[2023-03-16 19:25:56,672] [INFO] DFAST_QC pipeline started.
[2023-03-16 19:25:56,672] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 19:25:56,672] [INFO] DQC Reference Directory: /var/lib/cwl/stgc509b9ed-ff92-447c-b42d-bab71786b03e/dqc_reference
[2023-03-16 19:25:57,816] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 19:25:57,816] [INFO] Task started: Prodigal
[2023-03-16 19:25:57,817] [INFO] Running command: cat /var/lib/cwl/stg68e1cfb4-1264-4b61-99b2-5fc6bd83c711/OceanDNA-b3192.fa | prodigal -d OceanDNA-b3192/cds.fna -a OceanDNA-b3192/protein.faa -g 11 -q > /dev/null
[2023-03-16 19:26:12,883] [INFO] Task succeeded: Prodigal
[2023-03-16 19:26:12,884] [INFO] Task started: HMMsearch
[2023-03-16 19:26:12,884] [INFO] Running command: hmmsearch --tblout OceanDNA-b3192/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc509b9ed-ff92-447c-b42d-bab71786b03e/dqc_reference/reference_markers.hmm OceanDNA-b3192/protein.faa > /dev/null
[2023-03-16 19:26:13,168] [INFO] Task succeeded: HMMsearch
[2023-03-16 19:26:13,168] [INFO] Found 6/6 markers.
[2023-03-16 19:26:13,182] [INFO] Query marker FASTA was written to OceanDNA-b3192/markers.fasta
[2023-03-16 19:26:13,186] [INFO] Task started: Blastn
[2023-03-16 19:26:13,186] [INFO] Running command: blastn -query OceanDNA-b3192/markers.fasta -db /var/lib/cwl/stgc509b9ed-ff92-447c-b42d-bab71786b03e/dqc_reference/reference_markers.fasta -out OceanDNA-b3192/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 19:26:13,879] [INFO] Task succeeded: Blastn
[2023-03-16 19:26:13,880] [INFO] Selected 34 target genomes.
[2023-03-16 19:26:13,880] [INFO] Target genome list was writen to OceanDNA-b3192/target_genomes.txt
[2023-03-16 19:26:13,906] [INFO] Task started: fastANI
[2023-03-16 19:26:13,906] [INFO] Running command: fastANI --query /var/lib/cwl/stg68e1cfb4-1264-4b61-99b2-5fc6bd83c711/OceanDNA-b3192.fa --refList OceanDNA-b3192/target_genomes.txt --output OceanDNA-b3192/fastani_result.tsv --threads 1
[2023-03-16 19:26:53,804] [INFO] Task succeeded: fastANI
[2023-03-16 19:26:53,804] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc509b9ed-ff92-447c-b42d-bab71786b03e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 19:26:53,805] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc509b9ed-ff92-447c-b42d-bab71786b03e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 19:26:53,813] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 19:26:53,813] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 19:26:53,813] [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
Nocardioides soli	strain=DSM 105498	GCA_014191495.1	1036020	1036020	type	True	76.1395	58	563	95	below_threshold
Phycicoccus endophyticus	strain=IP6SC6	GCA_011326735.1	1690220	1690220	type	True	76.0205	52	563	95	below_threshold
Streptomyces violarus	strain=JCM 4534	GCA_014650255.1	67380	67380	type	True	76.0017	51	563	95	below_threshold
Phycicoccus endophyticus	strain=CGMCC 4.7300	GCA_014646175.1	1690220	1690220	type	True	75.9967	53	563	95	below_threshold
Motilibacter deserti	strain=E257	GCA_011250635.1	2714956	2714956	type	True	75.9743	60	563	95	below_threshold
Streptomyces violarus	strain=CECT 3237	GCA_014191845.1	67380	67380	type	True	75.9417	53	563	95	below_threshold
Embleya scabrispora	strain=DSM 41855	GCA_000372745.1	159449	159449	type	True	75.8648	50	563	95	below_threshold
Nocardioides nitrophenolicus	strain=DSM 15529	GCA_016907515.1	60489	60489	type	True	75.7737	55	563	95	below_threshold
Streptomyces albireticuli	strain=NRRL B1670	GCA_021228125.1	1940	1940	type	True	75.7373	58	563	95	below_threshold
Embleya hyalina	strain=NBRC 13850	GCA_003967355.1	516124	516124	type	True	75.7123	61	563	95	below_threshold
Streptomyces tibetensis	strain=XZ 46	GCA_007655005.1	2382123	2382123	type	True	75.5117	51	563	95	below_threshold
