[2024-01-25 17:41:50,662] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:41:50,664] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:41:50,665] [INFO] DQC Reference Directory: /var/lib/cwl/stg2a60e9ee-1304-4320-97b5-377d6721efd0/dqc_reference
[2024-01-25 17:41:51,825] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:41:51,826] [INFO] Task started: Prodigal
[2024-01-25 17:41:51,827] [INFO] Running command: gunzip -c /var/lib/cwl/stg98e0d678-546c-4d1f-8e22-a6fb0440466f/GCF_002902205.1_ASM290220v1_genomic.fna.gz | prodigal -d GCF_002902205.1_ASM290220v1_genomic.fna/cds.fna -a GCF_002902205.1_ASM290220v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:41:56,383] [INFO] Task succeeded: Prodigal
[2024-01-25 17:41:56,384] [INFO] Task started: HMMsearch
[2024-01-25 17:41:56,384] [INFO] Running command: hmmsearch --tblout GCF_002902205.1_ASM290220v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2a60e9ee-1304-4320-97b5-377d6721efd0/dqc_reference/reference_markers.hmm GCF_002902205.1_ASM290220v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:41:56,635] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:41:56,637] [INFO] Found 6/6 markers.
[2024-01-25 17:41:56,661] [INFO] Query marker FASTA was written to GCF_002902205.1_ASM290220v1_genomic.fna/markers.fasta
[2024-01-25 17:41:56,661] [INFO] Task started: Blastn
[2024-01-25 17:41:56,661] [INFO] Running command: blastn -query GCF_002902205.1_ASM290220v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2a60e9ee-1304-4320-97b5-377d6721efd0/dqc_reference/reference_markers.fasta -out GCF_002902205.1_ASM290220v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:41:57,245] [INFO] Task succeeded: Blastn
[2024-01-25 17:41:57,248] [INFO] Selected 9 target genomes.
[2024-01-25 17:41:57,248] [INFO] Target genome list was writen to GCF_002902205.1_ASM290220v1_genomic.fna/target_genomes.txt
[2024-01-25 17:41:57,256] [INFO] Task started: fastANI
[2024-01-25 17:41:57,256] [INFO] Running command: fastANI --query /var/lib/cwl/stg98e0d678-546c-4d1f-8e22-a6fb0440466f/GCF_002902205.1_ASM290220v1_genomic.fna.gz --refList GCF_002902205.1_ASM290220v1_genomic.fna/target_genomes.txt --output GCF_002902205.1_ASM290220v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:42:03,003] [INFO] Task succeeded: fastANI
[2024-01-25 17:42:03,003] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2a60e9ee-1304-4320-97b5-377d6721efd0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:42:03,003] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2a60e9ee-1304-4320-97b5-377d6721efd0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:42:03,010] [INFO] Found 8 fastANI hits (6 hits with ANI > threshold)
[2024-01-25 17:42:03,010] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:42:03,010] [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 aureus	strain=NCTC 08532	GCA_002902205.1	1280	1280	type	True	100.0	905	907	95	conclusive
Staphylococcus aureus	strain=FDAARGOS_773	GCA_006364675.1	1280	1280	type	True	99.9871	906	907	95	conclusive
Staphylococcus aureus	strain=PartF-Saureus-RM8376	GCA_022869625.1	1280	1280	type	True	99.987	906	907	95	conclusive
Staphylococcus aureus	strain=DSM 20231	GCA_001027105.1	1280	1280	type	True	99.9867	906	907	95	conclusive
Staphylococcus aureus	strain=DSM 20231	GCA_000330825.2	1280	1280	type	True	99.9839	900	907	95	conclusive
Staphylococcus aureus	strain=NBRC 100910	GCA_001544175.1	1280	1280	type	True	99.9813	894	907	95	conclusive
Staphylococcus taiwanensis	strain=NTUH-S172	GCA_020544305.1	2750012	2750012	type	True	79.0739	329	907	95	below_threshold
Macrococcus armenti	strain=JEK37	GCA_020097135.1	2875764	2875764	type	True	77.9989	85	907	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:42:03,011] [INFO] DFAST Taxonomy check result was written to GCF_002902205.1_ASM290220v1_genomic.fna/tc_result.tsv
[2024-01-25 17:42:03,012] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:42:03,012] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:42:03,012] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2a60e9ee-1304-4320-97b5-377d6721efd0/dqc_reference/checkm_data
[2024-01-25 17:42:03,013] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:42:03,041] [INFO] Task started: CheckM
[2024-01-25 17:42:03,041] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002902205.1_ASM290220v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002902205.1_ASM290220v1_genomic.fna/checkm_input GCF_002902205.1_ASM290220v1_genomic.fna/checkm_result
[2024-01-25 17:42:22,764] [INFO] Task succeeded: CheckM
[2024-01-25 17:42:22,765] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:42:22,800] [INFO] ===== Completeness check finished =====
[2024-01-25 17:42:22,801] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:42:22,801] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002902205.1_ASM290220v1_genomic.fna/markers.fasta)
[2024-01-25 17:42:22,801] [INFO] Task started: Blastn
[2024-01-25 17:42:22,801] [INFO] Running command: blastn -query GCF_002902205.1_ASM290220v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2a60e9ee-1304-4320-97b5-377d6721efd0/dqc_reference/reference_markers_gtdb.fasta -out GCF_002902205.1_ASM290220v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:42:23,606] [INFO] Task succeeded: Blastn
[2024-01-25 17:42:23,613] [INFO] Selected 7 target genomes.
[2024-01-25 17:42:23,614] [INFO] Target genome list was writen to GCF_002902205.1_ASM290220v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:42:23,615] [INFO] Task started: fastANI
[2024-01-25 17:42:23,616] [INFO] Running command: fastANI --query /var/lib/cwl/stg98e0d678-546c-4d1f-8e22-a6fb0440466f/GCF_002902205.1_ASM290220v1_genomic.fna.gz --refList GCF_002902205.1_ASM290220v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002902205.1_ASM290220v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:42:28,466] [INFO] Task succeeded: fastANI
[2024-01-25 17:42:28,473] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:42:28,473] [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_001027105.1	s__Staphylococcus aureus	99.9867	906	907	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	98.78	97.08	0.95	0.88	13059	conclusive
GCF_002902405.1	s__Staphylococcus schweitzeri	90.1943	817	907	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.10	98.12	0.97	0.94	9	-
GCF_015025035.1	s__Staphylococcus sp015025035	89.2497	801	907	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	98.24	97.61	0.95	0.93	11	-
GCF_000236925.1	s__Staphylococcus argenteus	88.6322	818	907	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.00	98.60	0.96	0.90	171	-
GCF_017357005.1	s__Staphylococcus simiae_A	80.8549	510	907	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	80.6565	499	907	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.97	99.96	0.98	0.96	3	-
GCF_001224225.1	s__Staphylococcus borealis	79.1211	319	907	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	98.37	97.44	0.93	0.89	22	-
--------------------------------------------------------------------------------
[2024-01-25 17:42:28,474] [INFO] GTDB search result was written to GCF_002902205.1_ASM290220v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:42:28,475] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:42:28,477] [INFO] DFAST_QC result json was written to GCF_002902205.1_ASM290220v1_genomic.fna/dqc_result.json
[2024-01-25 17:42:28,477] [INFO] DFAST_QC completed!
[2024-01-25 17:42:28,477] [INFO] Total running time: 0h0m38s