[2024-01-24 14:14:31,961] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:14:31,963] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:14:31,964] [INFO] DQC Reference Directory: /var/lib/cwl/stgfdac8c0e-a1cd-498e-a937-1e0c49713af0/dqc_reference
[2024-01-24 14:14:33,222] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:14:33,222] [INFO] Task started: Prodigal
[2024-01-24 14:14:33,223] [INFO] Running command: gunzip -c /var/lib/cwl/stgb77269b9-0c93-41c9-9eea-f185f35a77fe/GCF_004339465.1_ASM433946v1_genomic.fna.gz | prodigal -d GCF_004339465.1_ASM433946v1_genomic.fna/cds.fna -a GCF_004339465.1_ASM433946v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:14:47,906] [INFO] Task succeeded: Prodigal
[2024-01-24 14:14:47,906] [INFO] Task started: HMMsearch
[2024-01-24 14:14:47,906] [INFO] Running command: hmmsearch --tblout GCF_004339465.1_ASM433946v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfdac8c0e-a1cd-498e-a937-1e0c49713af0/dqc_reference/reference_markers.hmm GCF_004339465.1_ASM433946v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:14:48,249] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:14:48,250] [INFO] Found 6/6 markers.
[2024-01-24 14:14:48,290] [INFO] Query marker FASTA was written to GCF_004339465.1_ASM433946v1_genomic.fna/markers.fasta
[2024-01-24 14:14:48,290] [INFO] Task started: Blastn
[2024-01-24 14:14:48,290] [INFO] Running command: blastn -query GCF_004339465.1_ASM433946v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfdac8c0e-a1cd-498e-a937-1e0c49713af0/dqc_reference/reference_markers.fasta -out GCF_004339465.1_ASM433946v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:14:49,228] [INFO] Task succeeded: Blastn
[2024-01-24 14:14:49,232] [INFO] Selected 12 target genomes.
[2024-01-24 14:14:49,233] [INFO] Target genome list was writen to GCF_004339465.1_ASM433946v1_genomic.fna/target_genomes.txt
[2024-01-24 14:14:49,245] [INFO] Task started: fastANI
[2024-01-24 14:14:49,245] [INFO] Running command: fastANI --query /var/lib/cwl/stgb77269b9-0c93-41c9-9eea-f185f35a77fe/GCF_004339465.1_ASM433946v1_genomic.fna.gz --refList GCF_004339465.1_ASM433946v1_genomic.fna/target_genomes.txt --output GCF_004339465.1_ASM433946v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:15:01,925] [INFO] Task succeeded: fastANI
[2024-01-24 14:15:01,925] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfdac8c0e-a1cd-498e-a937-1e0c49713af0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:15:01,926] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfdac8c0e-a1cd-498e-a937-1e0c49713af0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:15:01,944] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:15:01,944] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:15:01,944] [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
Ancylobacter aquaticus	strain=DSM 101	GCA_004339465.1	100	100	type	True	100.0	1605	1605	95	conclusive
Ancylobacter rudongensis	strain=CGMCC 1.1761	GCA_900100155.1	177413	177413	type	True	90.2977	1242	1605	95	below_threshold
Ancylobacter dichloromethanicus	strain=VKM B-2484	GCA_018390645.1	518825	518825	type	True	88.2345	1156	1605	95	below_threshold
Starkeya koreensis	strain=Jip08	GCA_023016525.1	266121	266121	type	True	85.4773	1013	1605	95	below_threshold
Starkeya novella	strain=DSM 506	GCA_000092925.1	921	921	type	True	84.8724	1048	1605	95	below_threshold
Ancylobacter oerskovii	strain=CCM 7435	GCA_018390555.1	459519	459519	type	True	83.1667	957	1605	95	below_threshold
Bradyrhizobium acaciae	strain=10BB	GCA_020889785.1	2683706	2683706	type	True	77.3561	384	1605	95	below_threshold
Methylobacterium oryzihabitans	strain=TER-1	GCA_004004555.2	2499852	2499852	type	True	77.2488	452	1605	95	below_threshold
Methylobacterium crusticola	strain=KCTC 52305	GCA_022179145.1	1697972	1697972	type	True	76.8812	433	1605	95	below_threshold
Aureimonas phyllosphaerae	strain=DSM 25024	GCA_014196405.1	1166078	1166078	type	True	76.8599	283	1605	95	below_threshold
Afifella aestuarii	strain=JA968	GCA_004023665.1	1909496	1909496	type	True	76.7824	168	1605	95	below_threshold
Thermaurantiacus tibetensis	strain=SYSU G02173	GCA_015354055.1	2759035	2759035	type	True	75.6648	138	1605	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:15:01,946] [INFO] DFAST Taxonomy check result was written to GCF_004339465.1_ASM433946v1_genomic.fna/tc_result.tsv
