[2024-01-24 14:56:23,845] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:56:23,847] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:56:23,847] [INFO] DQC Reference Directory: /var/lib/cwl/stgc249e105-0991-4225-b269-8a0879e4e687/dqc_reference
[2024-01-24 14:56:26,555] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:56:26,556] [INFO] Task started: Prodigal
[2024-01-24 14:56:26,556] [INFO] Running command: gunzip -c /var/lib/cwl/stg010d367a-559c-4575-8c14-cdde76c64527/GCF_004331435.1_ASM433143v1_genomic.fna.gz | prodigal -d GCF_004331435.1_ASM433143v1_genomic.fna/cds.fna -a GCF_004331435.1_ASM433143v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:56:52,928] [INFO] Task succeeded: Prodigal
[2024-01-24 14:56:52,928] [INFO] Task started: HMMsearch
[2024-01-24 14:56:52,928] [INFO] Running command: hmmsearch --tblout GCF_004331435.1_ASM433143v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc249e105-0991-4225-b269-8a0879e4e687/dqc_reference/reference_markers.hmm GCF_004331435.1_ASM433143v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:56:53,444] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:56:53,446] [INFO] Found 6/6 markers.
[2024-01-24 14:56:53,524] [INFO] Query marker FASTA was written to GCF_004331435.1_ASM433143v1_genomic.fna/markers.fasta
[2024-01-24 14:56:53,524] [INFO] Task started: Blastn
[2024-01-24 14:56:53,524] [INFO] Running command: blastn -query GCF_004331435.1_ASM433143v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc249e105-0991-4225-b269-8a0879e4e687/dqc_reference/reference_markers.fasta -out GCF_004331435.1_ASM433143v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:56:54,867] [INFO] Task succeeded: Blastn
[2024-01-24 14:56:54,871] [INFO] Selected 12 target genomes.
[2024-01-24 14:56:54,871] [INFO] Target genome list was writen to GCF_004331435.1_ASM433143v1_genomic.fna/target_genomes.txt
[2024-01-24 14:56:54,882] [INFO] Task started: fastANI
[2024-01-24 14:56:54,882] [INFO] Running command: fastANI --query /var/lib/cwl/stg010d367a-559c-4575-8c14-cdde76c64527/GCF_004331435.1_ASM433143v1_genomic.fna.gz --refList GCF_004331435.1_ASM433143v1_genomic.fna/target_genomes.txt --output GCF_004331435.1_ASM433143v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:57:20,331] [INFO] Task succeeded: fastANI
[2024-01-24 14:57:20,332] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc249e105-0991-4225-b269-8a0879e4e687/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:57:20,332] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc249e105-0991-4225-b269-8a0879e4e687/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:57:20,346] [INFO] Found 12 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:57:20,347] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 14:57:20,347] [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 sindirgiensis	strain=DSM 27082	GCA_004331435.1	1124744	1124744	type	True	100.0	2935	2938	95	inconclusive
Kribbella speibonae	strain=YM55	GCA_004331375.1	1572660	1572660	type	True	95.5256	2595	2938	95	inconclusive
Kribbella soli	strain=KCTC 29219	GCA_004331345.1	1124743	1124743	type	True	92.0135	2430	2938	95	below_threshold
Kribbella shirazensis	strain=DSM 45490	GCA_011761605.1	1105143	1105143	type	True	88.0416	2176	2938	95	below_threshold
Kribbella aluminosa	strain=DSM 18824	GCA_017876295.1	416017	416017	type	True	87.0826	2042	2938	95	below_threshold
Kribbella jiaozuonensis	strain=NEAU-THZ27	GCA_005233875.1	2575441	2575441	type	True	86.8681	2082	2938	95	below_threshold
Kribbella jejuensis	strain=DSM 17305	GCA_006715085.1	236068	236068	type	True	86.754	1958	2938	95	below_threshold
Kribbella turkmenica	strain=16K104	GCA_004348725.1	2530375	2530375	type	True	84.5186	1636	2938	95	below_threshold
Kribbella capetownensis	strain=YM53	GCA_004331485.1	1572659	1572659	type	True	84.5014	1951	2938	95	below_threshold
Kribbella sandramycini	strain=DSM 15626	GCA_014207795.1	60450	60450	type	True	83.2264	1650	2938	95	below_threshold
Kribbella sandramycini	strain=ATCC 39419	GCA_013131805.1	60450	60450	type	True	83.2017	1633	2938	95	below_threshold
