[2024-01-25 19:49:20,515] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:49:20,517] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:49:20,517] [INFO] DQC Reference Directory: /var/lib/cwl/stg79364b8f-7bb8-4bac-8c56-0a3be489d3bf/dqc_reference
[2024-01-25 19:49:21,640] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:49:21,640] [INFO] Task started: Prodigal
[2024-01-25 19:49:21,640] [INFO] Running command: gunzip -c /var/lib/cwl/stg334e1065-2be1-4ed8-b148-9ed86e4dc49c/GCF_025995085.1_ASM2599508v1_genomic.fna.gz | prodigal -d GCF_025995085.1_ASM2599508v1_genomic.fna/cds.fna -a GCF_025995085.1_ASM2599508v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:49:28,970] [INFO] Task succeeded: Prodigal
[2024-01-25 19:49:28,971] [INFO] Task started: HMMsearch
[2024-01-25 19:49:28,971] [INFO] Running command: hmmsearch --tblout GCF_025995085.1_ASM2599508v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg79364b8f-7bb8-4bac-8c56-0a3be489d3bf/dqc_reference/reference_markers.hmm GCF_025995085.1_ASM2599508v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:49:29,220] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:49:29,221] [INFO] Found 6/6 markers.
[2024-01-25 19:49:29,278] [INFO] Query marker FASTA was written to GCF_025995085.1_ASM2599508v1_genomic.fna/markers.fasta
[2024-01-25 19:49:29,278] [INFO] Task started: Blastn
[2024-01-25 19:49:29,278] [INFO] Running command: blastn -query GCF_025995085.1_ASM2599508v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg79364b8f-7bb8-4bac-8c56-0a3be489d3bf/dqc_reference/reference_markers.fasta -out GCF_025995085.1_ASM2599508v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:49:30,107] [INFO] Task succeeded: Blastn
[2024-01-25 19:49:30,113] [INFO] Selected 13 target genomes.
[2024-01-25 19:49:30,113] [INFO] Target genome list was writen to GCF_025995085.1_ASM2599508v1_genomic.fna/target_genomes.txt
[2024-01-25 19:49:30,127] [INFO] Task started: fastANI
[2024-01-25 19:49:30,128] [INFO] Running command: fastANI --query /var/lib/cwl/stg334e1065-2be1-4ed8-b148-9ed86e4dc49c/GCF_025995085.1_ASM2599508v1_genomic.fna.gz --refList GCF_025995085.1_ASM2599508v1_genomic.fna/target_genomes.txt --output GCF_025995085.1_ASM2599508v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:49:38,494] [INFO] Task succeeded: fastANI
[2024-01-25 19:49:38,495] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg79364b8f-7bb8-4bac-8c56-0a3be489d3bf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:49:38,495] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg79364b8f-7bb8-4bac-8c56-0a3be489d3bf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:49:38,509] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:49:38,509] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:49:38,509] [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
Gluconobacter roseus	strain=NBRC 3990	GCA_006538885.1	586239	586239	type	True	99.9963	933	935	95	conclusive
Gluconobacter vitians	strain=LMG 31484	GCA_015244565.1	2728102	2728102	type	True	93.07	788	935	95	below_threshold
Gluconobacter oxydans	strain=NBRC 14819	GCA_006539685.1	442	442	type	True	90.3206	708	935	95	below_threshold
Gluconobacter oxydans	strain=DSM 3503	GCA_004346605.1	442	442	type	True	90.277	723	935	95	below_threshold
Gluconobacter oxydans	strain=LMG1408	GCA_015244575.1	442	442	type	True	90.2747	726	935	95	below_threshold
Gluconobacter potus	strain=R-71646	GCA_015244705.1	2724927	2724927	type	True	89.6734	763	935	95	below_threshold
Gluconobacter potus	strain=LMG 1764	GCA_001580675.1	2724927	2724927	type	True	89.6239	744	935	95	below_threshold
Gluconobacter aidae	strain=AC10	GCA_009547075.1	2662454	2662454	type	True	88.6832	711	935	95	below_threshold
Gluconobacter sphaericus	strain=NBRC 12467	GCA_006539125.1	574987	574987	type	True	87.162	684	935	95	below_threshold
Gluconobacter sphaericus	strain=LMG1414	GCA_015244605.1	574987	574987	type	True	87.0537	695	935	95	below_threshold
