[2024-01-25 19:39:20,675] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:39:20,677] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:39:20,677] [INFO] DQC Reference Directory: /var/lib/cwl/stg02f88cc0-eb75-4748-9313-8230844acb25/dqc_reference
[2024-01-25 19:39:21,839] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:39:21,840] [INFO] Task started: Prodigal
[2024-01-25 19:39:21,840] [INFO] Running command: gunzip -c /var/lib/cwl/stg9ef3e6f5-f37d-4800-b7b1-3f80fe53f354/GCF_001006765.1_ASM100676v1_genomic.fna.gz | prodigal -d GCF_001006765.1_ASM100676v1_genomic.fna/cds.fna -a GCF_001006765.1_ASM100676v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:39:26,413] [INFO] Task succeeded: Prodigal
[2024-01-25 19:39:26,413] [INFO] Task started: HMMsearch
[2024-01-25 19:39:26,413] [INFO] Running command: hmmsearch --tblout GCF_001006765.1_ASM100676v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg02f88cc0-eb75-4748-9313-8230844acb25/dqc_reference/reference_markers.hmm GCF_001006765.1_ASM100676v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:39:26,624] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:39:26,625] [INFO] Found 6/6 markers.
[2024-01-25 19:39:26,649] [INFO] Query marker FASTA was written to GCF_001006765.1_ASM100676v1_genomic.fna/markers.fasta
[2024-01-25 19:39:26,650] [INFO] Task started: Blastn
[2024-01-25 19:39:26,650] [INFO] Running command: blastn -query GCF_001006765.1_ASM100676v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg02f88cc0-eb75-4748-9313-8230844acb25/dqc_reference/reference_markers.fasta -out GCF_001006765.1_ASM100676v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:39:27,217] [INFO] Task succeeded: Blastn
[2024-01-25 19:39:27,219] [INFO] Selected 17 target genomes.
[2024-01-25 19:39:27,220] [INFO] Target genome list was writen to GCF_001006765.1_ASM100676v1_genomic.fna/target_genomes.txt
[2024-01-25 19:39:27,221] [INFO] Task started: fastANI
[2024-01-25 19:39:27,221] [INFO] Running command: fastANI --query /var/lib/cwl/stg9ef3e6f5-f37d-4800-b7b1-3f80fe53f354/GCF_001006765.1_ASM100676v1_genomic.fna.gz --refList GCF_001006765.1_ASM100676v1_genomic.fna/target_genomes.txt --output GCF_001006765.1_ASM100676v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:39:36,851] [INFO] Task succeeded: fastANI
[2024-01-25 19:39:36,851] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg02f88cc0-eb75-4748-9313-8230844acb25/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:39:36,851] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg02f88cc0-eb75-4748-9313-8230844acb25/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:39:36,863] [INFO] Found 15 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 19:39:36,863] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:39:36,863] [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 succinus subsp. succinus	strain=DSM 14617	GCA_001006765.1	224030	61015	type	True	100.0	922	926	95	conclusive
Staphylococcus succinus subsp. succinus	strain=DSM 14617	GCA_002902045.1	224030	61015	type	True	99.7988	759	926	95	conclusive
Staphylococcus equorum	strain=NCTC12414	GCA_900458565.1	246432	246432	type	True	81.6934	555	926	95	below_threshold
Staphylococcus equorum subsp. equorum	strain=NCTC 12414	GCA_003970515.1	29383	246432	type	True	81.6296	539	926	95	below_threshold
Staphylococcus equorum	strain=FDAARGOS_1149	GCA_016725305.1	246432	246432	type	True	81.6036	559	926	95	below_threshold
Staphylococcus equorum subsp. linens	strain=DSM 15097	GCA_002901955.1	201829	246432	type	True	81.5385	524	926	95	below_threshold
Staphylococcus saprophyticus	strain=ATCC 15305	GCA_001997165.1	29385	29385	type	True	81.279	510	926	95	below_threshold
Staphylococcus saprophyticus	strain=NCTC7292	GCA_900458885.1	29385	29385	type	True	81.2679	518	926	95	below_threshold
Staphylococcus saprophyticus	strain=NCTC 7292	GCA_002902025.2	29385	29385	type	True	81.2421	503	926	95	below_threshold
Staphylococcus shinii	strain=K22-5M	GCA_017583065.1	2912228	2912228	type	True	81.0854	535	926	95	below_threshold
Staphylococcus gallinarum	strain=DSM 20610	GCA_000875895.1	1293	1293	type	True	80.6445	524	926	95	below_threshold
Staphylococcus caeli	strain=82B	GCA_900097965.1	2201815	2201815	type	True	80.5459	464	926	95	below_threshold
Staphylococcus gallinarum	strain=NCTC 12195	GCA_003968815.1	1293	1293	type	True	80.3718	448	926	95	below_threshold
Staphylococcus aureus	strain=PartF-Saureus-RM8376	GCA_022869625.1	1280	1280	type	True	78.3214	255	926	95	below_threshold
