[2024-01-24 11:44:23,573] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:44:23,586] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:44:23,587] [INFO] DQC Reference Directory: /var/lib/cwl/stg2b8bc497-8bdf-4634-b7aa-9a7f71cfe4ba/dqc_reference
[2024-01-24 11:44:26,339] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:44:26,340] [INFO] Task started: Prodigal
[2024-01-24 11:44:26,340] [INFO] Running command: gunzip -c /var/lib/cwl/stgb454c292-1fcf-4faa-9606-063d3b4cee1a/GCF_024752335.1_ASM2475233v1_genomic.fna.gz | prodigal -d GCF_024752335.1_ASM2475233v1_genomic.fna/cds.fna -a GCF_024752335.1_ASM2475233v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:44:40,597] [INFO] Task succeeded: Prodigal
[2024-01-24 11:44:40,598] [INFO] Task started: HMMsearch
[2024-01-24 11:44:40,598] [INFO] Running command: hmmsearch --tblout GCF_024752335.1_ASM2475233v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2b8bc497-8bdf-4634-b7aa-9a7f71cfe4ba/dqc_reference/reference_markers.hmm GCF_024752335.1_ASM2475233v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:44:40,899] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:44:40,900] [INFO] Found 6/6 markers.
[2024-01-24 11:44:40,944] [INFO] Query marker FASTA was written to GCF_024752335.1_ASM2475233v1_genomic.fna/markers.fasta
[2024-01-24 11:44:40,945] [INFO] Task started: Blastn
[2024-01-24 11:44:40,945] [INFO] Running command: blastn -query GCF_024752335.1_ASM2475233v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2b8bc497-8bdf-4634-b7aa-9a7f71cfe4ba/dqc_reference/reference_markers.fasta -out GCF_024752335.1_ASM2475233v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:44:42,059] [INFO] Task succeeded: Blastn
[2024-01-24 11:44:42,062] [INFO] Selected 12 target genomes.
[2024-01-24 11:44:42,063] [INFO] Target genome list was writen to GCF_024752335.1_ASM2475233v1_genomic.fna/target_genomes.txt
[2024-01-24 11:44:42,068] [INFO] Task started: fastANI
[2024-01-24 11:44:42,068] [INFO] Running command: fastANI --query /var/lib/cwl/stgb454c292-1fcf-4faa-9606-063d3b4cee1a/GCF_024752335.1_ASM2475233v1_genomic.fna.gz --refList GCF_024752335.1_ASM2475233v1_genomic.fna/target_genomes.txt --output GCF_024752335.1_ASM2475233v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:44:55,727] [INFO] Task succeeded: fastANI
[2024-01-24 11:44:55,728] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2b8bc497-8bdf-4634-b7aa-9a7f71cfe4ba/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:44:55,728] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2b8bc497-8bdf-4634-b7aa-9a7f71cfe4ba/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:44:55,739] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:44:55,739] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:44:55,739] [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	85.4061	1030	1657	95	below_threshold
Starkeya koreensis	strain=Jip08	GCA_023016525.1	266121	266121	type	True	84.8027	975	1657	95	below_threshold
Ancylobacter dichloromethanicus	strain=VKM B-2484	GCA_018390645.1	518825	518825	type	True	84.3336	1005	1657	95	below_threshold
Ancylobacter oerskovii	strain=CCM 7435	GCA_018390555.1	459519	459519	type	True	83.897	986	1657	95	below_threshold
Ancylobacter sonchi	strain=VKM B-3145	GCA_018390695.1	1937790	1937790	type	True	83.8704	1022	1657	95	below_threshold
Ancylobacter rudongensis	strain=CGMCC 1.1761	GCA_900100155.1	177413	177413	type	True	83.7586	944	1657	95	below_threshold
Ancylobacter aquaticus	strain=DSM 101	GCA_004339465.1	100	100	type	True	83.4866	977	1657	95	below_threshold
Ancylobacter defluvii	strain=VKM B-2789	GCA_018390605.1	1282440	1282440	type	True	83.4567	989	1657	95	below_threshold
Xanthobacter tagetidis	strain=DSM 11105	GCA_014206845.1	60216	60216	type	True	79.6432	645	1657	95	below_threshold
Methylobacterium oryzihabitans	strain=TER-1	GCA_004004555.2	2499852	2499852	type	True	77.7695	595	1657	95	below_threshold
Methylobacterium goesingense	strain=DSM 21331	GCA_022179225.1	243690	243690	type	True	77.3913	385	1657	95	below_threshold
Methylobacterium crusticola	strain=KCTC 52305	GCA_022179145.1	1697972	1697972	type	True	77.2435	577	1657	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:44:55,741] [INFO] DFAST Taxonomy check result was written to GCF_024752335.1_ASM2475233v1_genomic.fna/tc_result.tsv
