[2024-01-24 13:46:01,496] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:46:01,498] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:46:01,498] [INFO] DQC Reference Directory: /var/lib/cwl/stgefc7cd32-bf80-4a61-968c-386a99164f7a/dqc_reference
[2024-01-24 13:46:02,783] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:46:02,784] [INFO] Task started: Prodigal
[2024-01-24 13:46:02,784] [INFO] Running command: gunzip -c /var/lib/cwl/stg74ebb24e-b2a7-48d3-96e0-cdd4151c9600/GCF_020883535.1_ASM2088353v1_genomic.fna.gz | prodigal -d GCF_020883535.1_ASM2088353v1_genomic.fna/cds.fna -a GCF_020883535.1_ASM2088353v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:46:07,828] [INFO] Task succeeded: Prodigal
[2024-01-24 13:46:07,828] [INFO] Task started: HMMsearch
[2024-01-24 13:46:07,829] [INFO] Running command: hmmsearch --tblout GCF_020883535.1_ASM2088353v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgefc7cd32-bf80-4a61-968c-386a99164f7a/dqc_reference/reference_markers.hmm GCF_020883535.1_ASM2088353v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:46:08,108] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:46:08,109] [INFO] Found 6/6 markers.
[2024-01-24 13:46:08,135] [INFO] Query marker FASTA was written to GCF_020883535.1_ASM2088353v1_genomic.fna/markers.fasta
[2024-01-24 13:46:08,135] [INFO] Task started: Blastn
[2024-01-24 13:46:08,135] [INFO] Running command: blastn -query GCF_020883535.1_ASM2088353v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgefc7cd32-bf80-4a61-968c-386a99164f7a/dqc_reference/reference_markers.fasta -out GCF_020883535.1_ASM2088353v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:46:08,831] [INFO] Task succeeded: Blastn
[2024-01-24 13:46:08,834] [INFO] Selected 22 target genomes.
[2024-01-24 13:46:08,835] [INFO] Target genome list was writen to GCF_020883535.1_ASM2088353v1_genomic.fna/target_genomes.txt
[2024-01-24 13:46:08,872] [INFO] Task started: fastANI
[2024-01-24 13:46:08,872] [INFO] Running command: fastANI --query /var/lib/cwl/stg74ebb24e-b2a7-48d3-96e0-cdd4151c9600/GCF_020883535.1_ASM2088353v1_genomic.fna.gz --refList GCF_020883535.1_ASM2088353v1_genomic.fna/target_genomes.txt --output GCF_020883535.1_ASM2088353v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:46:21,070] [INFO] Task succeeded: fastANI
[2024-01-24 13:46:21,070] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgefc7cd32-bf80-4a61-968c-386a99164f7a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:46:21,071] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgefc7cd32-bf80-4a61-968c-386a99164f7a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:46:21,088] [INFO] Found 20 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:46:21,088] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:46:21,088] [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=NCTC10530	GCA_900458195.1	46126	46126	type	True	81.4854	483	773	95	below_threshold
Staphylococcus hyicus	strain=ATCC 11249	GCA_000816085.1	1284	1284	type	True	81.3805	484	773	95	below_threshold
Staphylococcus hyicus	strain=NCTC10350	GCA_900474585.1	1284	1284	type	True	81.3667	485	773	95	below_threshold
Staphylococcus chromogenes	strain=ATCC 43764	GCA_017775145.1	46126	46126	type	True	81.2862	460	773	95	below_threshold
Staphylococcus agnetis	strain=DSM 23656	GCA_002901865.1	985762	985762	type	True	81.2705	451	773	95	below_threshold
Staphylococcus chromogenes	strain=CCM 3387	GCA_014635745.1	46126	46126	type	True	81.2566	465	773	95	below_threshold
Staphylococcus chromogenes	strain=NCTC 10530	GCA_002901945.1	46126	46126	type	True	81.2423	462	773	95	below_threshold
Staphylococcus hyicus	strain=CCUG 6509	GCA_003970475.1	1284	1284	type	True	80.9281	464	773	95	below_threshold
Staphylococcus pseudintermedius	strain=FDAARGOS_930	GCA_016026635.1	283734	283734	type	True	79.6379	269	773	95	below_threshold
Staphylococcus intermedius	strain=NCTC 11048	GCA_900458545.1	1285	1285	type	True	79.4349	283	773	95	below_threshold
Staphylococcus schleiferi	strain=NCTC12218	GCA_900458895.2	1295	1295	type	True	79.3058	282	773	95	below_threshold
Staphylococcus cornubiensis	strain=NW1	GCA_900183575.1	1986155	1986155	type	True	79.1438	262	773	95	below_threshold
Staphylococcus pseudintermedius	strain=CCUG 49543	GCA_002902125.1	283734	283734	type	True	79.0582	253	773	95	below_threshold
Staphylococcus pseudintermedius	strain=LMG 22219	GCA_001792775.2	283734	283734	type	True	79.0227	265	773	95	below_threshold
Staphylococcus lugdunensis	strain=NCTC12217	GCA_900478255.1	28035	28035	type	True	78.9771	148	773	95	below_threshold
Staphylococcus intermedius	strain=NCTC 11048	GCA_002902385.1	1285	1285	type	True	78.9567	263	773	95	below_threshold
Staphylococcus intermedius	strain=NCTC 11048	GCA_000308095.1	1285	1285	type	True	78.7677	251	773	95	below_threshold
Staphylococcus taiwanensis	strain=NTUH-S172	GCA_020544305.1	2750012	2750012	type	True	78.6702	183	773	95	below_threshold
Staphylococcus schweitzeri	strain=DSM 28300	GCA_014877095.1	1654388	1654388	type	True	78.1573	168	773	95	below_threshold
