[2024-01-24 11:34:41,453] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:34:41,464] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:34:41,465] [INFO] DQC Reference Directory: /var/lib/cwl/stgffb56f76-40fb-4cba-8ba6-3973364c8490/dqc_reference
[2024-01-24 11:34:42,813] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:34:42,813] [INFO] Task started: Prodigal
[2024-01-24 11:34:42,814] [INFO] Running command: gunzip -c /var/lib/cwl/stg6098c218-6af1-441f-bf3b-2ad8a9fe85f2/GCF_015775975.1_ASM1577597v1_genomic.fna.gz | prodigal -d GCF_015775975.1_ASM1577597v1_genomic.fna/cds.fna -a GCF_015775975.1_ASM1577597v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:34:47,679] [INFO] Task succeeded: Prodigal
[2024-01-24 11:34:47,679] [INFO] Task started: HMMsearch
[2024-01-24 11:34:47,679] [INFO] Running command: hmmsearch --tblout GCF_015775975.1_ASM1577597v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgffb56f76-40fb-4cba-8ba6-3973364c8490/dqc_reference/reference_markers.hmm GCF_015775975.1_ASM1577597v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:34:48,016] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:34:48,017] [INFO] Found 6/6 markers.
[2024-01-24 11:34:48,039] [INFO] Query marker FASTA was written to GCF_015775975.1_ASM1577597v1_genomic.fna/markers.fasta
[2024-01-24 11:34:48,040] [INFO] Task started: Blastn
[2024-01-24 11:34:48,040] [INFO] Running command: blastn -query GCF_015775975.1_ASM1577597v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgffb56f76-40fb-4cba-8ba6-3973364c8490/dqc_reference/reference_markers.fasta -out GCF_015775975.1_ASM1577597v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:34:48,629] [INFO] Task succeeded: Blastn
[2024-01-24 11:34:48,633] [INFO] Selected 10 target genomes.
[2024-01-24 11:34:48,633] [INFO] Target genome list was writen to GCF_015775975.1_ASM1577597v1_genomic.fna/target_genomes.txt
[2024-01-24 11:34:48,639] [INFO] Task started: fastANI
[2024-01-24 11:34:48,639] [INFO] Running command: fastANI --query /var/lib/cwl/stg6098c218-6af1-441f-bf3b-2ad8a9fe85f2/GCF_015775975.1_ASM1577597v1_genomic.fna.gz --refList GCF_015775975.1_ASM1577597v1_genomic.fna/target_genomes.txt --output GCF_015775975.1_ASM1577597v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:34:53,681] [INFO] Task succeeded: fastANI
[2024-01-24 11:34:53,682] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgffb56f76-40fb-4cba-8ba6-3973364c8490/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:34:53,682] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgffb56f76-40fb-4cba-8ba6-3973364c8490/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:34:53,688] [INFO] Found 6 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:34:53,688] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:34:53,688] [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 lloydii	strain=23_2_7_LY	GCA_015775975.1	2781774	2781774	type	True	100.0	856	856	95	conclusive
Staphylococcus kloosii	strain=NCTC12415	GCA_900458805.1	29384	29384	type	True	90.8764	751	856	95	below_threshold
Staphylococcus kloosii	strain=ATCC 43959	GCA_003019255.1	29384	29384	type	True	90.8713	752	856	95	below_threshold
Staphylococcus kloosii	strain=NCTC 12415	GCA_002902055.1	29384	29384	type	True	90.827	694	856	95	below_threshold
Staphylococcus durrellii	strain=27_4_6_LY	GCA_015594545.1	2781773	2781773	type	True	86.2984	707	856	95	below_threshold
Staphylococcus taiwanensis	strain=NTUH-S172	GCA_020544305.1	2750012	2750012	type	True	79.2398	266	856	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:34:53,690] [INFO] DFAST Taxonomy check result was written to GCF_015775975.1_ASM1577597v1_genomic.fna/tc_result.tsv
[2024-01-24 11:34:53,690] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:34:53,690] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:34:53,691] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgffb56f76-40fb-4cba-8ba6-3973364c8490/dqc_reference/checkm_data
