[2024-01-24 15:02:17,463] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:02:17,499] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:02:17,500] [INFO] DQC Reference Directory: /var/lib/cwl/stg5423bec5-3656-4662-8120-dcf2a85bd6c2/dqc_reference
[2024-01-24 15:02:18,829] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:02:18,830] [INFO] Task started: Prodigal
[2024-01-24 15:02:18,830] [INFO] Running command: gunzip -c /var/lib/cwl/stga6bd0019-c95d-489a-8e63-dda4991f661c/GCF_900142575.1_IMG-taxon_2667527448_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900142575.1_IMG-taxon_2667527448_annotated_assembly_genomic.fna/cds.fna -a GCF_900142575.1_IMG-taxon_2667527448_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:02:41,021] [INFO] Task succeeded: Prodigal
[2024-01-24 15:02:41,022] [INFO] Task started: HMMsearch
[2024-01-24 15:02:41,022] [INFO] Running command: hmmsearch --tblout GCF_900142575.1_IMG-taxon_2667527448_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5423bec5-3656-4662-8120-dcf2a85bd6c2/dqc_reference/reference_markers.hmm GCF_900142575.1_IMG-taxon_2667527448_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:02:41,375] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:02:41,376] [INFO] Found 6/6 markers.
[2024-01-24 15:02:41,446] [INFO] Query marker FASTA was written to GCF_900142575.1_IMG-taxon_2667527448_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 15:02:41,447] [INFO] Task started: Blastn
[2024-01-24 15:02:41,447] [INFO] Running command: blastn -query GCF_900142575.1_IMG-taxon_2667527448_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg5423bec5-3656-4662-8120-dcf2a85bd6c2/dqc_reference/reference_markers.fasta -out GCF_900142575.1_IMG-taxon_2667527448_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:02:42,806] [INFO] Task succeeded: Blastn
[2024-01-24 15:02:42,809] [INFO] Selected 13 target genomes.
[2024-01-24 15:02:42,809] [INFO] Target genome list was writen to GCF_900142575.1_IMG-taxon_2667527448_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 15:02:42,818] [INFO] Task started: fastANI
[2024-01-24 15:02:42,818] [INFO] Running command: fastANI --query /var/lib/cwl/stga6bd0019-c95d-489a-8e63-dda4991f661c/GCF_900142575.1_IMG-taxon_2667527448_annotated_assembly_genomic.fna.gz --refList GCF_900142575.1_IMG-taxon_2667527448_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900142575.1_IMG-taxon_2667527448_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:03:10,847] [INFO] Task succeeded: fastANI
[2024-01-24 15:03:10,847] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5423bec5-3656-4662-8120-dcf2a85bd6c2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:03:10,848] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5423bec5-3656-4662-8120-dcf2a85bd6c2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:03:10,863] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:03:10,863] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:03:10,863] [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
Actinacidiphila paucisporea	strain=CGMCC 4.2025	GCA_900142575.1	310782	310782	type	True	100.0	2678	2682	95	conclusive
Actinacidiphila bryophytorum	strain=DSM 42138	GCA_016916835.1	1436133	1436133	type	True	89.3638	1866	2682	95	below_threshold
Actinacidiphila bryophytorum	strain=DSM 42138	GCA_017164735.1	1436133	1436133	type	True	89.2225	1567	2682	95	below_threshold
Actinacidiphila epipremni	strain=PRB2-1	GCA_012034175.1	2053013	2053013	type	True	86.2365	1791	2682	95	below_threshold
Actinacidiphila rubida	strain=CGMCC 4.2026	GCA_900110255.1	310780	310780	type	True	83.4608	1615	2682	95	below_threshold
Actinacidiphila yanglinensis	strain=CGMCC 4.2023	GCA_900107965.1	310779	310779	type	True	83.1773	1608	2682	95	below_threshold
Actinacidiphila guanduensis	strain=CGMCC 4.2022	GCA_900103985.1	310781	310781	type	True	83.1494	1536	2682	95	below_threshold
Streptomyces parmotrematis	strain=Ptm05	GCA_019890615.1	2873249	2873249	type	True	80.8046	1125	2682	95	below_threshold
Actinacidiphila oryziradicis	strain=NEAU-C40	GCA_005047355.1	2571141	2571141	type	True	80.1998	1221	2682	95	below_threshold
Streptomyces lichenis	strain=LCR6-01	GCA_023218175.1	2306967	2306967	type	True	80.1556	1120	2682	95	below_threshold
Streptomyces inhibens	strain=NEAU-D10	GCA_003389455.1	2293571	2293571	type	True	79.9044	1069	2682	95	below_threshold
