[2024-01-25 20:13:35,381] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:13:35,384] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:13:35,384] [INFO] DQC Reference Directory: /var/lib/cwl/stgf61e9f52-384a-4aa0-b51e-b6d122589cf6/dqc_reference
[2024-01-25 20:13:36,511] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:13:36,512] [INFO] Task started: Prodigal
[2024-01-25 20:13:36,512] [INFO] Running command: gunzip -c /var/lib/cwl/stg5c363b17-d68f-4f85-a8d1-eddaace1420b/GCF_900457475.1_43781_H01_genomic.fna.gz | prodigal -d GCF_900457475.1_43781_H01_genomic.fna/cds.fna -a GCF_900457475.1_43781_H01_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:13:41,085] [INFO] Task succeeded: Prodigal
[2024-01-25 20:13:41,085] [INFO] Task started: HMMsearch
[2024-01-25 20:13:41,085] [INFO] Running command: hmmsearch --tblout GCF_900457475.1_43781_H01_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf61e9f52-384a-4aa0-b51e-b6d122589cf6/dqc_reference/reference_markers.hmm GCF_900457475.1_43781_H01_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:13:41,287] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:13:41,288] [INFO] Found 6/6 markers.
[2024-01-25 20:13:41,313] [INFO] Query marker FASTA was written to GCF_900457475.1_43781_H01_genomic.fna/markers.fasta
[2024-01-25 20:13:41,313] [INFO] Task started: Blastn
[2024-01-25 20:13:41,313] [INFO] Running command: blastn -query GCF_900457475.1_43781_H01_genomic.fna/markers.fasta -db /var/lib/cwl/stgf61e9f52-384a-4aa0-b51e-b6d122589cf6/dqc_reference/reference_markers.fasta -out GCF_900457475.1_43781_H01_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:13:41,898] [INFO] Task succeeded: Blastn
[2024-01-25 20:13:41,901] [INFO] Selected 11 target genomes.
[2024-01-25 20:13:41,901] [INFO] Target genome list was writen to GCF_900457475.1_43781_H01_genomic.fna/target_genomes.txt
[2024-01-25 20:13:41,911] [INFO] Task started: fastANI
[2024-01-25 20:13:41,912] [INFO] Running command: fastANI --query /var/lib/cwl/stg5c363b17-d68f-4f85-a8d1-eddaace1420b/GCF_900457475.1_43781_H01_genomic.fna.gz --refList GCF_900457475.1_43781_H01_genomic.fna/target_genomes.txt --output GCF_900457475.1_43781_H01_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:13:48,784] [INFO] Task succeeded: fastANI
[2024-01-25 20:13:48,785] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf61e9f52-384a-4aa0-b51e-b6d122589cf6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:13:48,785] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf61e9f52-384a-4aa0-b51e-b6d122589cf6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:13:48,791] [INFO] Found 9 fastANI hits (4 hits with ANI > threshold)
[2024-01-25 20:13:48,791] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:13:48,792] [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 argenteus	strain=NCTC13711	GCA_900457475.1	985002	985002	type	True	100.0	930	931	95	conclusive
Staphylococcus argenteus	strain=MSHR1132	GCA_000236925.1	985002	985002	type	True	99.995	928	931	95	conclusive
Staphylococcus argenteus	strain=DSM 28299	GCA_002901785.1	985002	985002	type	True	99.9563	900	931	95	conclusive
Staphylococcus argenteus	strain=DSM 28299	GCA_014877305.1	985002	985002	type	True	99.9436	908	931	95	conclusive
Staphylococcus schweitzeri	strain=DSM 28300	GCA_014877095.1	1654388	1654388	type	True	92.7775	827	931	95	below_threshold
Staphylococcus aureus	strain=PartF-Saureus-RM8376	GCA_022869625.1	1280	1280	type	True	88.756	817	931	95	below_threshold
Staphylococcus aureus	strain=DSM 20231	GCA_001027105.1	1280	1280	type	True	88.707	830	931	95	below_threshold
Staphylococcus aureus	strain=NCTC 08532	GCA_002902205.1	1280	1280	type	True	88.5358	824	931	95	below_threshold