[2024-01-24 11:34:53,692] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:34:53,717] [INFO] Task started: CheckM
[2024-01-24 11:34:53,717] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_015775975.1_ASM1577597v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_015775975.1_ASM1577597v1_genomic.fna/checkm_input GCF_015775975.1_ASM1577597v1_genomic.fna/checkm_result
[2024-01-24 11:35:14,938] [INFO] Task succeeded: CheckM
[2024-01-24 11:35:14,939] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:35:14,957] [INFO] ===== Completeness check finished =====
[2024-01-24 11:35:14,958] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:35:14,958] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_015775975.1_ASM1577597v1_genomic.fna/markers.fasta)
[2024-01-24 11:35:14,958] [INFO] Task started: Blastn
[2024-01-24 11:35:14,958] [INFO] Running command: blastn -query GCF_015775975.1_ASM1577597v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgffb56f76-40fb-4cba-8ba6-3973364c8490/dqc_reference/reference_markers_gtdb.fasta -out GCF_015775975.1_ASM1577597v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:35:15,794] [INFO] Task succeeded: Blastn
[2024-01-24 11:35:15,797] [INFO] Selected 15 target genomes.
[2024-01-24 11:35:15,798] [INFO] Target genome list was writen to GCF_015775975.1_ASM1577597v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:35:15,909] [INFO] Task started: fastANI
[2024-01-24 11:35:15,909] [INFO] Running command: fastANI --query /var/lib/cwl/stg6098c218-6af1-441f-bf3b-2ad8a9fe85f2/GCF_015775975.1_ASM1577597v1_genomic.fna.gz --refList GCF_015775975.1_ASM1577597v1_genomic.fna/target_genomes_gtdb.txt --output GCF_015775975.1_ASM1577597v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:35:24,418] [INFO] Task succeeded: fastANI
[2024-01-24 11:35:24,429] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:35:24,429] [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_015775975.1	s__Staphylococcus lloydii	100.0	856	856	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.39	98.19	0.98	0.95	4	conclusive
GCF_003019255.1	s__Staphylococcus kloosii	90.8817	751	856	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	98.99	96.08	0.96	0.89	9	-
GCF_015594545.1	s__Staphylococcus durrellii	86.3169	708	856	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	79.9458	399	856	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.12	98.73	0.94	0.91	41	-
GCF_016774515.1	s__Staphylococcus xylosus_A	79.8383	382	856	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.34	99.08	0.95	0.91	11	-
GCF_000010125.1	s__Staphylococcus saprophyticus	79.6461	385	856	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.41	98.75	0.94	0.91	167	-
GCF_002902235.1	s__Staphylococcus ureilyticus	79.2147	333	856	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	98.76	98.26	0.93	0.88	107	-
GCF_900458565.1	s__Staphylococcus equorum	79.2008	368	856	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	79.1179	370	856	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001431205.1	s__Staphylococcus sp001431205	79.0568	364	856	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001006765.1	s__Staphylococcus succinus	79.0419	354	856	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	97.99	95.53	0.94	0.89	24	-
GCF_002614725.1	s__Staphylococcus edaphicus	78.8925	346	856	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003970495.1	s__Staphylococcus pasteuri	78.8839	309	856	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	98.98	98.67	0.95	0.89	34	-
--------------------------------------------------------------------------------
[2024-01-24 11:35:24,431] [INFO] GTDB search result was written to GCF_015775975.1_ASM1577597v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:35:24,431] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:35:24,434] [INFO] DFAST_QC result json was written to GCF_015775975.1_ASM1577597v1_genomic.fna/dqc_result.json
[2024-01-24 11:35:24,434] [INFO] DFAST_QC completed!
[2024-01-24 11:35:24,434] [INFO] Total running time: 0h0m43s