[2024-01-24 12:05:50,435] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:05:50,437] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:05:50,437] [INFO] DQC Reference Directory: /var/lib/cwl/stg8edf6a86-4acb-4525-b49f-e17ec4dc2c32/dqc_reference
[2024-01-24 12:05:52,747] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:05:52,747] [INFO] Task started: Prodigal
[2024-01-24 12:05:52,747] [INFO] Running command: gunzip -c /var/lib/cwl/stgfc95201c-3021-4cbe-89ac-fe2b32a7d9fd/GCF_017775145.1_ASM1777514v1_genomic.fna.gz | prodigal -d GCF_017775145.1_ASM1777514v1_genomic.fna/cds.fna -a GCF_017775145.1_ASM1777514v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:05:57,332] [INFO] Task succeeded: Prodigal
[2024-01-24 12:05:57,332] [INFO] Task started: HMMsearch
[2024-01-24 12:05:57,333] [INFO] Running command: hmmsearch --tblout GCF_017775145.1_ASM1777514v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8edf6a86-4acb-4525-b49f-e17ec4dc2c32/dqc_reference/reference_markers.hmm GCF_017775145.1_ASM1777514v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:05:57,603] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:05:57,604] [INFO] Found 6/6 markers.
[2024-01-24 12:05:57,627] [INFO] Query marker FASTA was written to GCF_017775145.1_ASM1777514v1_genomic.fna/markers.fasta
[2024-01-24 12:05:57,631] [INFO] Task started: Blastn
[2024-01-24 12:05:57,631] [INFO] Running command: blastn -query GCF_017775145.1_ASM1777514v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8edf6a86-4acb-4525-b49f-e17ec4dc2c32/dqc_reference/reference_markers.fasta -out GCF_017775145.1_ASM1777514v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:06:00,682] [INFO] Task succeeded: Blastn
[2024-01-24 12:06:00,685] [INFO] Selected 12 target genomes.
[2024-01-24 12:06:00,686] [INFO] Target genome list was writen to GCF_017775145.1_ASM1777514v1_genomic.fna/target_genomes.txt
[2024-01-24 12:06:00,786] [INFO] Task started: fastANI
[2024-01-24 12:06:00,786] [INFO] Running command: fastANI --query /var/lib/cwl/stgfc95201c-3021-4cbe-89ac-fe2b32a7d9fd/GCF_017775145.1_ASM1777514v1_genomic.fna.gz --refList GCF_017775145.1_ASM1777514v1_genomic.fna/target_genomes.txt --output GCF_017775145.1_ASM1777514v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:06:06,636] [INFO] Task succeeded: fastANI
[2024-01-24 12:06:06,636] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8edf6a86-4acb-4525-b49f-e17ec4dc2c32/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:06:06,637] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8edf6a86-4acb-4525-b49f-e17ec4dc2c32/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:06:06,645] [INFO] Found 8 fastANI hits (4 hits with ANI > threshold)
[2024-01-24 12:06:06,645] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:06:06,646] [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 chromogenes	strain=ATCC 43764	GCA_017775145.1	46126	46126	type	True	100.0	743	745	95	conclusive
Staphylococcus chromogenes	strain=CCM 3387	GCA_014635745.1	46126	46126	type	True	99.9982	744	745	95	conclusive
Staphylococcus chromogenes	strain=NCTC10530	GCA_900458195.1	46126	46126	type	True	99.9966	745	745	95	conclusive
Staphylococcus chromogenes	strain=NCTC 10530	GCA_002901945.1	46126	46126	type	True	99.9393	702	745	95	conclusive
Staphylococcus agnetis	strain=DSM 23656	GCA_002901865.1	985762	985762	type	True	81.1836	485	745	95	below_threshold
Staphylococcus hyicus	strain=NCTC10350	GCA_900474585.1	1284	1284	type	True	81.1559	464	745	95	below_threshold
Staphylococcus intermedius	strain=NCTC 11048	GCA_000308095.1	1285	1285	type	True	79.2581	263	745	95	below_threshold
Staphylococcus capitis subsp. capitis	strain=DSM 20326	GCA_025272975.1	72758	29388	type	True	78.1011	160	745	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:06:06,647] [INFO] DFAST Taxonomy check result was written to GCF_017775145.1_ASM1777514v1_genomic.fna/tc_result.tsv
[2024-01-24 12:06:06,649] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:06:06,649] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:06:06,649] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8edf6a86-4acb-4525-b49f-e17ec4dc2c32/dqc_reference/checkm_data
[2024-01-24 12:06:06,650] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:06:06,674] [INFO] Task started: CheckM
