[2024-01-24 10:47:40,963] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:47:40,969] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:47:40,970] [INFO] DQC Reference Directory: /var/lib/cwl/stg9d357a2d-46c4-441c-b3a1-38f0bab0125c/dqc_reference
[2024-01-24 10:47:44,786] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:47:44,788] [INFO] Task started: Prodigal
[2024-01-24 10:47:44,789] [INFO] Running command: gunzip -c /var/lib/cwl/stgc1232ae5-d3c7-449c-8d88-fd3a11b1d892/GCF_003006155.1_ASM300615v1_genomic.fna.gz | prodigal -d GCF_003006155.1_ASM300615v1_genomic.fna/cds.fna -a GCF_003006155.1_ASM300615v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:47:57,244] [INFO] Task succeeded: Prodigal
[2024-01-24 10:47:57,245] [INFO] Task started: HMMsearch
[2024-01-24 10:47:57,245] [INFO] Running command: hmmsearch --tblout GCF_003006155.1_ASM300615v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9d357a2d-46c4-441c-b3a1-38f0bab0125c/dqc_reference/reference_markers.hmm GCF_003006155.1_ASM300615v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:47:57,502] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:47:57,504] [INFO] Found 6/6 markers.
[2024-01-24 10:47:57,542] [INFO] Query marker FASTA was written to GCF_003006155.1_ASM300615v1_genomic.fna/markers.fasta
[2024-01-24 10:47:57,543] [INFO] Task started: Blastn
[2024-01-24 10:47:57,543] [INFO] Running command: blastn -query GCF_003006155.1_ASM300615v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9d357a2d-46c4-441c-b3a1-38f0bab0125c/dqc_reference/reference_markers.fasta -out GCF_003006155.1_ASM300615v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:47:58,439] [INFO] Task succeeded: Blastn
[2024-01-24 10:47:58,442] [INFO] Selected 19 target genomes.
[2024-01-24 10:47:58,443] [INFO] Target genome list was writen to GCF_003006155.1_ASM300615v1_genomic.fna/target_genomes.txt
[2024-01-24 10:47:58,450] [INFO] Task started: fastANI
[2024-01-24 10:47:58,450] [INFO] Running command: fastANI --query /var/lib/cwl/stgc1232ae5-d3c7-449c-8d88-fd3a11b1d892/GCF_003006155.1_ASM300615v1_genomic.fna.gz --refList GCF_003006155.1_ASM300615v1_genomic.fna/target_genomes.txt --output GCF_003006155.1_ASM300615v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:48:16,513] [INFO] Task succeeded: fastANI
[2024-01-24 10:48:16,514] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9d357a2d-46c4-441c-b3a1-38f0bab0125c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:48:16,514] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9d357a2d-46c4-441c-b3a1-38f0bab0125c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:48:16,531] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 10:48:16,531] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:48:16,531] [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 tamaricis	strain=F01	GCA_003006155.1	1771309	1771309	type	True	100.0	1425	1425	95	conclusive
Salinicola endophyticus	strain=CPA92	GCA_003206575.1	1949083	1949083	type	True	93.2679	1268	1425	95	below_threshold
Salinicola lusitanus	strain=CR50	GCA_003206045.1	1949085	1949085	type	True	83.6624	972	1425	95	below_threshold
Salinicola acroporae	strain=LMG 28587	GCA_003206615.1	1541440	1541440	type	True	82.9985	943	1425	95	below_threshold
Salinicola peritrichatus	strain=JCM 18795	GCA_003206715.1	1267424	1267424	type	True	82.1652	858	1425	95	below_threshold
Salinicola salarius	strain=DSM 18044	GCA_003206135.1	430457	430457	type	True	81.845	837	1425	95	below_threshold
Salinicola halophilus	strain=CECT 5903	GCA_003206155.1	184065	184065	type	True	81.572	779	1425	95	below_threshold
Salinicola halophyticus	strain=CR45	GCA_003206695.1	1808881	1808881	type	True	81.4819	885	1425	95	below_threshold
Salinicola rhizosphaerae	strain=KCTC 32998	GCA_014652715.1	1443141	1443141	type	True	81.2071	825	1425	95	below_threshold
Salinicola aestuarinus	strain=CPA62	GCA_003206645.1	1949082	1949082	type	True	80.9205	771	1425	95	below_threshold
Halomonas denitrificans	strain=DSM 18045	GCA_003056305.1	370769	370769	type	True	80.3379	548	1425	95	below_threshold
Halomonas sulfidoxydans	strain=MCCC 1A11059	GCA_017868775.1	2733484	2733484	type	True	80.2692	558	1425	95	below_threshold
Halomonas halophila	strain=NBRC 102604	GCA_007989465.1	29573	29573	type	True	80.2588	559	1425	95	below_threshold
Halomonas saccharevitans	strain=CGMCC 1.6493	GCA_900116405.1	416872	416872	type	True	79.9838	484	1425	95	below_threshold
Halomonas tianxiuensis	strain=BC-M4-5	GCA_009834345.1	2497861	2497861	type	True	79.8019	508	1425	95	below_threshold
Halomonas campisalis	strain=A4	GCA_022341425.1	74661	74661	type	True	79.7953	519	1425	95	below_threshold
Halomonas ethanolica	strain=MCCC 1A11081	GCA_021404305.1	2733486	2733486	type	True	79.6297	528	1425	95	below_threshold