Staphylococcus taiwanensis	strain=NTUH-S172	GCA_020544305.1	2750012	2750012	type	True	79.7306	337	931	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:13:48,793] [INFO] DFAST Taxonomy check result was written to GCF_900457475.1_43781_H01_genomic.fna/tc_result.tsv
[2024-01-25 20:13:48,794] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:13:48,794] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:13:48,794] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf61e9f52-384a-4aa0-b51e-b6d122589cf6/dqc_reference/checkm_data
[2024-01-25 20:13:48,795] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:13:48,824] [INFO] Task started: CheckM
[2024-01-25 20:13:48,824] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900457475.1_43781_H01_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900457475.1_43781_H01_genomic.fna/checkm_input GCF_900457475.1_43781_H01_genomic.fna/checkm_result
[2024-01-25 20:14:09,210] [INFO] Task succeeded: CheckM
[2024-01-25 20:14:09,211] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:14:09,268] [INFO] ===== Completeness check finished =====
[2024-01-25 20:14:09,268] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:14:09,269] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900457475.1_43781_H01_genomic.fna/markers.fasta)
[2024-01-25 20:14:09,269] [INFO] Task started: Blastn
[2024-01-25 20:14:09,269] [INFO] Running command: blastn -query GCF_900457475.1_43781_H01_genomic.fna/markers.fasta -db /var/lib/cwl/stgf61e9f52-384a-4aa0-b51e-b6d122589cf6/dqc_reference/reference_markers_gtdb.fasta -out GCF_900457475.1_43781_H01_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:14:10,082] [INFO] Task succeeded: Blastn
[2024-01-25 20:14:10,085] [INFO] Selected 7 target genomes.
[2024-01-25 20:14:10,086] [INFO] Target genome list was writen to GCF_900457475.1_43781_H01_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:14:10,089] [INFO] Task started: fastANI
[2024-01-25 20:14:10,089] [INFO] Running command: fastANI --query /var/lib/cwl/stg5c363b17-d68f-4f85-a8d1-eddaace1420b/GCF_900457475.1_43781_H01_genomic.fna.gz --refList GCF_900457475.1_43781_H01_genomic.fna/target_genomes_gtdb.txt --output GCF_900457475.1_43781_H01_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:14:15,091] [INFO] Task succeeded: fastANI
[2024-01-25 20:14:15,098] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:14:15,098] [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_000236925.1	s__Staphylococcus argenteus	99.995	928	931	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.00	98.60	0.96	0.90	171	conclusive
GCF_015025035.1	s__Staphylococcus sp015025035	94.1399	836	931	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	98.24	97.61	0.95	0.93	11	-
GCF_002902405.1	s__Staphylococcus schweitzeri	92.7591	826	931	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.10	98.12	0.97	0.94	9	-
GCF_001027105.1	s__Staphylococcus aureus	88.7047	829	931	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	98.78	97.08	0.95	0.88	13059	-
GCF_017357005.1	s__Staphylococcus simiae_A	81.3707	515	931	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.94	99.91	0.98	0.98	6	-
GCF_002902085.1	s__Staphylococcus simiae	81.2179	481	931	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.97	99.96	0.98	0.96	3	-
GCF_002902725.1	s__Staphylococcus caprae	79.6779	348	931	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	98.57	98.10	0.94	0.91	18	-
--------------------------------------------------------------------------------
[2024-01-25 20:14:15,100] [INFO] GTDB search result was written to GCF_900457475.1_43781_H01_genomic.fna/result_gtdb.tsv
[2024-01-25 20:14:15,101] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:14:15,103] [INFO] DFAST_QC result json was written to GCF_900457475.1_43781_H01_genomic.fna/dqc_result.json
[2024-01-25 20:14:15,103] [INFO] DFAST_QC completed!
[2024-01-25 20:14:15,103] [INFO] Total running time: 0h0m40s