[2023-03-17 02:54:22,027] [INFO] DFAST_QC pipeline started.
[2023-03-17 02:54:22,027] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 02:54:22,027] [INFO] DQC Reference Directory: /var/lib/cwl/stg8648c1c3-8276-4187-92ee-b1a0604bb922/dqc_reference
[2023-03-17 02:54:23,265] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 02:54:23,266] [INFO] Task started: Prodigal
[2023-03-17 02:54:23,266] [INFO] Running command: cat /var/lib/cwl/stg8f9194e6-897c-468e-a353-6cbe671f5c4a/OceanDNA-b35179.fa | prodigal -d OceanDNA-b35179/cds.fna -a OceanDNA-b35179/protein.faa -g 11 -q > /dev/null
[2023-03-17 02:54:34,158] [INFO] Task succeeded: Prodigal
[2023-03-17 02:54:34,158] [INFO] Task started: HMMsearch
[2023-03-17 02:54:34,158] [INFO] Running command: hmmsearch --tblout OceanDNA-b35179/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8648c1c3-8276-4187-92ee-b1a0604bb922/dqc_reference/reference_markers.hmm OceanDNA-b35179/protein.faa > /dev/null
[2023-03-17 02:54:34,346] [INFO] Task succeeded: HMMsearch
[2023-03-17 02:54:34,347] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg8f9194e6-897c-468e-a353-6cbe671f5c4a/OceanDNA-b35179.fa]
[2023-03-17 02:54:34,368] [INFO] Query marker FASTA was written to OceanDNA-b35179/markers.fasta
[2023-03-17 02:54:34,369] [INFO] Task started: Blastn
[2023-03-17 02:54:34,369] [INFO] Running command: blastn -query OceanDNA-b35179/markers.fasta -db /var/lib/cwl/stg8648c1c3-8276-4187-92ee-b1a0604bb922/dqc_reference/reference_markers.fasta -out OceanDNA-b35179/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 02:54:34,974] [INFO] Task succeeded: Blastn
[2023-03-17 02:54:34,976] [INFO] Selected 17 target genomes.
[2023-03-17 02:54:34,976] [INFO] Target genome list was writen to OceanDNA-b35179/target_genomes.txt
[2023-03-17 02:54:35,033] [INFO] Task started: fastANI
[2023-03-17 02:54:35,033] [INFO] Running command: fastANI --query /var/lib/cwl/stg8f9194e6-897c-468e-a353-6cbe671f5c4a/OceanDNA-b35179.fa --refList OceanDNA-b35179/target_genomes.txt --output OceanDNA-b35179/fastani_result.tsv --threads 1
[2023-03-17 02:54:43,837] [INFO] Task succeeded: fastANI
[2023-03-17 02:54:43,837] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8648c1c3-8276-4187-92ee-b1a0604bb922/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 02:54:43,838] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8648c1c3-8276-4187-92ee-b1a0604bb922/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 02:54:43,845] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2023-03-17 02:54:43,845] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-17 02:54:43,845] [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
Kangiella geojedonensis	strain=YCS-5	GCA_000981765.1	914150	914150	type	True	97.859	618	647	95	conclusive
Kangiella taiwanensis	strain=KT1	GCA_020005165.1	1079179	1079179	type	True	81.448	451	647	95	below_threshold
Kangiella spongicola	strain=ATCC BAA-2076	GCA_003194565.2	796379	796379	type	True	79.058	293	647	95	below_threshold
Kangiella shandongensis	strain=PI	GCA_020005365.1	2763258	2763258	type	True	78.0685	227	647	95	below_threshold
Kangiella sediminilitoris	strain=KCTC 23892	GCA_001708405.1	1144748	1144748	type	True	77.9409	196	647	95	below_threshold
Kangiella koreensis	strain=DSM 16069	GCA_000024085.1	261964	261964	type	True	76.8397	90	647	95	below_threshold
Kangiella profundi	strain=CGMCC 1.12959	GCA_014640235.1	1561924	1561924	type	True	76.7335	90	647	95	below_threshold
Kangiella aquimarina	strain=DSM 16071	GCA_000374105.1	261965	261965	type	True	76.541	108	647	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 02:54:43,847] [INFO] DFAST Taxonomy check result was written to OceanDNA-b35179/tc_result.tsv
[2023-03-17 02:54:43,847] [INFO] ===== Taxonomy check completed =====