Halomonas aerodenitrificans	strain=MCCC 1A11058	GCA_021404405.1	2733483	2733483	type	True	79.5919	527	1425	95	below_threshold
Halomonas kenyensis	strain=DSM 17331	GCA_022341445.1	321266	321266	type	True	79.4183	474	1425	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:48:16,533] [INFO] DFAST Taxonomy check result was written to GCF_003006155.1_ASM300615v1_genomic.fna/tc_result.tsv
[2024-01-24 10:48:16,533] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:48:16,533] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:48:16,534] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9d357a2d-46c4-441c-b3a1-38f0bab0125c/dqc_reference/checkm_data
[2024-01-24 10:48:16,535] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:48:16,576] [INFO] Task started: CheckM
[2024-01-24 10:48:16,576] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003006155.1_ASM300615v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003006155.1_ASM300615v1_genomic.fna/checkm_input GCF_003006155.1_ASM300615v1_genomic.fna/checkm_result
[2024-01-24 10:48:55,324] [INFO] Task succeeded: CheckM
[2024-01-24 10:48:55,325] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:48:55,347] [INFO] ===== Completeness check finished =====
[2024-01-24 10:48:55,347] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:48:55,348] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003006155.1_ASM300615v1_genomic.fna/markers.fasta)
[2024-01-24 10:48:55,348] [INFO] Task started: Blastn
[2024-01-24 10:48:55,349] [INFO] Running command: blastn -query GCF_003006155.1_ASM300615v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9d357a2d-46c4-441c-b3a1-38f0bab0125c/dqc_reference/reference_markers_gtdb.fasta -out GCF_003006155.1_ASM300615v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:48:56,960] [INFO] Task succeeded: Blastn
[2024-01-24 10:48:56,964] [INFO] Selected 13 target genomes.
[2024-01-24 10:48:56,965] [INFO] Target genome list was writen to GCF_003006155.1_ASM300615v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:48:56,977] [INFO] Task started: fastANI
[2024-01-24 10:48:56,978] [INFO] Running command: fastANI --query /var/lib/cwl/stgc1232ae5-d3c7-449c-8d88-fd3a11b1d892/GCF_003006155.1_ASM300615v1_genomic.fna.gz --refList GCF_003006155.1_ASM300615v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003006155.1_ASM300615v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:49:10,263] [INFO] Task succeeded: fastANI
[2024-01-24 10:49:10,277] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:49:10,277] [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_003006155.1	s__Salinicola tamaricis	100.0	1425	1425	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Salinicola	95.0	99.82	99.82	0.99	0.99	2	conclusive
GCA_000737985.1	s__Salinicola sp000737985	94.0397	1232	1425	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Salinicola	95.0	96.18	96.18	0.88	0.88	2	-
GCF_003206575.1	s__Salinicola endophyticus	93.2592	1269	1425	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Salinicola	95.0	99.06	99.06	0.96	0.96	2	-
GCF_003206045.1	s__Salinicola lusitanus	83.6855	968	1425	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Salinicola	95.0	96.87	96.87	0.93	0.93	2	-
GCA_002695065.1	s__Salinicola sp002695065	82.9859	887	1425	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Salinicola	95.0	97.83	97.83	0.85	0.85	2	-
GCF_003206715.1	s__Salinicola peritrichatus	82.1709	858	1425	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Salinicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003206135.1	s__Salinicola salarius	81.8264	840	1425	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	81.8245	826	1425	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Salinicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003206155.1	s__Salinicola halophilus	81.5992	776	1425	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Salinicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014652715.1	s__Salinicola rhizosphaerae	81.216	824	1425	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Salinicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003056305.1	s__Halomonas denitrificans	80.2977	553	1425	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007989465.1	s__Halomonas halophila	80.2278	562	1425	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	98.43	97.59	0.92	0.89	4	-
GCF_003202205.1	s__Halomonas sp003202205	79.9353	556	1425	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 10:49:10,279] [INFO] GTDB search result was written to GCF_003006155.1_ASM300615v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:49:10,279] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:49:10,283] [INFO] DFAST_QC result json was written to GCF_003006155.1_ASM300615v1_genomic.fna/dqc_result.json
[2024-01-24 10:49:10,283] [INFO] DFAST_QC completed!
[2024-01-24 10:49:10,283] [INFO] Total running time: 0h1m29s