[2024-01-24 15:26:04,581] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:26:04,583] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:26:04,583] [INFO] DQC Reference Directory: /var/lib/cwl/stgf5c4d2a8-640d-4f89-8699-9bed689aebb8/dqc_reference
[2024-01-24 15:26:07,020] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:26:07,022] [INFO] Task started: Prodigal
[2024-01-24 15:26:07,022] [INFO] Running command: gunzip -c /var/lib/cwl/stg4f2cc084-481a-49af-bbe0-c3b0259c0a16/GCF_003206065.1_ASM320606v1_genomic.fna.gz | prodigal -d GCF_003206065.1_ASM320606v1_genomic.fna/cds.fna -a GCF_003206065.1_ASM320606v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:26:18,685] [INFO] Task succeeded: Prodigal
[2024-01-24 15:26:18,685] [INFO] Task started: HMMsearch
[2024-01-24 15:26:18,685] [INFO] Running command: hmmsearch --tblout GCF_003206065.1_ASM320606v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf5c4d2a8-640d-4f89-8699-9bed689aebb8/dqc_reference/reference_markers.hmm GCF_003206065.1_ASM320606v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:26:19,014] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:26:19,016] [INFO] Found 6/6 markers.
[2024-01-24 15:26:19,054] [INFO] Query marker FASTA was written to GCF_003206065.1_ASM320606v1_genomic.fna/markers.fasta
[2024-01-24 15:26:19,054] [INFO] Task started: Blastn
[2024-01-24 15:26:19,054] [INFO] Running command: blastn -query GCF_003206065.1_ASM320606v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf5c4d2a8-640d-4f89-8699-9bed689aebb8/dqc_reference/reference_markers.fasta -out GCF_003206065.1_ASM320606v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:26:19,926] [INFO] Task succeeded: Blastn
[2024-01-24 15:26:19,931] [INFO] Selected 13 target genomes.
[2024-01-24 15:26:19,931] [INFO] Target genome list was writen to GCF_003206065.1_ASM320606v1_genomic.fna/target_genomes.txt
[2024-01-24 15:26:19,938] [INFO] Task started: fastANI
[2024-01-24 15:26:19,938] [INFO] Running command: fastANI --query /var/lib/cwl/stg4f2cc084-481a-49af-bbe0-c3b0259c0a16/GCF_003206065.1_ASM320606v1_genomic.fna.gz --refList GCF_003206065.1_ASM320606v1_genomic.fna/target_genomes.txt --output GCF_003206065.1_ASM320606v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:26:31,884] [INFO] Task succeeded: fastANI
[2024-01-24 15:26:31,884] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf5c4d2a8-640d-4f89-8699-9bed689aebb8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:26:31,885] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf5c4d2a8-640d-4f89-8699-9bed689aebb8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:26:31,903] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:26:31,903] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:26:31,903] [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
Salinicola halimionae	strain=CPA60	GCA_003206065.1	1949081	1949081	type	True	100.0	1324	1326	95	conclusive
Salinicola halophyticus	strain=CR45	GCA_003206695.1	1808881	1808881	type	True	88.1695	1125	1326	95	below_threshold
Salinicola socius	strain=SMB35	GCA_001937195.1	404433	404433	type	True	84.3702	1059	1326	95	below_threshold
Salinicola socius	strain=DSM 19940	GCA_003206115.1	404433	404433	type	True	84.3256	1079	1326	95	below_threshold
Salinicola salarius	strain=DSM 18044	GCA_003206135.1	430457	430457	type	True	84.0207	978	1326	95	below_threshold
Salinicola lusitanus	strain=CR50	GCA_003206045.1	1949085	1949085	type	True	83.0364	1040	1326	95	below_threshold
Salinicola acroporae	strain=LMG 28587	GCA_003206615.1	1541440	1541440	type	True	82.9809	1023	1326	95	below_threshold
Salinicola peritrichatus	strain=JCM 18795	GCA_003206715.1	1267424	1267424	type	True	81.3506	826	1326	95	below_threshold
Halomonas sulfidoxydans	strain=MCCC 1A11059	GCA_017868775.1	2733484	2733484	type	True	78.527	316	1326	95	below_threshold
Halomonas aerodenitrificans	strain=MCCC 1A11058	GCA_021404405.1	2733483	2733483	type	True	78.392	331	1326	95	below_threshold
Halomonas ethanolica	strain=MCCC 1A11081	GCA_021404305.1	2733486	2733486	type	True	78.3634	325	1326	95	below_threshold
Chromohalobacter sarecensis	strain=DSM 15547	GCA_023061135.1	245294	245294	type	True	78.3587	343	1326	95	below_threshold
Chromohalobacter nigrandesensis	strain=DSM 14323	GCA_023061285.1	119863	119863	type	True	78.3412	345	1326	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:26:31,905] [INFO] DFAST Taxonomy check result was written to GCF_003206065.1_ASM320606v1_genomic.fna/tc_result.tsv
