[2024-01-24 12:14:49,211] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:14:49,212] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:14:49,213] [INFO] DQC Reference Directory: /var/lib/cwl/stg5c19e932-58b5-462b-ba1a-fb79961d5dc3/dqc_reference
[2024-01-24 12:14:50,563] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:14:50,564] [INFO] Task started: Prodigal
[2024-01-24 12:14:50,564] [INFO] Running command: gunzip -c /var/lib/cwl/stg06e44730-1a54-4d1e-9481-d0b52d4d4a49/GCF_014647675.1_ASM1464767v1_genomic.fna.gz | prodigal -d GCF_014647675.1_ASM1464767v1_genomic.fna/cds.fna -a GCF_014647675.1_ASM1464767v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:15:21,096] [INFO] Task succeeded: Prodigal
[2024-01-24 12:15:21,097] [INFO] Task started: HMMsearch
[2024-01-24 12:15:21,097] [INFO] Running command: hmmsearch --tblout GCF_014647675.1_ASM1464767v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5c19e932-58b5-462b-ba1a-fb79961d5dc3/dqc_reference/reference_markers.hmm GCF_014647675.1_ASM1464767v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:15:21,528] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:15:21,530] [INFO] Found 6/6 markers.
[2024-01-24 12:15:21,612] [INFO] Query marker FASTA was written to GCF_014647675.1_ASM1464767v1_genomic.fna/markers.fasta
[2024-01-24 12:15:21,613] [INFO] Task started: Blastn
[2024-01-24 12:15:21,613] [INFO] Running command: blastn -query GCF_014647675.1_ASM1464767v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5c19e932-58b5-462b-ba1a-fb79961d5dc3/dqc_reference/reference_markers.fasta -out GCF_014647675.1_ASM1464767v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:23,011] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:23,015] [INFO] Selected 22 target genomes.
[2024-01-24 12:15:23,015] [INFO] Target genome list was writen to GCF_014647675.1_ASM1464767v1_genomic.fna/target_genomes.txt
[2024-01-24 12:15:23,024] [INFO] Task started: fastANI
[2024-01-24 12:15:23,024] [INFO] Running command: fastANI --query /var/lib/cwl/stg06e44730-1a54-4d1e-9481-d0b52d4d4a49/GCF_014647675.1_ASM1464767v1_genomic.fna.gz --refList GCF_014647675.1_ASM1464767v1_genomic.fna/target_genomes.txt --output GCF_014647675.1_ASM1464767v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:16:11,607] [INFO] Task succeeded: fastANI
[2024-01-24 12:16:11,608] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5c19e932-58b5-462b-ba1a-fb79961d5dc3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:16:11,608] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5c19e932-58b5-462b-ba1a-fb79961d5dc3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:16:11,631] [INFO] Found 22 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:16:11,631] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:16:11,632] [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 scabichelini	strain=HC44	GCA_011045015.1	2711217	2711217	type	True	90.3878	2286	3379	95	below_threshold
Streptomyces sporangiiformans	strain=NEAU-SSA 1	GCA_003568675.1	2315329	2315329	type	True	87.8473	2189	3379	95	below_threshold
Streptomyces sporangiiformans	strain=NEAU-SSA 1	GCA_005768555.2	2315329	2315329	type	True	87.8353	2194	3379	95	below_threshold
Streptomyces montanus	strain=NEAU-C151	GCA_005786655.1	2580423	2580423	type	True	87.7714	2156	3379	95	below_threshold
Streptomyces umbrinus	strain=JCM 4521	GCA_014650195.1	67370	67370	type	True	86.0343	2220	3379	95	below_threshold
Streptomyces phaeochromogenes	strain=NRRL B-1248	GCA_001418655.1	1923	1923	type	True	85.9949	1972	3379	95	below_threshold
Streptomyces aurantiacus	strain=NRRL ISP-5412	GCA_001418335.1	47760	47760	type	True	85.233	1607	3379	95	below_threshold
Streptomyces dengpaensis	strain=XZHG99	GCA_002946835.1	2049881	2049881	type	True	84.7404	1678	3379	95	below_threshold
Streptomyces albiflavescens	strain=CGMCC 4.7111	GCA_014645835.1	1623582	1623582	type	True	84.4768	1940	3379	95	below_threshold
Streptomyces olivochromogenes	strain=DSM 40451	GCA_001514115.1	1963	1963	type	True	84.3368	1914	3379	95	below_threshold
Streptomyces mirabilis	strain=JCM 4551	GCA_014650275.1	68239	68239	suspected-type	True	84.2199	1976	3379	95	below_threshold
Streptomyces coeruleorubidus	strain=ATCC 13740	GCA_008705135.1	116188	116188	suspected-type	True	84.0886	1974	3379	95	below_threshold
Streptomyces blattellae	strain=TRM63209	GCA_009709555.1	2569855	2569855	type	True	83.952	1707	3379	95	below_threshold
Streptomyces azureus	strain=ATCC 14921	GCA_001270025.1	146537	146537	type	True	83.7781	1777	3379	95	below_threshold
Streptomyces deccanensis	strain=KCTC 19241	GCA_022385335.1	424188	424188	type	True	83.7584	1948	3379	95	below_threshold
Streptomyces caniscabiei	strain=NE06-02D	GCA_014930365.1	2746961	2746961	type	True	83.4901	1980	3379	95	below_threshold
Streptomyces populi	strain=A249	GCA_002911015.1	2058924	2058924	type	True	83.4744	1668	3379	95	below_threshold
Streptomyces triticiradicis	strain=NEAU-H2	GCA_008868685.1	2651189	2651189	type	True	83.3553	1707	3379	95	below_threshold
Streptomyces glomeratus	strain=DSM 41457	GCA_021462825.1	284452	284452	type	True	83.1947	1498	3379	95	below_threshold
Streptomyces bauhiniae	strain=Bv016	GCA_004784475.1	2340725	2340725	type	True	82.2545	1336	3379	95	below_threshold
