[2024-01-24 12:22:48,418] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:22:48,420] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:22:48,420] [INFO] DQC Reference Directory: /var/lib/cwl/stg187891b0-62dc-4b47-b719-b41f9aff75ad/dqc_reference
[2024-01-24 12:22:49,681] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:22:49,682] [INFO] Task started: Prodigal
[2024-01-24 12:22:49,682] [INFO] Running command: gunzip -c /var/lib/cwl/stg8155fa8c-5c10-4391-9ff1-5932d0028463/GCF_900458565.1_54984_E01_genomic.fna.gz | prodigal -d GCF_900458565.1_54984_E01_genomic.fna/cds.fna -a GCF_900458565.1_54984_E01_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:22:55,029] [INFO] Task succeeded: Prodigal
[2024-01-24 12:22:55,030] [INFO] Task started: HMMsearch
[2024-01-24 12:22:55,030] [INFO] Running command: hmmsearch --tblout GCF_900458565.1_54984_E01_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg187891b0-62dc-4b47-b719-b41f9aff75ad/dqc_reference/reference_markers.hmm GCF_900458565.1_54984_E01_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:22:55,255] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:22:55,256] [INFO] Found 6/6 markers.
[2024-01-24 12:22:55,284] [INFO] Query marker FASTA was written to GCF_900458565.1_54984_E01_genomic.fna/markers.fasta
[2024-01-24 12:22:55,285] [INFO] Task started: Blastn
[2024-01-24 12:22:55,285] [INFO] Running command: blastn -query GCF_900458565.1_54984_E01_genomic.fna/markers.fasta -db /var/lib/cwl/stg187891b0-62dc-4b47-b719-b41f9aff75ad/dqc_reference/reference_markers.fasta -out GCF_900458565.1_54984_E01_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:22:55,913] [INFO] Task succeeded: Blastn
[2024-01-24 12:22:55,916] [INFO] Selected 12 target genomes.
[2024-01-24 12:22:55,916] [INFO] Target genome list was writen to GCF_900458565.1_54984_E01_genomic.fna/target_genomes.txt
[2024-01-24 12:22:55,921] [INFO] Task started: fastANI
[2024-01-24 12:22:55,921] [INFO] Running command: fastANI --query /var/lib/cwl/stg8155fa8c-5c10-4391-9ff1-5932d0028463/GCF_900458565.1_54984_E01_genomic.fna.gz --refList GCF_900458565.1_54984_E01_genomic.fna/target_genomes.txt --output GCF_900458565.1_54984_E01_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:23:03,235] [INFO] Task succeeded: fastANI
[2024-01-24 12:23:03,236] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg187891b0-62dc-4b47-b719-b41f9aff75ad/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:23:03,236] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg187891b0-62dc-4b47-b719-b41f9aff75ad/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:23:03,248] [INFO] Found 11 fastANI hits (4 hits with ANI > threshold)
[2024-01-24 12:23:03,248] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:23:03,248] [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 equorum	strain=NCTC12414	GCA_900458565.1	246432	246432	type	True	100.0	915	917	95	conclusive
Staphylococcus equorum	strain=FDAARGOS_1149	GCA_016725305.1	246432	246432	type	True	99.9979	908	917	95	conclusive
Staphylococcus equorum subsp. equorum	strain=NCTC 12414	GCA_003970515.1	29383	246432	type	True	99.9151	824	917	95	conclusive
Staphylococcus equorum subsp. linens	strain=DSM 15097	GCA_002901955.1	201829	246432	type	True	99.0629	794	917	95	conclusive
Staphylococcus saprophyticus	strain=NCTC7292	GCA_900458885.1	29385	29385	type	True	81.7416	571	917	95	below_threshold
Staphylococcus succinus subsp. succinus	strain=DSM 14617	GCA_001006765.1	224030	61015	type	True	81.6165	556	917	95	below_threshold
Staphylococcus shinii	strain=K22-5M	GCA_017583065.1	2912228	2912228	type	True	81.564	585	917	95	below_threshold
Staphylococcus edaphicus	strain=CCM 8730	GCA_002614725.1	1955013	1955013	type	True	80.95	553	917	95	below_threshold
Bacillus mycoides	strain=DSM 2048	GCA_022630575.1	1405	1405	type	True	78.8423	59	917	95	below_threshold
Staphylococcus aureus	strain=PartF-Saureus-RM8376	GCA_022869625.1	1280	1280	type	True	78.5787	276	917	95	below_threshold
