[2024-01-24 13:13:11,149] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:13:11,150] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:13:11,151] [INFO] DQC Reference Directory: /var/lib/cwl/stg404efd66-d624-4713-816e-79118371dd9e/dqc_reference
[2024-01-24 13:13:12,488] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:13:12,488] [INFO] Task started: Prodigal
[2024-01-24 13:13:12,489] [INFO] Running command: gunzip -c /var/lib/cwl/stg4c057bdd-f6e5-45b4-81ce-aa02bddfa666/GCF_014645375.1_ASM1464537v1_genomic.fna.gz | prodigal -d GCF_014645375.1_ASM1464537v1_genomic.fna/cds.fna -a GCF_014645375.1_ASM1464537v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:13:29,875] [INFO] Task succeeded: Prodigal
[2024-01-24 13:13:29,875] [INFO] Task started: HMMsearch
[2024-01-24 13:13:29,875] [INFO] Running command: hmmsearch --tblout GCF_014645375.1_ASM1464537v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg404efd66-d624-4713-816e-79118371dd9e/dqc_reference/reference_markers.hmm GCF_014645375.1_ASM1464537v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:13:30,223] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:13:30,224] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg4c057bdd-f6e5-45b4-81ce-aa02bddfa666/GCF_014645375.1_ASM1464537v1_genomic.fna.gz]
[2024-01-24 13:13:30,274] [INFO] Query marker FASTA was written to GCF_014645375.1_ASM1464537v1_genomic.fna/markers.fasta
[2024-01-24 13:13:30,274] [INFO] Task started: Blastn
[2024-01-24 13:13:30,274] [INFO] Running command: blastn -query GCF_014645375.1_ASM1464537v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg404efd66-d624-4713-816e-79118371dd9e/dqc_reference/reference_markers.fasta -out GCF_014645375.1_ASM1464537v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:13:31,160] [INFO] Task succeeded: Blastn
[2024-01-24 13:13:31,163] [INFO] Selected 16 target genomes.
[2024-01-24 13:13:31,164] [INFO] Target genome list was writen to GCF_014645375.1_ASM1464537v1_genomic.fna/target_genomes.txt
[2024-01-24 13:13:31,431] [INFO] Task started: fastANI
[2024-01-24 13:13:31,432] [INFO] Running command: fastANI --query /var/lib/cwl/stg4c057bdd-f6e5-45b4-81ce-aa02bddfa666/GCF_014645375.1_ASM1464537v1_genomic.fna.gz --refList GCF_014645375.1_ASM1464537v1_genomic.fna/target_genomes.txt --output GCF_014645375.1_ASM1464537v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:13:47,649] [INFO] Task succeeded: fastANI
[2024-01-24 13:13:47,650] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg404efd66-d624-4713-816e-79118371dd9e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:13:47,650] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg404efd66-d624-4713-816e-79118371dd9e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:13:47,664] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:13:47,665] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:13:47,665] [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
Marinobacterium nitratireducens	strain=CGMCC 1.7286	GCA_014645375.1	518897	518897	type	True	100.0	1829	1831	95	conclusive
Marinobacterium rhizophilum	strain=DSM 18822	GCA_000378045.1	420402	420402	type	True	79.5121	704	1831	95	below_threshold
Marinobacterium aestuarii	strain=ST58-10	GCA_001651805.1	1821621	1821621	type	True	79.1514	675	1831	95	below_threshold
Marinobacterium arenosum	strain=CAU 1594	GCA_019795155.1	2862496	2862496	type	True	79.0015	496	1831	95	below_threshold
Marinobacterium zhoushanense	strain=CGMCC 1.15341	GCA_014641945.1	1679163	1679163	type	True	78.6152	430	1831	95	below_threshold
Marinobacterium profundum	strain=PAMC 27536	GCA_001528745.1	1714300	1714300	type	True	78.5062	602	1831	95	below_threshold
Marinobacterium georgiense	strain=DSM 11526	GCA_900107855.1	48076	48076	type	True	77.843	223	1831	95	below_threshold
Pseudomonas aromaticivorans	strain=MAP12	GCA_019097855.1	2849492	2849492	type	True	77.5813	307	1831	95	below_threshold
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	77.5647	350	1831	95	below_threshold
Pseudomonas thermotolerans	strain=DSM 14292	GCA_000364625.1	157784	157784	type	True	77.3615	290	1831	95	below_threshold
Pseudomonas aeruginosa	strain=DSM 50071	GCA_024169805.1	287	287	type	True	77.26	320	1831	95	below_threshold
Pseudomonas aeruginosa	strain=JCM 5962	GCA_022496575.1	287	287	type	True	77.2562	313	1831	95	below_threshold
Salinicola endophyticus	strain=CPA92	GCA_003206575.1	1949083	1949083	type	True	77.077	241	1831	95	below_threshold
