[2024-01-24 12:06:14,536] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:06:14,539] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:06:14,540] [INFO] DQC Reference Directory: /var/lib/cwl/stg5d511a8a-ace2-4f4e-b425-4c6ae451385c/dqc_reference
[2024-01-24 12:06:15,806] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:06:15,807] [INFO] Task started: Prodigal
[2024-01-24 12:06:15,807] [INFO] Running command: gunzip -c /var/lib/cwl/stg22daa887-c3e6-4c4a-a613-f10ddc1508bf/GCF_003206715.1_ASM320671v1_genomic.fna.gz | prodigal -d GCF_003206715.1_ASM320671v1_genomic.fna/cds.fna -a GCF_003206715.1_ASM320671v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:06:28,966] [INFO] Task succeeded: Prodigal
[2024-01-24 12:06:28,966] [INFO] Task started: HMMsearch
[2024-01-24 12:06:28,966] [INFO] Running command: hmmsearch --tblout GCF_003206715.1_ASM320671v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5d511a8a-ace2-4f4e-b425-4c6ae451385c/dqc_reference/reference_markers.hmm GCF_003206715.1_ASM320671v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:06:29,300] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:06:29,301] [INFO] Found 6/6 markers.
[2024-01-24 12:06:29,341] [INFO] Query marker FASTA was written to GCF_003206715.1_ASM320671v1_genomic.fna/markers.fasta
[2024-01-24 12:06:29,342] [INFO] Task started: Blastn
[2024-01-24 12:06:29,342] [INFO] Running command: blastn -query GCF_003206715.1_ASM320671v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5d511a8a-ace2-4f4e-b425-4c6ae451385c/dqc_reference/reference_markers.fasta -out GCF_003206715.1_ASM320671v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:06:30,293] [INFO] Task succeeded: Blastn
[2024-01-24 12:06:30,297] [INFO] Selected 24 target genomes.
[2024-01-24 12:06:30,298] [INFO] Target genome list was writen to GCF_003206715.1_ASM320671v1_genomic.fna/target_genomes.txt
[2024-01-24 12:06:30,313] [INFO] Task started: fastANI
[2024-01-24 12:06:30,314] [INFO] Running command: fastANI --query /var/lib/cwl/stg22daa887-c3e6-4c4a-a613-f10ddc1508bf/GCF_003206715.1_ASM320671v1_genomic.fna.gz --refList GCF_003206715.1_ASM320671v1_genomic.fna/target_genomes.txt --output GCF_003206715.1_ASM320671v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:06:51,889] [INFO] Task succeeded: fastANI
[2024-01-24 12:06:51,890] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5d511a8a-ace2-4f4e-b425-4c6ae451385c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:06:51,890] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5d511a8a-ace2-4f4e-b425-4c6ae451385c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:06:51,906] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:06:51,907] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:06:51,907] [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 peritrichatus	strain=JCM 18795	GCA_003206715.1	1267424	1267424	type	True	100.0	1484	1489	95	conclusive
Salinicola salarius	strain=DSM 18044	GCA_003206135.1	430457	430457	type	True	83.4336	903	1489	95	below_threshold
Salinicola endophyticus	strain=CPA92	GCA_003206575.1	1949083	1949083	type	True	82.542	857	1489	95	below_threshold
Salinicola lusitanus	strain=CR50	GCA_003206045.1	1949085	1949085	type	True	82.5162	921	1489	95	below_threshold
Salinicola acroporae	strain=LMG 28587	GCA_003206615.1	1541440	1541440	type	True	82.2939	928	1489	95	below_threshold
Salinicola tamaricis	strain=F01	GCA_003006155.1	1771309	1771309	type	True	82.1913	864	1489	95	below_threshold
Salinicola socius	strain=SMB35	GCA_001937195.1	404433	404433	type	True	82.0785	883	1489	95	below_threshold
Salinicola socius	strain=DSM 19940	GCA_003206115.1	404433	404433	type	True	82.0466	888	1489	95	below_threshold
Salinicola rhizosphaerae	strain=KCTC 32998	GCA_014652715.1	1443141	1443141	type	True	81.3297	804	1489	95	below_threshold
Halomonas sulfidoxydans	strain=MCCC 1A11059	GCA_017868775.1	2733484	2733484	type	True	79.6709	489	1489	95	below_threshold
Halomonas ethanolica	strain=MCCC 1A11081	GCA_021404305.1	2733486	2733486	type	True	79.3248	454	1489	95	below_threshold
Halomonas campisalis	strain=A4	GCA_022341425.1	74661	74661	type	True	79.1485	437	1489	95	below_threshold
Halomonas tianxiuensis	strain=BC-M4-5	GCA_009834345.1	2497861	2497861	type	True	78.9649	463	1489	95	below_threshold
Halomonas zhangzhouensis	strain=MCCC 1A11036	GCA_021404465.1	2733481	2733481	type	True	78.923	426	1489	95	below_threshold
Chromohalobacter sarecensis	strain=DSM 15547	GCA_023061135.1	245294	245294	type	True	78.767	411	1489	95	below_threshold
Halomonas urumqiensis	strain=BZ-SZ-XJ27	GCA_002879635.1	1684789	1684789	type	True	78.6147	379	1489	95	below_threshold
Halomonas urumqiensis	strain=CGMCC 1.12917	GCA_014653135.1	1684789	1684789	type	True	78.61	379	1489	95	below_threshold
Halomonas urumqiensis	strain=BZ-SZ-XJ27	GCA_003028575.1	1684789	1684789	type	True	78.6049	378	1489	95	below_threshold
Kushneria avicenniae	strain=DSM 23439	GCA_900112585.1	402385	402385	type	True	77.7856	301	1489	95	below_threshold
Alcanivorax mobilis	strain=MT13131	GCA_002864685.1	2019569	2019569	type	True	76.7928	152	1489	95	below_threshold
