[2024-01-25 18:13:20,744] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:13:20,750] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:13:20,750] [INFO] DQC Reference Directory: /var/lib/cwl/stg695a04af-4a17-45e1-a3a4-1ce3c81c0537/dqc_reference
[2024-01-25 18:13:21,909] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:13:21,910] [INFO] Task started: Prodigal
[2024-01-25 18:13:21,910] [INFO] Running command: gunzip -c /var/lib/cwl/stg01c5384e-0556-416c-924f-66cb1acc66c5/GCF_029023945.1_ASM2902394v1_genomic.fna.gz | prodigal -d GCF_029023945.1_ASM2902394v1_genomic.fna/cds.fna -a GCF_029023945.1_ASM2902394v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:13:25,945] [INFO] Task succeeded: Prodigal
[2024-01-25 18:13:25,945] [INFO] Task started: HMMsearch
[2024-01-25 18:13:25,945] [INFO] Running command: hmmsearch --tblout GCF_029023945.1_ASM2902394v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg695a04af-4a17-45e1-a3a4-1ce3c81c0537/dqc_reference/reference_markers.hmm GCF_029023945.1_ASM2902394v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:13:26,164] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:13:26,165] [INFO] Found 6/6 markers.
[2024-01-25 18:13:26,186] [INFO] Query marker FASTA was written to GCF_029023945.1_ASM2902394v1_genomic.fna/markers.fasta
[2024-01-25 18:13:26,186] [INFO] Task started: Blastn
[2024-01-25 18:13:26,186] [INFO] Running command: blastn -query GCF_029023945.1_ASM2902394v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg695a04af-4a17-45e1-a3a4-1ce3c81c0537/dqc_reference/reference_markers.fasta -out GCF_029023945.1_ASM2902394v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:13:26,769] [INFO] Task succeeded: Blastn
[2024-01-25 18:13:26,773] [INFO] Selected 10 target genomes.
[2024-01-25 18:13:26,773] [INFO] Target genome list was writen to GCF_029023945.1_ASM2902394v1_genomic.fna/target_genomes.txt
[2024-01-25 18:13:26,777] [INFO] Task started: fastANI
[2024-01-25 18:13:26,777] [INFO] Running command: fastANI --query /var/lib/cwl/stg01c5384e-0556-416c-924f-66cb1acc66c5/GCF_029023945.1_ASM2902394v1_genomic.fna.gz --refList GCF_029023945.1_ASM2902394v1_genomic.fna/target_genomes.txt --output GCF_029023945.1_ASM2902394v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:13:33,533] [INFO] Task succeeded: fastANI
[2024-01-25 18:13:33,534] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg695a04af-4a17-45e1-a3a4-1ce3c81c0537/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:13:33,534] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg695a04af-4a17-45e1-a3a4-1ce3c81c0537/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:13:33,541] [INFO] Found 8 fastANI hits (3 hits with ANI > threshold)
[2024-01-25 18:13:33,541] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:13:33,541] [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=ATCC 29970	GCA_006094395.1	1283	1283	type	True	99.9938	851	855	95	conclusive
Staphylococcus haemolyticus	strain=NCTC11042	GCA_900458595.1	1283	1283	type	True	99.9924	851	855	95	conclusive
Staphylococcus haemolyticus	strain=NCTC 11042	GCA_002901805.1	1283	1283	type	True	99.9315	788	855	95	conclusive
Staphylococcus borealis	strain=51-48	GCA_013345165.1	2742203	2742203	type	True	88.2739	755	855	95	below_threshold
Staphylococcus borealis	strain=51-48	GCA_001224225.1	2742203	2742203	type	True	88.0637	731	855	95	below_threshold
Staphylococcus taiwanensis	strain=NTUH-S172	GCA_020544305.1	2750012	2750012	type	True	83.8533	644	855	95	below_threshold
Staphylococcus aureus	strain=PartF-Saureus-RM8376	GCA_022869625.1	1280	1280	type	True	79.7382	305	855	95	below_threshold
Staphylococcus aureus	strain=NCTC 08532	GCA_002902205.1	1280	1280	type	True	79.1821	299	855	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:13:33,542] [INFO] DFAST Taxonomy check result was written to GCF_029023945.1_ASM2902394v1_genomic.fna/tc_result.tsv
[2024-01-25 18:13:33,543] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:13:33,543] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:13:33,543] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg695a04af-4a17-45e1-a3a4-1ce3c81c0537/dqc_reference/checkm_data
[2024-01-25 18:13:33,544] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:13:33,573] [INFO] Task started: CheckM
[2024-01-25 18:13:33,573] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_029023945.1_ASM2902394v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_029023945.1_ASM2902394v1_genomic.fna/checkm_input GCF_029023945.1_ASM2902394v1_genomic.fna/checkm_result
[2024-01-25 18:13:52,204] [INFO] Task succeeded: CheckM
[2024-01-25 18:13:52,205] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:13:52,225] [INFO] ===== Completeness check finished =====
[2024-01-25 18:13:52,225] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:13:52,226] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_029023945.1_ASM2902394v1_genomic.fna/markers.fasta)
[2024-01-25 18:13:52,226] [INFO] Task started: Blastn
[2024-01-25 18:13:52,226] [INFO] Running command: blastn -query GCF_029023945.1_ASM2902394v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg695a04af-4a17-45e1-a3a4-1ce3c81c0537/dqc_reference/reference_markers_gtdb.fasta -out GCF_029023945.1_ASM2902394v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:13:53,005] [INFO] Task succeeded: Blastn
[2024-01-25 18:13:53,008] [INFO] Selected 7 target genomes.
[2024-01-25 18:13:53,008] [INFO] Target genome list was writen to GCF_029023945.1_ASM2902394v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:13:53,010] [INFO] Task started: fastANI
[2024-01-25 18:13:53,010] [INFO] Running command: fastANI --query /var/lib/cwl/stg01c5384e-0556-416c-924f-66cb1acc66c5/GCF_029023945.1_ASM2902394v1_genomic.fna.gz --refList GCF_029023945.1_ASM2902394v1_genomic.fna/target_genomes_gtdb.txt --output GCF_029023945.1_ASM2902394v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:13:57,679] [INFO] Task succeeded: fastANI
[2024-01-25 18:13:57,685] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:13:57,685] [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	99.9938	851	855	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	88.0734	730	855	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	82.4092	574	855	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	82.217	531	855	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	82.0679	522	855	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	81.8762	538	855	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	81.5456	518	855	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.59	98.61	0.94	0.91	9	-
--------------------------------------------------------------------------------
[2024-01-25 18:13:57,686] [INFO] GTDB search result was written to GCF_029023945.1_ASM2902394v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:13:57,687] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:13:57,689] [INFO] DFAST_QC result json was written to GCF_029023945.1_ASM2902394v1_genomic.fna/dqc_result.json
[2024-01-25 18:13:57,689] [INFO] DFAST_QC completed!
[2024-01-25 18:13:57,689] [INFO] Total running time: 0h0m37s