[2024-01-24 15:26:31,906] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:26:31,906] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:26:31,907] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf5c4d2a8-640d-4f89-8699-9bed689aebb8/dqc_reference/checkm_data
[2024-01-24 15:26:31,908] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:26:31,952] [INFO] Task started: CheckM
[2024-01-24 15:26:31,954] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003206065.1_ASM320606v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003206065.1_ASM320606v1_genomic.fna/checkm_input GCF_003206065.1_ASM320606v1_genomic.fna/checkm_result
[2024-01-24 15:27:10,548] [INFO] Task succeeded: CheckM
[2024-01-24 15:27:10,549] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:27:10,567] [INFO] ===== Completeness check finished =====
[2024-01-24 15:27:10,567] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:27:10,568] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003206065.1_ASM320606v1_genomic.fna/markers.fasta)
[2024-01-24 15:27:10,569] [INFO] Task started: Blastn
[2024-01-24 15:27:10,569] [INFO] Running command: blastn -query GCF_003206065.1_ASM320606v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf5c4d2a8-640d-4f89-8699-9bed689aebb8/dqc_reference/reference_markers_gtdb.fasta -out GCF_003206065.1_ASM320606v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:27:12,080] [INFO] Task succeeded: Blastn
[2024-01-24 15:27:12,084] [INFO] Selected 10 target genomes.
[2024-01-24 15:27:12,084] [INFO] Target genome list was writen to GCF_003206065.1_ASM320606v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:27:12,092] [INFO] Task started: fastANI
[2024-01-24 15:27:12,092] [INFO] Running command: fastANI --query /var/lib/cwl/stg4f2cc084-481a-49af-bbe0-c3b0259c0a16/GCF_003206065.1_ASM320606v1_genomic.fna.gz --refList GCF_003206065.1_ASM320606v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003206065.1_ASM320606v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:27:22,438] [INFO] Task succeeded: fastANI
[2024-01-24 15:27:22,453] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:27:22,454] [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_003206065.1	s__Salinicola halimionae	100.0	1324	1326	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Salinicola	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003206695.1	s__Salinicola halophyticus	88.1695	1125	1326	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Salinicola	95.0	97.72	97.72	0.93	0.93	2	-
GCF_001937195.1	s__Salinicola socius	84.3602	1059	1326	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Salinicola	95.0	99.48	98.96	0.96	0.93	3	-
GCF_003206135.1	s__Salinicola salarius	84.0207	978	1326	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Salinicola	95.0	97.80	97.80	0.89	0.89	2	-
GCF_002179555.1	s__Salinicola salarius_A	83.9755	973	1326	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Salinicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002695065.1	s__Salinicola sp002695065	83.5995	972	1326	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Salinicola	95.0	97.83	97.83	0.85	0.85	2	-
GCF_008298015.1	s__Salinicola sp008298015	83.4251	1001	1326	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Salinicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003206045.1	s__Salinicola lusitanus	83.0407	1039	1326	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Salinicola	95.0	96.87	96.87	0.93	0.93	2	-
GCF_003206615.1	s__Salinicola acroporae	82.9809	1023	1326	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Salinicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003206715.1	s__Salinicola peritrichatus	81.3475	826	1326	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Salinicola	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:27:22,455] [INFO] GTDB search result was written to GCF_003206065.1_ASM320606v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:27:22,456] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:27:22,460] [INFO] DFAST_QC result json was written to GCF_003206065.1_ASM320606v1_genomic.fna/dqc_result.json
[2024-01-24 15:27:22,460] [INFO] DFAST_QC completed!
[2024-01-24 15:27:22,460] [INFO] Total running time: 0h1m18s