Staphylococcus shinii	strain=K22-5M	GCA_017583065.1	2912228	2912228	type	True	77.952	163	773	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:46:21,090] [INFO] DFAST Taxonomy check result was written to GCF_020883535.1_ASM2088353v1_genomic.fna/tc_result.tsv
[2024-01-24 13:46:21,091] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:46:21,091] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:46:21,091] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgefc7cd32-bf80-4a61-968c-386a99164f7a/dqc_reference/checkm_data
[2024-01-24 13:46:21,092] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:46:21,119] [INFO] Task started: CheckM
[2024-01-24 13:46:21,119] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_020883535.1_ASM2088353v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_020883535.1_ASM2088353v1_genomic.fna/checkm_input GCF_020883535.1_ASM2088353v1_genomic.fna/checkm_result
[2024-01-24 13:46:43,593] [INFO] Task succeeded: CheckM
[2024-01-24 13:46:43,594] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:46:43,612] [INFO] ===== Completeness check finished =====
[2024-01-24 13:46:43,613] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:46:43,613] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_020883535.1_ASM2088353v1_genomic.fna/markers.fasta)
[2024-01-24 13:46:43,614] [INFO] Task started: Blastn
[2024-01-24 13:46:43,614] [INFO] Running command: blastn -query GCF_020883535.1_ASM2088353v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgefc7cd32-bf80-4a61-968c-386a99164f7a/dqc_reference/reference_markers_gtdb.fasta -out GCF_020883535.1_ASM2088353v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:46:44,392] [INFO] Task succeeded: Blastn
[2024-01-24 13:46:44,396] [INFO] Selected 19 target genomes.
[2024-01-24 13:46:44,396] [INFO] Target genome list was writen to GCF_020883535.1_ASM2088353v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:46:44,420] [INFO] Task started: fastANI
[2024-01-24 13:46:44,420] [INFO] Running command: fastANI --query /var/lib/cwl/stg74ebb24e-b2a7-48d3-96e0-cdd4151c9600/GCF_020883535.1_ASM2088353v1_genomic.fna.gz --refList GCF_020883535.1_ASM2088353v1_genomic.fna/target_genomes_gtdb.txt --output GCF_020883535.1_ASM2088353v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:46:55,583] [INFO] Task succeeded: fastANI
[2024-01-24 13:46:55,597] [INFO] Found 17 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:46:55,597] [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_000816085.1	s__Staphylococcus hyicus	81.3528	486	773	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.46	99.24	0.96	0.94	9	-
GCF_002901865.1	s__Staphylococcus agnetis	81.2737	450	773	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	98.49	96.84	0.93	0.88	40	-
GCF_002901945.1	s__Staphylococcus chromogenes	81.2262	463	773	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	98.79	96.35	0.95	0.90	130	-
GCF_003019275.1	s__Staphylococcus muscae	79.5804	222	773	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.99	99.99	1.00	1.00	4	-
GCF_900636325.1	s__Staphylococcus delphini	79.4657	274	773	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	97.77	95.78	0.92	0.86	24	-
GCF_003012915.1	s__Staphylococcus felis	79.2988	227	773	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.05	98.64	0.95	0.91	31	-
GCA_900458895.2	s__Staphylococcus schleiferi	79.1751	279	773	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0878	99.86	99.80	0.99	0.98	25	-
GCF_900183575.1	s__Staphylococcus cornubiensis	79.1619	261	773	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001792775.2	s__Staphylococcus pseudintermedius	79.0642	262	773	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.31	98.36	0.94	0.88	431	-
GCF_002902385.1	s__Staphylococcus intermedius	78.957	262	773	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.80	99.54	0.96	0.94	8	-
GCF_000236925.1	s__Staphylococcus argenteus	78.9557	192	773	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.00	98.60	0.96	0.90	171	-
GCF_002901995.1	s__Staphylococcus coagulans	78.8251	244	773	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0878	98.48	97.57	0.97	0.93	43	-
GCF_002902145.1	s__Staphylococcus rostri	78.7849	211	773	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016238445.1	s__Staphylococcus sp016238445	78.5971	232	773	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002902405.1	s__Staphylococcus schweitzeri	78.2503	167	773	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.10	98.12	0.97	0.94	9	-
GCF_002901705.1	s__Staphylococcus lugdunensis	78.0566	143	773	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.51	99.34	0.98	0.96	70	-
GCF_015025035.1	s__Staphylococcus sp015025035	78.0148	187	773	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	98.24	97.61	0.95	0.93	11	-
--------------------------------------------------------------------------------
[2024-01-24 13:46:55,599] [INFO] GTDB search result was written to GCF_020883535.1_ASM2088353v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:46:55,600] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:46:55,605] [INFO] DFAST_QC result json was written to GCF_020883535.1_ASM2088353v1_genomic.fna/dqc_result.json
[2024-01-24 13:46:55,605] [INFO] DFAST_QC completed!
[2024-01-24 13:46:55,605] [INFO] Total running time: 0h0m54s