[2024-01-24 14:22:17,392] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:22:17,394] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:22:17,395] [INFO] DQC Reference Directory: /var/lib/cwl/stg8ec42a74-fd5f-4adf-8525-8cafe61e2d91/dqc_reference
[2024-01-24 14:22:18,634] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:22:18,635] [INFO] Task started: Prodigal
[2024-01-24 14:22:18,635] [INFO] Running command: gunzip -c /var/lib/cwl/stg52e5f999-26ee-4b31-a412-5ed87ac6d300/GCF_003667445.1_ASM366744v1_genomic.fna.gz | prodigal -d GCF_003667445.1_ASM366744v1_genomic.fna/cds.fna -a GCF_003667445.1_ASM366744v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:22:33,540] [INFO] Task succeeded: Prodigal
[2024-01-24 14:22:33,541] [INFO] Task started: HMMsearch
[2024-01-24 14:22:33,541] [INFO] Running command: hmmsearch --tblout GCF_003667445.1_ASM366744v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8ec42a74-fd5f-4adf-8525-8cafe61e2d91/dqc_reference/reference_markers.hmm GCF_003667445.1_ASM366744v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:22:33,853] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:22:33,854] [INFO] Found 6/6 markers.
[2024-01-24 14:22:33,904] [INFO] Query marker FASTA was written to GCF_003667445.1_ASM366744v1_genomic.fna/markers.fasta
[2024-01-24 14:22:33,904] [INFO] Task started: Blastn
[2024-01-24 14:22:33,905] [INFO] Running command: blastn -query GCF_003667445.1_ASM366744v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8ec42a74-fd5f-4adf-8525-8cafe61e2d91/dqc_reference/reference_markers.fasta -out GCF_003667445.1_ASM366744v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:22:34,846] [INFO] Task succeeded: Blastn
[2024-01-24 14:22:34,853] [INFO] Selected 8 target genomes.
[2024-01-24 14:22:34,853] [INFO] Target genome list was writen to GCF_003667445.1_ASM366744v1_genomic.fna/target_genomes.txt
[2024-01-24 14:22:34,860] [INFO] Task started: fastANI
[2024-01-24 14:22:34,860] [INFO] Running command: fastANI --query /var/lib/cwl/stg52e5f999-26ee-4b31-a412-5ed87ac6d300/GCF_003667445.1_ASM366744v1_genomic.fna.gz --refList GCF_003667445.1_ASM366744v1_genomic.fna/target_genomes.txt --output GCF_003667445.1_ASM366744v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:22:45,438] [INFO] Task succeeded: fastANI
[2024-01-24 14:22:45,439] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8ec42a74-fd5f-4adf-8525-8cafe61e2d91/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:22:45,439] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8ec42a74-fd5f-4adf-8525-8cafe61e2d91/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:22:45,452] [INFO] Found 8 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:22:45,452] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:22:45,452] [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
Xanthobacter tagetidis	strain=ATCC 700314	GCA_003667445.1	60216	60216	type	True	100.0	1617	1621	95	conclusive
Xanthobacter tagetidis	strain=DSM 11105	GCA_014206845.1	60216	60216	type	True	99.9986	1613	1621	95	conclusive
Xanthobacter dioxanivorans	strain=YN2	GCA_016807805.1	2528964	2528964	type	True	83.3957	957	1621	95	below_threshold
Xanthobacter aminoxidans	strain=ATCC BAA-299	GCA_023571765.1	186280	186280	type	True	83.2729	957	1621	95	below_threshold
Xanthobacter oligotrophicus	strain=29k	GCA_008364685.1	2607286	2607286	type	True	82.8959	896	1621	95	below_threshold
Xanthobacter autotrophicus	strain=DSM 432	GCA_005871085.1	280	280	type	True	82.8436	867	1621	95	below_threshold
Xanthobacter agilis	strain=LMG 16336	GCA_021730435.1	47492	47492	type	True	81.3549	777	1621	95	below_threshold
Starkeya koreensis	strain=Jip08	GCA_023016525.1	266121	266121	type	True	79.3043	609	1621	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:22:45,454] [INFO] DFAST Taxonomy check result was written to GCF_003667445.1_ASM366744v1_genomic.fna/tc_result.tsv
[2024-01-24 14:22:45,454] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:22:45,455] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:22:45,455] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8ec42a74-fd5f-4adf-8525-8cafe61e2d91/dqc_reference/checkm_data
[2024-01-24 14:22:45,456] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:22:45,515] [INFO] Task started: CheckM
[2024-01-24 14:22:45,515] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003667445.1_ASM366744v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003667445.1_ASM366744v1_genomic.fna/checkm_input GCF_003667445.1_ASM366744v1_genomic.fna/checkm_result
[2024-01-24 14:23:38,892] [INFO] Task succeeded: CheckM
[2024-01-24 14:23:38,894] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:23:38,919] [INFO] ===== Completeness check finished =====
[2024-01-24 14:23:38,919] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:23:38,920] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003667445.1_ASM366744v1_genomic.fna/markers.fasta)
[2024-01-24 14:23:38,920] [INFO] Task started: Blastn
[2024-01-24 14:23:38,920] [INFO] Running command: blastn -query GCF_003667445.1_ASM366744v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8ec42a74-fd5f-4adf-8525-8cafe61e2d91/dqc_reference/reference_markers_gtdb.fasta -out GCF_003667445.1_ASM366744v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:23:40,697] [INFO] Task succeeded: Blastn
[2024-01-24 14:23:40,701] [INFO] Selected 10 target genomes.
[2024-01-24 14:23:40,702] [INFO] Target genome list was writen to GCF_003667445.1_ASM366744v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:23:40,709] [INFO] Task started: fastANI
[2024-01-24 14:23:40,709] [INFO] Running command: fastANI --query /var/lib/cwl/stg52e5f999-26ee-4b31-a412-5ed87ac6d300/GCF_003667445.1_ASM366744v1_genomic.fna.gz --refList GCF_003667445.1_ASM366744v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003667445.1_ASM366744v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:23:54,482] [INFO] Task succeeded: fastANI
[2024-01-24 14:23:54,494] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:23:54,495] [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_003667445.1	s__Xanthobacter tagetidis	100.0	1617	1621	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Xanthobacter	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_000702385.1	s__Xanthobacter sp000702385	83.4335	967	1621	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Xanthobacter	95.0	96.09	96.09	0.89	0.89	2	-
GCF_016807805.1	s__Xanthobacter sp016807805	83.3808	958	1621	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Xanthobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017875275.1	s__Xanthobacter flavus	83.0951	946	1621	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Xanthobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012932745.1	s__Xanthobacter sp012932745	82.9915	959	1621	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Xanthobacter	95.0	97.23	97.23	0.90	0.90	2	-
GCF_012275355.1	s__Xanthobacter sp012275355	82.9181	927	1621	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Xanthobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_008364685.1	s__Xanthobacter sp008364685	82.849	903	1621	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	82.8416	887	1621	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Xanthobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005871085.1	s__Xanthobacter autotrophicus_A	82.8083	870	1621	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Xanthobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000473085.1	s__Azorhizobium doebereinerae	81.4085	851	1621	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Azorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:23:54,496] [INFO] GTDB search result was written to GCF_003667445.1_ASM366744v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:23:54,497] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:23:54,500] [INFO] DFAST_QC result json was written to GCF_003667445.1_ASM366744v1_genomic.fna/dqc_result.json
[2024-01-24 14:23:54,501] [INFO] DFAST_QC completed!
[2024-01-24 14:23:54,501] [INFO] Total running time: 0h1m37s