[2024-01-24 12:14:06,607] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:14:06,609] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:14:06,609] [INFO] DQC Reference Directory: /var/lib/cwl/stgcdd6748b-b569-4fba-8aa5-6f028ba88860/dqc_reference
[2024-01-24 12:14:07,890] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:14:07,891] [INFO] Task started: Prodigal
[2024-01-24 12:14:07,891] [INFO] Running command: gunzip -c /var/lib/cwl/stg69775db9-02cc-424a-bbf4-2346c8fac899/GCF_900217795.1_IMG-taxon_2740891832_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900217795.1_IMG-taxon_2740891832_annotated_assembly_genomic.fna/cds.fna -a GCF_900217795.1_IMG-taxon_2740891832_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:14:15,800] [INFO] Task succeeded: Prodigal
[2024-01-24 12:14:15,800] [INFO] Task started: HMMsearch
[2024-01-24 12:14:15,800] [INFO] Running command: hmmsearch --tblout GCF_900217795.1_IMG-taxon_2740891832_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcdd6748b-b569-4fba-8aa5-6f028ba88860/dqc_reference/reference_markers.hmm GCF_900217795.1_IMG-taxon_2740891832_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:14:16,176] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:14:16,178] [INFO] Found 6/6 markers.
[2024-01-24 12:14:16,210] [INFO] Query marker FASTA was written to GCF_900217795.1_IMG-taxon_2740891832_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 12:14:16,210] [INFO] Task started: Blastn
[2024-01-24 12:14:16,211] [INFO] Running command: blastn -query GCF_900217795.1_IMG-taxon_2740891832_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgcdd6748b-b569-4fba-8aa5-6f028ba88860/dqc_reference/reference_markers.fasta -out GCF_900217795.1_IMG-taxon_2740891832_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:14:16,816] [INFO] Task succeeded: Blastn
[2024-01-24 12:14:16,819] [INFO] Selected 19 target genomes.
[2024-01-24 12:14:16,819] [INFO] Target genome list was writen to GCF_900217795.1_IMG-taxon_2740891832_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 12:14:16,827] [INFO] Task started: fastANI
[2024-01-24 12:14:16,828] [INFO] Running command: fastANI --query /var/lib/cwl/stg69775db9-02cc-424a-bbf4-2346c8fac899/GCF_900217795.1_IMG-taxon_2740891832_annotated_assembly_genomic.fna.gz --refList GCF_900217795.1_IMG-taxon_2740891832_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900217795.1_IMG-taxon_2740891832_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:14:29,216] [INFO] Task succeeded: fastANI
[2024-01-24 12:14:29,216] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcdd6748b-b569-4fba-8aa5-6f028ba88860/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:14:29,217] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcdd6748b-b569-4fba-8aa5-6f028ba88860/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:14:29,231] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:14:29,232] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:14:29,232] [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
Ureibacillus chungkukjangi	strain=2RL32	GCA_003049615.1	1202712	1202712	type	True	79.5025	394	1336	95	below_threshold
Ureibacillus chungkukjangi	strain=KACC 16626	GCA_003217295.1	1202712	1202712	type	True	79.436	383	1336	95	below_threshold
Ureibacillus sinduriensis	strain=JCM 15800	GCA_002200845.1	561440	561440	type	True	79.2493	329	1336	95	below_threshold
Ureibacillus sinduriensis	strain=JCM 15800	GCA_000772955.1	561440	561440	type	True	79.2477	329	1336	95	below_threshold
Lysinibacillus composti	strain=MCCC 1A13240	GCA_003856865.1	720633	720633	type	True	79.2262	383	1336	95	below_threshold
Lysinibacillus composti	strain=DSM 24785	GCA_016908465.1	720633	720633	type	True	79.2045	385	1336	95	below_threshold
Ureibacillus acetophenoni	strain=JC23	GCA_900220965.1	614649	614649	type	True	78.9051	366	1336	95	below_threshold
Ureibacillus massiliensis	strain=CCUG 49529	GCA_000772965.1	292806	292806	type	True	78.8787	349	1336	95	below_threshold
Ureibacillus massiliensis	strain=4400831	GCA_002200855.1	292806	292806	type	True	78.8787	349	1336	95	below_threshold
Lysinibacillus varians	strain=NBRC 109424	GCA_005217815.1	1145276	1145276	suspected-type	True	78.5062	225	1336	95	below_threshold
Ureibacillus manganicus	strain=DSM 26584	GCA_002200865.1	1266064	1266064	type	True	78.4681	358	1336	95	below_threshold
Lysinibacillus tabacifolii	strain=KCTC 33042	GCA_005217585.1	1173107	1173107	suspected-type	True	78.4634	226	1336	95	below_threshold
Ureibacillus manganicus	strain=DSM 26584	GCA_000772945.1	1266064	1266064	type	True	78.4456	360	1336	95	below_threshold
Lysinibacillus varians	strain=GY32	GCA_000600105.1	1145276	1145276	suspected-type	True	78.4089	233	1336	95	below_threshold
Lysinibacillus mangiferihumi	strain=CCTCC AB 2010389	GCA_005217845.1	1130819	1130819	type	True	78.2923	223	1336	95	below_threshold
Lysinibacillus mangiferihumi	strain=M-GX18	GCA_003049665.1	1130819	1130819	type	True	78.1944	227	1336	95	below_threshold
Solibacillus faecavium	strain=A46	GCA_014836905.1	2762221	2762221	type	True	78.1096	208	1336	95	below_threshold
