[2024-01-25 18:54:35,709] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:54:35,710] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:54:35,710] [INFO] DQC Reference Directory: /var/lib/cwl/stgea9a96f9-f898-4b68-b02d-39435c8215b0/dqc_reference
[2024-01-25 18:54:36,867] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:54:36,868] [INFO] Task started: Prodigal
[2024-01-25 18:54:36,868] [INFO] Running command: gunzip -c /var/lib/cwl/stg582fad9f-aa87-4c9c-9f7d-9c2b21b37992/GCF_002901865.1_ASM290186v1_genomic.fna.gz | prodigal -d GCF_002901865.1_ASM290186v1_genomic.fna/cds.fna -a GCF_002901865.1_ASM290186v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:54:40,943] [INFO] Task succeeded: Prodigal
[2024-01-25 18:54:40,944] [INFO] Task started: HMMsearch
[2024-01-25 18:54:40,944] [INFO] Running command: hmmsearch --tblout GCF_002901865.1_ASM290186v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgea9a96f9-f898-4b68-b02d-39435c8215b0/dqc_reference/reference_markers.hmm GCF_002901865.1_ASM290186v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:54:41,147] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:54:41,148] [INFO] Found 6/6 markers.
[2024-01-25 18:54:41,170] [INFO] Query marker FASTA was written to GCF_002901865.1_ASM290186v1_genomic.fna/markers.fasta
[2024-01-25 18:54:41,170] [INFO] Task started: Blastn
[2024-01-25 18:54:41,170] [INFO] Running command: blastn -query GCF_002901865.1_ASM290186v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgea9a96f9-f898-4b68-b02d-39435c8215b0/dqc_reference/reference_markers.fasta -out GCF_002901865.1_ASM290186v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:54:41,733] [INFO] Task succeeded: Blastn
[2024-01-25 18:54:41,735] [INFO] Selected 12 target genomes.
[2024-01-25 18:54:41,736] [INFO] Target genome list was writen to GCF_002901865.1_ASM290186v1_genomic.fna/target_genomes.txt
[2024-01-25 18:54:41,745] [INFO] Task started: fastANI
[2024-01-25 18:54:41,745] [INFO] Running command: fastANI --query /var/lib/cwl/stg582fad9f-aa87-4c9c-9f7d-9c2b21b37992/GCF_002901865.1_ASM290186v1_genomic.fna.gz --refList GCF_002901865.1_ASM290186v1_genomic.fna/target_genomes.txt --output GCF_002901865.1_ASM290186v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:54:47,672] [INFO] Task succeeded: fastANI
[2024-01-25 18:54:47,672] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgea9a96f9-f898-4b68-b02d-39435c8215b0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:54:47,672] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgea9a96f9-f898-4b68-b02d-39435c8215b0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:54:47,680] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:54:47,680] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:54:47,680] [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 agnetis	strain=DSM 23656	GCA_002901865.1	985762	985762	type	True	100.0	763	767	95	conclusive
Staphylococcus hyicus	strain=CCUG 6509	GCA_003970475.1	1284	1284	type	True	86.7587	622	767	95	below_threshold
Staphylococcus hyicus	strain=ATCC 11249	GCA_000816085.1	1284	1284	type	True	86.7002	654	767	95	below_threshold
Staphylococcus hyicus	strain=NCTC10350	GCA_900474585.1	1284	1284	type	True	86.6909	656	767	95	below_threshold
Staphylococcus chromogenes	strain=NCTC10530	GCA_900458195.1	46126	46126	type	True	81.4185	466	767	95	below_threshold
Staphylococcus schleiferi subsp. schleiferi	strain=NCTC 12218	GCA_003968865.1	74707	1295	type	True	78.8502	256	767	95	below_threshold
Staphylococcus aureus	strain=PartF-Saureus-RM8376	GCA_022869625.1	1280	1280	type	True	78.2554	176	767	95	below_threshold
Staphylococcus aureus	strain=NCTC 08532	GCA_002902205.1	1280	1280	type	True	78.1106	174	767	95	below_threshold
Staphylococcus taiwanensis	strain=NTUH-S172	GCA_020544305.1	2750012	2750012	type	True	77.9591	172	767	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:54:47,682] [INFO] DFAST Taxonomy check result was written to GCF_002901865.1_ASM290186v1_genomic.fna/tc_result.tsv
