[2024-01-25 18:54:20,716] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:54:20,718] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:54:20,718] [INFO] DQC Reference Directory: /var/lib/cwl/stg5c4c89f1-1311-4481-bd66-290dd1f01e1f/dqc_reference
[2024-01-25 18:54:21,853] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:54:21,854] [INFO] Task started: Prodigal
[2024-01-25 18:54:21,854] [INFO] Running command: gunzip -c /var/lib/cwl/stg26bdb256-3b0e-4f6a-a05b-d2d685422b5d/GCF_002732165.1_ASM273216v1_genomic.fna.gz | prodigal -d GCF_002732165.1_ASM273216v1_genomic.fna/cds.fna -a GCF_002732165.1_ASM273216v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:54:26,175] [INFO] Task succeeded: Prodigal
[2024-01-25 18:54:26,175] [INFO] Task started: HMMsearch
[2024-01-25 18:54:26,175] [INFO] Running command: hmmsearch --tblout GCF_002732165.1_ASM273216v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5c4c89f1-1311-4481-bd66-290dd1f01e1f/dqc_reference/reference_markers.hmm GCF_002732165.1_ASM273216v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:54:26,382] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:54:26,383] [INFO] Found 6/6 markers.
[2024-01-25 18:54:26,407] [INFO] Query marker FASTA was written to GCF_002732165.1_ASM273216v1_genomic.fna/markers.fasta
[2024-01-25 18:54:26,408] [INFO] Task started: Blastn
[2024-01-25 18:54:26,408] [INFO] Running command: blastn -query GCF_002732165.1_ASM273216v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5c4c89f1-1311-4481-bd66-290dd1f01e1f/dqc_reference/reference_markers.fasta -out GCF_002732165.1_ASM273216v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:54:26,971] [INFO] Task succeeded: Blastn
[2024-01-25 18:54:26,974] [INFO] Selected 9 target genomes.
[2024-01-25 18:54:26,974] [INFO] Target genome list was writen to GCF_002732165.1_ASM273216v1_genomic.fna/target_genomes.txt
[2024-01-25 18:54:26,978] [INFO] Task started: fastANI
[2024-01-25 18:54:26,978] [INFO] Running command: fastANI --query /var/lib/cwl/stg26bdb256-3b0e-4f6a-a05b-d2d685422b5d/GCF_002732165.1_ASM273216v1_genomic.fna.gz --refList GCF_002732165.1_ASM273216v1_genomic.fna/target_genomes.txt --output GCF_002732165.1_ASM273216v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:54:32,214] [INFO] Task succeeded: fastANI
[2024-01-25 18:54:32,214] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5c4c89f1-1311-4481-bd66-290dd1f01e1f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:54:32,215] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5c4c89f1-1311-4481-bd66-290dd1f01e1f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:54:32,220] [INFO] Found 5 fastANI hits (3 hits with ANI > threshold)
[2024-01-25 18:54:32,220] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:54:32,220] [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
Staphylococcus xylosus	strain=CCM 2738	GCA_002732165.1	1288	1288	type	True	100.0	898	900	95	conclusive
Staphylococcus xylosus	strain=NCTC11043	GCA_900458755.1	1288	1288	type	True	99.9939	899	900	95	conclusive
Staphylococcus xylosus	strain=NCTC 11043	GCA_002901985.1	1288	1288	type	True	99.8599	791	900	95	conclusive
Staphylococcus pseudoxylosus	strain=S04009	GCA_003697915.1	2282419	2282419	type	True	93.3278	842	900	95	below_threshold
Staphylococcus shinii	strain=K22-5M	GCA_017583065.1	2912228	2912228	type	True	91.0232	830	900	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:54:32,222] [INFO] DFAST Taxonomy check result was written to GCF_002732165.1_ASM273216v1_genomic.fna/tc_result.tsv
[2024-01-25 18:54:32,222] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:54:32,223] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:54:32,223] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5c4c89f1-1311-4481-bd66-290dd1f01e1f/dqc_reference/checkm_data
[2024-01-25 18:54:32,223] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:54:32,252] [INFO] Task started: CheckM
[2024-01-25 18:54:32,253] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002732165.1_ASM273216v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002732165.1_ASM273216v1_genomic.fna/checkm_input GCF_002732165.1_ASM273216v1_genomic.fna/checkm_result
[2024-01-25 18:54:51,295] [INFO] Task succeeded: CheckM
[2024-01-25 18:54:51,296] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:54:51,322] [INFO] ===== Completeness check finished =====
[2024-01-25 18:54:51,322] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:54:51,322] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002732165.1_ASM273216v1_genomic.fna/markers.fasta)
[2024-01-25 18:54:51,322] [INFO] Task started: Blastn
[2024-01-25 18:54:51,323] [INFO] Running command: blastn -query GCF_002732165.1_ASM273216v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5c4c89f1-1311-4481-bd66-290dd1f01e1f/dqc_reference/reference_markers_gtdb.fasta -out GCF_002732165.1_ASM273216v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:54:52,133] [INFO] Task succeeded: Blastn
[2024-01-25 18:54:52,139] [INFO] Selected 7 target genomes.
[2024-01-25 18:54:52,139] [INFO] Target genome list was writen to GCF_002732165.1_ASM273216v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:54:52,141] [INFO] Task started: fastANI
[2024-01-25 18:54:52,141] [INFO] Running command: fastANI --query /var/lib/cwl/stg26bdb256-3b0e-4f6a-a05b-d2d685422b5d/GCF_002732165.1_ASM273216v1_genomic.fna.gz --refList GCF_002732165.1_ASM273216v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002732165.1_ASM273216v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:54:56,899] [INFO] Task succeeded: fastANI
[2024-01-25 18:54:56,905] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:54:56,905] [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_002732165.1	s__Staphylococcus xylosus	100.0	898	900	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	98.41	97.01	0.95	0.90	48	conclusive
GCF_003697915.1	s__Staphylococcus pseudoxylosus	93.3278	842	900	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	98.50	97.12	0.92	0.87	9	-
GCF_000338275.1	s__Staphylococcus xylosus_B	93.1258	841	900	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.09	97.23	0.94	0.90	8	-
GCF_016774515.1	s__Staphylococcus xylosus_A	91.0766	848	900	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.34	99.08	0.95	0.91	11	-
GCF_000010125.1	s__Staphylococcus saprophyticus	81.8001	587	900	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.41	98.75	0.94	0.91	167	-
GCF_013391405.1	s__Staphylococcus sp013391405	81.6981	594	900	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002614725.1	s__Staphylococcus edaphicus	81.6939	578	900	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:54:56,906] [INFO] GTDB search result was written to GCF_002732165.1_ASM273216v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:54:56,907] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:54:56,909] [INFO] DFAST_QC result json was written to GCF_002732165.1_ASM273216v1_genomic.fna/dqc_result.json
[2024-01-25 18:54:56,909] [INFO] DFAST_QC completed!
[2024-01-25 18:54:56,909] [INFO] Total running time: 0h0m36s