[2024-01-24 12:36:24,827] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:36:24,830] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:36:24,830] [INFO] DQC Reference Directory: /var/lib/cwl/stg324e1a53-6bbd-4385-b89b-1ece87cb2eea/dqc_reference
[2024-01-24 12:36:26,133] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:36:26,134] [INFO] Task started: Prodigal
[2024-01-24 12:36:26,135] [INFO] Running command: gunzip -c /var/lib/cwl/stg3e3ebfe7-ee2f-4ef3-9fea-9df81cb4079f/GCF_900458755.1_41665_D01_genomic.fna.gz | prodigal -d GCF_900458755.1_41665_D01_genomic.fna/cds.fna -a GCF_900458755.1_41665_D01_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:36:31,301] [INFO] Task succeeded: Prodigal
[2024-01-24 12:36:31,301] [INFO] Task started: HMMsearch
[2024-01-24 12:36:31,301] [INFO] Running command: hmmsearch --tblout GCF_900458755.1_41665_D01_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg324e1a53-6bbd-4385-b89b-1ece87cb2eea/dqc_reference/reference_markers.hmm GCF_900458755.1_41665_D01_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:36:31,551] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:36:31,552] [INFO] Found 6/6 markers.
[2024-01-24 12:36:31,578] [INFO] Query marker FASTA was written to GCF_900458755.1_41665_D01_genomic.fna/markers.fasta
[2024-01-24 12:36:31,578] [INFO] Task started: Blastn
[2024-01-24 12:36:31,578] [INFO] Running command: blastn -query GCF_900458755.1_41665_D01_genomic.fna/markers.fasta -db /var/lib/cwl/stg324e1a53-6bbd-4385-b89b-1ece87cb2eea/dqc_reference/reference_markers.fasta -out GCF_900458755.1_41665_D01_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:36:32,175] [INFO] Task succeeded: Blastn
[2024-01-24 12:36:32,178] [INFO] Selected 9 target genomes.
[2024-01-24 12:36:32,179] [INFO] Target genome list was writen to GCF_900458755.1_41665_D01_genomic.fna/target_genomes.txt
[2024-01-24 12:36:32,189] [INFO] Task started: fastANI
[2024-01-24 12:36:32,190] [INFO] Running command: fastANI --query /var/lib/cwl/stg3e3ebfe7-ee2f-4ef3-9fea-9df81cb4079f/GCF_900458755.1_41665_D01_genomic.fna.gz --refList GCF_900458755.1_41665_D01_genomic.fna/target_genomes.txt --output GCF_900458755.1_41665_D01_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:36:37,506] [INFO] Task succeeded: fastANI
[2024-01-24 12:36:37,506] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg324e1a53-6bbd-4385-b89b-1ece87cb2eea/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:36:37,506] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg324e1a53-6bbd-4385-b89b-1ece87cb2eea/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:36:37,512] [INFO] Found 5 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 12:36:37,513] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:36:37,513] [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=NCTC11043	GCA_900458755.1	1288	1288	type	True	100.0	931	932	95	conclusive
Staphylococcus xylosus	strain=CCM 2738	GCA_002732165.1	1288	1288	type	True	99.9856	895	932	95	conclusive
Staphylococcus xylosus	strain=NCTC 11043	GCA_002901985.1	1288	1288	type	True	99.8461	800	932	95	conclusive
Staphylococcus pseudoxylosus	strain=S04009	GCA_003697915.1	2282419	2282419	type	True	93.2846	855	932	95	below_threshold
Staphylococcus shinii	strain=K22-5M	GCA_017583065.1	2912228	2912228	type	True	91.0191	853	932	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:36:37,514] [INFO] DFAST Taxonomy check result was written to GCF_900458755.1_41665_D01_genomic.fna/tc_result.tsv
[2024-01-24 12:36:37,515] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:36:37,515] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:36:37,515] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg324e1a53-6bbd-4385-b89b-1ece87cb2eea/dqc_reference/checkm_data
[2024-01-24 12:36:37,516] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:36:37,548] [INFO] Task started: CheckM
[2024-01-24 12:36:37,549] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900458755.1_41665_D01_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900458755.1_41665_D01_genomic.fna/checkm_input GCF_900458755.1_41665_D01_genomic.fna/checkm_result
[2024-01-24 12:37:00,553] [INFO] Task succeeded: CheckM
[2024-01-24 12:37:00,554] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:37:00,573] [INFO] ===== Completeness check finished =====
[2024-01-24 12:37:00,574] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:37:00,574] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900458755.1_41665_D01_genomic.fna/markers.fasta)
[2024-01-24 12:37:00,575] [INFO] Task started: Blastn
[2024-01-24 12:37:00,575] [INFO] Running command: blastn -query GCF_900458755.1_41665_D01_genomic.fna/markers.fasta -db /var/lib/cwl/stg324e1a53-6bbd-4385-b89b-1ece87cb2eea/dqc_reference/reference_markers_gtdb.fasta -out GCF_900458755.1_41665_D01_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:37:01,365] [INFO] Task succeeded: Blastn
[2024-01-24 12:37:01,368] [INFO] Selected 7 target genomes.
[2024-01-24 12:37:01,369] [INFO] Target genome list was writen to GCF_900458755.1_41665_D01_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:37:01,374] [INFO] Task started: fastANI
[2024-01-24 12:37:01,375] [INFO] Running command: fastANI --query /var/lib/cwl/stg3e3ebfe7-ee2f-4ef3-9fea-9df81cb4079f/GCF_900458755.1_41665_D01_genomic.fna.gz --refList GCF_900458755.1_41665_D01_genomic.fna/target_genomes_gtdb.txt --output GCF_900458755.1_41665_D01_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:37:06,261] [INFO] Task succeeded: fastANI
[2024-01-24 12:37:06,268] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:37:06,268] [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	99.9856	895	932	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	93.2921	854	932	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	93.1788	838	932	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	91.1486	859	932	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	82.117	612	932	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.41	98.75	0.94	0.91	167	-
GCF_002614725.1	s__Staphylococcus edaphicus	81.8388	591	932	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013391405.1	s__Staphylococcus sp013391405	81.5984	613	932	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:37:06,270] [INFO] GTDB search result was written to GCF_900458755.1_41665_D01_genomic.fna/result_gtdb.tsv
[2024-01-24 12:37:06,271] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:37:06,273] [INFO] DFAST_QC result json was written to GCF_900458755.1_41665_D01_genomic.fna/dqc_result.json
[2024-01-24 12:37:06,274] [INFO] DFAST_QC completed!
[2024-01-24 12:37:06,274] [INFO] Total running time: 0h0m41s