Staphylococcus aureus	strain=NCTC 08532	GCA_002902205.1	1280	1280	type	True	78.2982	250	926	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:39:36,864] [INFO] DFAST Taxonomy check result was written to GCF_001006765.1_ASM100676v1_genomic.fna/tc_result.tsv
[2024-01-25 19:39:36,865] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:39:36,865] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:39:36,865] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg02f88cc0-eb75-4748-9313-8230844acb25/dqc_reference/checkm_data
[2024-01-25 19:39:36,866] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:39:36,898] [INFO] Task started: CheckM
[2024-01-25 19:39:36,898] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001006765.1_ASM100676v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001006765.1_ASM100676v1_genomic.fna/checkm_input GCF_001006765.1_ASM100676v1_genomic.fna/checkm_result
[2024-01-25 19:39:56,319] [INFO] Task succeeded: CheckM
[2024-01-25 19:39:56,320] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:39:56,335] [INFO] ===== Completeness check finished =====
[2024-01-25 19:39:56,335] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:39:56,336] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001006765.1_ASM100676v1_genomic.fna/markers.fasta)
[2024-01-25 19:39:56,336] [INFO] Task started: Blastn
[2024-01-25 19:39:56,336] [INFO] Running command: blastn -query GCF_001006765.1_ASM100676v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg02f88cc0-eb75-4748-9313-8230844acb25/dqc_reference/reference_markers_gtdb.fasta -out GCF_001006765.1_ASM100676v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:39:57,086] [INFO] Task succeeded: Blastn
[2024-01-25 19:39:57,089] [INFO] Selected 12 target genomes.
[2024-01-25 19:39:57,089] [INFO] Target genome list was writen to GCF_001006765.1_ASM100676v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:39:57,090] [INFO] Task started: fastANI
[2024-01-25 19:39:57,091] [INFO] Running command: fastANI --query /var/lib/cwl/stg9ef3e6f5-f37d-4800-b7b1-3f80fe53f354/GCF_001006765.1_ASM100676v1_genomic.fna.gz --refList GCF_001006765.1_ASM100676v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001006765.1_ASM100676v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:40:03,792] [INFO] Task succeeded: fastANI
[2024-01-25 19:40:03,801] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:40:03,801] [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_001006765.1	s__Staphylococcus succinus	100.0	922	926	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	97.99	95.53	0.94	0.89	24	conclusive
GCF_900458565.1	s__Staphylococcus equorum	81.6933	555	926	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.19	97.35	0.94	0.89	49	-
GCF_001747895.1	s__Staphylococcus equorum_A	81.6485	575	926	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	81.3741	582	926	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000010125.1	s__Staphylococcus saprophyticus	81.1448	510	926	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.41	98.75	0.94	0.91	167	-
GCF_016774515.1	s__Staphylococcus xylosus_A	80.9292	544	926	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.34	99.08	0.95	0.91	11	-
GCF_002732165.1	s__Staphylococcus xylosus	80.8644	520	926	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	98.41	97.01	0.95	0.90	48	-
GCF_013391405.1	s__Staphylococcus sp013391405	80.6967	514	926	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	80.6476	493	926	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000875895.1	s__Staphylococcus gallinarum	80.6445	524	926	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	98.63	98.14	0.94	0.91	25	-
GCF_900097965.1	s__Staphylococcus caeli	80.5509	464	926	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.99	99.99	1.00	1.00	2	-
GCF_002901845.1	s__Staphylococcus hominis	78.3311	265	926	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	97.87	96.99	0.93	0.86	183	-
--------------------------------------------------------------------------------
[2024-01-25 19:40:03,802] [INFO] GTDB search result was written to GCF_001006765.1_ASM100676v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:40:03,803] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:40:03,806] [INFO] DFAST_QC result json was written to GCF_001006765.1_ASM100676v1_genomic.fna/dqc_result.json
[2024-01-25 19:40:03,806] [INFO] DFAST_QC completed!
[2024-01-25 19:40:03,806] [INFO] Total running time: 0h0m43s