[2024-01-24 14:19:21,677] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:19:21,685] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:19:21,685] [INFO] DQC Reference Directory: /var/lib/cwl/stg13f0dc14-8178-4657-a804-a2d8c88ceccb/dqc_reference
[2024-01-24 14:19:23,548] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:19:23,549] [INFO] Task started: Prodigal
[2024-01-24 14:19:23,550] [INFO] Running command: gunzip -c /var/lib/cwl/stg9dc4cc9e-ebe1-45a1-8d11-45f1a6902852/GCF_009745975.1_ASM974597v1_genomic.fna.gz | prodigal -d GCF_009745975.1_ASM974597v1_genomic.fna/cds.fna -a GCF_009745975.1_ASM974597v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:19:43,703] [INFO] Task succeeded: Prodigal
[2024-01-24 14:19:43,703] [INFO] Task started: HMMsearch
[2024-01-24 14:19:43,703] [INFO] Running command: hmmsearch --tblout GCF_009745975.1_ASM974597v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg13f0dc14-8178-4657-a804-a2d8c88ceccb/dqc_reference/reference_markers.hmm GCF_009745975.1_ASM974597v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:19:44,300] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:19:44,302] [INFO] Found 6/6 markers.
[2024-01-24 14:19:44,374] [INFO] Query marker FASTA was written to GCF_009745975.1_ASM974597v1_genomic.fna/markers.fasta
[2024-01-24 14:19:44,375] [INFO] Task started: Blastn
[2024-01-24 14:19:44,375] [INFO] Running command: blastn -query GCF_009745975.1_ASM974597v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg13f0dc14-8178-4657-a804-a2d8c88ceccb/dqc_reference/reference_markers.fasta -out GCF_009745975.1_ASM974597v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:19:47,555] [INFO] Task succeeded: Blastn
[2024-01-24 14:19:47,559] [INFO] Selected 15 target genomes.
[2024-01-24 14:19:47,559] [INFO] Target genome list was writen to GCF_009745975.1_ASM974597v1_genomic.fna/target_genomes.txt
[2024-01-24 14:19:47,603] [INFO] Task started: fastANI
[2024-01-24 14:19:47,604] [INFO] Running command: fastANI --query /var/lib/cwl/stg9dc4cc9e-ebe1-45a1-8d11-45f1a6902852/GCF_009745975.1_ASM974597v1_genomic.fna.gz --refList GCF_009745975.1_ASM974597v1_genomic.fna/target_genomes.txt --output GCF_009745975.1_ASM974597v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:20:22,287] [INFO] Task succeeded: fastANI
[2024-01-24 14:20:22,288] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg13f0dc14-8178-4657-a804-a2d8c88ceccb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:20:22,289] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg13f0dc14-8178-4657-a804-a2d8c88ceccb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:20:22,352] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:20:22,352] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:20:22,352] [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
Actinokineospora pegani	strain=TRM 65233	GCA_009745975.1	2654637	2654637	type	True	100.0	2078	2089	95	conclusive
Actinokineospora spheciospongiae	strain=EG49	GCA_000564855.1	909613	909613	type	True	84.6074	1411	2089	95	below_threshold
Actinokineospora bangkokensis	strain=44EHW	GCA_001940455.1	1193682	1193682	type	True	83.7705	1363	2089	95	below_threshold
Actinokineospora baliensis	strain=DSM 45656	GCA_016907695.1	547056	547056	type	True	81.5633	1061	2089	95	below_threshold
Actinokineospora globicatena	strain=DSM 44256	GCA_024171945.1	103729	103729	type	True	81.5187	1102	2089	95	below_threshold
Actinokineospora terrae	strain=DSM 44260	GCA_900111175.1	155974	155974	type	True	81.4988	1108	2089	95	below_threshold
Actinokineospora cianjurensis	strain=DSM 45657	GCA_003663795.1	585224	585224	type	True	81.486	1096	2089	95	below_threshold
Actinokineospora alba	strain=DSM 45114	GCA_004362515.1	504798	504798	type	True	81.2313	1008	2089	95	below_threshold
Actinokineospora auranticolor	strain=YU 961-1	GCA_002934265.1	155976	155976	type	True	81.1929	1146	2089	95	below_threshold
Actinokineospora diospyrosa	strain=DSM 44255	GCA_024171925.1	103728	103728	type	True	81.1451	1080	2089	95	below_threshold
Actinokineospora fastidiosa	strain=JCM 3276	GCA_014648415.1	1816	1816	type	True	81.0837	1108	2089	95	below_threshold
Actinokineospora enzanensis	strain=DSM 44649	GCA_000374445.1	155975	155975	type	True	80.9812	1069	2089	95	below_threshold
Amycolatopsis thermalba	strain=NRRL B-24845	GCA_003385215.1	944492	944492	type	True	78.892	823	2089	95	below_threshold
Amycolatopsis acidiphila	strain=KCTC 39523	GCA_021391495.1	715473	715473	type	True	78.5481	795	2089	95	below_threshold