Streptomyces harenosi	strain=PRKS01-65	GCA_011008945.1	2697029	2697029	type	True	79.8452	1068	2682	95	below_threshold
Streptomyces buecherae	strain=AC541	GCA_014295035.1	2763006	2763006	type	True	79.6931	1136	2682	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:03:10,865] [INFO] DFAST Taxonomy check result was written to GCF_900142575.1_IMG-taxon_2667527448_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 15:03:10,865] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:03:10,865] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:03:10,866] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5423bec5-3656-4662-8120-dcf2a85bd6c2/dqc_reference/checkm_data
[2024-01-24 15:03:10,867] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:03:10,948] [INFO] Task started: CheckM
[2024-01-24 15:03:10,949] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900142575.1_IMG-taxon_2667527448_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900142575.1_IMG-taxon_2667527448_annotated_assembly_genomic.fna/checkm_input GCF_900142575.1_IMG-taxon_2667527448_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 15:04:56,903] [INFO] Task succeeded: CheckM
[2024-01-24 15:04:56,905] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:04:56,937] [INFO] ===== Completeness check finished =====
[2024-01-24 15:04:56,938] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:04:56,938] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900142575.1_IMG-taxon_2667527448_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 15:04:56,939] [INFO] Task started: Blastn
[2024-01-24 15:04:56,939] [INFO] Running command: blastn -query GCF_900142575.1_IMG-taxon_2667527448_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg5423bec5-3656-4662-8120-dcf2a85bd6c2/dqc_reference/reference_markers_gtdb.fasta -out GCF_900142575.1_IMG-taxon_2667527448_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:04:59,165] [INFO] Task succeeded: Blastn
[2024-01-24 15:04:59,169] [INFO] Selected 10 target genomes.
[2024-01-24 15:04:59,169] [INFO] Target genome list was writen to GCF_900142575.1_IMG-taxon_2667527448_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:04:59,178] [INFO] Task started: fastANI
[2024-01-24 15:04:59,178] [INFO] Running command: fastANI --query /var/lib/cwl/stga6bd0019-c95d-489a-8e63-dda4991f661c/GCF_900142575.1_IMG-taxon_2667527448_annotated_assembly_genomic.fna.gz --refList GCF_900142575.1_IMG-taxon_2667527448_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900142575.1_IMG-taxon_2667527448_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:05:23,198] [INFO] Task succeeded: fastANI
[2024-01-24 15:05:23,207] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:05:23,208] [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_900142575.1	s__Streptomyces paucisporeus	100.0	2678	2682	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_016916835.1	s__Streptomyces bryophytorum	89.3891	1863	2682	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.96	99.96	0.99	0.99	2	-
GCF_000701325.1	s__Streptomyces sp000701325	89.3008	1819	2682	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012034175.1	s__Streptomyces sp012034175	86.1987	1796	2682	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000721495.1	s__Streptomyces sp000721495	85.7827	1802	2682	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014596445.1	s__Streptomyces sp014596445	83.9378	1497	2682	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110255.1	s__Streptomyces rubidus	83.4893	1609	2682	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900107965.1	s__Streptomyces yanglinensis	83.1778	1608	2682	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009783685.1	s__Streptomyces sp009783685	83.0497	995	2682	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014295035.1	s__Streptomyces buecherae	79.7109	1135	2682	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.71	96.93	0.96	0.94	7	-
--------------------------------------------------------------------------------
[2024-01-24 15:05:23,209] [INFO] GTDB search result was written to GCF_900142575.1_IMG-taxon_2667527448_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 15:05:23,210] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:05:23,218] [INFO] DFAST_QC result json was written to GCF_900142575.1_IMG-taxon_2667527448_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 15:05:23,218] [INFO] DFAST_QC completed!
[2024-01-24 15:05:23,218] [INFO] Total running time: 0h3m6s