Acetobacter garciniae	strain=TBRC 12339	GCA_017377735.1	2817435	2817435	type	True	77.2225	136	935	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:49:38,510] [INFO] DFAST Taxonomy check result was written to GCF_025995085.1_ASM2599508v1_genomic.fna/tc_result.tsv
[2024-01-25 19:49:38,511] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:49:38,511] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:49:38,511] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg79364b8f-7bb8-4bac-8c56-0a3be489d3bf/dqc_reference/checkm_data
[2024-01-25 19:49:38,512] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:49:38,541] [INFO] Task started: CheckM
[2024-01-25 19:49:38,542] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025995085.1_ASM2599508v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025995085.1_ASM2599508v1_genomic.fna/checkm_input GCF_025995085.1_ASM2599508v1_genomic.fna/checkm_result
[2024-01-25 19:50:04,090] [INFO] Task succeeded: CheckM
[2024-01-25 19:50:04,090] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:50:04,103] [INFO] ===== Completeness check finished =====
[2024-01-25 19:50:04,103] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:50:04,104] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025995085.1_ASM2599508v1_genomic.fna/markers.fasta)
[2024-01-25 19:50:04,104] [INFO] Task started: Blastn
[2024-01-25 19:50:04,104] [INFO] Running command: blastn -query GCF_025995085.1_ASM2599508v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg79364b8f-7bb8-4bac-8c56-0a3be489d3bf/dqc_reference/reference_markers_gtdb.fasta -out GCF_025995085.1_ASM2599508v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:50:05,631] [INFO] Task succeeded: Blastn
[2024-01-25 19:50:05,635] [INFO] Selected 7 target genomes.
[2024-01-25 19:50:05,635] [INFO] Target genome list was writen to GCF_025995085.1_ASM2599508v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:50:05,650] [INFO] Task started: fastANI
[2024-01-25 19:50:05,650] [INFO] Running command: fastANI --query /var/lib/cwl/stg334e1065-2be1-4ed8-b148-9ed86e4dc49c/GCF_025995085.1_ASM2599508v1_genomic.fna.gz --refList GCF_025995085.1_ASM2599508v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025995085.1_ASM2599508v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:50:10,827] [INFO] Task succeeded: fastANI
[2024-01-25 19:50:10,833] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:50:10,833] [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_006538885.1	s__Gluconobacter roseus	99.9963	933	935	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconobacter	95.0	99.99	99.99	1.00	1.00	2	conclusive
GCF_015244565.1	s__Gluconobacter vitians	93.0866	787	935	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006539685.1	s__Gluconobacter oxydans	90.3312	708	935	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconobacter	95.0	98.14	96.18	0.93	0.85	13	-
GCF_001580675.1	s__Gluconobacter potus	89.6387	743	935	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconobacter	95.0	96.92	96.89	0.82	0.80	7	-
GCF_018811945.1	s__Gluconobacter sp018811945	89.3797	749	935	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009547075.1	s__Gluconobacter sp009547075	88.6832	711	935	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006539125.1	s__Gluconobacter sphaericus	87.1806	683	935	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconobacter	95.0	98.91	98.17	0.94	0.92	6	-
--------------------------------------------------------------------------------
[2024-01-25 19:50:10,835] [INFO] GTDB search result was written to GCF_025995085.1_ASM2599508v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:50:10,835] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:50:10,838] [INFO] DFAST_QC result json was written to GCF_025995085.1_ASM2599508v1_genomic.fna/dqc_result.json
[2024-01-25 19:50:10,838] [INFO] DFAST_QC completed!
[2024-01-25 19:50:10,838] [INFO] Total running time: 0h0m50s