[2023-03-18 08:55:17,519] [INFO] DFAST_QC pipeline started.
[2023-03-18 08:55:17,519] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 08:55:17,519] [INFO] DQC Reference Directory: /var/lib/cwl/stg9d7b4a69-ac45-4ceb-9312-ba7f73248338/dqc_reference
[2023-03-18 08:55:18,645] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 08:55:18,646] [INFO] Task started: Prodigal
[2023-03-18 08:55:18,646] [INFO] Running command: cat /var/lib/cwl/stg6bf25bb4-1a4f-4dad-a217-232e47d74e71/OceanDNA-b32084.fa | prodigal -d OceanDNA-b32084/cds.fna -a OceanDNA-b32084/protein.faa -g 11 -q > /dev/null
[2023-03-18 08:55:47,146] [INFO] Task succeeded: Prodigal
[2023-03-18 08:55:47,146] [INFO] Task started: HMMsearch
[2023-03-18 08:55:47,146] [INFO] Running command: hmmsearch --tblout OceanDNA-b32084/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9d7b4a69-ac45-4ceb-9312-ba7f73248338/dqc_reference/reference_markers.hmm OceanDNA-b32084/protein.faa > /dev/null
[2023-03-18 08:55:47,383] [INFO] Task succeeded: HMMsearch
[2023-03-18 08:55:47,383] [INFO] Found 6/6 markers.
[2023-03-18 08:55:47,411] [INFO] Query marker FASTA was written to OceanDNA-b32084/markers.fasta
[2023-03-18 08:55:47,412] [INFO] Task started: Blastn
[2023-03-18 08:55:47,412] [INFO] Running command: blastn -query OceanDNA-b32084/markers.fasta -db /var/lib/cwl/stg9d7b4a69-ac45-4ceb-9312-ba7f73248338/dqc_reference/reference_markers.fasta -out OceanDNA-b32084/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 08:55:48,157] [INFO] Task succeeded: Blastn
[2023-03-18 08:55:48,158] [INFO] Selected 18 target genomes.
[2023-03-18 08:55:48,159] [INFO] Target genome list was writen to OceanDNA-b32084/target_genomes.txt
[2023-03-18 08:55:48,169] [INFO] Task started: fastANI
[2023-03-18 08:55:48,169] [INFO] Running command: fastANI --query /var/lib/cwl/stg6bf25bb4-1a4f-4dad-a217-232e47d74e71/OceanDNA-b32084.fa --refList OceanDNA-b32084/target_genomes.txt --output OceanDNA-b32084/fastani_result.tsv --threads 1
[2023-03-18 08:56:03,736] [INFO] Task succeeded: fastANI
[2023-03-18 08:56:03,736] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9d7b4a69-ac45-4ceb-9312-ba7f73248338/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 08:56:03,737] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9d7b4a69-ac45-4ceb-9312-ba7f73248338/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 08:56:03,748] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 08:56:03,748] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 08:56:03,748] [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
Sphingobium terrigena	strain=EO9	GCA_003591655.1	2304063	2304063	type	True	85.2815	913	1497	95	below_threshold
Sphingobium psychrophilum	strain=AR-3-1	GCA_012927105.1	2728834	2728834	type	True	85.0465	964	1497	95	below_threshold
Sphingobium cupriresistens	strain=CCTCC AB 2011146	GCA_004152865.1	1132417	1132417	type	True	84.0952	829	1497	95	below_threshold
Sphingobium xenophagum	strain=NBRC 107872	GCA_000367345.1	121428	121428	type	True	84.0943	822	1497	95	below_threshold
Sphingobium limneticum	strain=DSM 25076	GCA_008710155.1	1007511	1007511	type	True	83.9682	878	1497	95	below_threshold
Sphingobium yanoikuyae	strain=ATCC 51230	GCA_000315525.1	13690	13690	suspected-type	True	83.3311	827	1497	95	below_threshold
Sphingobium scionense	strain=DSM 19371	GCA_014197035.1	1404341	1404341	type	True	82.8079	814	1497	95	below_threshold
Sphingobium lactosutens	strain=DS20	GCA_000445105.1	522773	522773	type	True	81.947	749	1497	95	below_threshold
Sphingobium indicum	strain=B90A	GCA_000264945.2	332055	332055	type	True	81.8992	662	1497	95	below_threshold
Sphingobium amiense	strain=DSM 16289	GCA_003967075.1	135719	135719	type	True	81.8632	713	1497	95	below_threshold
Sphingobium amiense	strain=NBRC 102518	GCA_001591305.1	135719	135719	type	True	81.819	687	1497	95	below_threshold
Sphingobium fuliginis	strain=DSM 18781	GCA_004152845.1	336203	336203	type	True	81.7496	687	1497	95	below_threshold
Sphingobium fuliginis	strain=CCM 7327	GCA_014636045.1	336203	336203	type	True	81.6639	691	1497	95	below_threshold
Sphingomonas changnyeongensis	strain=C33	GCA_009913435.1	2698679	2698679	type	True	77.8813	348	1497	95	below_threshold
Rhizorhabdus phycosphaerae	strain=MK52	GCA_011044255.1	2711156	2711156	type	True	77.814	319	1497	95	below_threshold
Sphingomonas flavalba	strain=ZLT-5	GCA_004796535.1	2559804	2559804	type	True	77.7064	311	1497	95	below_threshold
Sphingomonas cavernae	strain=K2R01-6	GCA_003590775.1	2320861	2320861	type	True	77.6703	311	1497	95	below_threshold
Sphingomonas baiyangensis	strain=L-1-4 w-11	GCA_005144715.1	2572576	2572576	type	True	77.3338	318	1497	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 08:56:03,748] [INFO] DFAST Taxonomy check result was written to OceanDNA-b32084/tc_result.tsv
