[2024-01-24 13:25:29,627] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:25:29,629] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:25:29,629] [INFO] DQC Reference Directory: /var/lib/cwl/stg67debb1d-36d3-4ff8-966b-2f3cdf6eb89f/dqc_reference
[2024-01-24 13:25:30,867] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:25:30,868] [INFO] Task started: Prodigal
[2024-01-24 13:25:30,868] [INFO] Running command: gunzip -c /var/lib/cwl/stg48fd08d5-0935-4a71-a225-fe0102115c77/GCF_900104475.1_IMG-taxon_2619619031_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900104475.1_IMG-taxon_2619619031_annotated_assembly_genomic.fna/cds.fna -a GCF_900104475.1_IMG-taxon_2619619031_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:25:46,381] [INFO] Task succeeded: Prodigal
[2024-01-24 13:25:46,382] [INFO] Task started: HMMsearch
[2024-01-24 13:25:46,382] [INFO] Running command: hmmsearch --tblout GCF_900104475.1_IMG-taxon_2619619031_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg67debb1d-36d3-4ff8-966b-2f3cdf6eb89f/dqc_reference/reference_markers.hmm GCF_900104475.1_IMG-taxon_2619619031_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:25:46,658] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:25:46,659] [INFO] Found 6/6 markers.
[2024-01-24 13:25:46,704] [INFO] Query marker FASTA was written to GCF_900104475.1_IMG-taxon_2619619031_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 13:25:46,704] [INFO] Task started: Blastn
[2024-01-24 13:25:46,704] [INFO] Running command: blastn -query GCF_900104475.1_IMG-taxon_2619619031_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg67debb1d-36d3-4ff8-966b-2f3cdf6eb89f/dqc_reference/reference_markers.fasta -out GCF_900104475.1_IMG-taxon_2619619031_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:25:47,987] [INFO] Task succeeded: Blastn
[2024-01-24 13:25:47,992] [INFO] Selected 11 target genomes.
[2024-01-24 13:25:47,993] [INFO] Target genome list was writen to GCF_900104475.1_IMG-taxon_2619619031_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 13:25:48,004] [INFO] Task started: fastANI
[2024-01-24 13:25:48,004] [INFO] Running command: fastANI --query /var/lib/cwl/stg48fd08d5-0935-4a71-a225-fe0102115c77/GCF_900104475.1_IMG-taxon_2619619031_annotated_assembly_genomic.fna.gz --refList GCF_900104475.1_IMG-taxon_2619619031_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900104475.1_IMG-taxon_2619619031_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:26:01,968] [INFO] Task succeeded: fastANI
[2024-01-24 13:26:01,969] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg67debb1d-36d3-4ff8-966b-2f3cdf6eb89f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:26:01,969] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg67debb1d-36d3-4ff8-966b-2f3cdf6eb89f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:26:01,978] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:26:01,979] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:26:01,979] [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
Actinopolyspora xinjiangensis	strain=DSM 46732	GCA_900104475.1	405564	405564	type	True	100.0	1659	1661	95	conclusive
Actinopolyspora erythraea	strain=YIM 90600	GCA_002263515.1	414996	414996	type	True	94.5236	1460	1661	95	below_threshold
Actinopolyspora erythraea	strain=YIM 90600	GCA_000763095.1	414996	414996	type	True	94.4832	1461	1661	95	below_threshold
Actinopolyspora alba	strain=DSM 45004	GCA_900112765.1	673379	673379	type	True	86.5602	1342	1661	95	below_threshold
Actinopolyspora righensis	strain=DSM 45501	GCA_900116555.1	995060	995060	type	True	86.5074	1319	1661	95	below_threshold
Actinopolyspora saharensis	strain=DSM 45459	GCA_900100925.1	995062	995062	type	True	82.1071	1013	1661	95	below_threshold
Saccharopolyspora erythraea	strain=NRRL 2338	GCA_000062885.1	1836	1836	type	True	79.1109	693	1661	95	below_threshold
Saccharopolyspora erythraea	strain=DSM 40517	GCA_002564065.1	1836	1836	type	True	79.0907	700	1661	95	below_threshold
Saccharopolyspora rectivirgula	strain=DSM 43747	GCA_000497205.1	28042	28042	type	True	78.6971	502	1661	95	below_threshold
Actinoalloteichus spitiensis	strain=RMV-1378	GCA_000239155.2	252394	252394	type	True	77.2806	317	1661	95	below_threshold
