[2024-01-24 14:55:24,476] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:55:24,478] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:55:24,478] [INFO] DQC Reference Directory: /var/lib/cwl/stgd7b12def-016f-48f0-8531-2442ae9bd31a/dqc_reference
[2024-01-24 14:55:25,686] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:55:25,687] [INFO] Task started: Prodigal
[2024-01-24 14:55:25,687] [INFO] Running command: gunzip -c /var/lib/cwl/stg38747432-a994-4821-9e40-aff3f6b5a510/GCF_900458595.1_36734_F01_genomic.fna.gz | prodigal -d GCF_900458595.1_36734_F01_genomic.fna/cds.fna -a GCF_900458595.1_36734_F01_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:55:30,270] [INFO] Task succeeded: Prodigal
[2024-01-24 14:55:30,271] [INFO] Task started: HMMsearch
[2024-01-24 14:55:30,271] [INFO] Running command: hmmsearch --tblout GCF_900458595.1_36734_F01_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd7b12def-016f-48f0-8531-2442ae9bd31a/dqc_reference/reference_markers.hmm GCF_900458595.1_36734_F01_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:55:30,503] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:55:30,505] [INFO] Found 6/6 markers.
[2024-01-24 14:55:30,532] [INFO] Query marker FASTA was written to GCF_900458595.1_36734_F01_genomic.fna/markers.fasta
[2024-01-24 14:55:30,533] [INFO] Task started: Blastn
[2024-01-24 14:55:30,533] [INFO] Running command: blastn -query GCF_900458595.1_36734_F01_genomic.fna/markers.fasta -db /var/lib/cwl/stgd7b12def-016f-48f0-8531-2442ae9bd31a/dqc_reference/reference_markers.fasta -out GCF_900458595.1_36734_F01_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:55:31,193] [INFO] Task succeeded: Blastn
[2024-01-24 14:55:31,196] [INFO] Selected 10 target genomes.
[2024-01-24 14:55:31,197] [INFO] Target genome list was writen to GCF_900458595.1_36734_F01_genomic.fna/target_genomes.txt
[2024-01-24 14:55:31,205] [INFO] Task started: fastANI
[2024-01-24 14:55:31,205] [INFO] Running command: fastANI --query /var/lib/cwl/stg38747432-a994-4821-9e40-aff3f6b5a510/GCF_900458595.1_36734_F01_genomic.fna.gz --refList GCF_900458595.1_36734_F01_genomic.fna/target_genomes.txt --output GCF_900458595.1_36734_F01_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:55:38,240] [INFO] Task succeeded: fastANI
[2024-01-24 14:55:38,241] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd7b12def-016f-48f0-8531-2442ae9bd31a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:55:38,241] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd7b12def-016f-48f0-8531-2442ae9bd31a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:55:38,251] [INFO] Found 8 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 14:55:38,251] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:55:38,251] [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 haemolyticus	strain=NCTC11042	GCA_900458595.1	1283	1283	type	True	100.0	853	854	95	conclusive
Staphylococcus haemolyticus	strain=ATCC 29970	GCA_006094395.1	1283	1283	type	True	99.9843	851	854	95	conclusive
Staphylococcus haemolyticus	strain=NCTC 11042	GCA_002901805.1	1283	1283	type	True	99.923	790	854	95	conclusive
Staphylococcus borealis	strain=51-48	GCA_013345165.1	2742203	2742203	type	True	88.2731	740	854	95	below_threshold
Staphylococcus borealis	strain=51-48	GCA_001224225.1	2742203	2742203	type	True	88.0477	736	854	95	below_threshold
Staphylococcus taiwanensis	strain=NTUH-S172	GCA_020544305.1	2750012	2750012	type	True	84.1598	631	854	95	below_threshold
Staphylococcus aureus	strain=PartF-Saureus-RM8376	GCA_022869625.1	1280	1280	type	True	79.6424	313	854	95	below_threshold
Staphylococcus aureus	strain=NCTC 08532	GCA_002902205.1	1280	1280	type	True	79.098	305	854	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:55:38,253] [INFO] DFAST Taxonomy check result was written to GCF_900458595.1_36734_F01_genomic.fna/tc_result.tsv