Streptomyces nymphaeiformis	strain=SFB5A	GCA_014203895.1	2663842	2663842	type	True	81.0237	1361	3379	95	below_threshold
Streptomyces mashuensis	strain=JCM 4059	GCA_014654785.1	33904	33904	type	True	80.0613	1114	3379	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:16:11,633] [INFO] DFAST Taxonomy check result was written to GCF_014647675.1_ASM1464767v1_genomic.fna/tc_result.tsv
[2024-01-24 12:16:11,634] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:16:11,634] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:16:11,634] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5c19e932-58b5-462b-ba1a-fb79961d5dc3/dqc_reference/checkm_data
[2024-01-24 12:16:11,636] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:16:11,731] [INFO] Task started: CheckM
[2024-01-24 12:16:11,732] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014647675.1_ASM1464767v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014647675.1_ASM1464767v1_genomic.fna/checkm_input GCF_014647675.1_ASM1464767v1_genomic.fna/checkm_result
[2024-01-24 12:17:47,169] [INFO] Task succeeded: CheckM
[2024-01-24 12:17:47,171] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 3.12%
Strain heterogeneity: 66.67%
--------------------------------------------------------------------------------
[2024-01-24 12:17:47,203] [INFO] ===== Completeness check finished =====
[2024-01-24 12:17:47,203] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:17:47,204] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014647675.1_ASM1464767v1_genomic.fna/markers.fasta)
[2024-01-24 12:17:47,204] [INFO] Task started: Blastn
[2024-01-24 12:17:47,204] [INFO] Running command: blastn -query GCF_014647675.1_ASM1464767v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5c19e932-58b5-462b-ba1a-fb79961d5dc3/dqc_reference/reference_markers_gtdb.fasta -out GCF_014647675.1_ASM1464767v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:17:49,442] [INFO] Task succeeded: Blastn
[2024-01-24 12:17:49,446] [INFO] Selected 16 target genomes.
[2024-01-24 12:17:49,447] [INFO] Target genome list was writen to GCF_014647675.1_ASM1464767v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:17:49,459] [INFO] Task started: fastANI
[2024-01-24 12:17:49,460] [INFO] Running command: fastANI --query /var/lib/cwl/stg06e44730-1a54-4d1e-9481-d0b52d4d4a49/GCF_014647675.1_ASM1464767v1_genomic.fna.gz --refList GCF_014647675.1_ASM1464767v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014647675.1_ASM1464767v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:18:28,205] [INFO] Task succeeded: fastANI
[2024-01-24 12:18:28,219] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:18:28,219] [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_014647675.1	s__Streptomyces flaveus	100.0	3378	3379	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.63	96.63	0.83	0.83	2	conclusive
GCF_011045025.1	s__Streptomyces ureilyticus	92.604	2317	3379	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011045015.1	s__Streptomyces scabichelini	90.3608	2288	3379	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005768555.2	s__Streptomyces sporangiiformans	87.8345	2193	3379	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.93	95.85	0.91	0.82	3	-
GCF_008905045.1	s__Streptomyces albicerus	87.0424	2254	3379	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007050945.1	s__Streptomyces sp007050945	86.1184	2233	3379	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016598615.1	s__Streptomyces sp016598615	86.1068	2164	3379	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001418655.1	s__Streptomyces phaeochromogenes	85.9266	1984	3379	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.97	95.89	0.88	0.87	3	-
GCF_014645835.1	s__Streptomyces albiflavescens	84.4739	1942	3379	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014650275.1	s__Streptomyces mirabilis	84.2316	1974	3379	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	96.2382	96.82	96.27	0.84	0.80	23	-
GCF_000717875.1	s__Streptomyces sp000717875	83.6442	1737	3379	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.70	99.70	0.96	0.96	2	-
GCF_008704515.1	s__Streptomyces viridosporus	83.2385	1521	3379	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.42	99.12	0.96	0.94	4	-
GCF_003143855.1	s__Streptomyces sp003143855	82.6877	1554	3379	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.17	95.17	0.79	0.79	2	-
GCF_009916105.1	s__Streptomyces sp009916105	81.209	1277	3379	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003386135.1	s__Streptomyces sp003386135	81.07	1363	3379	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.57	99.57	0.94	0.94	2	-
GCF_000830005.1	s__Streptomyces vietnamensis	81.0065	1398	3379	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:18:28,221] [INFO] GTDB search result was written to GCF_014647675.1_ASM1464767v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:18:28,221] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:18:28,227] [INFO] DFAST_QC result json was written to GCF_014647675.1_ASM1464767v1_genomic.fna/dqc_result.json
[2024-01-24 12:18:28,227] [INFO] DFAST_QC completed!
[2024-01-24 12:18:28,227] [INFO] Total running time: 0h3m39s