[2024-01-25 17:45:05,644] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:45:05,645] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:45:05,646] [INFO] DQC Reference Directory: /var/lib/cwl/stg79d4ebc7-5f6b-4398-925b-4521daa8ab5b/dqc_reference
[2024-01-25 17:45:06,794] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:45:06,795] [INFO] Task started: Prodigal
[2024-01-25 17:45:06,795] [INFO] Running command: gunzip -c /var/lib/cwl/stgfda57741-94fd-4e5a-8990-929dc94fbbb8/GCF_902703545.1_STARVERO_assembly_genomic.fna.gz | prodigal -d GCF_902703545.1_STARVERO_assembly_genomic.fna/cds.fna -a GCF_902703545.1_STARVERO_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:45:19,139] [INFO] Task succeeded: Prodigal
[2024-01-25 17:45:19,140] [INFO] Task started: HMMsearch
[2024-01-25 17:45:19,140] [INFO] Running command: hmmsearch --tblout GCF_902703545.1_STARVERO_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg79d4ebc7-5f6b-4398-925b-4521daa8ab5b/dqc_reference/reference_markers.hmm GCF_902703545.1_STARVERO_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:45:19,450] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:45:19,452] [INFO] Found 6/6 markers.
[2024-01-25 17:45:19,490] [INFO] Query marker FASTA was written to GCF_902703545.1_STARVERO_assembly_genomic.fna/markers.fasta
[2024-01-25 17:45:19,490] [INFO] Task started: Blastn
[2024-01-25 17:45:19,490] [INFO] Running command: blastn -query GCF_902703545.1_STARVERO_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg79d4ebc7-5f6b-4398-925b-4521daa8ab5b/dqc_reference/reference_markers.fasta -out GCF_902703545.1_STARVERO_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:45:20,536] [INFO] Task succeeded: Blastn
[2024-01-25 17:45:20,538] [INFO] Selected 11 target genomes.
[2024-01-25 17:45:20,539] [INFO] Target genome list was writen to GCF_902703545.1_STARVERO_assembly_genomic.fna/target_genomes.txt
[2024-01-25 17:45:20,544] [INFO] Task started: fastANI
[2024-01-25 17:45:20,544] [INFO] Running command: fastANI --query /var/lib/cwl/stgfda57741-94fd-4e5a-8990-929dc94fbbb8/GCF_902703545.1_STARVERO_assembly_genomic.fna.gz --refList GCF_902703545.1_STARVERO_assembly_genomic.fna/target_genomes.txt --output GCF_902703545.1_STARVERO_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:45:33,518] [INFO] Task succeeded: fastANI
[2024-01-25 17:45:33,518] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg79d4ebc7-5f6b-4398-925b-4521daa8ab5b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:45:33,518] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg79d4ebc7-5f6b-4398-925b-4521daa8ab5b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:45:33,526] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 17:45:33,526] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 17:45:33,526] [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
Starkeya novella	strain=DSM 506	GCA_000092925.1	921	921	type	True	87.2963	1082	1594	95	below_threshold
Starkeya koreensis	strain=Jip08	GCA_023016525.1	266121	266121	type	True	86.6893	985	1594	95	below_threshold
Ancylobacter dichloromethanicus	strain=VKM B-2484	GCA_018390645.1	518825	518825	type	True	85.5289	1022	1594	95	below_threshold
Ancylobacter rudongensis	strain=CGMCC 1.1761	GCA_900100155.1	177413	177413	type	True	85.2812	969	1594	95	below_threshold
Ancylobacter aquaticus	strain=DSM 101	GCA_004339465.1	100	100	type	True	84.8995	978	1594	95	below_threshold
Ancylobacter oerskovii	strain=CCM 7435	GCA_018390555.1	459519	459519	type	True	84.1771	961	1594	95	below_threshold
Ancylobacter sonchi	strain=VKM B-3145	GCA_018390695.1	1937790	1937790	type	True	84.0212	967	1594	95	below_threshold
Ancylobacter defluvii	strain=VKM B-2789	GCA_018390605.1	1282440	1282440	type	True	83.4245	936	1594	95	below_threshold
Bradyrhizobium betae	strain=CECT 5829	GCA_024806875.1	244734	244734	type	True	78.1421	454	1594	95	below_threshold
Salinarimonas soli	strain=BN140002	GCA_008386575.1	1638099	1638099	type	True	77.7817	388	1594	95	below_threshold
Bradyrhizobium cajani	strain=1010	GCA_009759665.1	1928661	1928661	type	True	77.7697	502	1594	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:45:33,530] [INFO] DFAST Taxonomy check result was written to GCF_902703545.1_STARVERO_assembly_genomic.fna/tc_result.tsv
