[2024-01-24 13:59:42,580] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:59:42,582] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:59:42,582] [INFO] DQC Reference Directory: /var/lib/cwl/stgf4e87e4c-475e-41fc-b3b2-a8fbdf72eef9/dqc_reference
[2024-01-24 13:59:43,880] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:59:43,880] [INFO] Task started: Prodigal
[2024-01-24 13:59:43,881] [INFO] Running command: gunzip -c /var/lib/cwl/stg46dcac57-7900-40ff-9396-1b262b91ed80/GCF_004785665.1_ASM478566v1_genomic.fna.gz | prodigal -d GCF_004785665.1_ASM478566v1_genomic.fna/cds.fna -a GCF_004785665.1_ASM478566v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:59:48,157] [INFO] Task succeeded: Prodigal
[2024-01-24 13:59:48,157] [INFO] Task started: HMMsearch
[2024-01-24 13:59:48,157] [INFO] Running command: hmmsearch --tblout GCF_004785665.1_ASM478566v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf4e87e4c-475e-41fc-b3b2-a8fbdf72eef9/dqc_reference/reference_markers.hmm GCF_004785665.1_ASM478566v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:59:48,409] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:59:48,410] [INFO] Found 6/6 markers.
[2024-01-24 13:59:48,437] [INFO] Query marker FASTA was written to GCF_004785665.1_ASM478566v1_genomic.fna/markers.fasta
[2024-01-24 13:59:48,438] [INFO] Task started: Blastn
[2024-01-24 13:59:48,438] [INFO] Running command: blastn -query GCF_004785665.1_ASM478566v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf4e87e4c-475e-41fc-b3b2-a8fbdf72eef9/dqc_reference/reference_markers.fasta -out GCF_004785665.1_ASM478566v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:59:49,118] [INFO] Task succeeded: Blastn
[2024-01-24 13:59:49,132] [INFO] Selected 10 target genomes.
[2024-01-24 13:59:49,133] [INFO] Target genome list was writen to GCF_004785665.1_ASM478566v1_genomic.fna/target_genomes.txt
[2024-01-24 13:59:49,142] [INFO] Task started: fastANI
[2024-01-24 13:59:49,142] [INFO] Running command: fastANI --query /var/lib/cwl/stg46dcac57-7900-40ff-9396-1b262b91ed80/GCF_004785665.1_ASM478566v1_genomic.fna.gz --refList GCF_004785665.1_ASM478566v1_genomic.fna/target_genomes.txt --output GCF_004785665.1_ASM478566v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:59:54,567] [INFO] Task succeeded: fastANI
[2024-01-24 13:59:54,567] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf4e87e4c-475e-41fc-b3b2-a8fbdf72eef9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:59:54,568] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf4e87e4c-475e-41fc-b3b2-a8fbdf72eef9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:59:54,578] [INFO] Found 8 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:59:54,578] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:59:54,578] [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 pragensis	strain=CCM 8529	GCA_004785665.1	1611836	1611836	type	True	100.0	806	807	95	conclusive
Staphylococcus pragensis	strain=CCM 8529	GCA_014635505.1	1611836	1611836	type	True	99.9687	793	807	95	conclusive
Staphylococcus petrasii	strain=CCM 8418	GCA_004684865.1	1276936	1276936	type	True	92.0226	717	807	95	below_threshold
Staphylococcus petrasii	strain=NCTC13835	GCA_900458665.1	1276936	1276936	type	True	91.9874	727	807	95	below_threshold
Staphylococcus petrasii	strain=CCUG 62727	GCA_002902565.1	1276936	1276936	type	True	91.9282	681	807	95	below_threshold
Staphylococcus taiwanensis	strain=NTUH-S172	GCA_020544305.1	2750012	2750012	type	True	82.675	585	807	95	below_threshold
Staphylococcus aureus	strain=PartF-Saureus-RM8376	GCA_022869625.1	1280	1280	type	True	79.1392	317	807	95	below_threshold
Staphylococcus aureus	strain=NCTC 08532	GCA_002902205.1	1280	1280	type	True	79.0474	310	807	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:59:54,580] [INFO] DFAST Taxonomy check result was written to GCF_004785665.1_ASM478566v1_genomic.fna/tc_result.tsv
