[2024-01-24 13:23:10,765] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:23:10,766] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:23:10,767] [INFO] DQC Reference Directory: /var/lib/cwl/stg2364d177-56f7-4cf1-962f-54e45cdabcf3/dqc_reference
[2024-01-24 13:23:12,111] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:23:12,112] [INFO] Task started: Prodigal
[2024-01-24 13:23:12,112] [INFO] Running command: gunzip -c /var/lib/cwl/stg6b904713-214a-44ce-98d2-dfb42a82c6f5/GCF_003970515.1_ASM397051v1_genomic.fna.gz | prodigal -d GCF_003970515.1_ASM397051v1_genomic.fna/cds.fna -a GCF_003970515.1_ASM397051v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:23:16,832] [INFO] Task succeeded: Prodigal
[2024-01-24 13:23:16,833] [INFO] Task started: HMMsearch
[2024-01-24 13:23:16,833] [INFO] Running command: hmmsearch --tblout GCF_003970515.1_ASM397051v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2364d177-56f7-4cf1-962f-54e45cdabcf3/dqc_reference/reference_markers.hmm GCF_003970515.1_ASM397051v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:23:17,068] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:23:17,070] [INFO] Found 6/6 markers.
[2024-01-24 13:23:17,103] [INFO] Query marker FASTA was written to GCF_003970515.1_ASM397051v1_genomic.fna/markers.fasta
[2024-01-24 13:23:17,103] [INFO] Task started: Blastn
[2024-01-24 13:23:17,103] [INFO] Running command: blastn -query GCF_003970515.1_ASM397051v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2364d177-56f7-4cf1-962f-54e45cdabcf3/dqc_reference/reference_markers.fasta -out GCF_003970515.1_ASM397051v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:23:17,730] [INFO] Task succeeded: Blastn
[2024-01-24 13:23:17,733] [INFO] Selected 12 target genomes.
[2024-01-24 13:23:17,734] [INFO] Target genome list was writen to GCF_003970515.1_ASM397051v1_genomic.fna/target_genomes.txt
[2024-01-24 13:23:17,758] [INFO] Task started: fastANI
[2024-01-24 13:23:17,758] [INFO] Running command: fastANI --query /var/lib/cwl/stg6b904713-214a-44ce-98d2-dfb42a82c6f5/GCF_003970515.1_ASM397051v1_genomic.fna.gz --refList GCF_003970515.1_ASM397051v1_genomic.fna/target_genomes.txt --output GCF_003970515.1_ASM397051v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:23:24,379] [INFO] Task succeeded: fastANI
[2024-01-24 13:23:24,379] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2364d177-56f7-4cf1-962f-54e45cdabcf3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:23:24,380] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2364d177-56f7-4cf1-962f-54e45cdabcf3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:23:24,391] [INFO] Found 10 fastANI hits (4 hits with ANI > threshold)
[2024-01-24 13:23:24,391] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:23:24,391] [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 equorum subsp. equorum	strain=NCTC 12414	GCA_003970515.1	29383	246432	type	True	100.0	829	837	95	conclusive
Staphylococcus equorum	strain=NCTC12414	GCA_900458565.1	246432	246432	type	True	99.996	835	837	95	conclusive
Staphylococcus equorum	strain=FDAARGOS_1149	GCA_016725305.1	246432	246432	type	True	99.9946	837	837	95	conclusive
Staphylococcus equorum subsp. linens	strain=DSM 15097	GCA_002901955.1	201829	246432	type	True	99.0933	755	837	95	conclusive
Staphylococcus succinus subsp. succinus	strain=DSM 14617	GCA_001006765.1	224030	61015	type	True	81.6922	523	837	95	below_threshold
Staphylococcus saprophyticus	strain=NCTC7292	GCA_900458885.1	29385	29385	type	True	81.4889	529	837	95	below_threshold
Staphylococcus shinii	strain=K22-5M	GCA_017583065.1	2912228	2912228	type	True	81.4098	578	837	95	below_threshold
Staphylococcus edaphicus	strain=CCM 8730	GCA_002614725.1	1955013	1955013	type	True	81.0099	508	837	95	below_threshold
Staphylococcus aureus	strain=PartF-Saureus-RM8376	GCA_022869625.1	1280	1280	type	True	78.1566	257	837	95	below_threshold
Staphylococcus aureus	strain=NCTC 08532	GCA_002902205.1	1280	1280	type	True	78.0932	257	837	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:23:24,393] [INFO] DFAST Taxonomy check result was written to GCF_003970515.1_ASM397051v1_genomic.fna/tc_result.tsv
