[2023-03-15 17:46:31,703] [INFO] DFAST_QC pipeline started.
[2023-03-15 17:46:31,704] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 17:46:31,704] [INFO] DQC Reference Directory: /var/lib/cwl/stg612297a8-9d1e-4aa6-a103-a13d350c10b0/dqc_reference
[2023-03-15 17:46:32,771] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 17:46:32,772] [INFO] Task started: Prodigal
[2023-03-15 17:46:32,772] [INFO] Running command: cat /var/lib/cwl/stg0f48757e-8921-4c95-8dc2-f621e15f01d7/OceanDNA-b32091.fa | prodigal -d OceanDNA-b32091/cds.fna -a OceanDNA-b32091/protein.faa -g 11 -q > /dev/null
[2023-03-15 17:46:48,557] [INFO] Task succeeded: Prodigal
[2023-03-15 17:46:48,557] [INFO] Task started: HMMsearch
[2023-03-15 17:46:48,557] [INFO] Running command: hmmsearch --tblout OceanDNA-b32091/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg612297a8-9d1e-4aa6-a103-a13d350c10b0/dqc_reference/reference_markers.hmm OceanDNA-b32091/protein.faa > /dev/null
[2023-03-15 17:46:48,734] [INFO] Task succeeded: HMMsearch
[2023-03-15 17:46:48,734] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg0f48757e-8921-4c95-8dc2-f621e15f01d7/OceanDNA-b32091.fa]
[2023-03-15 17:46:48,752] [INFO] Query marker FASTA was written to OceanDNA-b32091/markers.fasta
[2023-03-15 17:46:48,752] [INFO] Task started: Blastn
[2023-03-15 17:46:48,753] [INFO] Running command: blastn -query OceanDNA-b32091/markers.fasta -db /var/lib/cwl/stg612297a8-9d1e-4aa6-a103-a13d350c10b0/dqc_reference/reference_markers.fasta -out OceanDNA-b32091/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 17:46:49,554] [INFO] Task succeeded: Blastn
[2023-03-15 17:46:49,558] [INFO] Selected 16 target genomes.
[2023-03-15 17:46:49,558] [INFO] Target genome list was writen to OceanDNA-b32091/target_genomes.txt
[2023-03-15 17:46:49,569] [INFO] Task started: fastANI
[2023-03-15 17:46:49,569] [INFO] Running command: fastANI --query /var/lib/cwl/stg0f48757e-8921-4c95-8dc2-f621e15f01d7/OceanDNA-b32091.fa --refList OceanDNA-b32091/target_genomes.txt --output OceanDNA-b32091/fastani_result.tsv --threads 1
[2023-03-15 17:47:03,326] [INFO] Task succeeded: fastANI
[2023-03-15 17:47:03,327] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg612297a8-9d1e-4aa6-a103-a13d350c10b0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 17:47:03,327] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg612297a8-9d1e-4aa6-a103-a13d350c10b0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 17:47:03,337] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 17:47:03,337] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 17:47:03,337] [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	85.0925	615	804	95	below_threshold
Sphingobium xenophagum	strain=NBRC 107872	GCA_000367345.1	121428	121428	type	True	84.5449	592	804	95	below_threshold
Sphingobium psychrophilum	strain=AR-3-1	GCA_012927105.1	2728834	2728834	type	True	84.5002	648	804	95	below_threshold
Sphingobium cupriresistens	strain=CCTCC AB 2011146	GCA_004152865.1	1132417	1132417	type	True	84.0144	619	804	95	below_threshold
Sphingobium limneticum	strain=DSM 25076	GCA_008710155.1	1007511	1007511	type	True	83.5504	614	804	95	below_threshold
Sphingobium yanoikuyae	strain=ATCC 51230	GCA_000315525.1	13690	13690	suspected-type	True	82.9259	616	804	95	below_threshold
Sphingobium scionense	strain=DSM 19371	GCA_014197035.1	1404341	1404341	type	True	82.6423	614	804	95	below_threshold
Sphingobium amiense	strain=NBRC 102518	GCA_001591305.1	135719	135719	type	True	82.3149	526	804	95	below_threshold
Sphingobium amiense	strain=DSM 16289	GCA_003967075.1	135719	135719	type	True	82.2882	537	804	95	below_threshold
Sphingobium lactosutens	strain=DS20	GCA_000445105.1	522773	522773	type	True	82.1515	580	804	95	below_threshold
Sphingobium indicum	strain=B90A	GCA_000264945.2	332055	332055	type	True	81.9411	539	804	95	below_threshold
Sphingobium ummariense	strain=RL-3	GCA_000447205.1	420994	420994	type	True	81.2259	546	804	95	below_threshold
Sphingobium sufflavum	strain=HL-25	GCA_021403115.1	1129547	1129547	type	True	78.8156	332	804	95	below_threshold
Sphingomonas suaedae	strain=XS-10	GCA_007833215.1	2599297	2599297	type	True	78.2847	292	804	95	below_threshold
Sphingomonas changnyeongensis	strain=C33	GCA_009913435.1	2698679	2698679	type	True	78.0454	283	804	95	below_threshold
