[2024-01-24 14:28:15,872] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:28:15,874] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:28:15,875] [INFO] DQC Reference Directory: /var/lib/cwl/stg10b9fda7-1626-443e-9097-b77264d0e5f9/dqc_reference
[2024-01-24 14:28:17,938] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:28:17,939] [INFO] Task started: Prodigal
[2024-01-24 14:28:17,939] [INFO] Running command: gunzip -c /var/lib/cwl/stgc284e9ca-e58e-41ce-a7a8-95f2ad8061d1/GCF_005771435.1_ASM577143v1_genomic.fna.gz | prodigal -d GCF_005771435.1_ASM577143v1_genomic.fna/cds.fna -a GCF_005771435.1_ASM577143v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:28:32,167] [INFO] Task succeeded: Prodigal
[2024-01-24 14:28:32,167] [INFO] Task started: HMMsearch
[2024-01-24 14:28:32,167] [INFO] Running command: hmmsearch --tblout GCF_005771435.1_ASM577143v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg10b9fda7-1626-443e-9097-b77264d0e5f9/dqc_reference/reference_markers.hmm GCF_005771435.1_ASM577143v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:28:32,445] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:28:32,447] [INFO] Found 6/6 markers.
[2024-01-24 14:28:32,494] [INFO] Query marker FASTA was written to GCF_005771435.1_ASM577143v1_genomic.fna/markers.fasta
[2024-01-24 14:28:32,494] [INFO] Task started: Blastn
[2024-01-24 14:28:32,494] [INFO] Running command: blastn -query GCF_005771435.1_ASM577143v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg10b9fda7-1626-443e-9097-b77264d0e5f9/dqc_reference/reference_markers.fasta -out GCF_005771435.1_ASM577143v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:28:33,382] [INFO] Task succeeded: Blastn
[2024-01-24 14:28:33,386] [INFO] Selected 11 target genomes.
[2024-01-24 14:28:33,386] [INFO] Target genome list was writen to GCF_005771435.1_ASM577143v1_genomic.fna/target_genomes.txt
[2024-01-24 14:28:33,427] [INFO] Task started: fastANI
[2024-01-24 14:28:33,427] [INFO] Running command: fastANI --query /var/lib/cwl/stgc284e9ca-e58e-41ce-a7a8-95f2ad8061d1/GCF_005771435.1_ASM577143v1_genomic.fna.gz --refList GCF_005771435.1_ASM577143v1_genomic.fna/target_genomes.txt --output GCF_005771435.1_ASM577143v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:28:43,151] [INFO] Task succeeded: fastANI
[2024-01-24 14:28:43,151] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg10b9fda7-1626-443e-9097-b77264d0e5f9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:28:43,152] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg10b9fda7-1626-443e-9097-b77264d0e5f9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:28:43,162] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:28:43,163] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:28:43,163] [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
Microbulbifer harenosus	strain=HB161719	GCA_005771435.1	2576840	2576840	type	True	100.0	1524	1526	95	conclusive
Microbulbifer elongatus	strain=DSM 6810	GCA_022554105.1	86173	86173	type	True	81.5258	753	1526	95	below_threshold
Microbulbifer elongatus	strain=DSM 6810	GCA_021165935.1	86173	86173	type	True	81.4726	764	1526	95	below_threshold
Microbulbifer hydrolyticus	strain=IRE-31	GCA_009931115.1	48074	48074	type	True	81.2018	801	1526	95	below_threshold
Microbulbifer celer	strain=KCTC 12973	GCA_020991125.1	435905	435905	type	True	81.179	789	1526	95	below_threshold
Microbulbifer hydrolyticus	strain=DSM 11525	GCA_014202835.1	48074	48074	type	True	81.1699	814	1526	95	below_threshold
Microbulbifer mangrovi	strain=DD-13	GCA_002009015.1	927787	927787	type	True	80.938	753	1526	95	below_threshold
Microbulbifer marinus	strain=CGMCC 1.10657	GCA_900107725.1	658218	658218	type	True	79.6986	557	1526	95	below_threshold
Microbulbifer taiwanensis	strain=LMG 26125	GCA_014904815.1	986746	986746	type	True	79.6451	616	1526	95	below_threshold
Stutzerimonas degradans	strain=FDAARGOS_876	GCA_016028635.1	2968968	2968968	suspected-type	True	76.8637	120	1526	95	below_threshold
Stutzerimonas degradans	strain=DSM 50238	GCA_024448505.1	2968968	2968968	type	True	76.7951	116	1526	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:28:43,164] [INFO] DFAST Taxonomy check result was written to GCF_005771435.1_ASM577143v1_genomic.fna/tc_result.tsv
[2024-01-24 14:28:43,165] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:28:43,165] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:28:43,166] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg10b9fda7-1626-443e-9097-b77264d0e5f9/dqc_reference/checkm_data
