[2024-01-24 13:27:31,818] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:27:31,821] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:27:31,822] [INFO] DQC Reference Directory: /var/lib/cwl/stgf9ded6ed-4771-46a1-bb84-b6c6daba93db/dqc_reference
[2024-01-24 13:27:33,205] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:27:33,206] [INFO] Task started: Prodigal
[2024-01-24 13:27:33,207] [INFO] Running command: gunzip -c /var/lib/cwl/stg050c7dae-3ada-4b04-a2d8-0a52eb5c753b/GCF_014649115.1_ASM1464911v1_genomic.fna.gz | prodigal -d GCF_014649115.1_ASM1464911v1_genomic.fna/cds.fna -a GCF_014649115.1_ASM1464911v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:28:00,118] [INFO] Task succeeded: Prodigal
[2024-01-24 13:28:00,118] [INFO] Task started: HMMsearch
[2024-01-24 13:28:00,118] [INFO] Running command: hmmsearch --tblout GCF_014649115.1_ASM1464911v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf9ded6ed-4771-46a1-bb84-b6c6daba93db/dqc_reference/reference_markers.hmm GCF_014649115.1_ASM1464911v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:28:00,515] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:28:00,517] [INFO] Found 6/6 markers.
[2024-01-24 13:28:00,595] [INFO] Query marker FASTA was written to GCF_014649115.1_ASM1464911v1_genomic.fna/markers.fasta
[2024-01-24 13:28:00,595] [INFO] Task started: Blastn
[2024-01-24 13:28:00,595] [INFO] Running command: blastn -query GCF_014649115.1_ASM1464911v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf9ded6ed-4771-46a1-bb84-b6c6daba93db/dqc_reference/reference_markers.fasta -out GCF_014649115.1_ASM1464911v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:28:01,963] [INFO] Task succeeded: Blastn
[2024-01-24 13:28:01,967] [INFO] Selected 14 target genomes.
[2024-01-24 13:28:01,967] [INFO] Target genome list was writen to GCF_014649115.1_ASM1464911v1_genomic.fna/target_genomes.txt
[2024-01-24 13:28:01,973] [INFO] Task started: fastANI
[2024-01-24 13:28:01,973] [INFO] Running command: fastANI --query /var/lib/cwl/stg050c7dae-3ada-4b04-a2d8-0a52eb5c753b/GCF_014649115.1_ASM1464911v1_genomic.fna.gz --refList GCF_014649115.1_ASM1464911v1_genomic.fna/target_genomes.txt --output GCF_014649115.1_ASM1464911v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:28:34,170] [INFO] Task succeeded: fastANI
[2024-01-24 13:28:34,170] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf9ded6ed-4771-46a1-bb84-b6c6daba93db/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:28:34,171] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf9ded6ed-4771-46a1-bb84-b6c6daba93db/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:28:34,183] [INFO] Found 14 fastANI hits (5 hits with ANI > threshold)
[2024-01-24 13:28:34,183] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 13:28:34,183] [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
Streptomyces eurythermus	strain=JCM 4206	GCA_014649115.1	42237	42237	type	True	100.0	3020	3022	95	inconclusive
Streptomyces lavenduligriseus	strain=NRRL ISP-5487	GCA_000718625.1	67315	67315	type	True	96.9394	2419	3022	95	inconclusive
Streptomyces achromogenes subsp. achromogenes	strain=NRRL B-2120	GCA_000720835.1	67256	67255	type	True	95.2791	2352	3022	95	inconclusive
Streptomyces rubradiris	strain=JCM 4955	GCA_014656255.1	285531	285531	type	True	95.1667	2317	3022	95	inconclusive
Streptomyces rubradiris	strain=NBRC 14000	GCA_016860525.1	285531	285531	type	True	95.0835	2341	3022	95	inconclusive
Streptomyces spinosus	strain=SBTS01	GCA_020400655.1	2872623	2872623	type	True	89.114	1995	3022	95	below_threshold
Streptomyces barringtoniae	strain=JA03	GCA_020819595.1	2892029	2892029	type	True	87.3568	1847	3022	95	below_threshold
Streptomyces sennicomposti	strain=RCPT1-4	GCA_019890635.1	2873384	2873384	type	True	85.2532	1590	3022	95	below_threshold
Streptomyces harenosi	strain=PRKS01-65	GCA_011008945.1	2697029	2697029	type	True	84.8097	1552	3022	95	below_threshold
Streptomyces shenzhenensis	strain=DSM 42034	GCA_021462265.1	943815	943815	type	True	84.7157	1800	3022	95	below_threshold
Streptomyces jietaisiensis	strain=CGMCC 4.1859	GCA_900102095.1	235987	235987	type	True	83.2368	1502	3022	95	below_threshold
Actinacidiphila bryophytorum	strain=DSM 42138	GCA_017164735.1	1436133	1436133	type	True	79.9481	1061	3022	95	below_threshold
Actinacidiphila paucisporea	strain=CGMCC 4.2025	GCA_900142575.1	310782	310782	type	True	79.7178	1245	3022	95	below_threshold
Streptomyces albus subsp. albus	strain=NRRL B-1811	GCA_000725885.1	67257	1888	suspected-type	True	79.6709	1231	3022	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:28:34,185] [INFO] DFAST Taxonomy check result was written to GCF_014649115.1_ASM1464911v1_genomic.fna/tc_result.tsv