Nocardioides panacis	strain=G188	GCA_019039255.1	2849501	2849501	type	True	77.7039	541	2938	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:57:20,348] [INFO] DFAST Taxonomy check result was written to GCF_004331435.1_ASM433143v1_genomic.fna/tc_result.tsv
[2024-01-24 14:57:20,349] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:57:20,349] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:57:20,349] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc249e105-0991-4225-b269-8a0879e4e687/dqc_reference/checkm_data
[2024-01-24 14:57:20,350] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:57:20,431] [INFO] Task started: CheckM
[2024-01-24 14:57:20,431] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004331435.1_ASM433143v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004331435.1_ASM433143v1_genomic.fna/checkm_input GCF_004331435.1_ASM433143v1_genomic.fna/checkm_result
[2024-01-24 14:58:40,056] [INFO] Task succeeded: CheckM
[2024-01-24 14:58:40,058] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:58:40,084] [INFO] ===== Completeness check finished =====
[2024-01-24 14:58:40,084] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:58:40,084] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004331435.1_ASM433143v1_genomic.fna/markers.fasta)
[2024-01-24 14:58:40,085] [INFO] Task started: Blastn
[2024-01-24 14:58:40,085] [INFO] Running command: blastn -query GCF_004331435.1_ASM433143v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc249e105-0991-4225-b269-8a0879e4e687/dqc_reference/reference_markers_gtdb.fasta -out GCF_004331435.1_ASM433143v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:58:42,043] [INFO] Task succeeded: Blastn
[2024-01-24 14:58:42,046] [INFO] Selected 11 target genomes.
[2024-01-24 14:58:42,047] [INFO] Target genome list was writen to GCF_004331435.1_ASM433143v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:58:42,056] [INFO] Task started: fastANI
[2024-01-24 14:58:42,056] [INFO] Running command: fastANI --query /var/lib/cwl/stg010d367a-559c-4575-8c14-cdde76c64527/GCF_004331435.1_ASM433143v1_genomic.fna.gz --refList GCF_004331435.1_ASM433143v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004331435.1_ASM433143v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:59:07,826] [INFO] Task succeeded: fastANI
[2024-01-24 14:59:07,835] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:59:07,836] [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_004331435.1	s__Kribbella sindirgiensis	100.0	2935	2938	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Kribbellaceae;g__Kribbella	95.0	95.59	95.53	0.88	0.88	3	conclusive
GCF_004331345.1	s__Kribbella soli	92.0278	2428	2938	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	92.0264	2378	2938	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	91.6668	2279	2938	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Kribbellaceae;g__Kribbella	95.0	97.22	95.50	0.92	0.87	3	-
GCF_011761605.1	s__Kribbella shirazensis	88.0383	2177	2938	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	87.0774	2043	2938	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	86.864	2082	2938	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Kribbellaceae;g__Kribbella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004365875.1	s__Kribbella sp004365875	86.8014	2088	2938	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Kribbellaceae;g__Kribbella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004217145.1	s__Kribbella soli_A	86.717	2128	2938	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	86.6423	2047	2938	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	84.5301	1634	2938	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 14:59:07,837] [INFO] GTDB search result was written to GCF_004331435.1_ASM433143v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:59:07,838] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:59:07,841] [INFO] DFAST_QC result json was written to GCF_004331435.1_ASM433143v1_genomic.fna/dqc_result.json
[2024-01-24 14:59:07,842] [INFO] DFAST_QC completed!
[2024-01-24 14:59:07,842] [INFO] Total running time: 0h2m44s