[2024-01-24 10:47:09,048] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:47:09,060] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:47:09,060] [INFO] DQC Reference Directory: /var/lib/cwl/stg5979f468-1f25-462f-9b38-a980897e2066/dqc_reference
[2024-01-24 10:47:11,831] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:47:11,906] [INFO] Task started: Prodigal
[2024-01-24 10:47:11,907] [INFO] Running command: gunzip -c /var/lib/cwl/stg265e6806-a050-45a5-9427-2c21896e8f9c/GCF_006539685.1_ASM653968v1_genomic.fna.gz | prodigal -d GCF_006539685.1_ASM653968v1_genomic.fna/cds.fna -a GCF_006539685.1_ASM653968v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:47:19,418] [INFO] Task succeeded: Prodigal
[2024-01-24 10:47:19,419] [INFO] Task started: HMMsearch
[2024-01-24 10:47:19,419] [INFO] Running command: hmmsearch --tblout GCF_006539685.1_ASM653968v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5979f468-1f25-462f-9b38-a980897e2066/dqc_reference/reference_markers.hmm GCF_006539685.1_ASM653968v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:47:19,665] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:47:19,667] [INFO] Found 6/6 markers.
[2024-01-24 10:47:19,700] [INFO] Query marker FASTA was written to GCF_006539685.1_ASM653968v1_genomic.fna/markers.fasta
[2024-01-24 10:47:19,701] [INFO] Task started: Blastn
[2024-01-24 10:47:19,701] [INFO] Running command: blastn -query GCF_006539685.1_ASM653968v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5979f468-1f25-462f-9b38-a980897e2066/dqc_reference/reference_markers.fasta -out GCF_006539685.1_ASM653968v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:47:20,555] [INFO] Task succeeded: Blastn
[2024-01-24 10:47:20,560] [INFO] Selected 11 target genomes.
[2024-01-24 10:47:20,560] [INFO] Target genome list was writen to GCF_006539685.1_ASM653968v1_genomic.fna/target_genomes.txt
[2024-01-24 10:47:20,652] [INFO] Task started: fastANI
[2024-01-24 10:47:20,652] [INFO] Running command: fastANI --query /var/lib/cwl/stg265e6806-a050-45a5-9427-2c21896e8f9c/GCF_006539685.1_ASM653968v1_genomic.fna.gz --refList GCF_006539685.1_ASM653968v1_genomic.fna/target_genomes.txt --output GCF_006539685.1_ASM653968v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:47:28,432] [INFO] Task succeeded: fastANI
[2024-01-24 10:47:28,433] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5979f468-1f25-462f-9b38-a980897e2066/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:47:28,433] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5979f468-1f25-462f-9b38-a980897e2066/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:47:28,443] [INFO] Found 11 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 10:47:28,443] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:47:28,443] [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 oxydans	strain=NBRC 14819	GCA_006539685.1	442	442	type	True	100.0	858	859	95	conclusive
Gluconobacter oxydans	strain=LMG1408	GCA_015244575.1	442	442	type	True	99.9928	858	859	95	conclusive
Gluconobacter oxydans	strain=DSM 3503	GCA_004346605.1	442	442	type	True	99.9669	859	859	95	conclusive
Gluconobacter potus	strain=LMG 1764	GCA_001580675.1	2724927	2724927	type	True	94.731	771	859	95	below_threshold
Gluconobacter potus	strain=R-71646	GCA_015244705.1	2724927	2724927	type	True	94.6017	768	859	95	below_threshold
Gluconobacter aidae	strain=AC10	GCA_009547075.1	2662454	2662454	type	True	92.4668	723	859	95	below_threshold
Gluconobacter sphaericus	strain=NBRC 12467	GCA_006539125.1	574987	574987	type	True	90.649	725	859	95	below_threshold
Gluconobacter vitians	strain=LMG 31484	GCA_015244565.1	2728102	2728102	type	True	90.5223	742	859	95	below_threshold
Asaia lannensis	strain=NBRC 102526	GCA_024054035.1	415421	415421	type	True	77.7801	179	859	95	below_threshold
Acetobacter garciniae	strain=TBRC 12339	GCA_017377735.1	2817435	2817435	type	True	77.0876	142	859	95	below_threshold
Roseococcus pinisoli	strain=XZZS9	GCA_018413645.1	2835040	2835040	type	True	76.4364	87	859	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:47:28,445] [INFO] DFAST Taxonomy check result was written to GCF_006539685.1_ASM653968v1_genomic.fna/tc_result.tsv
[2024-01-24 10:47:28,445] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:47:28,445] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:47:28,446] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5979f468-1f25-462f-9b38-a980897e2066/dqc_reference/checkm_data
[2024-01-24 10:47:28,447] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:47:28,473] [INFO] Task started: CheckM
[2024-01-24 10:47:28,473] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_006539685.1_ASM653968v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_006539685.1_ASM653968v1_genomic.fna/checkm_input GCF_006539685.1_ASM653968v1_genomic.fna/checkm_result
[2024-01-24 10:47:56,912] [INFO] Task succeeded: CheckM
[2024-01-24 10:47:56,913] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:47:56,930] [INFO] ===== Completeness check finished =====
[2024-01-24 10:47:56,930] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:47:56,931] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_006539685.1_ASM653968v1_genomic.fna/markers.fasta)
[2024-01-24 10:47:56,931] [INFO] Task started: Blastn
[2024-01-24 10:47:56,931] [INFO] Running command: blastn -query GCF_006539685.1_ASM653968v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5979f468-1f25-462f-9b38-a980897e2066/dqc_reference/reference_markers_gtdb.fasta -out GCF_006539685.1_ASM653968v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:47:58,363] [INFO] Task succeeded: Blastn
[2024-01-24 10:47:58,367] [INFO] Selected 7 target genomes.
[2024-01-24 10:47:58,367] [INFO] Target genome list was writen to GCF_006539685.1_ASM653968v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:47:58,412] [INFO] Task started: fastANI
[2024-01-24 10:47:58,413] [INFO] Running command: fastANI --query /var/lib/cwl/stg265e6806-a050-45a5-9427-2c21896e8f9c/GCF_006539685.1_ASM653968v1_genomic.fna.gz --refList GCF_006539685.1_ASM653968v1_genomic.fna/target_genomes_gtdb.txt --output GCF_006539685.1_ASM653968v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:48:04,013] [INFO] Task succeeded: fastANI
[2024-01-24 10:48:04,020] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:48:04,021] [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_006539685.1	s__Gluconobacter oxydans	100.0	858	859	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconobacter	95.0	98.14	96.18	0.93	0.85	13	conclusive
GCF_001580675.1	s__Gluconobacter potus	94.7049	772	859	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	93.5966	784	859	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	92.4637	724	859	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	90.649	725	859	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconobacter	95.0	98.91	98.17	0.94	0.92	6	-
GCF_015244565.1	s__Gluconobacter vitians	90.5223	742	859	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006538885.1	s__Gluconobacter roseus	90.3804	711	859	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconobacter	95.0	99.99	99.99	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 10:48:04,022] [INFO] GTDB search result was written to GCF_006539685.1_ASM653968v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:48:04,023] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:48:04,026] [INFO] DFAST_QC result json was written to GCF_006539685.1_ASM653968v1_genomic.fna/dqc_result.json
[2024-01-24 10:48:04,026] [INFO] DFAST_QC completed!
[2024-01-24 10:48:04,026] [INFO] Total running time: 0h0m55s