Lysinibacillus contaminans	strain=DSM 25560	GCA_001278945.1	1293441	1293441	type	True	77.5093	197	1336	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:14:29,234] [INFO] DFAST Taxonomy check result was written to GCF_900217795.1_IMG-taxon_2740891832_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 12:14:29,235] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:14:29,235] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:14:29,236] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcdd6748b-b569-4fba-8aa5-6f028ba88860/dqc_reference/checkm_data
[2024-01-24 12:14:29,237] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:14:29,280] [INFO] Task started: CheckM
[2024-01-24 12:14:29,280] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900217795.1_IMG-taxon_2740891832_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900217795.1_IMG-taxon_2740891832_annotated_assembly_genomic.fna/checkm_input GCF_900217795.1_IMG-taxon_2740891832_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 12:15:00,136] [INFO] Task succeeded: CheckM
[2024-01-24 12:15:00,138] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:15:00,154] [INFO] ===== Completeness check finished =====
[2024-01-24 12:15:00,154] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:15:00,155] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900217795.1_IMG-taxon_2740891832_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 12:15:00,155] [INFO] Task started: Blastn
[2024-01-24 12:15:00,155] [INFO] Running command: blastn -query GCF_900217795.1_IMG-taxon_2740891832_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgcdd6748b-b569-4fba-8aa5-6f028ba88860/dqc_reference/reference_markers_gtdb.fasta -out GCF_900217795.1_IMG-taxon_2740891832_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:00,978] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:00,982] [INFO] Selected 11 target genomes.
[2024-01-24 12:15:00,982] [INFO] Target genome list was writen to GCF_900217795.1_IMG-taxon_2740891832_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:15:00,992] [INFO] Task started: fastANI
[2024-01-24 12:15:00,992] [INFO] Running command: fastANI --query /var/lib/cwl/stg69775db9-02cc-424a-bbf4-2346c8fac899/GCF_900217795.1_IMG-taxon_2740891832_annotated_assembly_genomic.fna.gz --refList GCF_900217795.1_IMG-taxon_2740891832_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900217795.1_IMG-taxon_2740891832_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:15:09,919] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:09,939] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:15:09,939] [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_900217795.1	s__Ureibacillus xyleni	100.0	1335	1336	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Ureibacillus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003628435.1	s__Ureibacillus endophyticus	85.5264	869	1336	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Ureibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003977595.1	s__Ureibacillus antri	81.0847	682	1336	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Ureibacillus	95.0	98.58	98.58	0.91	0.91	2	-
GCF_003966145.1	s__Ureibacillus telephonicus	80.2551	485	1336	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Ureibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003711845.1	s__Ureibacillus halotolerans	79.9097	436	1336	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Ureibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014836845.1	s__Ureibacillus sp014836845	79.6637	426	1336	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Ureibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005491425.1	s__Ureibacillus sp005491425	79.5358	432	1336	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Ureibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000772955.1	s__Ureibacillus sinduriensis	79.2635	328	1336	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Ureibacillus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000772965.1	s__Ureibacillus massiliensis	78.8787	349	1336	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Ureibacillus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003515775.1	s__Ureibacillus yapensis	78.8729	292	1336	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Ureibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003049665.1	s__Lysinibacillus mangiferihumi	78.1595	228	1336	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Lysinibacillus	96.9114	99.98	99.98	0.98	0.98	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:15:09,942] [INFO] GTDB search result was written to GCF_900217795.1_IMG-taxon_2740891832_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 12:15:09,942] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:15:09,946] [INFO] DFAST_QC result json was written to GCF_900217795.1_IMG-taxon_2740891832_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 12:15:09,947] [INFO] DFAST_QC completed!
[2024-01-24 12:15:09,947] [INFO] Total running time: 0h1m3s