[2024-01-24 13:58:10,259] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:58:10,260] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:58:10,261] [INFO] DQC Reference Directory: /var/lib/cwl/stg2dc39373-f749-40ab-8a70-090463b70e23/dqc_reference
[2024-01-24 13:58:11,360] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:58:11,360] [INFO] Task started: Prodigal
[2024-01-24 13:58:11,361] [INFO] Running command: gunzip -c /var/lib/cwl/stg762c959e-283b-4e61-8a8e-305ffd112a96/GCF_003019255.1_ASM301925v1_genomic.fna.gz | prodigal -d GCF_003019255.1_ASM301925v1_genomic.fna/cds.fna -a GCF_003019255.1_ASM301925v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:58:15,468] [INFO] Task succeeded: Prodigal
[2024-01-24 13:58:15,469] [INFO] Task started: HMMsearch
[2024-01-24 13:58:15,469] [INFO] Running command: hmmsearch --tblout GCF_003019255.1_ASM301925v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2dc39373-f749-40ab-8a70-090463b70e23/dqc_reference/reference_markers.hmm GCF_003019255.1_ASM301925v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:58:15,752] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:58:15,753] [INFO] Found 6/6 markers.
[2024-01-24 13:58:15,774] [INFO] Query marker FASTA was written to GCF_003019255.1_ASM301925v1_genomic.fna/markers.fasta
[2024-01-24 13:58:15,774] [INFO] Task started: Blastn
[2024-01-24 13:58:15,774] [INFO] Running command: blastn -query GCF_003019255.1_ASM301925v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2dc39373-f749-40ab-8a70-090463b70e23/dqc_reference/reference_markers.fasta -out GCF_003019255.1_ASM301925v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:16,519] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:16,521] [INFO] Selected 10 target genomes.
[2024-01-24 13:58:16,522] [INFO] Target genome list was writen to GCF_003019255.1_ASM301925v1_genomic.fna/target_genomes.txt
[2024-01-24 13:58:16,590] [INFO] Task started: fastANI
[2024-01-24 13:58:16,590] [INFO] Running command: fastANI --query /var/lib/cwl/stg762c959e-283b-4e61-8a8e-305ffd112a96/GCF_003019255.1_ASM301925v1_genomic.fna.gz --refList GCF_003019255.1_ASM301925v1_genomic.fna/target_genomes.txt --output GCF_003019255.1_ASM301925v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:58:22,163] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:22,163] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2dc39373-f749-40ab-8a70-090463b70e23/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:58:22,163] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2dc39373-f749-40ab-8a70-090463b70e23/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:58:22,169] [INFO] Found 6 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 13:58:22,169] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:58:22,169] [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 kloosii	strain=ATCC 43959	GCA_003019255.1	29384	29384	type	True	100.0	876	878	95	conclusive
Staphylococcus kloosii	strain=NCTC12415	GCA_900458805.1	29384	29384	type	True	99.9995	875	878	95	conclusive
Staphylococcus kloosii	strain=NCTC 12415	GCA_002902055.1	29384	29384	type	True	99.8967	803	878	95	conclusive
Staphylococcus lloydii	strain=23_2_7_LY	GCA_015775975.1	2781774	2781774	type	True	90.9204	750	878	95	below_threshold
Staphylococcus durrellii	strain=27_4_6_LY	GCA_015594545.1	2781773	2781773	type	True	86.6247	733	878	95	below_threshold
Staphylococcus taiwanensis	strain=NTUH-S172	GCA_020544305.1	2750012	2750012	type	True	79.172	268	878	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:58:22,170] [INFO] DFAST Taxonomy check result was written to GCF_003019255.1_ASM301925v1_genomic.fna/tc_result.tsv
[2024-01-24 13:58:22,171] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:58:22,171] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:58:22,171] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2dc39373-f749-40ab-8a70-090463b70e23/dqc_reference/checkm_data
[2024-01-24 13:58:22,171] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:58:22,198] [INFO] Task started: CheckM
[2024-01-24 13:58:22,198] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003019255.1_ASM301925v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003019255.1_ASM301925v1_genomic.fna/checkm_input GCF_003019255.1_ASM301925v1_genomic.fna/checkm_result
[2024-01-24 13:58:39,855] [INFO] Task succeeded: CheckM
[2024-01-24 13:58:39,856] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:58:39,870] [INFO] ===== Completeness check finished =====
[2024-01-24 13:58:39,870] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:58:39,870] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003019255.1_ASM301925v1_genomic.fna/markers.fasta)
[2024-01-24 13:58:39,871] [INFO] Task started: Blastn
[2024-01-24 13:58:39,871] [INFO] Running command: blastn -query GCF_003019255.1_ASM301925v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2dc39373-f749-40ab-8a70-090463b70e23/dqc_reference/reference_markers_gtdb.fasta -out GCF_003019255.1_ASM301925v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:40,604] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:40,607] [INFO] Selected 12 target genomes.
[2024-01-24 13:58:40,607] [INFO] Target genome list was writen to GCF_003019255.1_ASM301925v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:58:40,613] [INFO] Task started: fastANI
[2024-01-24 13:58:40,613] [INFO] Running command: fastANI --query /var/lib/cwl/stg762c959e-283b-4e61-8a8e-305ffd112a96/GCF_003019255.1_ASM301925v1_genomic.fna.gz --refList GCF_003019255.1_ASM301925v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003019255.1_ASM301925v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:58:47,029] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:47,037] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:58:47,037] [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_003019255.1	s__Staphylococcus kloosii	100.0	877	878	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	98.99	96.08	0.96	0.89	9	conclusive
GCF_015775975.1	s__Staphylococcus lloydii	90.9204	750	878	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	86.6076	732	878	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002902345.1	s__Staphylococcus arlettae	79.6826	389	878	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.12	98.73	0.94	0.91	41	-
GCF_900458565.1	s__Staphylococcus equorum	79.6025	372	878	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.19	97.35	0.94	0.89	49	-
GCF_013391405.1	s__Staphylococcus sp013391405	79.2152	360	878	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900097965.1	s__Staphylococcus caeli	79.133	355	878	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.99	99.99	1.00	1.00	2	-
GCF_001747895.1	s__Staphylococcus equorum_A	79.1224	369	878	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.34	98.64	0.94	0.92	4	-
GCF_002902325.1	s__Staphylococcus capitis	78.9848	259	878	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	97.07	96.40	0.94	0.88	151	-
GCF_002902365.1	s__Staphylococcus cohnii	78.9716	327	878	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	97.14	95.73	0.92	0.88	59	-
GCF_002614725.1	s__Staphylococcus edaphicus	78.9218	342	878	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002902725.1	s__Staphylococcus caprae	78.8708	260	878	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 13:58:47,038] [INFO] GTDB search result was written to GCF_003019255.1_ASM301925v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:58:47,039] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:58:47,041] [INFO] DFAST_QC result json was written to GCF_003019255.1_ASM301925v1_genomic.fna/dqc_result.json
[2024-01-24 13:58:47,041] [INFO] DFAST_QC completed!
[2024-01-24 13:58:47,042] [INFO] Total running time: 0h0m37s