[2024-01-24 14:38:49,874] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:38:49,875] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:38:49,875] [INFO] DQC Reference Directory: /var/lib/cwl/stg5266d55d-fc7c-4507-a3cb-13215dadc20e/dqc_reference
[2024-01-24 14:38:52,373] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:38:52,374] [INFO] Task started: Prodigal
[2024-01-24 14:38:52,375] [INFO] Running command: gunzip -c /var/lib/cwl/stg1cdf392e-1bf7-47eb-b3b9-cf08e80a2eb1/GCF_014648635.1_ASM1464863v1_genomic.fna.gz | prodigal -d GCF_014648635.1_ASM1464863v1_genomic.fna/cds.fna -a GCF_014648635.1_ASM1464863v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:39:22,541] [INFO] Task succeeded: Prodigal
[2024-01-24 14:39:22,542] [INFO] Task started: HMMsearch
[2024-01-24 14:39:22,542] [INFO] Running command: hmmsearch --tblout GCF_014648635.1_ASM1464863v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5266d55d-fc7c-4507-a3cb-13215dadc20e/dqc_reference/reference_markers.hmm GCF_014648635.1_ASM1464863v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:39:22,963] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:39:22,964] [INFO] Found 6/6 markers.
[2024-01-24 14:39:23,035] [INFO] Query marker FASTA was written to GCF_014648635.1_ASM1464863v1_genomic.fna/markers.fasta
[2024-01-24 14:39:23,035] [INFO] Task started: Blastn
[2024-01-24 14:39:23,035] [INFO] Running command: blastn -query GCF_014648635.1_ASM1464863v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5266d55d-fc7c-4507-a3cb-13215dadc20e/dqc_reference/reference_markers.fasta -out GCF_014648635.1_ASM1464863v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:39:24,471] [INFO] Task succeeded: Blastn
[2024-01-24 14:39:24,477] [INFO] Selected 18 target genomes.
[2024-01-24 14:39:24,478] [INFO] Target genome list was writen to GCF_014648635.1_ASM1464863v1_genomic.fna/target_genomes.txt
[2024-01-24 14:39:24,486] [INFO] Task started: fastANI
[2024-01-24 14:39:24,486] [INFO] Running command: fastANI --query /var/lib/cwl/stg1cdf392e-1bf7-47eb-b3b9-cf08e80a2eb1/GCF_014648635.1_ASM1464863v1_genomic.fna.gz --refList GCF_014648635.1_ASM1464863v1_genomic.fna/target_genomes.txt --output GCF_014648635.1_ASM1464863v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:40:08,833] [INFO] Task succeeded: fastANI
[2024-01-24 14:40:08,833] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5266d55d-fc7c-4507-a3cb-13215dadc20e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:40:08,834] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5266d55d-fc7c-4507-a3cb-13215dadc20e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:40:08,850] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:40:08,850] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:40:08,850] [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 olivaceoviridis	strain=JCM 4499	GCA_014650115.1	1921	1921	type	True	90.7303	2213	3002	95	below_threshold
Streptomyces corchorusii	strain=DSM 40340	GCA_001514055.1	1903	1903	type	True	90.6906	2197	3002	95	below_threshold
Streptomyces canarius	strain=JCM 4733	GCA_014650735.1	285453	285453	type	True	90.5509	2235	3002	95	below_threshold
Streptomyces spinosus	strain=SBTS01	GCA_020400655.1	2872623	2872623	type	True	90.3631	2118	3002	95	below_threshold
Streptomyces echinatus	strain=CECT 3313	GCA_014203595.1	67293	67293	type	True	89.9186	2145	3002	95	below_threshold
Streptomyces musisoli	strain=CH5-8	GCA_016741855.1	2802280	2802280	type	True	89.8759	2139	3002	95	below_threshold
Streptomyces echinatus	strain=JCM4574	GCA_020400685.1	67293	67293	type	True	89.8578	2117	3002	95	below_threshold
Streptomyces achromogenes subsp. achromogenes	strain=NRRL B-2120	GCA_000720835.1	67256	67255	type	True	89.4651	1967	3002	95	below_threshold
Streptomyces lavenduligriseus	strain=NRRL ISP-5487	GCA_000718625.1	67315	67315	type	True	89.3684	1977	3002	95	below_threshold
Streptomyces rubradiris	strain=JCM 4955	GCA_014656255.1	285531	285531	type	True	89.3023	2008	3002	95	below_threshold
Streptomyces rubradiris	strain=NBRC 14000	GCA_016860525.1	285531	285531	type	True	89.2798	2015	3002	95	below_threshold
Streptomyces eurythermus	strain=JCM 4206	GCA_014649115.1	42237	42237	type	True	89.252	2058	3002	95	below_threshold
Streptomyces barringtoniae	strain=JA03	GCA_020819595.1	2892029	2892029	type	True	88.189	2008	3002	95	below_threshold
Streptomyces durhamensis	strain=NRRL B-3309	GCA_000725475.1	68194	68194	type	True	88.1466	2069	3002	95	below_threshold
Streptomyces fodineus	strain=TW1S1	GCA_001735805.1	1904616	1904616	type	True	87.9937	2050	3002	95	below_threshold
Streptomyces shenzhenensis subsp. oryzicola	strain=W18L9	GCA_013870495.1	2749088	943815	type	True	85.4067	1412	3002	95	below_threshold
