[2024-01-25 18:07:05,760] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:07:05,762] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:07:05,762] [INFO] DQC Reference Directory: /var/lib/cwl/stg0e51a666-56e9-415e-bf66-62f12d3e65ba/dqc_reference
[2024-01-25 18:07:06,957] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:07:06,957] [INFO] Task started: Prodigal
[2024-01-25 18:07:06,957] [INFO] Running command: gunzip -c /var/lib/cwl/stg6dd5526e-3094-494b-9206-b46c7c297595/GCF_900458435.1_50279_A02_genomic.fna.gz | prodigal -d GCF_900458435.1_50279_A02_genomic.fna/cds.fna -a GCF_900458435.1_50279_A02_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:07:11,521] [INFO] Task succeeded: Prodigal
[2024-01-25 18:07:11,522] [INFO] Task started: HMMsearch
[2024-01-25 18:07:11,522] [INFO] Running command: hmmsearch --tblout GCF_900458435.1_50279_A02_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0e51a666-56e9-415e-bf66-62f12d3e65ba/dqc_reference/reference_markers.hmm GCF_900458435.1_50279_A02_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:07:11,754] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:07:11,756] [INFO] Found 6/6 markers.
[2024-01-25 18:07:11,778] [INFO] Query marker FASTA was written to GCF_900458435.1_50279_A02_genomic.fna/markers.fasta
[2024-01-25 18:07:11,778] [INFO] Task started: Blastn
[2024-01-25 18:07:11,778] [INFO] Running command: blastn -query GCF_900458435.1_50279_A02_genomic.fna/markers.fasta -db /var/lib/cwl/stg0e51a666-56e9-415e-bf66-62f12d3e65ba/dqc_reference/reference_markers.fasta -out GCF_900458435.1_50279_A02_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:07:12,360] [INFO] Task succeeded: Blastn
[2024-01-25 18:07:12,363] [INFO] Selected 10 target genomes.
[2024-01-25 18:07:12,363] [INFO] Target genome list was writen to GCF_900458435.1_50279_A02_genomic.fna/target_genomes.txt
[2024-01-25 18:07:12,369] [INFO] Task started: fastANI
[2024-01-25 18:07:12,369] [INFO] Running command: fastANI --query /var/lib/cwl/stg6dd5526e-3094-494b-9206-b46c7c297595/GCF_900458435.1_50279_A02_genomic.fna.gz --refList GCF_900458435.1_50279_A02_genomic.fna/target_genomes.txt --output GCF_900458435.1_50279_A02_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:07:18,283] [INFO] Task succeeded: fastANI
[2024-01-25 18:07:18,283] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0e51a666-56e9-415e-bf66-62f12d3e65ba/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:07:18,284] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0e51a666-56e9-415e-bf66-62f12d3e65ba/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:07:18,290] [INFO] Found 7 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 18:07:18,290] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:07:18,290] [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 carnosus	strain=NCTC13825	GCA_900458435.1	1281	1281	type	True	100.0	858	858	95	conclusive
Staphylococcus carnosus	strain=FDAARGOS_883	GCA_016028275.1	1281	1281	type	True	99.9997	856	858	95	conclusive
Staphylococcus condimenti	strain=NCTC13827	GCA_900637235.1	70255	70255	type	True	91.9759	793	858	95	below_threshold
Staphylococcus condimenti	strain=DSM 11674	GCA_001618885.1	70255	70255	type	True	91.9357	796	858	95	below_threshold
Staphylococcus condimenti	strain=DSM 11674	GCA_001014685.1	70255	70255	type	True	91.8858	762	858	95	below_threshold
Staphylococcus aureus	strain=PartF-Saureus-RM8376	GCA_022869625.1	1280	1280	type	True	79.352	221	858	95	below_threshold
Staphylococcus aureus	strain=NCTC 08532	GCA_002902205.1	1280	1280	type	True	78.6308	216	858	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:07:18,291] [INFO] DFAST Taxonomy check result was written to GCF_900458435.1_50279_A02_genomic.fna/tc_result.tsv
[2024-01-25 18:07:18,292] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:07:18,292] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:07:18,292] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0e51a666-56e9-415e-bf66-62f12d3e65ba/dqc_reference/checkm_data
[2024-01-25 18:07:18,293] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:07:18,320] [INFO] Task started: CheckM
[2024-01-25 18:07:18,321] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900458435.1_50279_A02_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900458435.1_50279_A02_genomic.fna/checkm_input GCF_900458435.1_50279_A02_genomic.fna/checkm_result
[2024-01-25 18:07:37,868] [INFO] Task succeeded: CheckM
[2024-01-25 18:07:37,869] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:07:37,886] [INFO] ===== Completeness check finished =====
[2024-01-25 18:07:37,886] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:07:37,887] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900458435.1_50279_A02_genomic.fna/markers.fasta)
[2024-01-25 18:07:37,887] [INFO] Task started: Blastn
[2024-01-25 18:07:37,887] [INFO] Running command: blastn -query GCF_900458435.1_50279_A02_genomic.fna/markers.fasta -db /var/lib/cwl/stg0e51a666-56e9-415e-bf66-62f12d3e65ba/dqc_reference/reference_markers_gtdb.fasta -out GCF_900458435.1_50279_A02_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:07:38,686] [INFO] Task succeeded: Blastn
[2024-01-25 18:07:38,689] [INFO] Selected 7 target genomes.
[2024-01-25 18:07:38,689] [INFO] Target genome list was writen to GCF_900458435.1_50279_A02_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:07:38,694] [INFO] Task started: fastANI
[2024-01-25 18:07:38,694] [INFO] Running command: fastANI --query /var/lib/cwl/stg6dd5526e-3094-494b-9206-b46c7c297595/GCF_900458435.1_50279_A02_genomic.fna.gz --refList GCF_900458435.1_50279_A02_genomic.fna/target_genomes_gtdb.txt --output GCF_900458435.1_50279_A02_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:07:43,226] [INFO] Task succeeded: fastANI
[2024-01-25 18:07:43,231] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:07:43,231] [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_900458435.1	s__Staphylococcus carnosus	100.0	858	858	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.71	99.56	0.96	0.93	12	conclusive
GCF_001618885.1	s__Staphylococcus condimenti	91.9357	796	858	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.75	99.00	0.98	0.93	11	-
GCA_900186985.1	s__Staphylococcus piscifermentans	85.3682	707	858	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	100.00	100.00	0.99	0.99	3	-
GCF_003718735.1	s__Staphylococcus debuckii	85.1319	698	858	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002902285.1	s__Staphylococcus simulans	81.281	486	858	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	98.92	98.61	0.93	0.91	77	-
GCF_003043455.1	s__Staphylococcus simulans_A	81.2713	473	858	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	98.25	98.25	0.90	0.90	2	-
GCF_002994445.1	s__Staphylococcus simulans_B	81.1043	500	858	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	96.89	96.89	0.92	0.92	2	-
--------------------------------------------------------------------------------
[2024-01-25 18:07:43,232] [INFO] GTDB search result was written to GCF_900458435.1_50279_A02_genomic.fna/result_gtdb.tsv
[2024-01-25 18:07:43,233] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:07:43,235] [INFO] DFAST_QC result json was written to GCF_900458435.1_50279_A02_genomic.fna/dqc_result.json
[2024-01-25 18:07:43,235] [INFO] DFAST_QC completed!
[2024-01-25 18:07:43,235] [INFO] Total running time: 0h0m37s