[2024-01-24 11:12:39,416] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:12:39,418] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:12:39,419] [INFO] DQC Reference Directory: /var/lib/cwl/stg71a810c5-7015-40c4-ab97-33d847399042/dqc_reference
[2024-01-24 11:12:40,903] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:12:40,904] [INFO] Task started: Prodigal
[2024-01-24 11:12:40,904] [INFO] Running command: gunzip -c /var/lib/cwl/stg80ea6a20-f9e4-4df3-9e23-7f00da430208/GCF_025994175.1_ASM2599417v1_genomic.fna.gz | prodigal -d GCF_025994175.1_ASM2599417v1_genomic.fna/cds.fna -a GCF_025994175.1_ASM2599417v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:12:50,622] [INFO] Task succeeded: Prodigal
[2024-01-24 11:12:50,622] [INFO] Task started: HMMsearch
[2024-01-24 11:12:50,623] [INFO] Running command: hmmsearch --tblout GCF_025994175.1_ASM2599417v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg71a810c5-7015-40c4-ab97-33d847399042/dqc_reference/reference_markers.hmm GCF_025994175.1_ASM2599417v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:12:50,905] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:12:50,906] [INFO] Found 6/6 markers.
[2024-01-24 11:12:50,940] [INFO] Query marker FASTA was written to GCF_025994175.1_ASM2599417v1_genomic.fna/markers.fasta
[2024-01-24 11:12:50,940] [INFO] Task started: Blastn
[2024-01-24 11:12:50,940] [INFO] Running command: blastn -query GCF_025994175.1_ASM2599417v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg71a810c5-7015-40c4-ab97-33d847399042/dqc_reference/reference_markers.fasta -out GCF_025994175.1_ASM2599417v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:12:51,667] [INFO] Task succeeded: Blastn
[2024-01-24 11:12:51,671] [INFO] Selected 16 target genomes.
[2024-01-24 11:12:51,672] [INFO] Target genome list was writen to GCF_025994175.1_ASM2599417v1_genomic.fna/target_genomes.txt
[2024-01-24 11:12:51,680] [INFO] Task started: fastANI
[2024-01-24 11:12:51,680] [INFO] Running command: fastANI --query /var/lib/cwl/stg80ea6a20-f9e4-4df3-9e23-7f00da430208/GCF_025994175.1_ASM2599417v1_genomic.fna.gz --refList GCF_025994175.1_ASM2599417v1_genomic.fna/target_genomes.txt --output GCF_025994175.1_ASM2599417v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:13:03,015] [INFO] Task succeeded: fastANI
[2024-01-24 11:13:03,016] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg71a810c5-7015-40c4-ab97-33d847399042/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:13:03,016] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg71a810c5-7015-40c4-ab97-33d847399042/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:13:03,034] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:13:03,034] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:13:03,034] [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
Asaia siamensis	strain=CCM 7132	GCA_014635085.1	110479	110479	type	True	99.999	1089	1089	95	conclusive
Asaia platycodi	strain=JCM 25414	GCA_000614545.1	610243	610243	type	True	85.6348	834	1089	95	below_threshold
Asaia prunellae	strain=JCM 25354	GCA_000613885.1	610245	610245	type	True	82.1186	647	1089	95	below_threshold
Asaia bogorensis	strain=NBRC 16594	GCA_001547995.1	91915	91915	suspected-type	True	82.0237	645	1089	95	below_threshold
Asaia bogorensis	strain=NBRC 16594	GCA_007989265.1	91915	91915	suspected-type	True	81.9665	649	1089	95	below_threshold
Asaia lannensis	strain=NBRC 102526	GCA_024054035.1	415421	415421	type	True	81.6794	642	1089	95	below_threshold
Asaia astilbis	strain=JCM 15831	GCA_000613845.1	610244	610244	type	True	81.0072	615	1089	95	below_threshold
Kozakia baliensis	strain=DSM 14400	GCA_001787335.1	153496	153496	type	True	78.1878	222	1089	95	below_threshold
Kozakia baliensis	strain=NBRC 16664	GCA_007989365.1	153496	153496	type	True	78.1562	217	1089	95	below_threshold
Gluconobacter kanchanaburiensis	strain=NBRC 103587	GCA_007988905.1	563199	563199	type	True	77.9119	152	1089	95	below_threshold
Gluconobacter cadivus	strain=LMG 1744	GCA_015244745.1	2728101	2728101	type	True	77.606	187	1089	95	below_threshold
Acetobacter garciniae	strain=TBRC 12339	GCA_017377735.1	2817435	2817435	type	True	77.2408	145	1089	95	below_threshold
Rhodovastum atsumiense	strain=G2-11	GCA_937425535.1	504468	504468	type	True	76.5425	106	1089	95	below_threshold
Acidiphilium iwatense	strain=KCTC 23505	GCA_021556475.1	768198	768198	type	True	76.0403	68	1089	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:13:03,037] [INFO] DFAST Taxonomy check result was written to GCF_025994175.1_ASM2599417v1_genomic.fna/tc_result.tsv
