[2023-06-29 00:38:44,591] [INFO] DFAST_QC pipeline started.
[2023-06-29 00:38:44,594] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 00:38:44,595] [INFO] DQC Reference Directory: /var/lib/cwl/stgbec9b824-03b5-4b32-b5a2-938ca59c0838/dqc_reference
[2023-06-29 00:38:45,833] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 00:38:45,834] [INFO] Task started: Prodigal
[2023-06-29 00:38:45,834] [INFO] Running command: gunzip -c /var/lib/cwl/stg961684a9-dc88-44c3-8dae-4ca30737566f/GCA_020093015.1_ASM2009301v1_genomic.fna.gz | prodigal -d GCA_020093015.1_ASM2009301v1_genomic.fna/cds.fna -a GCA_020093015.1_ASM2009301v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 00:38:50,240] [INFO] Task succeeded: Prodigal
[2023-06-29 00:38:50,240] [INFO] Task started: HMMsearch
[2023-06-29 00:38:50,240] [INFO] Running command: hmmsearch --tblout GCA_020093015.1_ASM2009301v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbec9b824-03b5-4b32-b5a2-938ca59c0838/dqc_reference/reference_markers.hmm GCA_020093015.1_ASM2009301v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 00:38:50,502] [INFO] Task succeeded: HMMsearch
[2023-06-29 00:38:50,503] [INFO] Found 6/6 markers.
[2023-06-29 00:38:50,531] [INFO] Query marker FASTA was written to GCA_020093015.1_ASM2009301v1_genomic.fna/markers.fasta
[2023-06-29 00:38:50,531] [INFO] Task started: Blastn
[2023-06-29 00:38:50,531] [INFO] Running command: blastn -query GCA_020093015.1_ASM2009301v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbec9b824-03b5-4b32-b5a2-938ca59c0838/dqc_reference/reference_markers.fasta -out GCA_020093015.1_ASM2009301v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 00:38:51,139] [INFO] Task succeeded: Blastn
[2023-06-29 00:38:51,144] [INFO] Selected 10 target genomes.
[2023-06-29 00:38:51,144] [INFO] Target genome list was writen to GCA_020093015.1_ASM2009301v1_genomic.fna/target_genomes.txt
[2023-06-29 00:38:51,147] [INFO] Task started: fastANI
[2023-06-29 00:38:51,147] [INFO] Running command: fastANI --query /var/lib/cwl/stg961684a9-dc88-44c3-8dae-4ca30737566f/GCA_020093015.1_ASM2009301v1_genomic.fna.gz --refList GCA_020093015.1_ASM2009301v1_genomic.fna/target_genomes.txt --output GCA_020093015.1_ASM2009301v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 00:38:56,480] [INFO] Task succeeded: fastANI
[2023-06-29 00:38:56,481] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbec9b824-03b5-4b32-b5a2-938ca59c0838/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 00:38:56,482] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbec9b824-03b5-4b32-b5a2-938ca59c0838/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 00:38:56,496] [INFO] Found 7 fastANI hits (5 hits with ANI > threshold)
[2023-06-29 00:38:56,497] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-29 00:38:56,497] [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 saprophyticus	strain=NCTC7292	GCA_900458885.1	29385	29385	type	True	99.5222	741	784	95	conclusive
Staphylococcus saprophyticus	strain=ATCC 15305	GCA_006094355.1	29385	29385	type	True	99.516	740	784	95	conclusive
Staphylococcus saprophyticus	strain=ATCC 15305	GCA_001997165.1	29385	29385	type	True	99.5001	737	784	95	conclusive
Staphylococcus saprophyticus	strain=ATCC 15305	GCA_000010125.1	29385	29385	type	True	99.4889	736	784	95	conclusive
Staphylococcus saprophyticus	strain=NCTC 7292	GCA_002902025.2	29385	29385	type	True	99.4624	709	784	95	conclusive
Staphylococcus shinii	strain=K22-5M	GCA_017583065.1	2912228	2912228	type	True	81.9561	575	784	95	below_threshold
Staphylococcus capitis subsp. capitis	strain=DSM 20326	GCA_025272975.1	72758	29388	type	True	78.2639	245	784	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 00:38:56,499] [INFO] DFAST Taxonomy check result was written to GCA_020093015.1_ASM2009301v1_genomic.fna/tc_result.tsv
[2023-06-29 00:38:56,500] [INFO] ===== Taxonomy check completed =====