[2023-03-17 02:54:43,847] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 02:54:43,847] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8648c1c3-8276-4187-92ee-b1a0604bb922/dqc_reference/checkm_data
[2023-03-17 02:54:43,848] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 02:54:43,871] [INFO] Task started: CheckM
[2023-03-17 02:54:43,871] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b35179/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b35179/checkm_input OceanDNA-b35179/checkm_result
[2023-03-17 02:55:14,753] [INFO] Task succeeded: CheckM
[2023-03-17 02:55:14,753] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 59.95%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 02:55:14,771] [INFO] ===== Completeness check finished =====
[2023-03-17 02:55:14,771] [INFO] ===== Start GTDB Search =====
[2023-03-17 02:55:14,771] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b35179/markers.fasta)
[2023-03-17 02:55:14,772] [INFO] Task started: Blastn
[2023-03-17 02:55:14,772] [INFO] Running command: blastn -query OceanDNA-b35179/markers.fasta -db /var/lib/cwl/stg8648c1c3-8276-4187-92ee-b1a0604bb922/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b35179/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 02:55:15,739] [INFO] Task succeeded: Blastn
[2023-03-17 02:55:15,739] [INFO] Selected 15 target genomes.
[2023-03-17 02:55:15,739] [INFO] Target genome list was writen to OceanDNA-b35179/target_genomes_gtdb.txt
[2023-03-17 02:55:15,749] [INFO] Task started: fastANI
[2023-03-17 02:55:15,749] [INFO] Running command: fastANI --query /var/lib/cwl/stg8f9194e6-897c-468e-a353-6cbe671f5c4a/OceanDNA-b35179.fa --refList OceanDNA-b35179/target_genomes_gtdb.txt --output OceanDNA-b35179/fastani_result_gtdb.tsv --threads 1
[2023-03-17 02:55:23,362] [INFO] Task succeeded: fastANI
[2023-03-17 02:55:23,367] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 02:55:23,368] [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_000981765.1	s__Kangiella geojedonensis	97.859	618	647	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Kangiellaceae;g__Kangiella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_003370465.1	s__Kangiella sp003370465	80.3701	247	647	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Kangiellaceae;g__Kangiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003194565.2	s__Kangiella spongicola	79.058	293	647	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Kangiellaceae;g__Kangiella	95.0	96.32	96.32	0.92	0.92	2	-
GCF_001708405.1	s__Kangiella sediminilitoris	77.9409	196	647	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Kangiellaceae;g__Kangiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000024085.1	s__Kangiella koreensis	76.8397	90	647	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Kangiellaceae;g__Kangiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002838765.1	s__Kangiella profundi	76.7576	89	647	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Kangiellaceae;g__Kangiella	95.0	100.00	100.00	1.00	1.00	2	-
GCA_013373015.1	s__Kangiella sp013373015	76.7272	81	647	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Kangiellaceae;g__Kangiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000374105.1	s__Kangiella aquimarina	76.541	108	647	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Kangiellaceae;g__Kangiella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 02:55:23,368] [INFO] GTDB search result was written to OceanDNA-b35179/result_gtdb.tsv
[2023-03-17 02:55:23,368] [INFO] ===== GTDB Search completed =====
[2023-03-17 02:55:23,369] [INFO] DFAST_QC result json was written to OceanDNA-b35179/dqc_result.json
[2023-03-17 02:55:23,369] [INFO] DFAST_QC completed!
[2023-03-17 02:55:23,369] [INFO] Total running time: 0h1m1s