[2024-01-24 13:31:44,217] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:31:44,220] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:31:44,220] [INFO] DQC Reference Directory: /var/lib/cwl/stgfa7c94e3-f8f1-4da5-aa54-d1218fce8374/dqc_reference
[2024-01-24 13:31:45,423] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:31:45,424] [INFO] Task started: Prodigal
[2024-01-24 13:31:45,424] [INFO] Running command: gunzip -c /var/lib/cwl/stg4823f067-9bae-44f1-aaef-24905b1c648c/GCF_900143005.1_IMG-taxon_2700988713_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900143005.1_IMG-taxon_2700988713_annotated_assembly_genomic.fna/cds.fna -a GCF_900143005.1_IMG-taxon_2700988713_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:32:13,114] [INFO] Task succeeded: Prodigal
[2024-01-24 13:32:13,114] [INFO] Task started: HMMsearch
[2024-01-24 13:32:13,115] [INFO] Running command: hmmsearch --tblout GCF_900143005.1_IMG-taxon_2700988713_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfa7c94e3-f8f1-4da5-aa54-d1218fce8374/dqc_reference/reference_markers.hmm GCF_900143005.1_IMG-taxon_2700988713_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:32:13,555] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:32:13,556] [INFO] Found 6/6 markers.
[2024-01-24 13:32:13,627] [INFO] Query marker FASTA was written to GCF_900143005.1_IMG-taxon_2700988713_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 13:32:13,627] [INFO] Task started: Blastn
[2024-01-24 13:32:13,627] [INFO] Running command: blastn -query GCF_900143005.1_IMG-taxon_2700988713_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgfa7c94e3-f8f1-4da5-aa54-d1218fce8374/dqc_reference/reference_markers.fasta -out GCF_900143005.1_IMG-taxon_2700988713_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:14,916] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:14,923] [INFO] Selected 16 target genomes.
[2024-01-24 13:32:14,924] [INFO] Target genome list was writen to GCF_900143005.1_IMG-taxon_2700988713_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 13:32:14,934] [INFO] Task started: fastANI
[2024-01-24 13:32:14,935] [INFO] Running command: fastANI --query /var/lib/cwl/stg4823f067-9bae-44f1-aaef-24905b1c648c/GCF_900143005.1_IMG-taxon_2700988713_annotated_assembly_genomic.fna.gz --refList GCF_900143005.1_IMG-taxon_2700988713_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900143005.1_IMG-taxon_2700988713_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:32:42,632] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:42,633] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfa7c94e3-f8f1-4da5-aa54-d1218fce8374/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:32:42,633] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfa7c94e3-f8f1-4da5-aa54-d1218fce8374/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:32:42,645] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:32:42,646] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:32:42,646] [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
Cryptosporangium aurantiacum	strain=DSM 46144	GCA_900143005.1	134849	134849	type	True	100.0	3170	3172	95	conclusive
Cryptosporangium arvum	strain=DSM 44712	GCA_000585375.1	80871	80871	type	True	83.3541	1942	3172	95	below_threshold
Cryptosporangium phraense	strain=A-T 5661	GCA_006912135.1	2593070	2593070	type	True	83.1042	1770	3172	95	below_threshold
Micromonospora aurantiaca	strain=ATCC 27029	GCA_003721415.1	47850	47850	type	True	76.7387	835	3172	95	below_threshold
Virgisporangium ochraceum	strain=NBRC 16418	GCA_016863655.1	65505	65505	type	True	76.4616	1035	3172	95	below_threshold
Actinoplanes cyaneus	strain=NBRC 14990	GCA_016862095.1	52696	52696	type	True	76.4522	917	3172	95	below_threshold
Fodinicola acaciae	strain=GKU 173	GCA_010993745.1	2681555	2681555	type	True	76.4271	690	3172	95	below_threshold
Prauserella rugosa	strain=DSM 43194	GCA_007829565.1	43354	43354	type	True	76.2842	459	3172	95	below_threshold
Amycolatopsis vancoresmycina	strain=DSM 44592	GCA_000388135.1	208444	208444	type	True	76.2582	805	3172	95	below_threshold
Streptoalloteichus tenebrarius	strain=DSM 40477	GCA_024171885.1	1933	1933	type	True	76.2331	613	3172	95	below_threshold
Sphaerisporangium krabiense	strain=DSM 45790	GCA_014200435.1	763782	763782	type	True	76.2	714	3172	95	below_threshold
Saccharopolyspora gloriosae	strain=DSM 45582	GCA_014203325.1	455344	455344	type	True	76.1896	664	3172	95	below_threshold
Prescottella agglutinans	strain=CCTCC AB2014297	GCA_004011865.1	1644129	1644129	type	True	76.1608	485	3172	95	below_threshold
Sphaerisporangium krabiense	strain=NBRC 107571	GCA_016863355.1	763782	763782	type	True	76.1348	707	3172	95	below_threshold
Actinomadura spongiicola	strain=LHW52907	GCA_003432485.1	2303421	2303421	type	True	76.0614	639	3172	95	below_threshold
Streptomyces armeniacus	strain=ATCC 15676	GCA_003355155.1	83291	83291	type	True	76.0315	673	3172	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:32:42,648] [INFO] DFAST Taxonomy check result was written to GCF_900143005.1_IMG-taxon_2700988713_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 13:32:42,648] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:32:42,648] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:32:42,649] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfa7c94e3-f8f1-4da5-aa54-d1218fce8374/dqc_reference/checkm_data