[2024-01-24 13:28:34,185] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:28:34,186] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:28:34,186] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf9ded6ed-4771-46a1-bb84-b6c6daba93db/dqc_reference/checkm_data
[2024-01-24 13:28:34,187] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:28:34,272] [INFO] Task started: CheckM
[2024-01-24 13:28:34,273] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014649115.1_ASM1464911v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014649115.1_ASM1464911v1_genomic.fna/checkm_input GCF_014649115.1_ASM1464911v1_genomic.fna/checkm_result
[2024-01-24 13:30:49,547] [INFO] Task succeeded: CheckM
[2024-01-24 13:30:49,548] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:30:49,572] [INFO] ===== Completeness check finished =====
[2024-01-24 13:30:49,572] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:30:49,573] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014649115.1_ASM1464911v1_genomic.fna/markers.fasta)
[2024-01-24 13:30:49,573] [INFO] Task started: Blastn
[2024-01-24 13:30:49,573] [INFO] Running command: blastn -query GCF_014649115.1_ASM1464911v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf9ded6ed-4771-46a1-bb84-b6c6daba93db/dqc_reference/reference_markers_gtdb.fasta -out GCF_014649115.1_ASM1464911v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:30:51,958] [INFO] Task succeeded: Blastn
[2024-01-24 13:30:51,963] [INFO] Selected 17 target genomes.
[2024-01-24 13:30:51,963] [INFO] Target genome list was writen to GCF_014649115.1_ASM1464911v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:30:51,973] [INFO] Task started: fastANI
[2024-01-24 13:30:51,974] [INFO] Running command: fastANI --query /var/lib/cwl/stg050c7dae-3ada-4b04-a2d8-0a52eb5c753b/GCF_014649115.1_ASM1464911v1_genomic.fna.gz --refList GCF_014649115.1_ASM1464911v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014649115.1_ASM1464911v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:31:31,751] [INFO] Task succeeded: fastANI
[2024-01-24 13:31:31,770] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:31:31,771] [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_014649115.1	s__Streptomyces eurythermus	100.0	3020	3022	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.2781	97.90	96.79	0.90	0.85	4	conclusive
GCF_000720835.1	s__Streptomyces achromogenes	95.2538	2355	3022	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.2781	N/A	N/A	N/A	N/A	1	-
GCF_016860525.1	s__Streptomyces rubradiris	95.1356	2335	3022	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.184	99.99	99.99	1.00	1.00	2	-
GCF_000718775.1	s__Streptomyces sp000718775	89.5613	1950	3022	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013046785.1	s__Streptomyces sp013046785	89.4038	1912	3022	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002155905.1	s__Streptomyces tricolor	89.3603	1702	3022	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.81	98.00	0.86	0.72	5	-
GCF_017526105.1	s__Streptomyces cyanogenus	89.3443	1948	3022	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000716535.1	s__Streptomyces flaveolus_A	89.319	2023	3022	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.26	98.84	0.94	0.91	9	-
GCF_014650115.1	s__Streptomyces olivaceoviridis	89.2701	2045	3022	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.78	96.54	0.86	0.85	6	-
GCF_014648635.1	s__Streptomyces cinerochromogenes	89.252	2068	3022	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016741855.1	s__Streptomyces musisoli	89.1052	2010	3022	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009604455.1	s__Streptomyces sp009604455	87.2941	1903	3022	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001735805.1	s__Streptomyces fodineus	87.144	1869	3022	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001514215.1	s__Streptomyces bungoensis	86.7243	1788	3022	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003270085.1	s__Streptomyces triticisoli	84.8118	1395	3022	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019049285.1	s__Streptomyces sp019049285	84.0133	1712	3022	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001278075.1	s__Streptomyces pristinaespiralis	81.1133	1418	3022	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.86	99.72	0.99	0.98	3	-
--------------------------------------------------------------------------------
[2024-01-24 13:31:31,773] [INFO] GTDB search result was written to GCF_014649115.1_ASM1464911v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:31:31,774] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:31:31,778] [INFO] DFAST_QC result json was written to GCF_014649115.1_ASM1464911v1_genomic.fna/dqc_result.json
[2024-01-24 13:31:31,779] [INFO] DFAST_QC completed!
[2024-01-24 13:31:31,779] [INFO] Total running time: 0h3m60s