Staphylococcus aureus	strain=NCTC 08532	GCA_002902205.1	1280	1280	type	True	78.1858	268	917	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:23:03,257] [INFO] DFAST Taxonomy check result was written to GCF_900458565.1_54984_E01_genomic.fna/tc_result.tsv
[2024-01-24 12:23:03,259] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:23:03,259] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:23:03,259] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg187891b0-62dc-4b47-b719-b41f9aff75ad/dqc_reference/checkm_data
[2024-01-24 12:23:03,261] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:23:03,290] [INFO] Task started: CheckM
[2024-01-24 12:23:03,291] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900458565.1_54984_E01_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900458565.1_54984_E01_genomic.fna/checkm_input GCF_900458565.1_54984_E01_genomic.fna/checkm_result
[2024-01-24 12:23:25,132] [INFO] Task succeeded: CheckM
[2024-01-24 12:23:25,133] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:23:25,154] [INFO] ===== Completeness check finished =====
[2024-01-24 12:23:25,154] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:23:25,154] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900458565.1_54984_E01_genomic.fna/markers.fasta)
[2024-01-24 12:23:25,155] [INFO] Task started: Blastn
[2024-01-24 12:23:25,155] [INFO] Running command: blastn -query GCF_900458565.1_54984_E01_genomic.fna/markers.fasta -db /var/lib/cwl/stg187891b0-62dc-4b47-b719-b41f9aff75ad/dqc_reference/reference_markers_gtdb.fasta -out GCF_900458565.1_54984_E01_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:23:25,904] [INFO] Task succeeded: Blastn
[2024-01-24 12:23:25,907] [INFO] Selected 10 target genomes.
[2024-01-24 12:23:25,907] [INFO] Target genome list was writen to GCF_900458565.1_54984_E01_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:23:25,914] [INFO] Task started: fastANI
[2024-01-24 12:23:25,914] [INFO] Running command: fastANI --query /var/lib/cwl/stg8155fa8c-5c10-4391-9ff1-5932d0028463/GCF_900458565.1_54984_E01_genomic.fna.gz --refList GCF_900458565.1_54984_E01_genomic.fna/target_genomes_gtdb.txt --output GCF_900458565.1_54984_E01_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:23:32,175] [INFO] Task succeeded: fastANI
[2024-01-24 12:23:32,189] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:23:32,189] [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_900458565.1	s__Staphylococcus equorum	100.0	915	917	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.19	97.35	0.94	0.89	49	conclusive
GCF_001747895.1	s__Staphylococcus equorum_A	94.6872	828	917	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	93.1498	799	917	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016774515.1	s__Staphylococcus xylosus_A	81.6064	599	917	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.34	99.08	0.95	0.91	11	-
GCF_001006765.1	s__Staphylococcus succinus	81.6038	557	917	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	97.99	95.53	0.94	0.89	24	-
GCF_000010125.1	s__Staphylococcus saprophyticus	81.5625	578	917	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.41	98.75	0.94	0.91	167	-
GCF_003697915.1	s__Staphylococcus pseudoxylosus	81.2164	591	917	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	98.50	97.12	0.92	0.87	9	-
GCF_013391405.1	s__Staphylococcus sp013391405	81.1534	561	917	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	80.9503	553	917	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900097965.1	s__Staphylococcus caeli	80.9274	496	917	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.99	99.99	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:23:32,191] [INFO] GTDB search result was written to GCF_900458565.1_54984_E01_genomic.fna/result_gtdb.tsv
[2024-01-24 12:23:32,192] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:23:32,197] [INFO] DFAST_QC result json was written to GCF_900458565.1_54984_E01_genomic.fna/dqc_result.json
[2024-01-24 12:23:32,198] [INFO] DFAST_QC completed!
[2024-01-24 12:23:32,198] [INFO] Total running time: 0h0m44s