Streptomyces tibetensis	strain=XZ 46	GCA_005869865.1	2382123	2382123	type	True	75.5117	51	563	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 19:26:53,814] [INFO] DFAST Taxonomy check result was written to OceanDNA-b3192/tc_result.tsv
[2023-03-16 19:26:53,815] [INFO] ===== Taxonomy check completed =====
[2023-03-16 19:26:53,815] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 19:26:53,816] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc509b9ed-ff92-447c-b42d-bab71786b03e/dqc_reference/checkm_data
[2023-03-16 19:26:53,817] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 19:26:54,076] [INFO] Task started: CheckM
[2023-03-16 19:26:54,076] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b3192/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b3192/checkm_input OceanDNA-b3192/checkm_result
[2023-03-16 19:27:34,620] [INFO] Task succeeded: CheckM
[2023-03-16 19:27:34,621] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.38%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 19:27:34,623] [INFO] ===== Completeness check finished =====
[2023-03-16 19:27:34,623] [INFO] ===== Start GTDB Search =====
[2023-03-16 19:27:34,623] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b3192/markers.fasta)
[2023-03-16 19:27:34,625] [INFO] Task started: Blastn
[2023-03-16 19:27:34,625] [INFO] Running command: blastn -query OceanDNA-b3192/markers.fasta -db /var/lib/cwl/stgc509b9ed-ff92-447c-b42d-bab71786b03e/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b3192/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 19:27:35,641] [INFO] Task succeeded: Blastn
[2023-03-16 19:27:35,642] [INFO] Selected 7 target genomes.
[2023-03-16 19:27:35,643] [INFO] Target genome list was writen to OceanDNA-b3192/target_genomes_gtdb.txt
[2023-03-16 19:27:35,656] [INFO] Task started: fastANI
[2023-03-16 19:27:35,656] [INFO] Running command: fastANI --query /var/lib/cwl/stg68e1cfb4-1264-4b61-99b2-5fc6bd83c711/OceanDNA-b3192.fa --refList OceanDNA-b3192/target_genomes_gtdb.txt --output OceanDNA-b3192/fastani_result_gtdb.tsv --threads 1
[2023-03-16 19:27:38,634] [INFO] Task succeeded: fastANI
[2023-03-16 19:27:38,639] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 19:27:38,639] [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_002729215.1	s__S36-B12 sp002729215	98.0778	491	563	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__S36-B12;g__S36-B12	95.0	98.32	97.43	0.87	0.81	12	conclusive
GCA_002728915.1	s__S36-B12 sp002728915	90.911	441	563	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__S36-B12;g__S36-B12	95.0	99.13	98.99	0.85	0.80	4	-
GCA_012103605.1	s__S36-B12 sp012103605	90.7161	434	563	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__S36-B12;g__S36-B12	95.0	95.57	95.57	0.76	0.76	2	-
GCA_010029945.1	s__S36-B12 sp010029945	90.3301	364	563	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__S36-B12;g__S36-B12	95.0	98.25	98.18	0.79	0.75	5	-
GCA_002694095.1	s__S36-B12 sp002694095	89.9355	444	563	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__S36-B12;g__S36-B12	95.0	97.65	97.49	0.82	0.80	3	-
GCA_018402235.1	s__S36-B12 sp018402235	77.7897	151	563	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__S36-B12;g__S36-B12	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009699015.1	s__WLND01 sp009699015	76.1443	76	563	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__S36-B12;g__WLND01	95.0	98.95	98.95	0.81	0.81	2	-
--------------------------------------------------------------------------------
[2023-03-16 19:27:38,640] [INFO] GTDB search result was written to OceanDNA-b3192/result_gtdb.tsv
[2023-03-16 19:27:38,640] [INFO] ===== GTDB Search completed =====
[2023-03-16 19:27:38,641] [INFO] DFAST_QC result json was written to OceanDNA-b3192/dqc_result.json
[2023-03-16 19:27:38,641] [INFO] DFAST_QC completed!
[2023-03-16 19:27:38,641] [INFO] Total running time: 0h1m42s