[2024-01-24 12:14:34,724] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:14:34,726] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:14:34,726] [INFO] DQC Reference Directory: /var/lib/cwl/stg0d38fb3c-43aa-4838-b267-154c70de5b8d/dqc_reference
[2024-01-24 12:14:36,134] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:14:36,135] [INFO] Task started: Prodigal
[2024-01-24 12:14:36,136] [INFO] Running command: gunzip -c /var/lib/cwl/stgd6d56d25-2280-489f-846c-885570e4908b/GCF_003206115.1_ASM320611v1_genomic.fna.gz | prodigal -d GCF_003206115.1_ASM320611v1_genomic.fna/cds.fna -a GCF_003206115.1_ASM320611v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:14:47,923] [INFO] Task succeeded: Prodigal
[2024-01-24 12:14:47,923] [INFO] Task started: HMMsearch
[2024-01-24 12:14:47,923] [INFO] Running command: hmmsearch --tblout GCF_003206115.1_ASM320611v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0d38fb3c-43aa-4838-b267-154c70de5b8d/dqc_reference/reference_markers.hmm GCF_003206115.1_ASM320611v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:14:48,206] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:14:48,207] [INFO] Found 6/6 markers.
[2024-01-24 12:14:48,249] [INFO] Query marker FASTA was written to GCF_003206115.1_ASM320611v1_genomic.fna/markers.fasta
[2024-01-24 12:14:48,249] [INFO] Task started: Blastn
[2024-01-24 12:14:48,249] [INFO] Running command: blastn -query GCF_003206115.1_ASM320611v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0d38fb3c-43aa-4838-b267-154c70de5b8d/dqc_reference/reference_markers.fasta -out GCF_003206115.1_ASM320611v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:14:49,239] [INFO] Task succeeded: Blastn
[2024-01-24 12:14:49,244] [INFO] Selected 13 target genomes.
[2024-01-24 12:14:49,245] [INFO] Target genome list was writen to GCF_003206115.1_ASM320611v1_genomic.fna/target_genomes.txt
[2024-01-24 12:14:49,250] [INFO] Task started: fastANI
[2024-01-24 12:14:49,250] [INFO] Running command: fastANI --query /var/lib/cwl/stgd6d56d25-2280-489f-846c-885570e4908b/GCF_003206115.1_ASM320611v1_genomic.fna.gz --refList GCF_003206115.1_ASM320611v1_genomic.fna/target_genomes.txt --output GCF_003206115.1_ASM320611v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:15:02,632] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:02,633] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0d38fb3c-43aa-4838-b267-154c70de5b8d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:15:02,633] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0d38fb3c-43aa-4838-b267-154c70de5b8d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:15:02,649] [INFO] Found 13 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:15:02,649] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:15:02,650] [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 socius	strain=DSM 19940	GCA_003206115.1	404433	404433	type	True	100.0	1343	1346	95	conclusive
Salinicola socius	strain=SMB35	GCA_001937195.1	404433	404433	type	True	99.9833	1328	1346	95	conclusive
Salinicola halophyticus	strain=CR45	GCA_003206695.1	1808881	1808881	type	True	86.6565	1078	1346	95	below_threshold
Salinicola salarius	strain=DSM 18044	GCA_003206135.1	430457	430457	type	True	85.8217	1025	1346	95	below_threshold
Salinicola lusitanus	strain=CR50	GCA_003206045.1	1949085	1949085	type	True	84.6062	1117	1346	95	below_threshold
Salinicola halimionae	strain=CPA60	GCA_003206065.1	1949081	1949081	type	True	84.5322	1050	1346	95	below_threshold
Salinicola acroporae	strain=LMG 28587	GCA_003206615.1	1541440	1541440	type	True	84.3744	1096	1346	95	below_threshold
Salinicola peritrichatus	strain=JCM 18795	GCA_003206715.1	1267424	1267424	type	True	82.0829	873	1346	95	below_threshold
Halomonas campisalis	strain=A4	GCA_022341425.1	74661	74661	type	True	78.6157	337	1346	95	below_threshold
Halomonas sulfidoxydans	strain=MCCC 1A11059	GCA_017868775.1	2733484	2733484	type	True	78.5007	421	1346	95	below_threshold
Halomonas kenyensis	strain=DSM 17331	GCA_022341445.1	321266	321266	type	True	78.4946	345	1346	95	below_threshold