Pseudonocardia acaciae	strain=DSM 45401	GCA_000620785.1	551276	551276	type	True	76.6268	457	1661	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:26:01,980] [INFO] DFAST Taxonomy check result was written to GCF_900104475.1_IMG-taxon_2619619031_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 13:26:01,981] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:26:01,981] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:26:01,981] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg67debb1d-36d3-4ff8-966b-2f3cdf6eb89f/dqc_reference/checkm_data
[2024-01-24 13:26:01,982] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:26:02,031] [INFO] Task started: CheckM
[2024-01-24 13:26:02,031] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900104475.1_IMG-taxon_2619619031_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900104475.1_IMG-taxon_2619619031_annotated_assembly_genomic.fna/checkm_input GCF_900104475.1_IMG-taxon_2619619031_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 13:26:49,163] [INFO] Task succeeded: CheckM
[2024-01-24 13:26:49,165] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:26:49,184] [INFO] ===== Completeness check finished =====
[2024-01-24 13:26:49,185] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:26:49,185] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900104475.1_IMG-taxon_2619619031_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 13:26:49,186] [INFO] Task started: Blastn
[2024-01-24 13:26:49,186] [INFO] Running command: blastn -query GCF_900104475.1_IMG-taxon_2619619031_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg67debb1d-36d3-4ff8-966b-2f3cdf6eb89f/dqc_reference/reference_markers_gtdb.fasta -out GCF_900104475.1_IMG-taxon_2619619031_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:26:50,919] [INFO] Task succeeded: Blastn
[2024-01-24 13:26:50,923] [INFO] Selected 7 target genomes.
[2024-01-24 13:26:50,923] [INFO] Target genome list was writen to GCF_900104475.1_IMG-taxon_2619619031_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:26:50,936] [INFO] Task started: fastANI
[2024-01-24 13:26:50,936] [INFO] Running command: fastANI --query /var/lib/cwl/stg48fd08d5-0935-4a71-a225-fe0102115c77/GCF_900104475.1_IMG-taxon_2619619031_annotated_assembly_genomic.fna.gz --refList GCF_900104475.1_IMG-taxon_2619619031_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900104475.1_IMG-taxon_2619619031_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:27:00,433] [INFO] Task succeeded: fastANI
[2024-01-24 13:27:00,447] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:27:00,448] [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_900104475.1	s__Actinopolyspora xinjiangensis	100.0	1659	1661	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinopolyspora	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002263515.1	s__Actinopolyspora erythraea	94.5115	1461	1661	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinopolyspora	95.0	99.98	99.98	0.99	0.99	2	-
GCF_900112765.1	s__Actinopolyspora alba	86.5682	1341	1661	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinopolyspora	95.8717	N/A	N/A	N/A	N/A	1	-
GCF_900116555.1	s__Actinopolyspora righensis	86.4822	1322	1661	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinopolyspora	95.8717	98.44	98.44	0.91	0.91	2	-
GCF_900101095.1	s__Actinopolyspora mzabensis	86.1693	1300	1661	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinopolyspora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900100925.1	s__Actinopolyspora saharensis	82.1191	1012	1661	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinopolyspora	95.0	98.98	98.97	0.92	0.92	3	-
GCF_006716775.1	s__Actinopolyspora sp006716775	81.7654	1018	1661	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinopolyspora	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:27:00,449] [INFO] GTDB search result was written to GCF_900104475.1_IMG-taxon_2619619031_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 13:27:00,450] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:27:00,452] [INFO] DFAST_QC result json was written to GCF_900104475.1_IMG-taxon_2619619031_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 13:27:00,453] [INFO] DFAST_QC completed!
[2024-01-24 13:27:00,453] [INFO] Total running time: 0h1m31s