[2024-01-25 19:10:05,530] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:10:05,531] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:10:05,531] [INFO] DQC Reference Directory: /var/lib/cwl/stg30936154-976e-487b-a128-7123a57a2fc2/dqc_reference
[2024-01-25 19:10:06,659] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:10:06,660] [INFO] Task started: Prodigal
[2024-01-25 19:10:06,660] [INFO] Running command: gunzip -c /var/lib/cwl/stgbfa2af82-6025-473d-9dad-7ac68ae25098/GCF_000473085.1_ASM47308v1_genomic.fna.gz | prodigal -d GCF_000473085.1_ASM47308v1_genomic.fna/cds.fna -a GCF_000473085.1_ASM47308v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:10:22,527] [INFO] Task succeeded: Prodigal
[2024-01-25 19:10:22,527] [INFO] Task started: HMMsearch
[2024-01-25 19:10:22,527] [INFO] Running command: hmmsearch --tblout GCF_000473085.1_ASM47308v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg30936154-976e-487b-a128-7123a57a2fc2/dqc_reference/reference_markers.hmm GCF_000473085.1_ASM47308v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:10:22,851] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:10:22,852] [INFO] Found 6/6 markers.
[2024-01-25 19:10:22,897] [INFO] Query marker FASTA was written to GCF_000473085.1_ASM47308v1_genomic.fna/markers.fasta
[2024-01-25 19:10:22,897] [INFO] Task started: Blastn
[2024-01-25 19:10:22,897] [INFO] Running command: blastn -query GCF_000473085.1_ASM47308v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg30936154-976e-487b-a128-7123a57a2fc2/dqc_reference/reference_markers.fasta -out GCF_000473085.1_ASM47308v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:10:23,867] [INFO] Task succeeded: Blastn
[2024-01-25 19:10:23,872] [INFO] Selected 12 target genomes.
[2024-01-25 19:10:23,872] [INFO] Target genome list was writen to GCF_000473085.1_ASM47308v1_genomic.fna/target_genomes.txt
[2024-01-25 19:10:23,889] [INFO] Task started: fastANI
[2024-01-25 19:10:23,889] [INFO] Running command: fastANI --query /var/lib/cwl/stgbfa2af82-6025-473d-9dad-7ac68ae25098/GCF_000473085.1_ASM47308v1_genomic.fna.gz --refList GCF_000473085.1_ASM47308v1_genomic.fna/target_genomes.txt --output GCF_000473085.1_ASM47308v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:10:39,158] [INFO] Task succeeded: fastANI
[2024-01-25 19:10:39,158] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg30936154-976e-487b-a128-7123a57a2fc2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:10:39,159] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg30936154-976e-487b-a128-7123a57a2fc2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:10:39,167] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:10:39,167] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:10:39,168] [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
Azorhizobium doebereinerae	strain=UFLA1-100	GCA_000473085.1	281091	281091	type	True	100.0	1889	1898	95	conclusive
Azorhizobium oxalatiphilum	strain=CCM 7897	GCA_014635325.1	980631	980631	type	True	84.8079	1321	1898	95	below_threshold
Azorhizobium caulinodans	strain=ORS 571	GCA_000010525.1	7	7	type	True	84.7288	1290	1898	95	below_threshold
Xanthobacter oligotrophicus	strain=29k	GCA_008364685.1	2607286	2607286	type	True	81.7211	931	1898	95	below_threshold
Xanthobacter aminoxidans	strain=ATCC BAA-299	GCA_023571765.1	186280	186280	type	True	81.5993	926	1898	95	below_threshold
Xanthobacter autotrophicus	strain=DSM 432	GCA_005871085.1	280	280	type	True	81.5464	869	1898	95	below_threshold
Xanthobacter dioxanivorans	strain=YN2	GCA_016807805.1	2528964	2528964	type	True	81.5103	932	1898	95	below_threshold
Xanthobacter tagetidis	strain=ATCC 700314	GCA_003667445.1	60216	60216	type	True	81.4885	842	1898	95	below_threshold
Xanthobacter tagetidis	strain=DSM 11105	GCA_014206845.1	60216	60216	type	True	81.4202	857	1898	95	below_threshold
Xanthobacter agilis	strain=LMG 16336	GCA_021730435.1	47492	47492	type	True	80.4588	748	1898	95	below_threshold
Starkeya novella	strain=DSM 506	GCA_000092925.1	921	921	type	True	79.4634	664	1898	95	below_threshold
Phreatobacter cathodiphilus	strain=S-12	GCA_003008515.1	1868589	1868589	type	True	77.8012	523	1898	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:10:39,169] [INFO] DFAST Taxonomy check result was written to GCF_000473085.1_ASM47308v1_genomic.fna/tc_result.tsv
[2024-01-25 19:10:39,170] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:10:39,170] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:10:39,170] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg30936154-976e-487b-a128-7123a57a2fc2/dqc_reference/checkm_data