Lentzea tibetensis	strain=FXJ1.1311	GCA_007845675.1	2591470	2591470	type	True	78.3948	868	2089	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:20:22,354] [INFO] DFAST Taxonomy check result was written to GCF_009745975.1_ASM974597v1_genomic.fna/tc_result.tsv
[2024-01-24 14:20:22,355] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:20:22,355] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:20:22,355] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg13f0dc14-8178-4657-a804-a2d8c88ceccb/dqc_reference/checkm_data
[2024-01-24 14:20:22,360] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:20:22,459] [INFO] Task started: CheckM
[2024-01-24 14:20:22,459] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009745975.1_ASM974597v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009745975.1_ASM974597v1_genomic.fna/checkm_input GCF_009745975.1_ASM974597v1_genomic.fna/checkm_result
[2024-01-24 14:21:42,926] [INFO] Task succeeded: CheckM
[2024-01-24 14:21:42,928] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:21:42,953] [INFO] ===== Completeness check finished =====
[2024-01-24 14:21:42,954] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:21:42,954] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009745975.1_ASM974597v1_genomic.fna/markers.fasta)
[2024-01-24 14:21:42,955] [INFO] Task started: Blastn
[2024-01-24 14:21:42,955] [INFO] Running command: blastn -query GCF_009745975.1_ASM974597v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg13f0dc14-8178-4657-a804-a2d8c88ceccb/dqc_reference/reference_markers_gtdb.fasta -out GCF_009745975.1_ASM974597v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:21:47,165] [INFO] Task succeeded: Blastn
[2024-01-24 14:21:47,169] [INFO] Selected 10 target genomes.
[2024-01-24 14:21:47,169] [INFO] Target genome list was writen to GCF_009745975.1_ASM974597v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:21:47,177] [INFO] Task started: fastANI
[2024-01-24 14:21:47,178] [INFO] Running command: fastANI --query /var/lib/cwl/stg9dc4cc9e-ebe1-45a1-8d11-45f1a6902852/GCF_009745975.1_ASM974597v1_genomic.fna.gz --refList GCF_009745975.1_ASM974597v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009745975.1_ASM974597v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:22:09,301] [INFO] Task succeeded: fastANI
[2024-01-24 14:22:09,345] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:22:09,346] [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_009745975.1	s__Actinokineospora pegani	100.0	2078	2089	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinokineospora	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003182415.1	s__Actinokineospora mzabensis	84.6123	1476	2089	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinokineospora	95.0	98.96	98.96	0.95	0.95	2	-
GCF_001940455.1	s__Actinokineospora bangkokensis	83.741	1369	2089	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinokineospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016907695.1	s__Actinokineospora baliensis	81.6056	1056	2089	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinokineospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900111175.1	s__Actinokineospora terrae	81.4829	1111	2089	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinokineospora	95.0	95.61	95.61	0.89	0.89	2	-
GCF_004362515.1	s__Actinokineospora alba	81.2262	1009	2089	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinokineospora	95.0	100.00	100.00	1.00	1.00	3	-
GCF_002934265.1	s__Actinokineospora auranticolor	81.1911	1150	2089	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinokineospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014648415.1	s__Actinokineospora fastidiosa	81.0204	1121	2089	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinokineospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000374445.1	s__Actinokineospora enzanensis	80.9631	1072	2089	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinokineospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003002815.1	s__Umezawaea tangerina	78.7225	1048	2089	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Umezawaea	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:22:09,348] [INFO] GTDB search result was written to GCF_009745975.1_ASM974597v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:22:09,348] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:22:09,352] [INFO] DFAST_QC result json was written to GCF_009745975.1_ASM974597v1_genomic.fna/dqc_result.json
[2024-01-24 14:22:09,352] [INFO] DFAST_QC completed!
[2024-01-24 14:22:09,352] [INFO] Total running time: 0h2m48s