[2024-01-24 13:17:05,545] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:17:05,547] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:17:05,548] [INFO] DQC Reference Directory: /var/lib/cwl/stg273d4333-d56c-4d4b-a76f-0f70bc04a75e/dqc_reference
[2024-01-24 13:17:06,932] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:17:06,933] [INFO] Task started: Prodigal
[2024-01-24 13:17:06,933] [INFO] Running command: gunzip -c /var/lib/cwl/stgf5177df3-1b91-456a-b48b-64ddb5f3e25d/GCF_002838765.1_ASM283876v1_genomic.fna.gz | prodigal -d GCF_002838765.1_ASM283876v1_genomic.fna/cds.fna -a GCF_002838765.1_ASM283876v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:17:13,600] [INFO] Task succeeded: Prodigal
[2024-01-24 13:17:13,601] [INFO] Task started: HMMsearch
[2024-01-24 13:17:13,601] [INFO] Running command: hmmsearch --tblout GCF_002838765.1_ASM283876v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg273d4333-d56c-4d4b-a76f-0f70bc04a75e/dqc_reference/reference_markers.hmm GCF_002838765.1_ASM283876v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:17:13,869] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:17:13,870] [INFO] Found 6/6 markers.
[2024-01-24 13:17:13,893] [INFO] Query marker FASTA was written to GCF_002838765.1_ASM283876v1_genomic.fna/markers.fasta
[2024-01-24 13:17:13,893] [INFO] Task started: Blastn
[2024-01-24 13:17:13,893] [INFO] Running command: blastn -query GCF_002838765.1_ASM283876v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg273d4333-d56c-4d4b-a76f-0f70bc04a75e/dqc_reference/reference_markers.fasta -out GCF_002838765.1_ASM283876v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:17:14,600] [INFO] Task succeeded: Blastn
[2024-01-24 13:17:14,603] [INFO] Selected 15 target genomes.
[2024-01-24 13:17:14,603] [INFO] Target genome list was writen to GCF_002838765.1_ASM283876v1_genomic.fna/target_genomes.txt
[2024-01-24 13:17:14,609] [INFO] Task started: fastANI
[2024-01-24 13:17:14,609] [INFO] Running command: fastANI --query /var/lib/cwl/stgf5177df3-1b91-456a-b48b-64ddb5f3e25d/GCF_002838765.1_ASM283876v1_genomic.fna.gz --refList GCF_002838765.1_ASM283876v1_genomic.fna/target_genomes.txt --output GCF_002838765.1_ASM283876v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:17:26,958] [INFO] Task succeeded: fastANI
[2024-01-24 13:17:26,959] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg273d4333-d56c-4d4b-a76f-0f70bc04a75e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:17:26,959] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg273d4333-d56c-4d4b-a76f-0f70bc04a75e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:17:26,967] [INFO] Found 7 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:17:26,967] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:17:26,967] [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 profundi	strain=FT102	GCA_002838765.1	1561924	1561924	type	True	100.0	884	884	95	conclusive
Kangiella profundi	strain=CGMCC 1.12959	GCA_014640235.1	1561924	1561924	type	True	99.9962	882	884	95	conclusive
Kangiella aquimarina	strain=DSM 16071	GCA_000374105.1	261965	261965	type	True	88.9076	788	884	95	below_threshold
Kangiella koreensis	strain=DSM 16069	GCA_000024085.1	261964	261964	type	True	81.7983	604	884	95	below_threshold
Kangiella geojedonensis	strain=YCS-5	GCA_000981765.1	914150	914150	type	True	78.4775	144	884	95	below_threshold
Kangiella taiwanensis	strain=KT1	GCA_020005165.1	1079179	1079179	type	True	78.3441	151	884	95	below_threshold
Kangiella shandongensis	strain=PI	GCA_020005365.1	2763258	2763258	type	True	77.9753	159	884	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:17:26,969] [INFO] DFAST Taxonomy check result was written to GCF_002838765.1_ASM283876v1_genomic.fna/tc_result.tsv
[2024-01-24 13:17:26,970] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:17:26,970] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:17:26,970] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg273d4333-d56c-4d4b-a76f-0f70bc04a75e/dqc_reference/checkm_data
[2024-01-24 13:17:26,972] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:17:27,004] [INFO] Task started: CheckM
[2024-01-24 13:17:27,004] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002838765.1_ASM283876v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002838765.1_ASM283876v1_genomic.fna/checkm_input GCF_002838765.1_ASM283876v1_genomic.fna/checkm_result
[2024-01-24 13:17:53,399] [INFO] Task succeeded: CheckM
[2024-01-24 13:17:53,400] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:17:53,421] [INFO] ===== Completeness check finished =====
[2024-01-24 13:17:53,421] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:17:53,421] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002838765.1_ASM283876v1_genomic.fna/markers.fasta)
[2024-01-24 13:17:53,422] [INFO] Task started: Blastn
[2024-01-24 13:17:53,422] [INFO] Running command: blastn -query GCF_002838765.1_ASM283876v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg273d4333-d56c-4d4b-a76f-0f70bc04a75e/dqc_reference/reference_markers_gtdb.fasta -out GCF_002838765.1_ASM283876v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:17:54,522] [INFO] Task succeeded: Blastn
[2024-01-24 13:17:54,526] [INFO] Selected 10 target genomes.
[2024-01-24 13:17:54,526] [INFO] Target genome list was writen to GCF_002838765.1_ASM283876v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:17:54,534] [INFO] Task started: fastANI
[2024-01-24 13:17:54,534] [INFO] Running command: fastANI --query /var/lib/cwl/stgf5177df3-1b91-456a-b48b-64ddb5f3e25d/GCF_002838765.1_ASM283876v1_genomic.fna.gz --refList GCF_002838765.1_ASM283876v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002838765.1_ASM283876v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:18:01,010] [INFO] Task succeeded: fastANI
[2024-01-24 13:18:01,020] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:18:01,021] [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_002838765.1	s__Kangiella profundi	100.0	884	884	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Kangiellaceae;g__Kangiella	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_000374105.1	s__Kangiella aquimarina	88.9076	788	884	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Kangiellaceae;g__Kangiella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014762745.1	s__Kangiella sp014762745	84.2118	639	884	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	81.8002	604	884	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	78.6271	146	884	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Kangiellaceae;g__Kangiella	95.0	96.32	96.32	0.92	0.92	2	-
GCF_000981765.1	s__Kangiella geojedonensis	78.3495	143	884	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Kangiellaceae;g__Kangiella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013373015.1	s__Kangiella sp013373015	77.2567	142	884	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Kangiellaceae;g__Kangiella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:18:01,023] [INFO] GTDB search result was written to GCF_002838765.1_ASM283876v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:18:01,023] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:18:01,026] [INFO] DFAST_QC result json was written to GCF_002838765.1_ASM283876v1_genomic.fna/dqc_result.json
[2024-01-24 13:18:01,026] [INFO] DFAST_QC completed!
[2024-01-24 13:18:01,026] [INFO] Total running time: 0h0m55s