[2024-01-24 11:13:03,038] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:13:03,038] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:13:03,039] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg71a810c5-7015-40c4-ab97-33d847399042/dqc_reference/checkm_data
[2024-01-24 11:13:03,040] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:13:03,081] [INFO] Task started: CheckM
[2024-01-24 11:13:03,082] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025994175.1_ASM2599417v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025994175.1_ASM2599417v1_genomic.fna/checkm_input GCF_025994175.1_ASM2599417v1_genomic.fna/checkm_result
[2024-01-24 11:13:36,656] [INFO] Task succeeded: CheckM
[2024-01-24 11:13:36,658] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:13:36,678] [INFO] ===== Completeness check finished =====
[2024-01-24 11:13:36,678] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:13:36,678] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025994175.1_ASM2599417v1_genomic.fna/markers.fasta)
[2024-01-24 11:13:36,679] [INFO] Task started: Blastn
[2024-01-24 11:13:36,679] [INFO] Running command: blastn -query GCF_025994175.1_ASM2599417v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg71a810c5-7015-40c4-ab97-33d847399042/dqc_reference/reference_markers_gtdb.fasta -out GCF_025994175.1_ASM2599417v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:13:37,816] [INFO] Task succeeded: Blastn
[2024-01-24 11:13:37,819] [INFO] Selected 14 target genomes.
[2024-01-24 11:13:37,820] [INFO] Target genome list was writen to GCF_025994175.1_ASM2599417v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:13:37,831] [INFO] Task started: fastANI
[2024-01-24 11:13:37,831] [INFO] Running command: fastANI --query /var/lib/cwl/stg80ea6a20-f9e4-4df3-9e23-7f00da430208/GCF_025994175.1_ASM2599417v1_genomic.fna.gz --refList GCF_025994175.1_ASM2599417v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025994175.1_ASM2599417v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:13:47,958] [INFO] Task succeeded: fastANI
[2024-01-24 11:13:47,969] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:13:47,970] [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_014635085.1	s__Asaia siamensis	99.999	1089	1089	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Asaia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000614545.1	s__Asaia platycodi	85.6348	834	1089	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Asaia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000613885.1	s__Asaia prunellae	82.1073	648	1089	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Asaia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001547995.1	s__Asaia bogorensis	82.0354	644	1089	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Asaia	95.0	96.55	95.04	0.93	0.88	6	-
GCF_003994335.1	s__Asaia sp003994335	82.0295	665	1089	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Asaia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900465345.1	s__Asaia bogorensis_A	81.9899	642	1089	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Asaia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000613845.1	s__Asaia astilbis	81.0034	616	1089	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Asaia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007988945.1	s__Swaminathania salitolerans	80.404	485	1089	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Swaminathania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013376175.1	s__Ameyamaea chiangmaiensis	78.3882	157	1089	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Ameyamaea	95.0	99.99	99.99	0.99	0.99	2	-
GCF_001787335.1	s__Kozakia baliensis	78.1878	222	1089	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Kozakia	95.0	98.19	97.27	0.93	0.89	4	-
GCF_018256155.1	s__Gluconobacter sp018256155	77.7497	190	1089	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015244745.1	s__Gluconobacter cadivus	77.606	187	1089	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconobacter	95.0	96.53	96.31	0.92	0.90	5	-
--------------------------------------------------------------------------------
[2024-01-24 11:13:47,972] [INFO] GTDB search result was written to GCF_025994175.1_ASM2599417v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:13:47,977] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:13:47,982] [INFO] DFAST_QC result json was written to GCF_025994175.1_ASM2599417v1_genomic.fna/dqc_result.json
[2024-01-24 11:13:47,983] [INFO] DFAST_QC completed!
[2024-01-24 11:13:47,983] [INFO] Total running time: 0h1m9s