Streptomyces shenzhenensis	strain=DSM 42034	GCA_021462265.1	943815	943815	type	True	85.2182	1916	3002	95	below_threshold
Streptomyces harenosi	strain=PRKS01-65	GCA_011008945.1	2697029	2697029	type	True	84.6875	1512	3002	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:40:08,860] [INFO] DFAST Taxonomy check result was written to GCF_014648635.1_ASM1464863v1_genomic.fna/tc_result.tsv
[2024-01-24 14:40:08,861] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:40:08,861] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:40:08,861] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5266d55d-fc7c-4507-a3cb-13215dadc20e/dqc_reference/checkm_data
[2024-01-24 14:40:08,863] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:40:08,948] [INFO] Task started: CheckM
[2024-01-24 14:40:08,952] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014648635.1_ASM1464863v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014648635.1_ASM1464863v1_genomic.fna/checkm_input GCF_014648635.1_ASM1464863v1_genomic.fna/checkm_result
[2024-01-24 14:42:30,713] [INFO] Task succeeded: CheckM
[2024-01-24 14:42:30,714] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:42:30,740] [INFO] ===== Completeness check finished =====
[2024-01-24 14:42:30,741] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:42:30,741] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014648635.1_ASM1464863v1_genomic.fna/markers.fasta)
[2024-01-24 14:42:30,742] [INFO] Task started: Blastn
[2024-01-24 14:42:30,742] [INFO] Running command: blastn -query GCF_014648635.1_ASM1464863v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5266d55d-fc7c-4507-a3cb-13215dadc20e/dqc_reference/reference_markers_gtdb.fasta -out GCF_014648635.1_ASM1464863v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:42:32,992] [INFO] Task succeeded: Blastn
[2024-01-24 14:42:32,996] [INFO] Selected 13 target genomes.
[2024-01-24 14:42:32,997] [INFO] Target genome list was writen to GCF_014648635.1_ASM1464863v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:42:33,012] [INFO] Task started: fastANI
[2024-01-24 14:42:33,012] [INFO] Running command: fastANI --query /var/lib/cwl/stg1cdf392e-1bf7-47eb-b3b9-cf08e80a2eb1/GCF_014648635.1_ASM1464863v1_genomic.fna.gz --refList GCF_014648635.1_ASM1464863v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014648635.1_ASM1464863v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:43:06,737] [INFO] Task succeeded: fastANI
[2024-01-24 14:43:06,751] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:43:06,752] [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_014648635.1	s__Streptomyces cinerochromogenes	100.0	3000	3002	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_002155905.1	s__Streptomyces tricolor	91.8037	1812	3002	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	91.462	2198	3002	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000720135.1	s__Streptomyces sp000720135	91.2003	2244	3002	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.69	98.69	0.94	0.94	2	-
GCF_000716535.1	s__Streptomyces flaveolus_A	90.973	2186	3002	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.26	98.84	0.94	0.91	9	-
GCF_002920615.1	s__Streptomyces sp002920615	90.8204	2142	3002	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.01	97.01	0.88	0.88	2	-
GCF_014650115.1	s__Streptomyces olivaceoviridis	90.7723	2207	3002	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.78	96.54	0.86	0.85	6	-
GCF_013046785.1	s__Streptomyces sp013046785	90.7404	2069	3002	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014649295.1	s__Streptomyces libani_A	90.6389	2110	3002	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	89.8759	2139	3002	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000720835.1	s__Streptomyces achromogenes	89.4676	1966	3002	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	89.2891	2013	3002	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.184	99.99	99.99	1.00	1.00	2	-
GCF_014649115.1	s__Streptomyces eurythermus	89.2718	2057	3002	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.2781	97.90	96.79	0.90	0.85	4	-
--------------------------------------------------------------------------------
[2024-01-24 14:43:06,753] [INFO] GTDB search result was written to GCF_014648635.1_ASM1464863v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:43:06,754] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:43:06,768] [INFO] DFAST_QC result json was written to GCF_014648635.1_ASM1464863v1_genomic.fna/dqc_result.json
[2024-01-24 14:43:06,769] [INFO] DFAST_QC completed!
[2024-01-24 14:43:06,769] [INFO] Total running time: 0h4m17s