[2023-03-18 08:56:03,749] [INFO] ===== Taxonomy check completed =====
[2023-03-18 08:56:03,749] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 08:56:03,749] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9d7b4a69-ac45-4ceb-9312-ba7f73248338/dqc_reference/checkm_data
[2023-03-18 08:56:03,749] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 08:56:03,755] [INFO] Task started: CheckM
[2023-03-18 08:56:03,756] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b32084/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b32084/checkm_input OceanDNA-b32084/checkm_result
[2023-03-18 08:57:12,430] [INFO] Task succeeded: CheckM
[2023-03-18 08:57:12,430] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 08:57:12,435] [INFO] ===== Completeness check finished =====
[2023-03-18 08:57:12,435] [INFO] ===== Start GTDB Search =====
[2023-03-18 08:57:12,436] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b32084/markers.fasta)
[2023-03-18 08:57:12,437] [INFO] Task started: Blastn
[2023-03-18 08:57:12,437] [INFO] Running command: blastn -query OceanDNA-b32084/markers.fasta -db /var/lib/cwl/stg9d7b4a69-ac45-4ceb-9312-ba7f73248338/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b32084/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 08:57:13,854] [INFO] Task succeeded: Blastn
[2023-03-18 08:57:13,856] [INFO] Selected 19 target genomes.
[2023-03-18 08:57:13,856] [INFO] Target genome list was writen to OceanDNA-b32084/target_genomes_gtdb.txt
[2023-03-18 08:57:13,881] [INFO] Task started: fastANI
[2023-03-18 08:57:13,881] [INFO] Running command: fastANI --query /var/lib/cwl/stg6bf25bb4-1a4f-4dad-a217-232e47d74e71/OceanDNA-b32084.fa --refList OceanDNA-b32084/target_genomes_gtdb.txt --output OceanDNA-b32084/fastani_result_gtdb.tsv --threads 1
[2023-03-18 08:57:33,760] [INFO] Task succeeded: fastANI
[2023-03-18 08:57:33,771] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 08:57:33,771] [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_000588875.1	s__Sphingobium sp000588875	97.0388	1202	1497	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002312805.1	s__Sphingobium sp002312805	91.4703	1072	1497	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	95.45	95.45	0.84	0.84	2	-
GCF_001713415.1	s__Sphingobium sp001713415	91.0247	1013	1497	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	95.59	95.59	0.75	0.75	2	-
GCF_003591655.1	s__Sphingobium sp003591655	85.2897	911	1497	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012927105.1	s__Sphingobium psychrophilum	85.0204	967	1497	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014280435.1	s__Sphingobium sp014280435	84.2659	876	1497	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000382885.1	s__Sphingobium japonicum_C	84.1541	733	1497	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004152865.1	s__Sphingobium cupriresistens	84.107	828	1497	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	98.64	98.49	0.81	0.81	3	-
GCA_016463275.1	s__Sphingobium sp016463275	84.0248	594	1497	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008710155.1	s__Sphingobium limneticum	83.9657	880	1497	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	98.69	97.69	0.91	0.88	5	-
GCF_000315525.1	s__Sphingobium yanoikuyae	83.3064	828	1497	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	96.25	95.31	0.82	0.72	34	-
GCA_013822485.1	s__Sphingobium sp013822485	83.2566	656	1497	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009720145.1	s__Sphingobium sp009720145	83.2486	790	1497	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000508185.1	s__Sphingobium sp000508185	83.0072	768	1497	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013393185.1	s__Sphingobium lactosutens_A	82.8947	809	1497	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900111125.1	s__Sphingobium sp900111125	82.8886	833	1497	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014203965.1	s__Sphingobium sp014203965	82.8675	828	1497	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014197035.1	s__Sphingobium scionense	82.8205	812	1497	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109095.1	s__Sphingobium sp900109095	82.7985	823	1497	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 08:57:33,772] [INFO] GTDB search result was written to OceanDNA-b32084/result_gtdb.tsv
[2023-03-18 08:57:33,772] [INFO] ===== GTDB Search completed =====
[2023-03-18 08:57:33,774] [INFO] DFAST_QC result json was written to OceanDNA-b32084/dqc_result.json
[2023-03-18 08:57:33,775] [INFO] DFAST_QC completed!
[2023-03-18 08:57:33,775] [INFO] Total running time: 0h2m16s