936d8-241e-4b2a-b6f2-88a26415a30a/OceanDNA-b30559.fa --refList OceanDNA-b30559/target_genomes.txt --output OceanDNA-b30559/fastani_result.tsv --threads 1
[2023-03-18 02:28:05,695] [INFO] Task succeeded: fastANI
[2023-03-18 02:28:05,695] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg05f809fb-8831-42a8-8ce7-87f8f869f90e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 02:28:05,695] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg05f809fb-8831-42a8-8ce7-87f8f869f90e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 02:28:05,707] [INFO] Found 21 fastANI hits (2 hits with ANI > threshold)
[2023-03-18 02:28:05,707] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-18 02:28:05,707] [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
Thalassobacter stenotrophicus	strain=DSM 16310	GCA_900141945.1	266809	266809	type	True	96.4447	589	610	95	conclusive
Thalassobacter stenotrophicus	strain=CECT 5294	GCA_001458315.1	266809	266809	type	True	96.4414	593	610	95	conclusive
Marivita cryptomonadis	strain=CL-SK44	GCA_002115725.1	505252	505252	type	True	76.4719	86	610	95	below_threshold
Falsiruegeria litorea	strain=CECT 7639	GCA_900172225.1	1280831	1280831	type	True	76.4338	81	610	95	below_threshold
Aestuariivita boseongensis	strain=BS-B2	GCA_001262635.1	1470562	1470562	type	True	76.313	74	610	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	76.2558	55	610	95	below_threshold
Pseudoprimorskyibacter insulae	strain=CECT 8871	GCA_900302505.1	1695997	1695997	type	True	76.2247	100	610	95	below_threshold
Litoreibacter albidus	strain=DSM 26922	GCA_900107015.1	670155	670155	type	True	76.2069	76	610	95	below_threshold
Rhodovulum adriaticum	strain=DSM 2781	GCA_016583705.1	35804	35804	type	True	76.2033	61	610	95	below_threshold
Tabrizicola sediminis	strain=DRYC-M-16	GCA_004745575.1	2486418	2486418	type	True	76.1544	64	610	95	below_threshold
Antarcticimicrobium luteum	strain=318-1	GCA_004358185.1	2547397	2547397	type	True	76.0775	75	610	95	below_threshold
Thalassobius mangrovi	strain=GS-10	GCA_009857745.1	2692236	2692236	type	True	76.0664	93	610	95	below_threshold
Tabrizicola alkalilacus	strain=DJC	GCA_003443995.1	2305252	2305252	type	True	76.0382	68	610	95	below_threshold
Roseovarius confluentis	strain=SAG6	GCA_002917925.1	1852027	1852027	type	True	75.9602	72	610	95	below_threshold
Roseivivax lentus	strain=DSM 29430	GCA_900156805.1	633194	633194	type	True	75.9071	62	610	95	below_threshold
Pelagimonas phthalicica	strain=DSM 26923	GCA_004364805.1	1037362	1037362	type	True	75.8907	73	610	95	below_threshold
Shimia marina	strain=DSM 26895	GCA_900112745.1	321267	321267	type	True	75.8844	67	610	95	below_threshold
Sulfitobacter marinus	strain=DSM 23422	GCA_900116285.1	394264	394264	type	True	75.8586	79	610	95	below_threshold
Shimia marina	strain=CECT 7688	GCA_001458175.1	321267	321267	type	True	75.8095	67	610	95	below_threshold
Salipiger pallidus	strain=CGMCC 1.15762	GCA_014643635.1	1775170	1775170	type	True	75.7262	65	610	95	below_threshold
Rhabdonatronobacter sediminivivens	strain=IM2376	GCA_013415485.1	2743469	2743469	type	True	75.567	55	610	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 02:28:05,708] [INFO] DFAST Taxonomy check result was written to OceanDNA-b30559/tc_result.tsv
[2023-03-18 02:28:05,708] [INFO] ===== Taxonomy check completed =====
[2023-03-18 02:28:05,708] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 02:28:05,708] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg05f809fb-8831-42a8-8ce7-87f8f869f90e/dqc_reference/checkm_data
[2023-03-18 02:28:05,709] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 02:28:05,713] [INFO] Task started: CheckM
[2023-03-18 02:28:05,713] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b30559/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b30559/checkm_input OceanDNA-b30559/checkm_result
[2023-03-18 02:28:42,082] [INFO] Task succeeded: CheckM
[2023-03-18 02:28:42,082] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 72.93%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 02:28:42,084] [INFO] ===== Completeness check finished =====
[2023-03-18 02:28:42,085] [INFO] ===== Start GTDB Search =====
[2023-03-18 02:28:42,085] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b30559/markers.fasta)
[2023-03-18 02:28:42,085] [INFO] Task started: Blastn
[2023-03-18 02:28:42,085] [INFO] Running command: blastn -query OceanDNA-b30559/markers.fasta -db /var/lib/cwl/stg05f809fb-8831-42a8-8ce7-87f8f869f90e/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b30559/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 02:28:43,153] [INFO] Task succeeded: Blastn
[2023-03-18 02:28:43,154] [INFO] Selected 25 target genomes.