[2024-01-24 13:23:24,394] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:23:24,394] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:23:24,394] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2364d177-56f7-4cf1-962f-54e45cdabcf3/dqc_reference/checkm_data
[2024-01-24 13:23:24,395] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:23:24,423] [INFO] Task started: CheckM
[2024-01-24 13:23:24,424] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003970515.1_ASM397051v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003970515.1_ASM397051v1_genomic.fna/checkm_input GCF_003970515.1_ASM397051v1_genomic.fna/checkm_result
[2024-01-24 13:23:44,215] [INFO] Task succeeded: CheckM
[2024-01-24 13:23:44,216] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:23:44,234] [INFO] ===== Completeness check finished =====
[2024-01-24 13:23:44,234] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:23:44,234] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003970515.1_ASM397051v1_genomic.fna/markers.fasta)
[2024-01-24 13:23:44,235] [INFO] Task started: Blastn
[2024-01-24 13:23:44,235] [INFO] Running command: blastn -query GCF_003970515.1_ASM397051v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2364d177-56f7-4cf1-962f-54e45cdabcf3/dqc_reference/reference_markers_gtdb.fasta -out GCF_003970515.1_ASM397051v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:23:45,021] [INFO] Task succeeded: Blastn
[2024-01-24 13:23:45,024] [INFO] Selected 10 target genomes.
[2024-01-24 13:23:45,025] [INFO] Target genome list was writen to GCF_003970515.1_ASM397051v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:23:45,037] [INFO] Task started: fastANI
[2024-01-24 13:23:45,037] [INFO] Running command: fastANI --query /var/lib/cwl/stg6b904713-214a-44ce-98d2-dfb42a82c6f5/GCF_003970515.1_ASM397051v1_genomic.fna.gz --refList GCF_003970515.1_ASM397051v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003970515.1_ASM397051v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:23:50,801] [INFO] Task succeeded: fastANI
[2024-01-24 13:23:50,810] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:23:50,810] [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_900458565.1	s__Staphylococcus equorum	99.996	835	837	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.19	97.35	0.94	0.89	49	conclusive
GCF_001747895.1	s__Staphylococcus equorum_A	94.885	775	837	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.34	98.64	0.94	0.92	4	-
GCF_001431205.1	s__Staphylococcus sp001431205	93.244	750	837	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001006765.1	s__Staphylococcus succinus	81.7092	521	837	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	97.99	95.53	0.94	0.89	24	-
GCF_000010125.1	s__Staphylococcus saprophyticus	81.3864	534	837	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.41	98.75	0.94	0.91	167	-
GCF_016774515.1	s__Staphylococcus xylosus_A	81.2418	562	837	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.34	99.08	0.95	0.91	11	-
GCF_003697915.1	s__Staphylococcus pseudoxylosus	81.1543	560	837	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	98.50	97.12	0.92	0.87	9	-
GCF_013391405.1	s__Staphylococcus sp013391405	81.1247	532	837	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	81.0018	509	837	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900097965.1	s__Staphylococcus caeli	80.8426	463	837	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.99	99.99	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:23:50,811] [INFO] GTDB search result was written to GCF_003970515.1_ASM397051v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:23:50,812] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:23:50,815] [INFO] DFAST_QC result json was written to GCF_003970515.1_ASM397051v1_genomic.fna/dqc_result.json
[2024-01-24 13:23:50,815] [INFO] DFAST_QC completed!
[2024-01-24 13:23:50,815] [INFO] Total running time: 0h0m40s