[2024-01-24 12:16:08,686] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:16:08,688] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:16:08,688] [INFO] DQC Reference Directory: /var/lib/cwl/stg56330df7-6fcf-4584-b508-e43fa6fc0d25/dqc_reference
[2024-01-24 12:16:10,061] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:16:10,062] [INFO] Task started: Prodigal
[2024-01-24 12:16:10,062] [INFO] Running command: gunzip -c /var/lib/cwl/stga3232771-d260-4d54-8033-d7dc09a21b66/GCF_002902345.1_ASM290234v1_genomic.fna.gz | prodigal -d GCF_002902345.1_ASM290234v1_genomic.fna/cds.fna -a GCF_002902345.1_ASM290234v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:16:14,953] [INFO] Task succeeded: Prodigal
[2024-01-24 12:16:14,954] [INFO] Task started: HMMsearch
[2024-01-24 12:16:14,954] [INFO] Running command: hmmsearch --tblout GCF_002902345.1_ASM290234v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg56330df7-6fcf-4584-b508-e43fa6fc0d25/dqc_reference/reference_markers.hmm GCF_002902345.1_ASM290234v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:16:15,212] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:16:15,213] [INFO] Found 6/6 markers.
[2024-01-24 12:16:15,240] [INFO] Query marker FASTA was written to GCF_002902345.1_ASM290234v1_genomic.fna/markers.fasta
[2024-01-24 12:16:15,240] [INFO] Task started: Blastn
[2024-01-24 12:16:15,240] [INFO] Running command: blastn -query GCF_002902345.1_ASM290234v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg56330df7-6fcf-4584-b508-e43fa6fc0d25/dqc_reference/reference_markers.fasta -out GCF_002902345.1_ASM290234v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:16:15,858] [INFO] Task succeeded: Blastn
[2024-01-24 12:16:15,861] [INFO] Selected 16 target genomes.
[2024-01-24 12:16:15,862] [INFO] Target genome list was writen to GCF_002902345.1_ASM290234v1_genomic.fna/target_genomes.txt
[2024-01-24 12:16:15,867] [INFO] Task started: fastANI
[2024-01-24 12:16:15,867] [INFO] Running command: fastANI --query /var/lib/cwl/stga3232771-d260-4d54-8033-d7dc09a21b66/GCF_002902345.1_ASM290234v1_genomic.fna.gz --refList GCF_002902345.1_ASM290234v1_genomic.fna/target_genomes.txt --output GCF_002902345.1_ASM290234v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:16:25,534] [INFO] Task succeeded: fastANI
[2024-01-24 12:16:25,535] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg56330df7-6fcf-4584-b508-e43fa6fc0d25/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:16:25,535] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg56330df7-6fcf-4584-b508-e43fa6fc0d25/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:16:25,547] [INFO] Found 13 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:16:25,547] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:16:25,548] [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 arlettae	strain=NCTC 12413	GCA_002902345.1	29378	29378	type	True	100.0	877	877	95	conclusive
Staphylococcus arlettae	strain=NCTC12413	GCA_900457375.1	29378	29378	type	True	99.9678	876	877	95	conclusive
Staphylococcus lloydii	strain=23_2_7_LY	GCA_015775975.1	2781774	2781774	type	True	79.9316	402	877	95	below_threshold
Staphylococcus kloosii	strain=ATCC 43959	GCA_003019255.1	29384	29384	type	True	79.6886	400	877	95	below_threshold
Staphylococcus durrellii	strain=27_4_6_LY	GCA_015594545.1	2781773	2781773	type	True	79.6796	390	877	95	below_threshold
Staphylococcus kloosii	strain=NCTC 12415	GCA_002902055.1	29384	29384	type	True	79.5802	391	877	95	below_threshold
Staphylococcus xylosus	strain=NCTC 11043	GCA_002901985.1	1288	1288	type	True	79.3338	349	877	95	below_threshold
Staphylococcus xylosus	strain=CCM 2738	GCA_002732165.1	1288	1288	type	True	79.2465	382	877	95	below_threshold
Staphylococcus xylosus	strain=NCTC11043	GCA_900458755.1	1288	1288	type	True	79.2014	382	877	95	below_threshold
Staphylococcus caprae	strain=NCTC12196	GCA_900458385.1	29380	29380	type	True	78.8564	241	877	95	below_threshold
Staphylococcus caprae	strain=NCTC 12196	GCA_002902725.1	29380	29380	type	True	78.8533	233	877	95	below_threshold
Staphylococcus taiwanensis	strain=NTUH-S172	GCA_020544305.1	2750012	2750012	type	True	78.7657	246	877	95	below_threshold
Staphylococcus capitis subsp. capitis	strain=DSM 20326	GCA_025272975.1	72758	29388	type	True	78.666	247	877	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:16:25,550] [INFO] DFAST Taxonomy check result was written to GCF_002902345.1_ASM290234v1_genomic.fna/tc_result.tsv