Salinicola tamaricis	strain=F01	GCA_003006155.1	1771309	1771309	type	True	76.9146	238	1831	95	below_threshold
Guyparkeria hydrothermalis	strain=R3	GCA_023555375.1	923	923	type	True	76.5764	105	1831	95	below_threshold
Halomonas korlensis	strain=CGMCC 1.6981	GCA_900116705.1	463301	463301	type	True	76.4934	188	1831	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:13:47,667] [INFO] DFAST Taxonomy check result was written to GCF_014645375.1_ASM1464537v1_genomic.fna/tc_result.tsv
[2024-01-24 13:13:47,667] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:13:47,667] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:13:47,668] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg404efd66-d624-4713-816e-79118371dd9e/dqc_reference/checkm_data
[2024-01-24 13:13:47,669] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:13:47,727] [INFO] Task started: CheckM
[2024-01-24 13:13:47,727] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014645375.1_ASM1464537v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014645375.1_ASM1464537v1_genomic.fna/checkm_input GCF_014645375.1_ASM1464537v1_genomic.fna/checkm_result
[2024-01-24 13:14:35,671] [INFO] Task succeeded: CheckM
[2024-01-24 13:14:35,673] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:14:35,697] [INFO] ===== Completeness check finished =====
[2024-01-24 13:14:35,697] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:14:35,698] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014645375.1_ASM1464537v1_genomic.fna/markers.fasta)
[2024-01-24 13:14:35,698] [INFO] Task started: Blastn
[2024-01-24 13:14:35,698] [INFO] Running command: blastn -query GCF_014645375.1_ASM1464537v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg404efd66-d624-4713-816e-79118371dd9e/dqc_reference/reference_markers_gtdb.fasta -out GCF_014645375.1_ASM1464537v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:14:37,247] [INFO] Task succeeded: Blastn
[2024-01-24 13:14:37,251] [INFO] Selected 10 target genomes.
[2024-01-24 13:14:37,251] [INFO] Target genome list was writen to GCF_014645375.1_ASM1464537v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:14:37,259] [INFO] Task started: fastANI
[2024-01-24 13:14:37,259] [INFO] Running command: fastANI --query /var/lib/cwl/stg4c057bdd-f6e5-45b4-81ce-aa02bddfa666/GCF_014645375.1_ASM1464537v1_genomic.fna.gz --refList GCF_014645375.1_ASM1464537v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014645375.1_ASM1464537v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:14:47,146] [INFO] Task succeeded: fastANI
[2024-01-24 13:14:47,162] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:14:47,163] [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_014645375.1	s__Marinobacterium_A nitratireducens	100.0	1829	1831	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium_A	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_013373085.1	s__Marinobacterium_A sp013373085	83.7919	1149	1831	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000378045.1	s__Marinobacterium_A rhizophilum	79.5294	700	1831	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001651805.1	s__Marinobacterium_A aestuarii	79.1614	672	1831	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019084545.1	s__Marinobacterium sp019084545	79.1056	459	1831	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003250495.1	s__Marinobacterium sp003250495	78.9598	357	1831	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001528745.1	s__Marinobacterium_A profundum	78.5063	602	1831	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003206575.1	s__Salinicola endophyticus	77.0824	242	1831	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Salinicola	95.0	99.06	99.06	0.96	0.96	2	-
GCF_003006155.1	s__Salinicola tamaricis	76.9031	241	1831	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Salinicola	95.0	99.82	99.82	0.99	0.99	2	-
GCF_000299335.2	s__Alcanivorax_A pacificus	76.6041	167	1831	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:14:47,164] [INFO] GTDB search result was written to GCF_014645375.1_ASM1464537v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:14:47,165] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:14:47,168] [INFO] DFAST_QC result json was written to GCF_014645375.1_ASM1464537v1_genomic.fna/dqc_result.json
[2024-01-24 13:14:47,168] [INFO] DFAST_QC completed!
[2024-01-24 13:14:47,168] [INFO] Total running time: 0h1m36s