[2023-03-16 18:28:42,317] [INFO] DFAST_QC pipeline started.
[2023-03-16 18:28:42,318] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 18:28:42,318] [INFO] DQC Reference Directory: /var/lib/cwl/stg6690fc9f-ca2b-4e4c-a66c-3d5072f4cb9a/dqc_reference
[2023-03-16 18:28:43,459] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 18:28:43,460] [INFO] Task started: Prodigal
[2023-03-16 18:28:43,460] [INFO] Running command: cat /var/lib/cwl/stg53cd42a7-d8bb-4364-8297-e66b2d9016c1/OceanDNA-b35168.fa | prodigal -d OceanDNA-b35168/cds.fna -a OceanDNA-b35168/protein.faa -g 11 -q > /dev/null
[2023-03-16 18:29:04,391] [INFO] Task succeeded: Prodigal
[2023-03-16 18:29:04,392] [INFO] Task started: HMMsearch
[2023-03-16 18:29:04,392] [INFO] Running command: hmmsearch --tblout OceanDNA-b35168/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6690fc9f-ca2b-4e4c-a66c-3d5072f4cb9a/dqc_reference/reference_markers.hmm OceanDNA-b35168/protein.faa > /dev/null
[2023-03-16 18:29:04,679] [INFO] Task succeeded: HMMsearch
[2023-03-16 18:29:04,679] [INFO] Found 6/6 markers.
[2023-03-16 18:29:04,699] [INFO] Query marker FASTA was written to OceanDNA-b35168/markers.fasta
[2023-03-16 18:29:04,700] [INFO] Task started: Blastn
[2023-03-16 18:29:04,700] [INFO] Running command: blastn -query OceanDNA-b35168/markers.fasta -db /var/lib/cwl/stg6690fc9f-ca2b-4e4c-a66c-3d5072f4cb9a/dqc_reference/reference_markers.fasta -out OceanDNA-b35168/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 18:29:05,292] [INFO] Task succeeded: Blastn
[2023-03-16 18:29:05,293] [INFO] Selected 26 target genomes.
[2023-03-16 18:29:05,294] [INFO] Target genome list was writen to OceanDNA-b35168/target_genomes.txt
[2023-03-16 18:29:05,311] [INFO] Task started: fastANI
[2023-03-16 18:29:05,311] [INFO] Running command: fastANI --query /var/lib/cwl/stg53cd42a7-d8bb-4364-8297-e66b2d9016c1/OceanDNA-b35168.fa --refList OceanDNA-b35168/target_genomes.txt --output OceanDNA-b35168/fastani_result.tsv --threads 1
[2023-03-16 18:29:24,817] [INFO] Task succeeded: fastANI
[2023-03-16 18:29:24,817] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6690fc9f-ca2b-4e4c-a66c-3d5072f4cb9a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 18:29:24,818] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6690fc9f-ca2b-4e4c-a66c-3d5072f4cb9a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 18:29:24,823] [INFO] Found 5 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 18:29:24,823] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 18:29:24,823] [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 aquimarina	strain=DSM 16071	GCA_000374105.1	261965	261965	type	True	77.3568	82	882	95	below_threshold
Kangiella profundi	strain=FT102	GCA_002838765.1	1561924	1561924	type	True	77.2601	79	882	95	below_threshold
Kangiella profundi	strain=CGMCC 1.12959	GCA_014640235.1	1561924	1561924	type	True	77.224	82	882	95	below_threshold
Kangiella spongicola	strain=ATCC BAA-2076	GCA_003194565.2	796379	796379	type	True	77.166	79	882	95	below_threshold
Kangiella koreensis	strain=DSM 16069	GCA_000024085.1	261964	261964	type	True	76.6126	99	882	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 18:29:24,824] [INFO] DFAST Taxonomy check result was written to OceanDNA-b35168/tc_result.tsv
[2023-03-16 18:29:24,824] [INFO] ===== Taxonomy check completed =====
[2023-03-16 18:29:24,824] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 18:29:24,824] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6690fc9f-ca2b-4e4c-a66c-3d5072f4cb9a/dqc_reference/checkm_data
[2023-03-16 18:29:24,825] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 18:29:24,955] [INFO] Task started: CheckM
[2023-03-16 18:29:24,955] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b35168/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b35168/checkm_input OceanDNA-b35168/checkm_result
[2023-03-16 18:30:10,855] [INFO] Task succeeded: CheckM
[2023-03-16 18:30:10,855] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 58.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 18:30:10,858] [INFO] ===== Completeness check finished =====
[2023-03-16 18:30:10,858] [INFO] ===== Start GTDB Search =====
[2023-03-16 18:30:10,859] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b35168/markers.fasta)
[2023-03-16 18:30:10,860] [INFO] Task started: Blastn
[2023-03-16 18:30:10,860] [INFO] Running command: blastn -query OceanDNA-b35168/markers.fasta -db /var/lib/cwl/stg6690fc9f-ca2b-4e4c-a66c-3d5072f4cb9a/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b35168/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 18:30:11,824] [INFO] Task succeeded: Blastn
[2023-03-16 18:30:11,825] [INFO] Selected 29 target genomes.
[2023-03-16 18:30:11,826] [INFO] Target genome list was writen to OceanDNA-b35168/target_genomes_gtdb.txt
[2023-03-16 18:30:11,905] [INFO] Task started: fastANI
[2023-03-16 18:30:11,905] [INFO] Running command: fastANI --query /var/lib/cwl/stg53cd42a7-d8bb-4364-8297-e66b2d9016c1/OceanDNA-b35168.fa --refList OceanDNA-b35168/target_genomes_gtdb.txt --output OceanDNA-b35168/fastani_result_gtdb.tsv --threads 1
[2023-03-16 18:30:27,670] [INFO] Task succeeded: fastANI
[2023-03-16 18:30:27,675] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 18:30:27,675] [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_013373015.1	s__Kangiella sp013373015	77.9221	194	882	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	77.3568	82	882	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	77.2245	80	882	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Kangiellaceae;g__Kangiella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_009674675.1	s__Kangiella sp009674675	77.1953	100	882	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	77.1642	80	882	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Kangiellaceae;g__Kangiella	95.0	96.32	96.32	0.92	0.92	2	-
GCF_000024085.1	s__Kangiella koreensis	76.6084	98	882	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Kangiellaceae;g__Kangiella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 18:30:27,675] [INFO] GTDB search result was written to OceanDNA-b35168/result_gtdb.tsv
[2023-03-16 18:30:27,675] [INFO] ===== GTDB Search completed =====
[2023-03-16 18:30:27,676] [INFO] DFAST_QC result json was written to OceanDNA-b35168/dqc_result.json
[2023-03-16 18:30:27,676] [INFO] DFAST_QC completed!
[2023-03-16 18:30:27,676] [INFO] Total running time: 0h1m45s