[2024-01-24 13:59:54,580] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:59:54,580] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:59:54,581] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf4e87e4c-475e-41fc-b3b2-a8fbdf72eef9/dqc_reference/checkm_data
[2024-01-24 13:59:54,581] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:59:54,607] [INFO] Task started: CheckM
[2024-01-24 13:59:54,607] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004785665.1_ASM478566v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004785665.1_ASM478566v1_genomic.fna/checkm_input GCF_004785665.1_ASM478566v1_genomic.fna/checkm_result
[2024-01-24 14:00:14,455] [INFO] Task succeeded: CheckM
[2024-01-24 14:00:14,457] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:00:14,475] [INFO] ===== Completeness check finished =====
[2024-01-24 14:00:14,475] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:00:14,475] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004785665.1_ASM478566v1_genomic.fna/markers.fasta)
[2024-01-24 14:00:14,476] [INFO] Task started: Blastn
[2024-01-24 14:00:14,476] [INFO] Running command: blastn -query GCF_004785665.1_ASM478566v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf4e87e4c-475e-41fc-b3b2-a8fbdf72eef9/dqc_reference/reference_markers_gtdb.fasta -out GCF_004785665.1_ASM478566v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:00:15,242] [INFO] Task succeeded: Blastn
[2024-01-24 14:00:15,245] [INFO] Selected 8 target genomes.
[2024-01-24 14:00:15,246] [INFO] Target genome list was writen to GCF_004785665.1_ASM478566v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:00:15,253] [INFO] Task started: fastANI
[2024-01-24 14:00:15,253] [INFO] Running command: fastANI --query /var/lib/cwl/stg46dcac57-7900-40ff-9396-1b262b91ed80/GCF_004785665.1_ASM478566v1_genomic.fna.gz --refList GCF_004785665.1_ASM478566v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004785665.1_ASM478566v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:00:20,061] [INFO] Task succeeded: fastANI
[2024-01-24 14:00:20,075] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:00:20,076] [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_004785665.1	s__Staphylococcus pragensis	100.0	806	807	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.69	99.09	0.98	0.94	4	conclusive
GCA_002902575.1	s__Staphylococcus croceilyticus	92.0172	661	807	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.95	99.95	1.00	1.00	2	-
GCF_002902565.1	s__Staphylococcus petrasii	91.9282	681	807	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	98.66	97.62	0.95	0.85	8	-
GCF_003035445.1	s__Staphylococcus devriesei_A	82.3377	570	807	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	97.92	97.92	0.95	0.95	2	-
GCF_006094395.1	s__Staphylococcus haemolyticus	82.2282	590	807	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	98.59	96.62	0.93	0.87	385	-
GCF_001224225.1	s__Staphylococcus borealis	82.157	620	807	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	98.37	97.44	0.93	0.89	22	-
GCF_002902625.1	s__Staphylococcus devriesei	82.0844	522	807	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.59	98.61	0.94	0.91	9	-
GCF_002901845.1	s__Staphylococcus hominis	81.3358	492	807	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	97.87	96.99	0.93	0.86	183	-
--------------------------------------------------------------------------------
[2024-01-24 14:00:20,077] [INFO] GTDB search result was written to GCF_004785665.1_ASM478566v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:00:20,078] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:00:20,081] [INFO] DFAST_QC result json was written to GCF_004785665.1_ASM478566v1_genomic.fna/dqc_result.json
[2024-01-24 14:00:20,081] [INFO] DFAST_QC completed!
[2024-01-24 14:00:20,082] [INFO] Total running time: 0h0m38s