[2024-01-24 14:39:14,771] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:39:14,773] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:39:14,773] [INFO] DQC Reference Directory: /var/lib/cwl/stgd536d05a-0aea-4633-a326-f420720d2002/dqc_reference
[2024-01-24 14:39:16,201] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:39:16,202] [INFO] Task started: Prodigal
[2024-01-24 14:39:16,202] [INFO] Running command: gunzip -c /var/lib/cwl/stgb8fc083a-e0ea-4240-959d-dfc657bd75c4/GCF_004331465.1_ASM433146v1_genomic.fna.gz | prodigal -d GCF_004331465.1_ASM433146v1_genomic.fna/cds.fna -a GCF_004331465.1_ASM433146v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:39:45,744] [INFO] Task succeeded: Prodigal
[2024-01-24 14:39:45,745] [INFO] Task started: HMMsearch
[2024-01-24 14:39:45,745] [INFO] Running command: hmmsearch --tblout GCF_004331465.1_ASM433146v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd536d05a-0aea-4633-a326-f420720d2002/dqc_reference/reference_markers.hmm GCF_004331465.1_ASM433146v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:39:46,291] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:39:46,293] [INFO] Found 6/6 markers.
[2024-01-24 14:39:46,374] [INFO] Query marker FASTA was written to GCF_004331465.1_ASM433146v1_genomic.fna/markers.fasta
[2024-01-24 14:39:46,375] [INFO] Task started: Blastn
[2024-01-24 14:39:46,375] [INFO] Running command: blastn -query GCF_004331465.1_ASM433146v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd536d05a-0aea-4633-a326-f420720d2002/dqc_reference/reference_markers.fasta -out GCF_004331465.1_ASM433146v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:39:47,644] [INFO] Task succeeded: Blastn
[2024-01-24 14:39:47,649] [INFO] Selected 13 target genomes.
[2024-01-24 14:39:47,650] [INFO] Target genome list was writen to GCF_004331465.1_ASM433146v1_genomic.fna/target_genomes.txt
[2024-01-24 14:39:47,657] [INFO] Task started: fastANI
[2024-01-24 14:39:47,657] [INFO] Running command: fastANI --query /var/lib/cwl/stgb8fc083a-e0ea-4240-959d-dfc657bd75c4/GCF_004331465.1_ASM433146v1_genomic.fna.gz --refList GCF_004331465.1_ASM433146v1_genomic.fna/target_genomes.txt --output GCF_004331465.1_ASM433146v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:40:17,579] [INFO] Task succeeded: fastANI
[2024-01-24 14:40:17,579] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd536d05a-0aea-4633-a326-f420720d2002/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:40:17,580] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd536d05a-0aea-4633-a326-f420720d2002/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:40:17,591] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:40:17,591] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:40:17,591] [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
Kribbella pittospori	strain=NRRL B-24813	GCA_004331465.1	722689	722689	type	True	100.0	3133	3135	95	conclusive
Kribbella capetownensis	strain=YM53	GCA_004331485.1	1572659	1572659	type	True	93.8979	2610	3135	95	below_threshold
Kribbella turkmenica	strain=16K104	GCA_004348725.1	2530375	2530375	type	True	85.4888	1740	3135	95	below_threshold
Kribbella jiaozuonensis	strain=NEAU-THZ27	GCA_005233875.1	2575441	2575441	type	True	84.6305	2002	3135	95	below_threshold
Kribbella soli	strain=KCTC 29219	GCA_004331345.1	1124743	1124743	type	True	84.6138	2004	3135	95	below_threshold
Kribbella sindirgiensis	strain=DSM 27082	GCA_004331435.1	1124744	1124744	type	True	84.4765	1968	3135	95	below_threshold
Kribbella speibonae	strain=YM55	GCA_004331375.1	1572660	1572660	type	True	84.4654	2015	3135	95	below_threshold
Kribbella shirazensis	strain=DSM 45490	GCA_011761605.1	1105143	1105143	type	True	84.385	1937	3135	95	below_threshold
Kribbella aluminosa	strain=DSM 18824	GCA_017876295.1	416017	416017	type	True	83.9721	1821	3135	95	below_threshold
Kribbella solani	strain=DSM 17294	GCA_014205295.1	236067	236067	type	True	83.6577	1653	3135	95	below_threshold
Kribbella sandramycini	strain=DSM 15626	GCA_014207795.1	60450	60450	type	True	83.214	1623	3135	95	below_threshold
Kribbella sandramycini	strain=ATCC 39419	GCA_013131805.1	60450	60450	type	True	83.2117	1624	3135	95	below_threshold
Nocardioides panacis	strain=G188	GCA_019039255.1	2849501	2849501	type	True	77.754	561	3135	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:40:17,593] [INFO] DFAST Taxonomy check result was written to GCF_004331465.1_ASM433146v1_genomic.fna/tc_result.tsv
[2024-01-24 14:40:17,594] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:40:17,594] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:40:17,594] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd536d05a-0aea-4633-a326-f420720d2002/dqc_reference/checkm_data
[2024-01-24 14:40:17,595] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:40:17,684] [INFO] Task started: CheckM
