[2024-01-25 19:53:50,395] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:53:50,397] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:53:50,397] [INFO] DQC Reference Directory: /var/lib/cwl/stg6b46071d-6c73-442c-9349-f439b2e44eb3/dqc_reference
[2024-01-25 19:53:51,530] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:53:51,531] [INFO] Task started: Prodigal
[2024-01-25 19:53:51,531] [INFO] Running command: gunzip -c /var/lib/cwl/stgdb141394-52ac-4f8b-99fa-1e5b03fa556b/GCF_029024945.1_ASM2902494v1_genomic.fna.gz | prodigal -d GCF_029024945.1_ASM2902494v1_genomic.fna/cds.fna -a GCF_029024945.1_ASM2902494v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:53:56,433] [INFO] Task succeeded: Prodigal
[2024-01-25 19:53:56,433] [INFO] Task started: HMMsearch
[2024-01-25 19:53:56,433] [INFO] Running command: hmmsearch --tblout GCF_029024945.1_ASM2902494v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6b46071d-6c73-442c-9349-f439b2e44eb3/dqc_reference/reference_markers.hmm GCF_029024945.1_ASM2902494v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:53:56,696] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:53:56,697] [INFO] Found 6/6 markers.
[2024-01-25 19:53:56,721] [INFO] Query marker FASTA was written to GCF_029024945.1_ASM2902494v1_genomic.fna/markers.fasta
[2024-01-25 19:53:56,722] [INFO] Task started: Blastn
[2024-01-25 19:53:56,722] [INFO] Running command: blastn -query GCF_029024945.1_ASM2902494v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6b46071d-6c73-442c-9349-f439b2e44eb3/dqc_reference/reference_markers.fasta -out GCF_029024945.1_ASM2902494v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:53:57,310] [INFO] Task succeeded: Blastn
[2024-01-25 19:53:57,313] [INFO] Selected 17 target genomes.
[2024-01-25 19:53:57,314] [INFO] Target genome list was writen to GCF_029024945.1_ASM2902494v1_genomic.fna/target_genomes.txt
[2024-01-25 19:53:57,322] [INFO] Task started: fastANI
[2024-01-25 19:53:57,322] [INFO] Running command: fastANI --query /var/lib/cwl/stgdb141394-52ac-4f8b-99fa-1e5b03fa556b/GCF_029024945.1_ASM2902494v1_genomic.fna.gz --refList GCF_029024945.1_ASM2902494v1_genomic.fna/target_genomes.txt --output GCF_029024945.1_ASM2902494v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:54:07,009] [INFO] Task succeeded: fastANI
[2024-01-25 19:54:07,009] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6b46071d-6c73-442c-9349-f439b2e44eb3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:54:07,009] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6b46071d-6c73-442c-9349-f439b2e44eb3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:54:07,018] [INFO] Found 15 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 19:54:07,019] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:54:07,019] [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 succinus subsp. succinus	strain=DSM 14617	GCA_001006765.1	224030	61015	type	True	99.9796	906	943	95	conclusive
Staphylococcus succinus subsp. succinus	strain=DSM 14617	GCA_002902045.1	224030	61015	type	True	99.7965	764	943	95	conclusive
Staphylococcus equorum	strain=NCTC12414	GCA_900458565.1	246432	246432	type	True	81.9575	575	943	95	below_threshold
Staphylococcus equorum	strain=FDAARGOS_1149	GCA_016725305.1	246432	246432	type	True	81.9458	578	943	95	below_threshold
Staphylococcus equorum subsp. linens	strain=DSM 15097	GCA_002901955.1	201829	246432	type	True	81.6389	544	943	95	below_threshold
Staphylococcus equorum subsp. equorum	strain=NCTC 12414	GCA_003970515.1	29383	246432	type	True	81.6362	536	943	95	below_threshold
Staphylococcus saprophyticus	strain=NCTC7292	GCA_900458885.1	29385	29385	type	True	81.6348	538	943	95	below_threshold
Staphylococcus saprophyticus	strain=NCTC 7292	GCA_002902025.2	29385	29385	type	True	81.3813	500	943	95	below_threshold
Staphylococcus saprophyticus	strain=ATCC 15305	GCA_001997165.1	29385	29385	type	True	81.373	520	943	95	below_threshold
Staphylococcus xylosus	strain=NCTC11043	GCA_900458755.1	1288	1288	type	True	81.205	546	943	95	below_threshold
Staphylococcus shinii	strain=K22-5M	GCA_017583065.1	2912228	2912228	type	True	80.9491	568	943	95	below_threshold
Staphylococcus gallinarum	strain=DSM 20610	GCA_000875895.1	1293	1293	type	True	80.6487	510	943	95	below_threshold
Staphylococcus gallinarum	strain=NCTC 12195	GCA_003968815.1	1293	1293	type	True	80.6436	440	943	95	below_threshold
Staphylococcus aureus	strain=PartF-Saureus-RM8376	GCA_022869625.1	1280	1280	type	True	79.0003	267	943	95	below_threshold