[2024-01-24 12:06:06,674] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017775145.1_ASM1777514v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017775145.1_ASM1777514v1_genomic.fna/checkm_input GCF_017775145.1_ASM1777514v1_genomic.fna/checkm_result
[2024-01-24 12:06:30,637] [INFO] Task succeeded: CheckM
[2024-01-24 12:06:30,638] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:06:30,676] [INFO] ===== Completeness check finished =====
[2024-01-24 12:06:30,676] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:06:30,677] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017775145.1_ASM1777514v1_genomic.fna/markers.fasta)
[2024-01-24 12:06:30,677] [INFO] Task started: Blastn
[2024-01-24 12:06:30,677] [INFO] Running command: blastn -query GCF_017775145.1_ASM1777514v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8edf6a86-4acb-4525-b49f-e17ec4dc2c32/dqc_reference/reference_markers_gtdb.fasta -out GCF_017775145.1_ASM1777514v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:06:31,421] [INFO] Task succeeded: Blastn
[2024-01-24 12:06:31,426] [INFO] Selected 15 target genomes.
[2024-01-24 12:06:31,426] [INFO] Target genome list was writen to GCF_017775145.1_ASM1777514v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:06:31,440] [INFO] Task started: fastANI
[2024-01-24 12:06:31,440] [INFO] Running command: fastANI --query /var/lib/cwl/stgfc95201c-3021-4cbe-89ac-fe2b32a7d9fd/GCF_017775145.1_ASM1777514v1_genomic.fna.gz --refList GCF_017775145.1_ASM1777514v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017775145.1_ASM1777514v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:06:39,131] [INFO] Task succeeded: fastANI
[2024-01-24 12:06:39,143] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:06:39,143] [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_002901945.1	s__Staphylococcus chromogenes	99.9393	702	745	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	98.79	96.35	0.95	0.90	130	conclusive
GCF_002901865.1	s__Staphylococcus agnetis	81.1701	486	745	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	98.49	96.84	0.93	0.88	40	-
GCF_000816085.1	s__Staphylococcus hyicus	81.1418	465	745	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.46	99.24	0.96	0.94	9	-
GCF_002902385.1	s__Staphylococcus intermedius	79.4134	271	745	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.80	99.54	0.96	0.94	8	-
GCF_001792775.2	s__Staphylococcus pseudintermedius	79.3763	267	745	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.31	98.36	0.94	0.88	431	-
GCF_900636325.1	s__Staphylococcus delphini	79.2782	261	745	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	97.77	95.78	0.92	0.86	24	-
GCF_900183575.1	s__Staphylococcus cornubiensis	79.1839	270	745	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010365305.1	s__Staphylococcus sp010365305	79.1394	279	745	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	79.0779	262	745	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0878	99.86	99.80	0.99	0.98	25	-
GCF_003019275.1	s__Staphylococcus muscae	78.9189	217	745	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.99	99.99	1.00	1.00	4	-
GCF_002901995.1	s__Staphylococcus coagulans	78.7829	256	745	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0878	98.48	97.57	0.97	0.93	43	-
GCF_016238445.1	s__Staphylococcus sp016238445	78.7404	250	745	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002902145.1	s__Staphylococcus rostri	78.7116	225	745	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000934465.1	s__Staphylococcus microti	78.6065	220	745	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.99	99.97	0.98	0.96	3	-
GCF_002902725.1	s__Staphylococcus caprae	77.9412	162	745	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	98.57	98.10	0.94	0.91	18	-
--------------------------------------------------------------------------------
[2024-01-24 12:06:39,145] [INFO] GTDB search result was written to GCF_017775145.1_ASM1777514v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:06:39,145] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:06:39,148] [INFO] DFAST_QC result json was written to GCF_017775145.1_ASM1777514v1_genomic.fna/dqc_result.json
[2024-01-24 12:06:39,148] [INFO] DFAST_QC completed!
[2024-01-24 12:06:39,148] [INFO] Total running time: 0h0m49s