[2024-01-24 11:44:55,742] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:44:55,742] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:44:55,742] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2b8bc497-8bdf-4634-b7aa-9a7f71cfe4ba/dqc_reference/checkm_data
[2024-01-24 11:44:55,743] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:44:55,791] [INFO] Task started: CheckM
[2024-01-24 11:44:55,791] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024752335.1_ASM2475233v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024752335.1_ASM2475233v1_genomic.fna/checkm_input GCF_024752335.1_ASM2475233v1_genomic.fna/checkm_result
[2024-01-24 11:45:40,899] [INFO] Task succeeded: CheckM
[2024-01-24 11:45:40,900] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:45:40,920] [INFO] ===== Completeness check finished =====
[2024-01-24 11:45:40,921] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:45:40,921] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024752335.1_ASM2475233v1_genomic.fna/markers.fasta)
[2024-01-24 11:45:40,922] [INFO] Task started: Blastn
[2024-01-24 11:45:40,922] [INFO] Running command: blastn -query GCF_024752335.1_ASM2475233v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2b8bc497-8bdf-4634-b7aa-9a7f71cfe4ba/dqc_reference/reference_markers_gtdb.fasta -out GCF_024752335.1_ASM2475233v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:45:43,177] [INFO] Task succeeded: Blastn
[2024-01-24 11:45:43,180] [INFO] Selected 12 target genomes.
[2024-01-24 11:45:43,180] [INFO] Target genome list was writen to GCF_024752335.1_ASM2475233v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:45:43,190] [INFO] Task started: fastANI
[2024-01-24 11:45:43,191] [INFO] Running command: fastANI --query /var/lib/cwl/stgb454c292-1fcf-4faa-9606-063d3b4cee1a/GCF_024752335.1_ASM2475233v1_genomic.fna.gz --refList GCF_024752335.1_ASM2475233v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024752335.1_ASM2475233v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:45:56,708] [INFO] Task succeeded: fastANI
[2024-01-24 11:45:56,722] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 11:45:56,723] [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_000092925.1	s__Starkeya novella	85.3854	1032	1657	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Starkeya	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017872635.1	s__Starkeya sp017872635	85.0305	999	1657	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Starkeya	95.0	100.00	100.00	1.00	1.00	2	-
GCF_009223885.1	s__Ancylobacter sp009223885	85.0094	957	1657	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Ancylobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010669125.1	s__Ancyclobacter_A pratisalsi	84.8658	1105	1657	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Ancyclobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007559435.1	s__Starkeya sp007559435	84.8594	964	1657	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Starkeya	95.0	98.55	98.55	0.95	0.95	2	-
GCF_018390645.1	s__Ancylobacter dichloromethanicus	84.323	1007	1657	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	83.9643	896	1657	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	83.9225	939	1657	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Angulomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018390555.1	s__Ancylobacter_B oerskovii	83.9188	984	1657	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Ancylobacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014195655.1	s__Angulomicrobium tetraedrale	83.8024	982	1657	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Angulomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000702305.1	s__GCF-000702305 sp000702305	83.7355	932	1657	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__GCF-000702305	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018390605.1	s__Ancylobacter_B defluvii	83.4549	991	1657	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Ancylobacter_B	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:45:56,724] [INFO] GTDB search result was written to GCF_024752335.1_ASM2475233v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:45:56,725] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:45:56,728] [INFO] DFAST_QC result json was written to GCF_024752335.1_ASM2475233v1_genomic.fna/dqc_result.json
[2024-01-24 11:45:56,728] [INFO] DFAST_QC completed!
[2024-01-24 11:45:56,728] [INFO] Total running time: 0h1m33s