[2024-01-24 11:21:07,416] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:21:07,418] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:21:07,418] [INFO] DQC Reference Directory: /var/lib/cwl/stg4c3dee42-0bdd-4d39-834d-30f1a3d59535/dqc_reference
[2024-01-24 11:21:11,969] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:21:11,970] [INFO] Task started: Prodigal
[2024-01-24 11:21:11,970] [INFO] Running command: gunzip -c /var/lib/cwl/stgb04a59e0-1db5-4cf8-9702-9476c1f274b4/GCF_015594545.1_ASM1559454v1_genomic.fna.gz | prodigal -d GCF_015594545.1_ASM1559454v1_genomic.fna/cds.fna -a GCF_015594545.1_ASM1559454v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:21:16,651] [INFO] Task succeeded: Prodigal
[2024-01-24 11:21:16,652] [INFO] Task started: HMMsearch
[2024-01-24 11:21:16,652] [INFO] Running command: hmmsearch --tblout GCF_015594545.1_ASM1559454v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4c3dee42-0bdd-4d39-834d-30f1a3d59535/dqc_reference/reference_markers.hmm GCF_015594545.1_ASM1559454v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:21:16,927] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:21:16,928] [INFO] Found 6/6 markers.
[2024-01-24 11:21:16,951] [INFO] Query marker FASTA was written to GCF_015594545.1_ASM1559454v1_genomic.fna/markers.fasta
[2024-01-24 11:21:16,951] [INFO] Task started: Blastn
[2024-01-24 11:21:16,951] [INFO] Running command: blastn -query GCF_015594545.1_ASM1559454v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4c3dee42-0bdd-4d39-834d-30f1a3d59535/dqc_reference/reference_markers.fasta -out GCF_015594545.1_ASM1559454v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:21:19,106] [INFO] Task succeeded: Blastn
[2024-01-24 11:21:19,110] [INFO] Selected 10 target genomes.
[2024-01-24 11:21:19,110] [INFO] Target genome list was writen to GCF_015594545.1_ASM1559454v1_genomic.fna/target_genomes.txt
[2024-01-24 11:21:19,234] [INFO] Task started: fastANI
[2024-01-24 11:21:19,234] [INFO] Running command: fastANI --query /var/lib/cwl/stgb04a59e0-1db5-4cf8-9702-9476c1f274b4/GCF_015594545.1_ASM1559454v1_genomic.fna.gz --refList GCF_015594545.1_ASM1559454v1_genomic.fna/target_genomes.txt --output GCF_015594545.1_ASM1559454v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:21:24,391] [INFO] Task succeeded: fastANI
[2024-01-24 11:21:24,392] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4c3dee42-0bdd-4d39-834d-30f1a3d59535/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:21:24,393] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4c3dee42-0bdd-4d39-834d-30f1a3d59535/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:21:24,402] [INFO] Found 6 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:21:24,402] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:21:24,403] [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 durrellii	strain=27_4_6_LY	GCA_015594545.1	2781773	2781773	type	True	100.0	874	876	95	conclusive
Staphylococcus kloosii	strain=NCTC12415	GCA_900458805.1	29384	29384	type	True	86.8363	702	876	95	below_threshold
Staphylococcus kloosii	strain=ATCC 43959	GCA_003019255.1	29384	29384	type	True	86.7545	716	876	95	below_threshold
Staphylococcus kloosii	strain=NCTC 12415	GCA_002902055.1	29384	29384	type	True	86.4398	678	876	95	below_threshold
Staphylococcus lloydii	strain=23_2_7_LY	GCA_015775975.1	2781774	2781774	type	True	86.3269	693	876	95	below_threshold
Staphylococcus taiwanensis	strain=NTUH-S172	GCA_020544305.1	2750012	2750012	type	True	79.0324	249	876	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:21:24,404] [INFO] DFAST Taxonomy check result was written to GCF_015594545.1_ASM1559454v1_genomic.fna/tc_result.tsv
[2024-01-24 11:21:24,404] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:21:24,405] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:21:24,405] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4c3dee42-0bdd-4d39-834d-30f1a3d59535/dqc_reference/checkm_data
[2024-01-24 11:21:24,406] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:21:24,431] [INFO] Task started: CheckM
[2024-01-24 11:21:24,431] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_015594545.1_ASM1559454v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_015594545.1_ASM1559454v1_genomic.fna/checkm_input GCF_015594545.1_ASM1559454v1_genomic.fna/checkm_result
[2024-01-24 11:21:47,047] [INFO] Task succeeded: CheckM
[2024-01-24 11:21:47,050] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:21:47,069] [INFO] ===== Completeness check finished =====
[2024-01-24 11:21:47,070] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:21:47,070] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_015594545.1_ASM1559454v1_genomic.fna/markers.fasta)
[2024-01-24 11:21:47,071] [INFO] Task started: Blastn
[2024-01-24 11:21:47,071] [INFO] Running command: blastn -query GCF_015594545.1_ASM1559454v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4c3dee42-0bdd-4d39-834d-30f1a3d59535/dqc_reference/reference_markers_gtdb.fasta -out GCF_015594545.1_ASM1559454v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:21:47,881] [INFO] Task succeeded: Blastn
[2024-01-24 11:21:47,884] [INFO] Selected 11 target genomes.
[2024-01-24 11:21:47,884] [INFO] Target genome list was writen to GCF_015594545.1_ASM1559454v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:21:47,903] [INFO] Task started: fastANI
[2024-01-24 11:21:47,903] [INFO] Running command: fastANI --query /var/lib/cwl/stgb04a59e0-1db5-4cf8-9702-9476c1f274b4/GCF_015594545.1_ASM1559454v1_genomic.fna.gz --refList GCF_015594545.1_ASM1559454v1_genomic.fna/target_genomes_gtdb.txt --output GCF_015594545.1_ASM1559454v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:21:54,350] [INFO] Task succeeded: fastANI
[2024-01-24 11:21:54,365] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:21:54,366] [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_015594545.1	s__Staphylococcus durrellii	100.0	874	876	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003019255.1	s__Staphylococcus kloosii	86.7465	715	876	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	98.99	96.08	0.96	0.89	9	-
GCF_015775975.1	s__Staphylococcus lloydii	86.3269	693	876	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.39	98.19	0.98	0.95	4	-
GCF_900458565.1	s__Staphylococcus equorum	79.715	359	876	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.19	97.35	0.94	0.89	49	-
GCF_002902345.1	s__Staphylococcus arlettae	79.6568	385	876	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	79.5146	352	876	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.34	99.08	0.95	0.91	11	-
GCF_003491325.1	s__Staphylococcus warneri_A	79.3305	254	876	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.32	98.95	0.94	0.90	22	-
GCF_013391405.1	s__Staphylococcus sp013391405	79.0012	326	876	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002614725.1	s__Staphylococcus edaphicus	78.8811	318	876	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000875895.1	s__Staphylococcus gallinarum	78.8422	338	876	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	98.63	98.14	0.94	0.91	25	-
GCF_002902085.1	s__Staphylococcus simiae	78.4185	239	876	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.97	99.96	0.98	0.96	3	-
--------------------------------------------------------------------------------
[2024-01-24 11:21:54,367] [INFO] GTDB search result was written to GCF_015594545.1_ASM1559454v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:21:54,368] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:21:54,371] [INFO] DFAST_QC result json was written to GCF_015594545.1_ASM1559454v1_genomic.fna/dqc_result.json
[2024-01-24 11:21:54,371] [INFO] DFAST_QC completed!
[2024-01-24 11:21:54,371] [INFO] Total running time: 0h0m47s