[2023-03-18 02:28:43,154] [INFO] Target genome list was writen to OceanDNA-b30559/target_genomes_gtdb.txt
[2023-03-18 02:28:43,170] [INFO] Task started: fastANI
[2023-03-18 02:28:43,170] [INFO] Running command: fastANI --query /var/lib/cwl/stg449936d8-241e-4b2a-b6f2-88a26415a30a/OceanDNA-b30559.fa --refList OceanDNA-b30559/target_genomes_gtdb.txt --output OceanDNA-b30559/fastani_result_gtdb.tsv --threads 1
[2023-03-18 02:28:59,326] [INFO] Task succeeded: fastANI
[2023-03-18 02:28:59,340] [INFO] Found 25 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 02:28:59,341] [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_001458315.1	s__Thalassobacter stenotrophicus	96.4414	593	610	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobacter	95.0	98.03	96.21	0.91	0.88	5	conclusive
GCF_009363255.1	s__Roseivivax sp009363255	76.7702	65	610	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseivivax	95.0	99.55	99.55	0.94	0.94	2	-
GCF_017743975.1	s__Ruegeria sp017743975	76.5436	73	610	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005938225.1	s__Arenibacterium halophilum	76.4484	82	610	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Arenibacterium	95.0	96.35	96.35	0.87	0.87	2	-
GCF_013030265.1	s__Ruegeria arenilitoris_E	76.3936	52	610	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002285415.1	s__Actibacterium pelagium	76.3338	64	610	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Actibacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000814005.1	s__Ruegeria sp000814005	76.3247	54	610	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001262635.1	s__Aestuariivita boseongensis	76.313	74	610	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aestuariivita	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017743735.1	s__Shimia sp017743735	76.2712	65	610	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia	95.0	95.87	95.63	0.93	0.93	3	-
GCF_013032095.1	s__Ruegeria atlantica_E	76.2598	68	610	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004345735.1	s__Rhodovulum adriaticum	76.2318	60	610	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	99.99	99.99	0.99	0.99	2	-
GCF_001292625.1	s__Shimia sp001292625	76.2088	62	610	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900113875.1	s__Jannaschia pohangensis	76.1259	97	610	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Jannaschia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_006227805.1	s__Aestuariivita sp006227805	76.0941	50	610	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aestuariivita	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004358185.1	s__Antarcticimicrobium luteum	76.0775	75	610	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Antarcticimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002701395.1	s__Rhodobacter_B sp002701395	76.0769	85	610	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodobacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009363655.1	s__Roseovarius sp009363655	76.0752	62	610	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	98.13	98.13	0.93	0.93	2	-
GCF_009857745.1	s__Thalassobius mangrovi	76.062	92	610	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000423645.1	s__Sediminimonas qiaohouensis	76.0417	70	610	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sediminimonas	95.0	97.45	97.45	0.91	0.91	2	-
GCF_900110705.1	s__Loktanella sp900110705	76.0082	66	610	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Loktanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013032005.1	s__Ruegeria atlantica_A	76.0026	74	610	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	98.11	97.00	0.94	0.90	12	-
GCF_002917925.1	s__Roseovarius confluentis	75.9281	71	610	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	98.93	98.93	0.93	0.93	2	-
GCF_900156805.1	s__Roseivivax lentus	75.8668	60	610	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseivivax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004364805.1	s__Pelagimonas phthalicica	75.858	72	610	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pelagimonas	95.0	97.63	95.26	0.94	0.87	3	-
GCA_016123485.1	s__Halocynthiibacter sp016123485	75.8315	51	610	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Halocynthiibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 02:28:59,341] [INFO] GTDB search result was written to OceanDNA-b30559/result_gtdb.tsv
[2023-03-18 02:28:59,341] [INFO] ===== GTDB Search completed =====
[2023-03-18 02:28:59,343] [INFO] DFAST_QC result json was written to OceanDNA-b30559/dqc_result.json
[2023-03-18 02:28:59,343] [INFO] DFAST_QC completed!
[2023-03-18 02:28:59,344] [INFO] Total running time: 0h1m22s