Alcanivorax limicola	strain=JB21	GCA_019931215.1	2874102	2874102	type	True	76.2972	85	1489	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:06:51,910] [INFO] DFAST Taxonomy check result was written to GCF_003206715.1_ASM320671v1_genomic.fna/tc_result.tsv
[2024-01-24 12:06:51,911] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:06:51,911] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:06:51,911] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5d511a8a-ace2-4f4e-b425-4c6ae451385c/dqc_reference/checkm_data
[2024-01-24 12:06:51,912] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:06:51,958] [INFO] Task started: CheckM
[2024-01-24 12:06:51,958] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003206715.1_ASM320671v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003206715.1_ASM320671v1_genomic.fna/checkm_input GCF_003206715.1_ASM320671v1_genomic.fna/checkm_result
[2024-01-24 12:07:33,859] [INFO] Task succeeded: CheckM
[2024-01-24 12:07:33,860] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:07:33,884] [INFO] ===== Completeness check finished =====
[2024-01-24 12:07:33,884] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:07:33,885] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003206715.1_ASM320671v1_genomic.fna/markers.fasta)
[2024-01-24 12:07:33,885] [INFO] Task started: Blastn
[2024-01-24 12:07:33,885] [INFO] Running command: blastn -query GCF_003206715.1_ASM320671v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5d511a8a-ace2-4f4e-b425-4c6ae451385c/dqc_reference/reference_markers_gtdb.fasta -out GCF_003206715.1_ASM320671v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:07:35,327] [INFO] Task succeeded: Blastn
[2024-01-24 12:07:35,332] [INFO] Selected 19 target genomes.
[2024-01-24 12:07:35,332] [INFO] Target genome list was writen to GCF_003206715.1_ASM320671v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:07:35,349] [INFO] Task started: fastANI
[2024-01-24 12:07:35,350] [INFO] Running command: fastANI --query /var/lib/cwl/stg22daa887-c3e6-4c4a-a613-f10ddc1508bf/GCF_003206715.1_ASM320671v1_genomic.fna.gz --refList GCF_003206715.1_ASM320671v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003206715.1_ASM320671v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:07:52,496] [INFO] Task succeeded: fastANI
[2024-01-24 12:07:52,516] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:07:52,516] [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_003206715.1	s__Salinicola peritrichatus	100.0	1484	1489	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_002179555.1	s__Salinicola salarius_A	83.886	962	1489	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	83.4219	904	1489	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Salinicola	95.0	97.80	97.80	0.89	0.89	2	-
GCA_002695065.1	s__Salinicola sp002695065	82.8672	888	1489	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Salinicola	95.0	97.83	97.83	0.85	0.85	2	-
GCF_003206575.1	s__Salinicola endophyticus	82.5236	859	1489	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	82.5014	923	1489	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Salinicola	95.0	96.87	96.87	0.93	0.93	2	-
GCA_000737985.1	s__Salinicola sp000737985	82.4181	858	1489	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Salinicola	95.0	96.18	96.18	0.88	0.88	2	-
GCF_003206615.1	s__Salinicola acroporae	82.3081	926	1489	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Salinicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003206695.1	s__Salinicola halophyticus	82.1708	855	1489	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Salinicola	95.0	97.72	97.72	0.93	0.93	2	-
GCF_003006155.1	s__Salinicola tamaricis	82.1622	867	1489	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Salinicola	95.0	99.82	99.82	0.99	0.99	2	-
GCF_001937195.1	s__Salinicola socius	82.0755	884	1489	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Salinicola	95.0	99.48	98.96	0.96	0.93	3	-
GCF_014652715.1	s__Salinicola rhizosphaerae	81.3464	802	1489	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Salinicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001971685.1	s__Halomonas_B sp001971685	79.743	510	1489	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000761475.1	s__Chromohalobacter israelensis	79.2485	531	1489	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Chromohalobacter	95.0	98.07	97.76	0.86	0.85	6	-
GCF_900112585.1	s__Kushneria avicenniae	77.7856	301	1489	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Kushneria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002864685.1	s__Alcanivorax mobilis	76.7772	153	1489	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	98.57	98.57	0.96	0.96	2	-
GCA_004299705.1	s__66-474 sp004299705	75.7019	66	1489	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__66-474	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:07:52,518] [INFO] GTDB search result was written to GCF_003206715.1_ASM320671v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:07:52,518] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:07:52,523] [INFO] DFAST_QC result json was written to GCF_003206715.1_ASM320671v1_genomic.fna/dqc_result.json
[2024-01-24 12:07:52,523] [INFO] DFAST_QC completed!
[2024-01-24 12:07:52,523] [INFO] Total running time: 0h1m38s