[2024-01-24 11:30:49,459] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:30:49,461] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:30:49,461] [INFO] DQC Reference Directory: /var/lib/cwl/stgd70f8f8c-8040-4000-a4b3-7e3c29d9cc0f/dqc_reference
[2024-01-24 11:30:50,670] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:30:50,674] [INFO] Task started: Prodigal
[2024-01-24 11:30:50,674] [INFO] Running command: gunzip -c /var/lib/cwl/stg4ff3c397-1df7-4a3f-ad3e-571578b17e6e/GCF_014640595.1_ASM1464059v1_genomic.fna.gz | prodigal -d GCF_014640595.1_ASM1464059v1_genomic.fna/cds.fna -a GCF_014640595.1_ASM1464059v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:31:00,401] [INFO] Task succeeded: Prodigal
[2024-01-24 11:31:00,402] [INFO] Task started: HMMsearch
[2024-01-24 11:31:00,402] [INFO] Running command: hmmsearch --tblout GCF_014640595.1_ASM1464059v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd70f8f8c-8040-4000-a4b3-7e3c29d9cc0f/dqc_reference/reference_markers.hmm GCF_014640595.1_ASM1464059v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:31:00,651] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:31:00,653] [INFO] Found 6/6 markers.
[2024-01-24 11:31:00,683] [INFO] Query marker FASTA was written to GCF_014640595.1_ASM1464059v1_genomic.fna/markers.fasta
[2024-01-24 11:31:00,684] [INFO] Task started: Blastn
[2024-01-24 11:31:00,684] [INFO] Running command: blastn -query GCF_014640595.1_ASM1464059v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd70f8f8c-8040-4000-a4b3-7e3c29d9cc0f/dqc_reference/reference_markers.fasta -out GCF_014640595.1_ASM1464059v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:31:01,723] [INFO] Task succeeded: Blastn
[2024-01-24 11:31:01,727] [INFO] Selected 15 target genomes.
[2024-01-24 11:31:01,728] [INFO] Target genome list was writen to GCF_014640595.1_ASM1464059v1_genomic.fna/target_genomes.txt
[2024-01-24 11:31:01,747] [INFO] Task started: fastANI
[2024-01-24 11:31:01,748] [INFO] Running command: fastANI --query /var/lib/cwl/stg4ff3c397-1df7-4a3f-ad3e-571578b17e6e/GCF_014640595.1_ASM1464059v1_genomic.fna.gz --refList GCF_014640595.1_ASM1464059v1_genomic.fna/target_genomes.txt --output GCF_014640595.1_ASM1464059v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:31:11,626] [INFO] Task succeeded: fastANI
[2024-01-24 11:31:11,626] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd70f8f8c-8040-4000-a4b3-7e3c29d9cc0f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:31:11,627] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd70f8f8c-8040-4000-a4b3-7e3c29d9cc0f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:31:11,639] [INFO] Found 15 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:31:11,640] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:31:11,640] [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
Pseudoclavibacter endophyticus	strain=CGMCC 1.15081	GCA_014640595.1	1778590	1778590	type	True	100.0	1082	1083	95	conclusive
Pseudoclavibacter endophyticus	strain=EGI 60007	GCA_008831085.1	1778590	1778590	type	True	99.9995	1081	1083	95	conclusive
Pseudoclavibacter chungangensis	strain=DSM 23821	GCA_013410545.1	587635	587635	type	True	78.9425	428	1083	95	below_threshold
Pseudoclavibacter chungangensis	strain=DSM 23821	GCA_008831135.1	587635	587635	type	True	78.9205	430	1083	95	below_threshold
Pseudoclavibacter terrae	strain=THG-MD12	GCA_008831075.1	1530195	1530195	type	True	78.3128	324	1083	95	below_threshold
Gulosibacter faecalis	strain=B187	GCA_000381765.1	272240	272240	type	True	77.7905	323	1083	95	below_threshold
Agromyces aurantiacus	strain=DSM 14598	GCA_016907355.1	165814	165814	type	True	77.7855	338	1083	95	below_threshold
Agromyces cavernae	strain=SYSU K20354	GCA_021044935.1	2898659	2898659	type	True	77.5161	316	1083	95	below_threshold
Agromyces agglutinans	strain=CFH 90414	GCA_009647605.1	2662258	2662258	type	True	77.4959	335	1083	95	below_threshold
Gulosibacter macacae	strain=YIM 102482-1	GCA_003865375.1	2488791	2488791	type	True	77.492	210	1083	95	below_threshold
Gryllotalpicola ginsengisoli	strain=DSM 22003	GCA_000419445.1	444608	444608	type	True	77.4871	251	1083	95	below_threshold
Agromyces humatus	strain=JCM 14319	GCA_021228295.1	279573	279573	type	True	77.4356	309	1083	95	below_threshold
Clavibacter michiganensis	strain=LMG7333	GCA_021216655.1	28447	28447	suspected-type	True	77.3207	287	1083	95	below_threshold
Clavibacter michiganensis subsp. insidiosus	strain=ATCC 10253	GCA_003076355.1	33014	28447	type	True	77.2159	293	1083	95	below_threshold
Microbacterium rhizomatis	strain=JCM 30598	GCA_008710745.1	1631477	1631477	type	True	77.1842	209	1083	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:31:11,642] [INFO] DFAST Taxonomy check result was written to GCF_014640595.1_ASM1464059v1_genomic.fna/tc_result.tsv
[2024-01-24 11:31:11,643] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:31:11,643] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:31:11,644] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd70f8f8c-8040-4000-a4b3-7e3c29d9cc0f/dqc_reference/checkm_data
[2024-01-24 11:31:11,646] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:31:11,684] [INFO] Task started: CheckM
