[2024-01-24 13:48:43,402] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:48:43,404] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:48:43,404] [INFO] DQC Reference Directory: /var/lib/cwl/stg2ea87706-e912-466e-8fe3-04621fd5e20c/dqc_reference
[2024-01-24 13:48:44,736] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:48:44,737] [INFO] Task started: Prodigal
[2024-01-24 13:48:44,737] [INFO] Running command: gunzip -c /var/lib/cwl/stge41c8f68-8ba7-4637-8884-af5443b31091/GCF_002902305.1_ASM290230v1_genomic.fna.gz | prodigal -d GCF_002902305.1_ASM290230v1_genomic.fna/cds.fna -a GCF_002902305.1_ASM290230v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:48:49,978] [INFO] Task succeeded: Prodigal
[2024-01-24 13:48:49,979] [INFO] Task started: HMMsearch
[2024-01-24 13:48:49,979] [INFO] Running command: hmmsearch --tblout GCF_002902305.1_ASM290230v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2ea87706-e912-466e-8fe3-04621fd5e20c/dqc_reference/reference_markers.hmm GCF_002902305.1_ASM290230v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:48:50,238] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:48:50,239] [INFO] Found 6/6 markers.
[2024-01-24 13:48:50,265] [INFO] Query marker FASTA was written to GCF_002902305.1_ASM290230v1_genomic.fna/markers.fasta
[2024-01-24 13:48:50,265] [INFO] Task started: Blastn
[2024-01-24 13:48:50,266] [INFO] Running command: blastn -query GCF_002902305.1_ASM290230v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2ea87706-e912-466e-8fe3-04621fd5e20c/dqc_reference/reference_markers.fasta -out GCF_002902305.1_ASM290230v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:48:50,863] [INFO] Task succeeded: Blastn
[2024-01-24 13:48:50,866] [INFO] Selected 19 target genomes.
[2024-01-24 13:48:50,866] [INFO] Target genome list was writen to GCF_002902305.1_ASM290230v1_genomic.fna/target_genomes.txt
[2024-01-24 13:48:50,886] [INFO] Task started: fastANI
[2024-01-24 13:48:50,886] [INFO] Running command: fastANI --query /var/lib/cwl/stge41c8f68-8ba7-4637-8884-af5443b31091/GCF_002902305.1_ASM290230v1_genomic.fna.gz --refList GCF_002902305.1_ASM290230v1_genomic.fna/target_genomes.txt --output GCF_002902305.1_ASM290230v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:49:00,210] [INFO] Task succeeded: fastANI
[2024-01-24 13:49:00,211] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2ea87706-e912-466e-8fe3-04621fd5e20c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:49:00,212] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2ea87706-e912-466e-8fe3-04621fd5e20c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:49:00,230] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:49:00,231] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:49:00,231] [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 argensis	strain=DSM 29875	GCA_002902305.1	1607738	1607738	type	True	100.0	809	809	95	conclusive
Staphylococcus pettenkoferi	strain=CCUG 51270	GCA_002902685.1	170573	170573	type	True	92.296	721	809	95	below_threshold
Staphylococcus pettenkoferi	strain=FDAARGOS_1071	GCA_016127935.1	170573	170573	type	True	92.2758	749	809	95	below_threshold
Staphylococcus pragensis	strain=CCM 8529	GCA_004785665.1	1611836	1611836	type	True	78.5796	193	809	95	below_threshold
Staphylococcus arlettae	strain=NCTC12413	GCA_900457375.1	29378	29378	type	True	78.554	161	809	95	below_threshold
Staphylococcus pragensis	strain=CCM 8529	GCA_014635505.1	1611836	1611836	type	True	78.5229	190	809	95	below_threshold
Staphylococcus petrasii	strain=NCTC13835	GCA_900458665.1	1276936	1276936	type	True	78.472	208	809	95	below_threshold
Staphylococcus croceilyticus	strain=CCUG 62728	GCA_002902575.1	319942	319942	type	True	78.4429	191	809	95	below_threshold
Staphylococcus arlettae	strain=NCTC 12413	GCA_002902345.1	29378	29378	type	True	78.4349	162	809	95	below_threshold
Staphylococcus petrasii	strain=CCUG 62727	GCA_002902565.1	1276936	1276936	type	True	78.4048	200	809	95	below_threshold
Staphylococcus aureus	strain=PartF-Saureus-RM8376	GCA_022869625.1	1280	1280	type	True	78.3959	135	809	95	below_threshold
Staphylococcus aureus	strain=NCTC 08532	GCA_002902205.1	1280	1280	type	True	78.3018	137	809	95	below_threshold
Staphylococcus croceilyticus	strain=CCM 8421	GCA_004684875.1	319942	319942	type	True	78.2768	200	809	95	below_threshold
Macrococcus goetzii	strain=CCM 4927	GCA_002742385.2	1891097	1891097	type	True	78.1416	61	809	95	below_threshold
Staphylococcus durrellii	strain=27_4_6_LY	GCA_015594545.1	2781773	2781773	type	True	78.0978	157	809	95	below_threshold
Staphylococcus xylosus	strain=NCTC11043	GCA_900458755.1	1288	1288	type	True	78.0388	178	809	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:49:00,233] [INFO] DFAST Taxonomy check result was written to GCF_002902305.1_ASM290230v1_genomic.fna/tc_result.tsv
[2024-01-24 13:49:00,233] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:49:00,234] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:49:00,234] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2ea87706-e912-466e-8fe3-04621fd5e20c/dqc_reference/checkm_data
[2024-01-24 13:49:00,235] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:49:00,260] [INFO] Task started: CheckM
[2024-01-24 13:49:00,260] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002902305.1_ASM290230v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002902305.1_ASM290230v1_genomic.fna/checkm_input GCF_002902305.1_ASM290230v1_genomic.fna/checkm_result
[2024-01-24 13:49:22,586] [INFO] Task succeeded: CheckM
[2024-01-24 13:49:22,588] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:49:22,607] [INFO] ===== Completeness check finished =====
[2024-01-24 13:49:22,607] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:49:22,608] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002902305.1_ASM290230v1_genomic.fna/markers.fasta)
[2024-01-24 13:49:22,608] [INFO] Task started: Blastn
[2024-01-24 13:49:22,608] [INFO] Running command: blastn -query GCF_002902305.1_ASM290230v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2ea87706-e912-466e-8fe3-04621fd5e20c/dqc_reference/reference_markers_gtdb.fasta -out GCF_002902305.1_ASM290230v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:23,408] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:23,413] [INFO] Selected 19 target genomes.
