[2024-01-24 14:42:02,523] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:42:02,526] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:42:02,527] [INFO] DQC Reference Directory: /var/lib/cwl/stga9408088-508a-4bc3-b179-6e5bc78a1bee/dqc_reference
[2024-01-24 14:42:03,883] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:42:03,884] [INFO] Task started: Prodigal
[2024-01-24 14:42:03,885] [INFO] Running command: gunzip -c /var/lib/cwl/stg93bc89e4-6075-463e-8d64-999e816eaf9e/GCF_000981765.1_ASM98176v1_genomic.fna.gz | prodigal -d GCF_000981765.1_ASM98176v1_genomic.fna/cds.fna -a GCF_000981765.1_ASM98176v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:42:09,924] [INFO] Task succeeded: Prodigal
[2024-01-24 14:42:09,925] [INFO] Task started: HMMsearch
[2024-01-24 14:42:09,925] [INFO] Running command: hmmsearch --tblout GCF_000981765.1_ASM98176v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga9408088-508a-4bc3-b179-6e5bc78a1bee/dqc_reference/reference_markers.hmm GCF_000981765.1_ASM98176v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:42:10,154] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:42:10,156] [INFO] Found 6/6 markers.
[2024-01-24 14:42:10,182] [INFO] Query marker FASTA was written to GCF_000981765.1_ASM98176v1_genomic.fna/markers.fasta
[2024-01-24 14:42:10,182] [INFO] Task started: Blastn
[2024-01-24 14:42:10,182] [INFO] Running command: blastn -query GCF_000981765.1_ASM98176v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga9408088-508a-4bc3-b179-6e5bc78a1bee/dqc_reference/reference_markers.fasta -out GCF_000981765.1_ASM98176v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:42:10,931] [INFO] Task succeeded: Blastn
[2024-01-24 14:42:10,935] [INFO] Selected 15 target genomes.
[2024-01-24 14:42:10,936] [INFO] Target genome list was writen to GCF_000981765.1_ASM98176v1_genomic.fna/target_genomes.txt
[2024-01-24 14:42:10,957] [INFO] Task started: fastANI
[2024-01-24 14:42:10,957] [INFO] Running command: fastANI --query /var/lib/cwl/stg93bc89e4-6075-463e-8d64-999e816eaf9e/GCF_000981765.1_ASM98176v1_genomic.fna.gz --refList GCF_000981765.1_ASM98176v1_genomic.fna/target_genomes.txt --output GCF_000981765.1_ASM98176v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:42:18,482] [INFO] Task succeeded: fastANI
[2024-01-24 14:42:18,483] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga9408088-508a-4bc3-b179-6e5bc78a1bee/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:42:18,483] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga9408088-508a-4bc3-b179-6e5bc78a1bee/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:42:18,494] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:42:18,495] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:42:18,495] [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	100.0	829	831	95	conclusive
Kangiella taiwanensis	strain=KT1	GCA_020005165.1	1079179	1079179	type	True	82.2897	560	831	95	below_threshold
Kangiella spongicola	strain=ATCC BAA-2076	GCA_003194565.2	796379	796379	type	True	80.2039	403	831	95	below_threshold
Kangiella sediminilitoris	strain=KCTC 23892	GCA_001708405.1	1144748	1144748	type	True	79.888	272	831	95	below_threshold
Kangiella shandongensis	strain=PI	GCA_020005365.1	2763258	2763258	type	True	79.3861	321	831	95	below_threshold
Kangiella koreensis	strain=DSM 16069	GCA_000024085.1	261964	261964	type	True	78.4783	158	831	95	below_threshold
Kangiella aquimarina	strain=DSM 16071	GCA_000374105.1	261965	261965	type	True	77.9841	145	831	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:42:18,497] [INFO] DFAST Taxonomy check result was written to GCF_000981765.1_ASM98176v1_genomic.fna/tc_result.tsv
[2024-01-24 14:42:18,497] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:42:18,497] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:42:18,498] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga9408088-508a-4bc3-b179-6e5bc78a1bee/dqc_reference/checkm_data
[2024-01-24 14:42:18,499] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:42:18,527] [INFO] Task started: CheckM
[2024-01-24 14:42:18,528] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000981765.1_ASM98176v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000981765.1_ASM98176v1_genomic.fna/checkm_input GCF_000981765.1_ASM98176v1_genomic.fna/checkm_result
[2024-01-24 14:42:43,514] [INFO] Task succeeded: CheckM
[2024-01-24 14:42:43,516] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:42:43,532] [INFO] ===== Completeness check finished =====
[2024-01-24 14:42:43,533] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:42:43,533] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000981765.1_ASM98176v1_genomic.fna/markers.fasta)
[2024-01-24 14:42:43,533] [INFO] Task started: Blastn
[2024-01-24 14:42:43,534] [INFO] Running command: blastn -query GCF_000981765.1_ASM98176v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga9408088-508a-4bc3-b179-6e5bc78a1bee/dqc_reference/reference_markers_gtdb.fasta -out GCF_000981765.1_ASM98176v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:42:44,670] [INFO] Task succeeded: Blastn
[2024-01-24 14:42:44,674] [INFO] Selected 17 target genomes.
[2024-01-24 14:42:44,674] [INFO] Target genome list was writen to GCF_000981765.1_ASM98176v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:42:44,688] [INFO] Task started: fastANI
[2024-01-24 14:42:44,689] [INFO] Running command: fastANI --query /var/lib/cwl/stg93bc89e4-6075-463e-8d64-999e816eaf9e/GCF_000981765.1_ASM98176v1_genomic.fna.gz --refList GCF_000981765.1_ASM98176v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000981765.1_ASM98176v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:42:53,740] [INFO] Task succeeded: fastANI
[2024-01-24 14:42:53,748] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:42:53,749] [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	100.0	829	831	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	81.6912	301	831	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	80.2094	401	831	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	79.9092	274	831	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	78.5263	148	831	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Kangiellaceae;g__Kangiella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000024085.1	s__Kangiella koreensis	78.4458	158	831	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	77.9841	145	831	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	77.5917	148	831	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	77.3017	132	831	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 14:42:53,750] [INFO] GTDB search result was written to GCF_000981765.1_ASM98176v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:42:53,751] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:42:53,754] [INFO] DFAST_QC result json was written to GCF_000981765.1_ASM98176v1_genomic.fna/dqc_result.json
[2024-01-24 14:42:53,754] [INFO] DFAST_QC completed!
[2024-01-24 14:42:53,754] [INFO] Total running time: 0h0m51s