Chromohalobacter nigrandesensis	strain=DSM 14323	GCA_023061285.1	119863	119863	type	True	78.4396	394	1346	95	below_threshold
Halomonas aerodenitrificans	strain=MCCC 1A11058	GCA_021404405.1	2733483	2733483	type	True	78.3885	393	1346	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:15:02,652] [INFO] DFAST Taxonomy check result was written to GCF_003206115.1_ASM320611v1_genomic.fna/tc_result.tsv
[2024-01-24 12:15:02,653] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:15:02,653] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:15:02,653] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0d38fb3c-43aa-4838-b267-154c70de5b8d/dqc_reference/checkm_data
[2024-01-24 12:15:02,655] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:15:02,698] [INFO] Task started: CheckM
[2024-01-24 12:15:02,699] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003206115.1_ASM320611v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003206115.1_ASM320611v1_genomic.fna/checkm_input GCF_003206115.1_ASM320611v1_genomic.fna/checkm_result
[2024-01-24 12:15:41,836] [INFO] Task succeeded: CheckM
[2024-01-24 12:15:41,838] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:15:41,861] [INFO] ===== Completeness check finished =====
[2024-01-24 12:15:41,861] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:15:41,862] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003206115.1_ASM320611v1_genomic.fna/markers.fasta)
[2024-01-24 12:15:41,862] [INFO] Task started: Blastn
[2024-01-24 12:15:41,863] [INFO] Running command: blastn -query GCF_003206115.1_ASM320611v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0d38fb3c-43aa-4838-b267-154c70de5b8d/dqc_reference/reference_markers_gtdb.fasta -out GCF_003206115.1_ASM320611v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:43,515] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:43,517] [INFO] Selected 10 target genomes.
[2024-01-24 12:15:43,518] [INFO] Target genome list was writen to GCF_003206115.1_ASM320611v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:15:43,524] [INFO] Task started: fastANI
[2024-01-24 12:15:43,524] [INFO] Running command: fastANI --query /var/lib/cwl/stgd6d56d25-2280-489f-846c-885570e4908b/GCF_003206115.1_ASM320611v1_genomic.fna.gz --refList GCF_003206115.1_ASM320611v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003206115.1_ASM320611v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:15:53,519] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:53,534] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:15:53,534] [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_001937195.1	s__Salinicola socius	99.9833	1328	1346	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Salinicola	95.0	99.48	98.96	0.96	0.93	3	conclusive
GCF_003206695.1	s__Salinicola halophyticus	86.6476	1079	1346	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Salinicola	95.0	97.72	97.72	0.93	0.93	2	-
GCF_003206135.1	s__Salinicola salarius	85.8159	1026	1346	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	85.7388	999	1346	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	85.6837	1056	1346	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	85.3302	1044	1346	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	84.6131	1116	1346	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Salinicola	95.0	96.87	96.87	0.93	0.93	2	-
GCF_003206065.1	s__Salinicola halimionae	84.5322	1050	1346	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Salinicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003206615.1	s__Salinicola acroporae	84.3703	1096	1346	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	82.0979	872	1346	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 12:15:53,536] [INFO] GTDB search result was written to GCF_003206115.1_ASM320611v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:15:53,536] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:15:53,539] [INFO] DFAST_QC result json was written to GCF_003206115.1_ASM320611v1_genomic.fna/dqc_result.json
[2024-01-24 12:15:53,539] [INFO] DFAST_QC completed!
[2024-01-24 12:15:53,539] [INFO] Total running time: 0h1m19s