[2024-01-24 13:49:23,413] [INFO] Target genome list was writen to GCF_002902305.1_ASM290230v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:49:23,432] [INFO] Task started: fastANI
[2024-01-24 13:49:23,433] [INFO] Running command: fastANI --query /var/lib/cwl/stge41c8f68-8ba7-4637-8884-af5443b31091/GCF_002902305.1_ASM290230v1_genomic.fna.gz --refList GCF_002902305.1_ASM290230v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002902305.1_ASM290230v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:49:32,123] [INFO] Task succeeded: fastANI
[2024-01-24 13:49:32,150] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:49:32,150] [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_002902305.1	s__Staphylococcus argensis	100.0	809	809	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.94	99.94	1.00	1.00	8	conclusive
GCF_002902685.1	s__Staphylococcus pettenkoferi	92.3035	720	809	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	97.48	96.01	0.95	0.89	21	-
GCF_006742205.1	s__Staphylococcus epidermidis	78.6419	140	809	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.01	96.59	0.94	0.83	1079	-
GCF_004785665.1	s__Staphylococcus pragensis	78.5998	192	809	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.69	99.09	0.98	0.94	4	-
GCF_003043455.1	s__Staphylococcus simulans_A	78.5859	153	809	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	98.25	98.25	0.90	0.90	2	-
GCA_002902575.1	s__Staphylococcus croceilyticus	78.462	190	809	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.95	99.95	1.00	1.00	2	-
GCF_002902345.1	s__Staphylococcus arlettae	78.4349	162	809	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.12	98.73	0.94	0.91	41	-
GCF_002902565.1	s__Staphylococcus petrasii	78.4228	199	809	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	98.66	97.62	0.95	0.85	8	-
GCF_015775975.1	s__Staphylococcus lloydii	78.3718	192	809	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.39	98.19	0.98	0.95	4	-
GCF_013391405.1	s__Staphylococcus sp013391405	78.3025	184	809	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002902285.1	s__Staphylococcus simulans	78.292	180	809	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	98.92	98.61	0.93	0.91	77	-
GCF_001224225.1	s__Staphylococcus borealis	78.2778	172	809	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	98.37	97.44	0.93	0.89	22	-
GCF_003019255.1	s__Staphylococcus kloosii	78.2254	203	809	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	98.99	96.08	0.96	0.89	9	-
GCF_900097965.1	s__Staphylococcus caeli	78.1754	181	809	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.99	99.99	1.00	1.00	2	-
GCF_015594545.1	s__Staphylococcus durrellii	78.1663	157	809	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002742385.2	s__Macrococcus_B goetzii	78.1416	61	809	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Macrococcus_B	95.5758	96.60	96.57	0.86	0.86	4	-
GCF_002902365.1	s__Staphylococcus cohnii	78.0956	169	809	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	97.14	95.73	0.92	0.88	59	-
GCF_001006765.1	s__Staphylococcus succinus	78.0189	172	809	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	97.99	95.53	0.94	0.89	24	-
GCF_002732165.1	s__Staphylococcus xylosus	78.0172	175	809	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	98.41	97.01	0.95	0.90	48	-
--------------------------------------------------------------------------------
[2024-01-24 13:49:32,152] [INFO] GTDB search result was written to GCF_002902305.1_ASM290230v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:49:32,153] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:49:32,159] [INFO] DFAST_QC result json was written to GCF_002902305.1_ASM290230v1_genomic.fna/dqc_result.json
[2024-01-24 13:49:32,159] [INFO] DFAST_QC completed!
[2024-01-24 13:49:32,160] [INFO] Total running time: 0h0m49s