[2024-01-24 14:38:46,552] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:38:46,554] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:38:46,555] [INFO] DQC Reference Directory: /var/lib/cwl/stg94b11962-5073-4a83-b8e0-3fd8fb0b1132/dqc_reference
[2024-01-24 14:38:47,924] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:38:47,925] [INFO] Task started: Prodigal
[2024-01-24 14:38:47,926] [INFO] Running command: gunzip -c /var/lib/cwl/stg456d8b30-b7cb-4121-a78d-0fe997b98e1a/GCF_003697915.1_ASM369791v1_genomic.fna.gz | prodigal -d GCF_003697915.1_ASM369791v1_genomic.fna/cds.fna -a GCF_003697915.1_ASM369791v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:38:53,453] [INFO] Task succeeded: Prodigal
[2024-01-24 14:38:53,454] [INFO] Task started: HMMsearch
[2024-01-24 14:38:53,454] [INFO] Running command: hmmsearch --tblout GCF_003697915.1_ASM369791v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg94b11962-5073-4a83-b8e0-3fd8fb0b1132/dqc_reference/reference_markers.hmm GCF_003697915.1_ASM369791v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:38:53,742] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:38:53,743] [INFO] Found 6/6 markers.
[2024-01-24 14:38:53,773] [INFO] Query marker FASTA was written to GCF_003697915.1_ASM369791v1_genomic.fna/markers.fasta
[2024-01-24 14:38:53,774] [INFO] Task started: Blastn
[2024-01-24 14:38:53,774] [INFO] Running command: blastn -query GCF_003697915.1_ASM369791v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg94b11962-5073-4a83-b8e0-3fd8fb0b1132/dqc_reference/reference_markers.fasta -out GCF_003697915.1_ASM369791v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:38:54,422] [INFO] Task succeeded: Blastn
[2024-01-24 14:38:54,426] [INFO] Selected 9 target genomes.
[2024-01-24 14:38:54,427] [INFO] Target genome list was writen to GCF_003697915.1_ASM369791v1_genomic.fna/target_genomes.txt
[2024-01-24 14:38:54,436] [INFO] Task started: fastANI
[2024-01-24 14:38:54,437] [INFO] Running command: fastANI --query /var/lib/cwl/stg456d8b30-b7cb-4121-a78d-0fe997b98e1a/GCF_003697915.1_ASM369791v1_genomic.fna.gz --refList GCF_003697915.1_ASM369791v1_genomic.fna/target_genomes.txt --output GCF_003697915.1_ASM369791v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:38:59,669] [INFO] Task succeeded: fastANI
[2024-01-24 14:38:59,670] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg94b11962-5073-4a83-b8e0-3fd8fb0b1132/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:38:59,670] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg94b11962-5073-4a83-b8e0-3fd8fb0b1132/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:38:59,681] [INFO] Found 6 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:38:59,682] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:38:59,682] [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 pseudoxylosus	strain=S04009	GCA_003697915.1	2282419	2282419	type	True	100.0	980	983	95	conclusive
Staphylococcus xylosus	strain=NCTC 11043	GCA_002901985.1	1288	1288	type	True	93.2683	756	983	95	below_threshold
Staphylococcus xylosus	strain=NCTC11043	GCA_900458755.1	1288	1288	type	True	93.2596	859	983	95	below_threshold
Staphylococcus xylosus	strain=CCM 2738	GCA_002732165.1	1288	1288	type	True	93.2458	852	983	95	below_threshold
Staphylococcus shinii	strain=K22-5M	GCA_017583065.1	2912228	2912228	type	True	91.9654	870	983	95	below_threshold
Staphylococcus taiwanensis	strain=NTUH-S172	GCA_020544305.1	2750012	2750012	type	True	78.7165	249	983	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:38:59,686] [INFO] DFAST Taxonomy check result was written to GCF_003697915.1_ASM369791v1_genomic.fna/tc_result.tsv
[2024-01-24 14:38:59,686] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:38:59,687] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:38:59,687] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg94b11962-5073-4a83-b8e0-3fd8fb0b1132/dqc_reference/checkm_data
[2024-01-24 14:38:59,688] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:38:59,722] [INFO] Task started: CheckM
[2024-01-24 14:38:59,723] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003697915.1_ASM369791v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003697915.1_ASM369791v1_genomic.fna/checkm_input GCF_003697915.1_ASM369791v1_genomic.fna/checkm_result
[2024-01-24 14:39:23,407] [INFO] Task succeeded: CheckM
[2024-01-24 14:39:23,408] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:39:23,427] [INFO] ===== Completeness check finished =====
[2024-01-24 14:39:23,427] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:39:23,427] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003697915.1_ASM369791v1_genomic.fna/markers.fasta)
[2024-01-24 14:39:23,428] [INFO] Task started: Blastn
[2024-01-24 14:39:23,428] [INFO] Running command: blastn -query GCF_003697915.1_ASM369791v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg94b11962-5073-4a83-b8e0-3fd8fb0b1132/dqc_reference/reference_markers_gtdb.fasta -out GCF_003697915.1_ASM369791v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:39:24,205] [INFO] Task succeeded: Blastn
[2024-01-24 14:39:24,208] [INFO] Selected 8 target genomes.
[2024-01-24 14:39:24,209] [INFO] Target genome list was writen to GCF_003697915.1_ASM369791v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:39:24,216] [INFO] Task started: fastANI
[2024-01-24 14:39:24,216] [INFO] Running command: fastANI --query /var/lib/cwl/stg456d8b30-b7cb-4121-a78d-0fe997b98e1a/GCF_003697915.1_ASM369791v1_genomic.fna.gz --refList GCF_003697915.1_ASM369791v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003697915.1_ASM369791v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:39:29,815] [INFO] Task succeeded: fastANI
[2024-01-24 14:39:29,824] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:39:29,824] [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_003697915.1	s__Staphylococcus pseudoxylosus	100.0	980	983	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	98.50	97.12	0.92	0.87	9	conclusive
GCF_000338275.1	s__Staphylococcus xylosus_B	94.8681	865	983	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.09	97.23	0.94	0.90	8	-
GCF_002732165.1	s__Staphylococcus xylosus	93.2458	852	983	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	98.41	97.01	0.95	0.90	48	-
GCF_016774515.1	s__Staphylococcus xylosus_A	92.0002	874	983	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	82.0372	599	983	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.41	98.75	0.94	0.91	167	-
GCF_002614725.1	s__Staphylococcus edaphicus	81.9142	575	983	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013391405.1	s__Staphylococcus sp013391405	81.8827	593	983	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	81.2939	590	983	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.19	97.35	0.94	0.89	49	-
--------------------------------------------------------------------------------
[2024-01-24 14:39:29,826] [INFO] GTDB search result was written to GCF_003697915.1_ASM369791v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:39:29,827] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:39:29,830] [INFO] DFAST_QC result json was written to GCF_003697915.1_ASM369791v1_genomic.fna/dqc_result.json
[2024-01-24 14:39:29,830] [INFO] DFAST_QC completed!
[2024-01-24 14:39:29,830] [INFO] Total running time: 0h0m43s