[2024-01-24 13:32:42,649] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:32:42,733] [INFO] Task started: CheckM
[2024-01-24 13:32:42,733] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900143005.1_IMG-taxon_2700988713_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900143005.1_IMG-taxon_2700988713_annotated_assembly_genomic.fna/checkm_input GCF_900143005.1_IMG-taxon_2700988713_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 13:34:03,954] [INFO] Task succeeded: CheckM
[2024-01-24 13:34:03,955] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:34:03,988] [INFO] ===== Completeness check finished =====
[2024-01-24 13:34:03,988] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:34:03,989] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900143005.1_IMG-taxon_2700988713_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 13:34:03,989] [INFO] Task started: Blastn
[2024-01-24 13:34:03,989] [INFO] Running command: blastn -query GCF_900143005.1_IMG-taxon_2700988713_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgfa7c94e3-f8f1-4da5-aa54-d1218fce8374/dqc_reference/reference_markers_gtdb.fasta -out GCF_900143005.1_IMG-taxon_2700988713_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:34:05,922] [INFO] Task succeeded: Blastn
[2024-01-24 13:34:05,926] [INFO] Selected 16 target genomes.
[2024-01-24 13:34:05,927] [INFO] Target genome list was writen to GCF_900143005.1_IMG-taxon_2700988713_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:34:05,950] [INFO] Task started: fastANI
[2024-01-24 13:34:05,951] [INFO] Running command: fastANI --query /var/lib/cwl/stg4823f067-9bae-44f1-aaef-24905b1c648c/GCF_900143005.1_IMG-taxon_2700988713_annotated_assembly_genomic.fna.gz --refList GCF_900143005.1_IMG-taxon_2700988713_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900143005.1_IMG-taxon_2700988713_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:34:32,900] [INFO] Task succeeded: fastANI
[2024-01-24 13:34:32,917] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:34:32,917] [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_900143005.1	s__Cryptosporangium aurantiacum	100.0	3170	3172	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Cryptosporangiaceae;g__Cryptosporangium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000585375.1	s__Cryptosporangium arvum	83.3845	1936	3172	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Cryptosporangiaceae;g__Cryptosporangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006912135.1	s__Cryptosporangium phraense	83.0801	1774	3172	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Cryptosporangiaceae;g__Cryptosporangium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009380105.1	s__WHSM01 sp009380105	76.7843	423	3172	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__WHSM01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902805565.1	s__CADCTP01 sp902805565	76.6113	607	3172	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__CADCTP01;g__CADCTP01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003999975.1	s__Actinoplanes sp003999975	76.5422	825	3172	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016862095.1	s__Actinoplanes cyaneus	76.4808	902	3172	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016863655.1	s__Virgisporangium ochraceum	76.4544	1039	3172	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Virgisporangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000716785.1	s__Amycolatopsis vancoresmycina	76.2115	919	3172	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	99.98	99.98	1.00	1.00	2	-
GCF_001570405.1	s__Microtetraspora niveoalba	76.1985	729	3172	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Microtetraspora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014200435.1	s__Sphaerisporangium krabiense	76.1897	713	3172	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Sphaerisporangium	95.0	100.00	100.00	0.99	0.99	2	-
GCF_003432485.1	s__Spirillospora sp003432485	76.0751	635	3172	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009793335.1	s__Spirillospora sp009793335	76.0745	927	3172	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006874475.1	s__Microbispora hainanensis	76.0594	711	3172	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Microbispora	95.0	95.41	95.40	0.85	0.85	4	-
GCF_006351005.1	s__Miniimonas arenae	75.7645	346	3172	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Beutenbergiaceae;g__Miniimonas	95.0	98.18	97.40	0.91	0.83	3	-
GCF_003991205.1	s__Georgenia sp003991205	75.6629	390	3172	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Georgenia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:34:32,919] [INFO] GTDB search result was written to GCF_900143005.1_IMG-taxon_2700988713_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 13:34:32,919] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:34:32,923] [INFO] DFAST_QC result json was written to GCF_900143005.1_IMG-taxon_2700988713_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 13:34:32,923] [INFO] DFAST_QC completed!
[2024-01-24 13:34:32,923] [INFO] Total running time: 0h2m49s