[2024-01-25 19:10:39,171] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:10:39,225] [INFO] Task started: CheckM
[2024-01-25 19:10:39,225] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000473085.1_ASM47308v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000473085.1_ASM47308v1_genomic.fna/checkm_input GCF_000473085.1_ASM47308v1_genomic.fna/checkm_result
[2024-01-25 19:11:45,937] [INFO] Task succeeded: CheckM
[2024-01-25 19:11:45,938] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:11:45,959] [INFO] ===== Completeness check finished =====
[2024-01-25 19:11:45,959] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:11:45,960] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000473085.1_ASM47308v1_genomic.fna/markers.fasta)
[2024-01-25 19:11:45,961] [INFO] Task started: Blastn
[2024-01-25 19:11:45,961] [INFO] Running command: blastn -query GCF_000473085.1_ASM47308v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg30936154-976e-487b-a128-7123a57a2fc2/dqc_reference/reference_markers_gtdb.fasta -out GCF_000473085.1_ASM47308v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:11:47,669] [INFO] Task succeeded: Blastn
[2024-01-25 19:11:47,672] [INFO] Selected 15 target genomes.
[2024-01-25 19:11:47,672] [INFO] Target genome list was writen to GCF_000473085.1_ASM47308v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:11:47,695] [INFO] Task started: fastANI
[2024-01-25 19:11:47,695] [INFO] Running command: fastANI --query /var/lib/cwl/stgbfa2af82-6025-473d-9dad-7ac68ae25098/GCF_000473085.1_ASM47308v1_genomic.fna.gz --refList GCF_000473085.1_ASM47308v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000473085.1_ASM47308v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:12:06,982] [INFO] Task succeeded: fastANI
[2024-01-25 19:12:06,995] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:12:06,997] [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_000473085.1	s__Azorhizobium doebereinerae	100.0	1888	1898	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Azorhizobium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014635325.1	s__Azorhizobium oxalatiphilum	84.828	1318	1898	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Azorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000010525.1	s__Azorhizobium caulinodans	84.7838	1281	1898	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Azorhizobium	95.0	97.54	97.54	0.94	0.94	2	-
GCA_013911975.1	s__Aquabacter sp013911975	81.8826	844	1898	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Aquabacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008364685.1	s__Xanthobacter sp008364685	81.716	932	1898	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Xanthobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000702385.1	s__Xanthobacter sp000702385	81.5923	929	1898	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Xanthobacter	95.0	96.09	96.09	0.89	0.89	2	-
GCF_005871085.1	s__Xanthobacter autotrophicus_A	81.5161	872	1898	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Xanthobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000017645.1	s__Xanthobacter autotrophicus	81.5097	911	1898	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Xanthobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003993795.1	s__Aquabacter cavernae	81.4985	847	1898	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Aquabacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003667445.1	s__Xanthobacter tagetidis	81.4372	848	1898	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Xanthobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCA_002257205.1	s__NCEH01 sp002257205	81.4083	595	1898	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__NCEH01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017742835.1	s__Aquabacter sp017742835	81.3764	903	1898	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Aquabacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002279855.1	s__Aquabacter sp002279855	81.3015	620	1898	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Aquabacter	95.0	98.44	97.78	0.75	0.72	3	-
GCF_004346185.1	s__Aquabacter spiritensis	80.0447	760	1898	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Aquabacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:12:07,000] [INFO] GTDB search result was written to GCF_000473085.1_ASM47308v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:12:07,000] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:12:07,004] [INFO] DFAST_QC result json was written to GCF_000473085.1_ASM47308v1_genomic.fna/dqc_result.json
[2024-01-25 19:12:07,004] [INFO] DFAST_QC completed!
[2024-01-25 19:12:07,004] [INFO] Total running time: 0h2m1s