[2024-01-25 18:54:47,683] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:54:47,683] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:54:47,683] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgea9a96f9-f898-4b68-b02d-39435c8215b0/dqc_reference/checkm_data
[2024-01-25 18:54:47,684] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:54:47,711] [INFO] Task started: CheckM
[2024-01-25 18:54:47,711] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002901865.1_ASM290186v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002901865.1_ASM290186v1_genomic.fna/checkm_input GCF_002901865.1_ASM290186v1_genomic.fna/checkm_result
[2024-01-25 18:55:06,682] [INFO] Task succeeded: CheckM
[2024-01-25 18:55:06,683] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:55:06,711] [INFO] ===== Completeness check finished =====
[2024-01-25 18:55:06,711] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:55:06,711] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002901865.1_ASM290186v1_genomic.fna/markers.fasta)
[2024-01-25 18:55:06,712] [INFO] Task started: Blastn
[2024-01-25 18:55:06,712] [INFO] Running command: blastn -query GCF_002901865.1_ASM290186v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgea9a96f9-f898-4b68-b02d-39435c8215b0/dqc_reference/reference_markers_gtdb.fasta -out GCF_002901865.1_ASM290186v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:55:07,486] [INFO] Task succeeded: Blastn
[2024-01-25 18:55:07,492] [INFO] Selected 13 target genomes.
[2024-01-25 18:55:07,492] [INFO] Target genome list was writen to GCF_002901865.1_ASM290186v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:55:07,507] [INFO] Task started: fastANI
[2024-01-25 18:55:07,507] [INFO] Running command: fastANI --query /var/lib/cwl/stg582fad9f-aa87-4c9c-9f7d-9c2b21b37992/GCF_002901865.1_ASM290186v1_genomic.fna.gz --refList GCF_002901865.1_ASM290186v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002901865.1_ASM290186v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:55:14,088] [INFO] Task succeeded: fastANI
[2024-01-25 18:55:14,096] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:55:14,097] [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_002901865.1	s__Staphylococcus agnetis	100.0	763	767	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	98.49	96.84	0.93	0.88	40	conclusive
GCF_000816085.1	s__Staphylococcus hyicus	86.7002	654	767	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.46	99.24	0.96	0.94	9	-
GCF_002901945.1	s__Staphylococcus chromogenes	81.3681	461	767	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	98.79	96.35	0.95	0.90	130	-
GCF_900183575.1	s__Staphylococcus cornubiensis	79.1013	268	767	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900458895.2	s__Staphylococcus schleiferi	79.0733	258	767	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0878	99.86	99.80	0.99	0.98	25	-
GCF_010365305.1	s__Staphylococcus sp010365305	78.9652	262	767	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013463155.1	s__Staphylococcus sp013463155	78.8698	221	767	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002902385.1	s__Staphylococcus intermedius	78.8687	273	767	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.80	99.54	0.96	0.94	8	-
GCF_002901995.1	s__Staphylococcus coagulans	78.8196	256	767	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0878	98.48	97.57	0.97	0.93	43	-
GCF_002101335.1	s__Staphylococcus lutrae	78.4279	247	767	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.99	99.99	1.00	1.00	2	-
GCF_015025035.1	s__Staphylococcus sp015025035	78.1845	177	767	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	98.24	97.61	0.95	0.93	11	-
--------------------------------------------------------------------------------
[2024-01-25 18:55:14,098] [INFO] GTDB search result was written to GCF_002901865.1_ASM290186v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:55:14,099] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:55:14,101] [INFO] DFAST_QC result json was written to GCF_002901865.1_ASM290186v1_genomic.fna/dqc_result.json
[2024-01-25 18:55:14,102] [INFO] DFAST_QC completed!
[2024-01-25 18:55:14,102] [INFO] Total running time: 0h0m38s