[2024-01-24 14:40:17,685] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004331465.1_ASM433146v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004331465.1_ASM433146v1_genomic.fna/checkm_input GCF_004331465.1_ASM433146v1_genomic.fna/checkm_result
[2024-01-24 14:41:51,117] [INFO] Task succeeded: CheckM
[2024-01-24 14:41:51,118] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 5.21%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:41:51,148] [INFO] ===== Completeness check finished =====
[2024-01-24 14:41:51,149] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:41:51,149] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004331465.1_ASM433146v1_genomic.fna/markers.fasta)
[2024-01-24 14:41:51,150] [INFO] Task started: Blastn
[2024-01-24 14:41:51,150] [INFO] Running command: blastn -query GCF_004331465.1_ASM433146v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd536d05a-0aea-4633-a326-f420720d2002/dqc_reference/reference_markers_gtdb.fasta -out GCF_004331465.1_ASM433146v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:41:53,130] [INFO] Task succeeded: Blastn
[2024-01-24 14:41:53,133] [INFO] Selected 15 target genomes.
[2024-01-24 14:41:53,133] [INFO] Target genome list was writen to GCF_004331465.1_ASM433146v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:41:53,144] [INFO] Task started: fastANI
[2024-01-24 14:41:53,144] [INFO] Running command: fastANI --query /var/lib/cwl/stgb8fc083a-e0ea-4240-959d-dfc657bd75c4/GCF_004331465.1_ASM433146v1_genomic.fna.gz --refList GCF_004331465.1_ASM433146v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004331465.1_ASM433146v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:42:30,128] [INFO] Task succeeded: fastANI
[2024-01-24 14:42:30,150] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:42:30,150] [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_004331465.1	s__Kribbella pittospori	100.0	3133	3135	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Kribbellaceae;g__Kribbella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_004331485.1	s__Kribbella sp004331485	93.9028	2609	3135	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Kribbellaceae;g__Kribbella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004342025.1	s__Kribbella sp004342025	85.7384	2144	3135	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Kribbellaceae;g__Kribbella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004348725.1	s__Kribbella sp004348725	85.474	1743	3135	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Kribbellaceae;g__Kribbella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004345665.1	s__Kribbella sp004345665	85.0961	1856	3135	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Kribbellaceae;g__Kribbella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005233875.1	s__Kribbella sp005233875	84.6312	2002	3135	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Kribbellaceae;g__Kribbella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004216905.1	s__Kribbella sp004216905	84.6243	1968	3135	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Kribbellaceae;g__Kribbella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004331345.1	s__Kribbella soli	84.6014	2009	3135	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Kribbellaceae;g__Kribbella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004366075.1	s__Kribbella sp004366075	84.54	1951	3135	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Kribbellaceae;g__Kribbella	95.0	97.22	95.50	0.92	0.87	3	-
GCF_004331435.1	s__Kribbella sindirgiensis	84.4715	1969	3135	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Kribbellaceae;g__Kribbella	95.0	95.59	95.53	0.88	0.88	3	-
GCF_004217145.1	s__Kribbella soli_A	84.4314	2027	3135	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Kribbellaceae;g__Kribbella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011761605.1	s__Kribbella shirazensis	84.3552	1943	3135	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Kribbellaceae;g__Kribbella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004365355.1	s__Kribbella sp004365355	84.3477	1972	3135	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Kribbellaceae;g__Kribbella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017876295.1	s__Kribbella aluminosa	84.005	1813	3135	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Kribbellaceae;g__Kribbella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004348455.1	s__Kribbella albertanoniae	83.185	1641	3135	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Kribbellaceae;g__Kribbella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:42:30,152] [INFO] GTDB search result was written to GCF_004331465.1_ASM433146v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:42:30,153] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:42:30,157] [INFO] DFAST_QC result json was written to GCF_004331465.1_ASM433146v1_genomic.fna/dqc_result.json
[2024-01-24 14:42:30,157] [INFO] DFAST_QC completed!
[2024-01-24 14:42:30,157] [INFO] Total running time: 0h3m15s