Novosphingobium umbonatum	strain=FSY-9	GCA_004005905.1	1908524	1908524	type	True	76.9441	185	804	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 17:47:03,339] [INFO] DFAST Taxonomy check result was written to OceanDNA-b32091/tc_result.tsv
[2023-03-15 17:47:03,340] [INFO] ===== Taxonomy check completed =====
[2023-03-15 17:47:03,340] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 17:47:03,340] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg612297a8-9d1e-4aa6-a103-a13d350c10b0/dqc_reference/checkm_data
[2023-03-15 17:47:03,341] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 17:47:03,346] [INFO] Task started: CheckM
[2023-03-15 17:47:03,346] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b32091/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b32091/checkm_input OceanDNA-b32091/checkm_result
[2023-03-15 17:47:43,204] [INFO] Task succeeded: CheckM
[2023-03-15 17:47:43,205] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 50.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 17:47:43,208] [INFO] ===== Completeness check finished =====
[2023-03-15 17:47:43,208] [INFO] ===== Start GTDB Search =====
[2023-03-15 17:47:43,209] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b32091/markers.fasta)
[2023-03-15 17:47:43,210] [INFO] Task started: Blastn
[2023-03-15 17:47:43,210] [INFO] Running command: blastn -query OceanDNA-b32091/markers.fasta -db /var/lib/cwl/stg612297a8-9d1e-4aa6-a103-a13d350c10b0/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b32091/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 17:47:44,734] [INFO] Task succeeded: Blastn
[2023-03-15 17:47:44,734] [INFO] Selected 15 target genomes.
[2023-03-15 17:47:44,734] [INFO] Target genome list was writen to OceanDNA-b32091/target_genomes_gtdb.txt
[2023-03-15 17:47:44,775] [INFO] Task started: fastANI
[2023-03-15 17:47:44,775] [INFO] Running command: fastANI --query /var/lib/cwl/stg0f48757e-8921-4c95-8dc2-f621e15f01d7/OceanDNA-b32091.fa --refList OceanDNA-b32091/target_genomes_gtdb.txt --output OceanDNA-b32091/fastani_result_gtdb.tsv --threads 1
[2023-03-15 17:47:57,642] [INFO] Task succeeded: fastANI
[2023-03-15 17:47:57,651] [INFO] Found 15 fastANI hits (2 hits with ANI > circumscription radius)
[2023-03-15 17:47:57,651] [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_001713415.1	s__Sphingobium sp001713415	96.1512	762	804	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	95.59	95.59	0.75	0.75	2	inconclusive
GCF_002312805.1	s__Sphingobium sp002312805	95.3124	734	804	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	95.45	95.45	0.84	0.84	2	inconclusive
GCF_000588875.1	s__Sphingobium sp000588875	91.3956	685	804	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003591655.1	s__Sphingobium sp003591655	85.0965	615	804	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	84.9512	529	804	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016463275.1	s__Sphingobium sp016463275	84.6644	460	804	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	84.48	602	804	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	83.999	621	804	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	98.64	98.49	0.81	0.81	3	-
GCF_009720145.1	s__Sphingobium sp009720145	83.7896	601	804	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013822485.1	s__Sphingobium sp013822485	83.7658	466	804	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	83.5504	614	804	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	98.69	97.69	0.91	0.88	5	-
GCF_001421665.1	s__Sphingobium sp001421665	83.4704	624	804	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000315525.1	s__Sphingobium yanoikuyae	82.9076	617	804	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	96.25	95.31	0.82	0.72	34	-
GCF_003967075.1	s__Sphingobium amiense	82.3174	535	804	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	99.99	99.99	1.00	1.00	2	-
GCF_000447205.1	s__Sphingobium ummariense	81.2377	545	804	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 17:47:57,652] [INFO] GTDB search result was written to OceanDNA-b32091/result_gtdb.tsv
[2023-03-15 17:47:57,652] [INFO] ===== GTDB Search completed =====
[2023-03-15 17:47:57,653] [INFO] DFAST_QC result json was written to OceanDNA-b32091/dqc_result.json
[2023-03-15 17:47:57,654] [INFO] DFAST_QC completed!
[2023-03-15 17:47:57,654] [INFO] Total running time: 0h1m26s