Staphylococcus aureus	strain=NCTC 08532	GCA_002902205.1	1280	1280	type	True	78.4298	250	943	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:54:07,020] [INFO] DFAST Taxonomy check result was written to GCF_029024945.1_ASM2902494v1_genomic.fna/tc_result.tsv
[2024-01-25 19:54:07,020] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:54:07,021] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:54:07,021] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6b46071d-6c73-442c-9349-f439b2e44eb3/dqc_reference/checkm_data
[2024-01-25 19:54:07,021] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:54:07,050] [INFO] Task started: CheckM
[2024-01-25 19:54:07,050] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_029024945.1_ASM2902494v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_029024945.1_ASM2902494v1_genomic.fna/checkm_input GCF_029024945.1_ASM2902494v1_genomic.fna/checkm_result
[2024-01-25 19:54:27,526] [INFO] Task succeeded: CheckM
[2024-01-25 19:54:27,527] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:54:27,543] [INFO] ===== Completeness check finished =====
[2024-01-25 19:54:27,543] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:54:27,543] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_029024945.1_ASM2902494v1_genomic.fna/markers.fasta)
[2024-01-25 19:54:27,544] [INFO] Task started: Blastn
[2024-01-25 19:54:27,544] [INFO] Running command: blastn -query GCF_029024945.1_ASM2902494v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6b46071d-6c73-442c-9349-f439b2e44eb3/dqc_reference/reference_markers_gtdb.fasta -out GCF_029024945.1_ASM2902494v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:54:28,326] [INFO] Task succeeded: Blastn
[2024-01-25 19:54:28,329] [INFO] Selected 12 target genomes.
[2024-01-25 19:54:28,329] [INFO] Target genome list was writen to GCF_029024945.1_ASM2902494v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:54:28,338] [INFO] Task started: fastANI
[2024-01-25 19:54:28,338] [INFO] Running command: fastANI --query /var/lib/cwl/stgdb141394-52ac-4f8b-99fa-1e5b03fa556b/GCF_029024945.1_ASM2902494v1_genomic.fna.gz --refList GCF_029024945.1_ASM2902494v1_genomic.fna/target_genomes_gtdb.txt --output GCF_029024945.1_ASM2902494v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:54:35,917] [INFO] Task succeeded: fastANI
[2024-01-25 19:54:35,927] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:54:35,927] [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_001006765.1	s__Staphylococcus succinus	99.9796	906	943	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	97.99	95.53	0.94	0.89	24	conclusive
GCF_900458565.1	s__Staphylococcus equorum	81.9584	575	943	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.19	97.35	0.94	0.89	49	-
GCF_001747895.1	s__Staphylococcus equorum_A	81.7836	575	943	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	81.638	589	943	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000010125.1	s__Staphylococcus saprophyticus	81.6324	522	943	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	81.1856	573	943	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.34	99.08	0.95	0.91	11	-
GCF_002732165.1	s__Staphylococcus xylosus	80.9779	530	943	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	98.41	97.01	0.95	0.90	48	-
GCF_013391405.1	s__Staphylococcus sp013391405	80.8697	500	943	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	80.657	498	943	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000875895.1	s__Staphylococcus gallinarum	80.6289	512	943	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	98.63	98.14	0.94	0.91	25	-
GCF_900097965.1	s__Staphylococcus caeli	80.4994	471	943	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.99	99.99	1.00	1.00	2	-
GCF_002901845.1	s__Staphylococcus hominis	78.5819	261	943	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	97.87	96.99	0.93	0.86	183	-
--------------------------------------------------------------------------------
[2024-01-25 19:54:35,929] [INFO] GTDB search result was written to GCF_029024945.1_ASM2902494v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:54:35,929] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:54:35,933] [INFO] DFAST_QC result json was written to GCF_029024945.1_ASM2902494v1_genomic.fna/dqc_result.json
[2024-01-25 19:54:35,933] [INFO] DFAST_QC completed!
[2024-01-25 19:54:35,933] [INFO] Total running time: 0h0m46s