[2024-01-24 12:16:25,550] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:16:25,550] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:16:25,551] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg56330df7-6fcf-4584-b508-e43fa6fc0d25/dqc_reference/checkm_data
[2024-01-24 12:16:25,552] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:16:25,585] [INFO] Task started: CheckM
[2024-01-24 12:16:25,585] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002902345.1_ASM290234v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002902345.1_ASM290234v1_genomic.fna/checkm_input GCF_002902345.1_ASM290234v1_genomic.fna/checkm_result
[2024-01-24 12:16:47,382] [INFO] Task succeeded: CheckM
[2024-01-24 12:16:47,383] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:16:47,404] [INFO] ===== Completeness check finished =====
[2024-01-24 12:16:47,405] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:16:47,405] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002902345.1_ASM290234v1_genomic.fna/markers.fasta)
[2024-01-24 12:16:47,405] [INFO] Task started: Blastn
[2024-01-24 12:16:47,406] [INFO] Running command: blastn -query GCF_002902345.1_ASM290234v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg56330df7-6fcf-4584-b508-e43fa6fc0d25/dqc_reference/reference_markers_gtdb.fasta -out GCF_002902345.1_ASM290234v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:16:48,224] [INFO] Task succeeded: Blastn
[2024-01-24 12:16:48,230] [INFO] Selected 16 target genomes.
[2024-01-24 12:16:48,230] [INFO] Target genome list was writen to GCF_002902345.1_ASM290234v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:16:48,237] [INFO] Task started: fastANI
[2024-01-24 12:16:48,238] [INFO] Running command: fastANI --query /var/lib/cwl/stga3232771-d260-4d54-8033-d7dc09a21b66/GCF_002902345.1_ASM290234v1_genomic.fna.gz --refList GCF_002902345.1_ASM290234v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002902345.1_ASM290234v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:16:56,498] [INFO] Task succeeded: fastANI
[2024-01-24 12:16:56,509] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:16:56,510] [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_002902345.1	s__Staphylococcus arlettae	100.0	877	877	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.12	98.73	0.94	0.91	41	conclusive
GCF_015775975.1	s__Staphylococcus lloydii	79.9179	403	877	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.39	98.19	0.98	0.95	4	-
GCF_015594545.1	s__Staphylococcus durrellii	79.6933	389	877	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003019255.1	s__Staphylococcus kloosii	79.6886	400	877	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	98.99	96.08	0.96	0.89	9	-
GCF_000010125.1	s__Staphylococcus saprophyticus	79.5409	374	877	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.41	98.75	0.94	0.91	167	-
GCF_002732165.1	s__Staphylococcus xylosus	79.2824	379	877	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	98.41	97.01	0.95	0.90	48	-
GCF_900097965.1	s__Staphylococcus caeli	79.2577	346	877	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.99	99.99	1.00	1.00	2	-
GCF_001006765.1	s__Staphylococcus succinus	79.2238	372	877	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	97.99	95.53	0.94	0.89	24	-
GCF_013391405.1	s__Staphylococcus sp013391405	79.0099	369	877	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900458565.1	s__Staphylococcus equorum	79.0077	384	877	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.19	97.35	0.94	0.89	49	-
GCF_002902725.1	s__Staphylococcus caprae	78.8829	232	877	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	98.57	98.10	0.94	0.91	18	-
GCF_015025035.1	s__Staphylococcus sp015025035	78.6767	243	877	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	98.24	97.61	0.95	0.93	11	-
GCF_003970495.1	s__Staphylococcus pasteuri	78.6571	279	877	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	98.98	98.67	0.95	0.89	34	-
GCF_002902325.1	s__Staphylococcus capitis	78.5976	236	877	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	97.07	96.40	0.94	0.88	151	-
--------------------------------------------------------------------------------
[2024-01-24 12:16:56,512] [INFO] GTDB search result was written to GCF_002902345.1_ASM290234v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:16:56,513] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:16:56,516] [INFO] DFAST_QC result json was written to GCF_002902345.1_ASM290234v1_genomic.fna/dqc_result.json
[2024-01-24 12:16:56,516] [INFO] DFAST_QC completed!
[2024-01-24 12:16:56,516] [INFO] Total running time: 0h0m48s