[2023-06-29 00:38:56,500] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 00:38:56,500] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbec9b824-03b5-4b32-b5a2-938ca59c0838/dqc_reference/checkm_data
[2023-06-29 00:38:56,502] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 00:38:56,535] [INFO] Task started: CheckM
[2023-06-29 00:38:56,536] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_020093015.1_ASM2009301v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_020093015.1_ASM2009301v1_genomic.fna/checkm_input GCA_020093015.1_ASM2009301v1_genomic.fna/checkm_result
[2023-06-29 00:39:17,605] [INFO] Task succeeded: CheckM
[2023-06-29 00:39:17,607] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-29 00:39:17,632] [INFO] ===== Completeness check finished =====
[2023-06-29 00:39:17,632] [INFO] ===== Start GTDB Search =====
[2023-06-29 00:39:17,633] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_020093015.1_ASM2009301v1_genomic.fna/markers.fasta)
[2023-06-29 00:39:17,633] [INFO] Task started: Blastn
[2023-06-29 00:39:17,633] [INFO] Running command: blastn -query GCA_020093015.1_ASM2009301v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbec9b824-03b5-4b32-b5a2-938ca59c0838/dqc_reference/reference_markers_gtdb.fasta -out GCA_020093015.1_ASM2009301v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 00:39:18,401] [INFO] Task succeeded: Blastn
[2023-06-29 00:39:18,405] [INFO] Selected 10 target genomes.
[2023-06-29 00:39:18,406] [INFO] Target genome list was writen to GCA_020093015.1_ASM2009301v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 00:39:18,411] [INFO] Task started: fastANI
[2023-06-29 00:39:18,412] [INFO] Running command: fastANI --query /var/lib/cwl/stg961684a9-dc88-44c3-8dae-4ca30737566f/GCA_020093015.1_ASM2009301v1_genomic.fna.gz --refList GCA_020093015.1_ASM2009301v1_genomic.fna/target_genomes_gtdb.txt --output GCA_020093015.1_ASM2009301v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 00:39:24,519] [INFO] Task succeeded: fastANI
[2023-06-29 00:39:24,533] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 00:39:24,533] [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_000010125.1	s__Staphylococcus saprophyticus	99.4889	736	784	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.41	98.75	0.94	0.91	167	conclusive
GCF_013391405.1	s__Staphylococcus sp013391405	89.8882	674	784	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	85.3587	642	784	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003697915.1	s__Staphylococcus pseudoxylosus	82.08	554	784	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	98.50	97.12	0.92	0.87	9	-
GCF_016774515.1	s__Staphylococcus xylosus_A	82.0094	575	784	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.34	99.08	0.95	0.91	11	-
GCF_000338275.1	s__Staphylococcus xylosus_B	81.9403	568	784	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.09	97.23	0.94	0.90	8	-
GCF_900097965.1	s__Staphylococcus caeli	81.8301	525	784	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.99	99.99	1.00	1.00	2	-
GCF_002732165.1	s__Staphylococcus xylosus	81.7756	571	784	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	98.41	97.01	0.95	0.90	48	-
GCF_900458565.1	s__Staphylococcus equorum	81.1311	530	784	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.19	97.35	0.94	0.89	49	-
GCF_001006765.1	s__Staphylococcus succinus	81.1283	454	784	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	97.99	95.53	0.94	0.89	24	-
--------------------------------------------------------------------------------
[2023-06-29 00:39:24,535] [INFO] GTDB search result was written to GCA_020093015.1_ASM2009301v1_genomic.fna/result_gtdb.tsv
[2023-06-29 00:39:24,536] [INFO] ===== GTDB Search completed =====
[2023-06-29 00:39:24,539] [INFO] DFAST_QC result json was written to GCA_020093015.1_ASM2009301v1_genomic.fna/dqc_result.json
[2023-06-29 00:39:24,539] [INFO] DFAST_QC completed!
[2023-06-29 00:39:24,539] [INFO] Total running time: 0h0m40s