[2024-01-24 14:55:38,253] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:55:38,254] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:55:38,254] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd7b12def-016f-48f0-8531-2442ae9bd31a/dqc_reference/checkm_data
[2024-01-24 14:55:38,255] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:55:38,296] [INFO] Task started: CheckM
[2024-01-24 14:55:38,296] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900458595.1_36734_F01_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900458595.1_36734_F01_genomic.fna/checkm_input GCF_900458595.1_36734_F01_genomic.fna/checkm_result
[2024-01-24 14:56:00,172] [INFO] Task succeeded: CheckM
[2024-01-24 14:56:00,173] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:56:00,189] [INFO] ===== Completeness check finished =====
[2024-01-24 14:56:00,190] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:56:00,190] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900458595.1_36734_F01_genomic.fna/markers.fasta)
[2024-01-24 14:56:00,190] [INFO] Task started: Blastn
[2024-01-24 14:56:00,190] [INFO] Running command: blastn -query GCF_900458595.1_36734_F01_genomic.fna/markers.fasta -db /var/lib/cwl/stgd7b12def-016f-48f0-8531-2442ae9bd31a/dqc_reference/reference_markers_gtdb.fasta -out GCF_900458595.1_36734_F01_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:56:01,062] [INFO] Task succeeded: Blastn
[2024-01-24 14:56:01,065] [INFO] Selected 7 target genomes.
[2024-01-24 14:56:01,065] [INFO] Target genome list was writen to GCF_900458595.1_36734_F01_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:56:01,071] [INFO] Task started: fastANI
[2024-01-24 14:56:01,071] [INFO] Running command: fastANI --query /var/lib/cwl/stg38747432-a994-4821-9e40-aff3f6b5a510/GCF_900458595.1_36734_F01_genomic.fna.gz --refList GCF_900458595.1_36734_F01_genomic.fna/target_genomes_gtdb.txt --output GCF_900458595.1_36734_F01_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:56:05,941] [INFO] Task succeeded: fastANI
[2024-01-24 14:56:05,948] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:56:05,948] [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_006094395.1	s__Staphylococcus haemolyticus	99.9843	851	854	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	98.59	96.62	0.93	0.87	385	conclusive
GCF_001224225.1	s__Staphylococcus borealis	88.0323	737	854	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	98.37	97.44	0.93	0.89	22	-
GCF_004785665.1	s__Staphylococcus pragensis	82.3034	570	854	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.69	99.09	0.98	0.94	4	-
GCF_002902565.1	s__Staphylococcus petrasii	82.1897	542	854	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	98.66	97.62	0.95	0.85	8	-
GCA_002902575.1	s__Staphylococcus croceilyticus	82.1755	519	854	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.95	99.95	1.00	1.00	2	-
GCF_003035445.1	s__Staphylococcus devriesei_A	81.7816	543	854	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	97.92	97.92	0.95	0.95	2	-
GCF_002902625.1	s__Staphylococcus devriesei	81.4756	515	854	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.59	98.61	0.94	0.91	9	-
--------------------------------------------------------------------------------
[2024-01-24 14:56:05,950] [INFO] GTDB search result was written to GCF_900458595.1_36734_F01_genomic.fna/result_gtdb.tsv
[2024-01-24 14:56:05,951] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:56:05,954] [INFO] DFAST_QC result json was written to GCF_900458595.1_36734_F01_genomic.fna/dqc_result.json
[2024-01-24 14:56:05,954] [INFO] DFAST_QC completed!
[2024-01-24 14:56:05,954] [INFO] Total running time: 0h0m41s