[2024-01-24 14:15:01,947] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:15:01,947] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:15:01,947] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfdac8c0e-a1cd-498e-a937-1e0c49713af0/dqc_reference/checkm_data
[2024-01-24 14:15:01,948] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:15:01,994] [INFO] Task started: CheckM
[2024-01-24 14:15:01,994] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004339465.1_ASM433946v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004339465.1_ASM433946v1_genomic.fna/checkm_input GCF_004339465.1_ASM433946v1_genomic.fna/checkm_result
[2024-01-24 14:15:48,970] [INFO] Task succeeded: CheckM
[2024-01-24 14:15:48,971] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:15:48,990] [INFO] ===== Completeness check finished =====
[2024-01-24 14:15:48,991] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:15:48,991] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004339465.1_ASM433946v1_genomic.fna/markers.fasta)
[2024-01-24 14:15:48,991] [INFO] Task started: Blastn
[2024-01-24 14:15:48,992] [INFO] Running command: blastn -query GCF_004339465.1_ASM433946v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfdac8c0e-a1cd-498e-a937-1e0c49713af0/dqc_reference/reference_markers_gtdb.fasta -out GCF_004339465.1_ASM433946v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:15:50,844] [INFO] Task succeeded: Blastn
[2024-01-24 14:15:50,847] [INFO] Selected 10 target genomes.
[2024-01-24 14:15:50,847] [INFO] Target genome list was writen to GCF_004339465.1_ASM433946v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:15:50,850] [INFO] Task started: fastANI
[2024-01-24 14:15:50,850] [INFO] Running command: fastANI --query /var/lib/cwl/stgb77269b9-0c93-41c9-9eea-f185f35a77fe/GCF_004339465.1_ASM433946v1_genomic.fna.gz --refList GCF_004339465.1_ASM433946v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004339465.1_ASM433946v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:16:01,379] [INFO] Task succeeded: fastANI
[2024-01-24 14:16:01,389] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:16:01,389] [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_004339465.1	s__Ancylobacter aquaticus	100.0	1605	1605	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Ancylobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900100155.1	s__Ancylobacter rudongensis	90.3102	1241	1605	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Ancylobacter	95.0	96.36	96.36	0.88	0.88	2	-
GCA_000378025.1	s__Ancylobacter sp000378025	90.1887	1276	1605	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Ancylobacter	95.0	99.99	99.99	1.00	1.00	2	-
GCF_018390645.1	s__Ancylobacter dichloromethanicus	88.2413	1155	1605	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Ancylobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009223885.1	s__Ancylobacter sp009223885	85.8616	979	1605	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Ancylobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000092925.1	s__Starkeya novella	84.8861	1046	1605	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	84.7947	1029	1605	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Starkeya	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900113065.1	s__Aureimonas phyllosphaerae	76.7832	290	1605	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aureimonas	95.0	99.99	99.99	0.99	0.99	3	-
GCF_004023665.1	s__Afifella aestuarii	76.7546	170	1605	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Afifellaceae;g__Afifella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015354055.1	s__Thermaurantiacus tibetensis	75.6648	138	1605	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Thermaurantiacus	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:16:01,391] [INFO] GTDB search result was written to GCF_004339465.1_ASM433946v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:16:01,391] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:16:01,395] [INFO] DFAST_QC result json was written to GCF_004339465.1_ASM433946v1_genomic.fna/dqc_result.json
[2024-01-24 14:16:01,396] [INFO] DFAST_QC completed!
[2024-01-24 14:16:01,396] [INFO] Total running time: 0h1m29s