[2024-01-24 11:31:11,684] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014640595.1_ASM1464059v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014640595.1_ASM1464059v1_genomic.fna/checkm_input GCF_014640595.1_ASM1464059v1_genomic.fna/checkm_result
[2024-01-24 11:32:02,361] [INFO] Task succeeded: CheckM
[2024-01-24 11:32:02,363] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:32:02,384] [INFO] ===== Completeness check finished =====
[2024-01-24 11:32:02,384] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:32:02,385] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014640595.1_ASM1464059v1_genomic.fna/markers.fasta)
[2024-01-24 11:32:02,385] [INFO] Task started: Blastn
[2024-01-24 11:32:02,385] [INFO] Running command: blastn -query GCF_014640595.1_ASM1464059v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd70f8f8c-8040-4000-a4b3-7e3c29d9cc0f/dqc_reference/reference_markers_gtdb.fasta -out GCF_014640595.1_ASM1464059v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:32:04,022] [INFO] Task succeeded: Blastn
[2024-01-24 11:32:04,026] [INFO] Selected 18 target genomes.
[2024-01-24 11:32:04,026] [INFO] Target genome list was writen to GCF_014640595.1_ASM1464059v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:32:04,039] [INFO] Task started: fastANI
[2024-01-24 11:32:04,039] [INFO] Running command: fastANI --query /var/lib/cwl/stg4ff3c397-1df7-4a3f-ad3e-571578b17e6e/GCF_014640595.1_ASM1464059v1_genomic.fna.gz --refList GCF_014640595.1_ASM1464059v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014640595.1_ASM1464059v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:32:15,163] [INFO] Task succeeded: fastANI
[2024-01-24 11:32:15,179] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:32:15,180] [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_008831085.1	s__Pseudoclavibacter endophyticus	99.9995	1081	1083	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Pseudoclavibacter	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_013410545.1	s__Pseudoclavibacter chungangensis	78.892	433	1083	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Pseudoclavibacter	95.0	99.99	99.99	0.99	0.99	2	-
GCA_910822395.1	s__Pseudoclavibacter sp910822395	78.8133	369	1083	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Pseudoclavibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008831075.1	s__Pseudoclavibacter terrae	78.3368	322	1083	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Pseudoclavibacter	95.0	96.82	96.82	0.88	0.88	2	-
GCF_002931555.1	s__Pseudoclavibacter sp002931555	78.2494	335	1083	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Pseudoclavibacter	95.0	98.27	98.05	0.90	0.88	3	-
GCA_012719255.1	s__Gulosibacter sp012719255	78.087	315	1083	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Gulosibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900163695.1	s__Gulosibacter sp900163695	77.9653	340	1083	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Gulosibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900626105.1	s__Gulosibacter sp900626105	77.7516	287	1083	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Gulosibacter	95.0	98.80	98.80	0.92	0.92	2	-
GCF_000381765.1	s__Gulosibacter faecalis	77.743	327	1083	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Gulosibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016907355.1	s__Agromyces aurantiacus	77.737	343	1083	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008122505.1	s__Agromyces sp008122505	77.7214	341	1083	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000419445.1	s__Gryllotalpicola ginsengisoli	77.4871	251	1083	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Gryllotalpicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009807095.1	s__Rathayibacter sp009807095	77.478	290	1083	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rathayibacter	95.0	99.31	99.31	0.97	0.97	2	-
GCF_014648575.1	s__Agromyces mediolanus	77.4751	349	1083	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003627075.1	s__Protaetiibacter intestinalis	77.3742	298	1083	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Protaetiibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900167575.1	s__Okibacterium fritillariae	77.3487	214	1083	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Okibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003627055.1	s__Gryllotalpicola protaetiae	77.2618	256	1083	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Gryllotalpicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013205025.1	s__Rathayibacter sp013205025	77.2204	309	1083	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rathayibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:32:15,182] [INFO] GTDB search result was written to GCF_014640595.1_ASM1464059v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:32:15,182] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:32:15,186] [INFO] DFAST_QC result json was written to GCF_014640595.1_ASM1464059v1_genomic.fna/dqc_result.json
[2024-01-24 11:32:15,186] [INFO] DFAST_QC completed!
[2024-01-24 11:32:15,186] [INFO] Total running time: 0h1m26s