[2024-01-25 17:45:33,531] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:45:33,531] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:45:33,531] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg79d4ebc7-5f6b-4398-925b-4521daa8ab5b/dqc_reference/checkm_data
[2024-01-25 17:45:33,532] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:45:33,578] [INFO] Task started: CheckM
[2024-01-25 17:45:33,579] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_902703545.1_STARVERO_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_902703545.1_STARVERO_assembly_genomic.fna/checkm_input GCF_902703545.1_STARVERO_assembly_genomic.fna/checkm_result
[2024-01-25 17:46:22,683] [INFO] Task succeeded: CheckM
[2024-01-25 17:46:22,684] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:46:22,705] [INFO] ===== Completeness check finished =====
[2024-01-25 17:46:22,705] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:46:22,706] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_902703545.1_STARVERO_assembly_genomic.fna/markers.fasta)
[2024-01-25 17:46:22,706] [INFO] Task started: Blastn
[2024-01-25 17:46:22,706] [INFO] Running command: blastn -query GCF_902703545.1_STARVERO_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg79d4ebc7-5f6b-4398-925b-4521daa8ab5b/dqc_reference/reference_markers_gtdb.fasta -out GCF_902703545.1_STARVERO_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:46:24,929] [INFO] Task succeeded: Blastn
[2024-01-25 17:46:24,932] [INFO] Selected 10 target genomes.
[2024-01-25 17:46:24,932] [INFO] Target genome list was writen to GCF_902703545.1_STARVERO_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:46:24,967] [INFO] Task started: fastANI
[2024-01-25 17:46:24,967] [INFO] Running command: fastANI --query /var/lib/cwl/stgfda57741-94fd-4e5a-8990-929dc94fbbb8/GCF_902703545.1_STARVERO_assembly_genomic.fna.gz --refList GCF_902703545.1_STARVERO_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_902703545.1_STARVERO_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:46:36,632] [INFO] Task succeeded: fastANI
[2024-01-25 17:46:36,639] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:46:36,639] [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_007559435.1	s__Starkeya sp007559435	98.5081	1324	1594	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Starkeya	95.0	98.55	98.55	0.95	0.95	2	conclusive
GCF_017872635.1	s__Starkeya sp017872635	87.3055	1057	1594	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Starkeya	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000092925.1	s__Starkeya novella	87.2845	1084	1594	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Starkeya	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009223885.1	s__Ancylobacter sp009223885	86.905	1009	1594	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Ancylobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018390645.1	s__Ancylobacter dichloromethanicus	85.5363	1020	1594	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Ancylobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900100155.1	s__Ancylobacter rudongensis	85.2595	971	1594	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Ancylobacter	95.0	96.36	96.36	0.88	0.88	2	-
GCF_004339465.1	s__Ancylobacter aquaticus	84.908	977	1594	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Ancylobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003241485.1	s__Angulomicrobium novellum_A	84.6983	922	1594	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Angulomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018449475.1	s__Angulomicrobium sp018449475	84.4454	932	1594	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Angulomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014195655.1	s__Angulomicrobium tetraedrale	84.1845	947	1594	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Angulomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:46:36,642] [INFO] GTDB search result was written to GCF_902703545.1_STARVERO_assembly_genomic.fna/result_gtdb.tsv
[2024-01-25 17:46:36,642] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:46:36,645] [INFO] DFAST_QC result json was written to GCF_902703545.1_STARVERO_assembly_genomic.fna/dqc_result.json
[2024-01-25 17:46:36,645] [INFO] DFAST_QC completed!
[2024-01-25 17:46:36,645] [INFO] Total running time: 0h1m31s