[2024-01-24 14:28:43,167] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:28:43,216] [INFO] Task started: CheckM
[2024-01-24 14:28:43,216] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_005771435.1_ASM577143v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_005771435.1_ASM577143v1_genomic.fna/checkm_input GCF_005771435.1_ASM577143v1_genomic.fna/checkm_result
[2024-01-24 14:29:26,683] [INFO] Task succeeded: CheckM
[2024-01-24 14:29:26,685] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:29:26,704] [INFO] ===== Completeness check finished =====
[2024-01-24 14:29:26,704] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:29:26,704] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_005771435.1_ASM577143v1_genomic.fna/markers.fasta)
[2024-01-24 14:29:26,705] [INFO] Task started: Blastn
[2024-01-24 14:29:26,705] [INFO] Running command: blastn -query GCF_005771435.1_ASM577143v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg10b9fda7-1626-443e-9097-b77264d0e5f9/dqc_reference/reference_markers_gtdb.fasta -out GCF_005771435.1_ASM577143v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:29:28,190] [INFO] Task succeeded: Blastn
[2024-01-24 14:29:28,193] [INFO] Selected 12 target genomes.
[2024-01-24 14:29:28,193] [INFO] Target genome list was writen to GCF_005771435.1_ASM577143v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:29:28,210] [INFO] Task started: fastANI
[2024-01-24 14:29:28,211] [INFO] Running command: fastANI --query /var/lib/cwl/stgc284e9ca-e58e-41ce-a7a8-95f2ad8061d1/GCF_005771435.1_ASM577143v1_genomic.fna.gz --refList GCF_005771435.1_ASM577143v1_genomic.fna/target_genomes_gtdb.txt --output GCF_005771435.1_ASM577143v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:29:39,779] [INFO] Task succeeded: fastANI
[2024-01-24 14:29:39,790] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:29:39,790] [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_005771435.1	s__Microbulbifer harenosus	100.0	1524	1526	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Microbulbifer	95.0	98.17	98.17	0.93	0.93	2	conclusive
GCF_002959965.1	s__Microbulbifer pacificus	84.5227	971	1526	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Microbulbifer	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009903625.1	s__Microbulbifer sp009903625	81.633	829	1526	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Microbulbifer	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017303155.1	s__Microbulbifer salipaludis	81.4782	716	1526	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Microbulbifer	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013367775.1	s__Microbulbifer sp013367775	81.4606	842	1526	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Microbulbifer	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000708675.1	s__Microbulbifer sp000708675	81.4051	749	1526	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Microbulbifer	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001639145.1	s__Microbulbifer sp001639145	81.3425	755	1526	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Microbulbifer	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009931115.1	s__Microbulbifer hydrolyticus	81.1963	801	1526	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Microbulbifer	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002009015.1	s__Microbulbifer mangrovi	80.9314	753	1526	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Microbulbifer	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000220505.1	s__Microbulbifer agarilyticus_B	80.6807	614	1526	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Microbulbifer	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900107725.1	s__Microbulbifer marinus	79.7077	556	1526	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Microbulbifer	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014904815.1	s__Microbulbifer taiwanensis	79.6645	613	1526	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Microbulbifer	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:29:39,792] [INFO] GTDB search result was written to GCF_005771435.1_ASM577143v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:29:39,793] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:29:39,796] [INFO] DFAST_QC result json was written to GCF_005771435.1_ASM577143v1_genomic.fna/dqc_result.json
[2024-01-24 14:29:39,796] [INFO] DFAST_QC completed!
[2024-01-24 14:29:39,796] [INFO] Total running time: 0h1m24s