[2024-01-24 14:22:01,673] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:22:01,675] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:22:01,675] [INFO] DQC Reference Directory: /var/lib/cwl/stg4d8660b2-ba22-450f-9957-4db04da31ff5/dqc_reference
[2024-01-24 14:22:02,907] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:22:02,908] [INFO] Task started: Prodigal
[2024-01-24 14:22:02,908] [INFO] Running command: gunzip -c /var/lib/cwl/stg01a8ae43-6e85-4658-8ca4-aa57173e2adf/GCF_009709575.1_ASM970957v1_genomic.fna.gz | prodigal -d GCF_009709575.1_ASM970957v1_genomic.fna/cds.fna -a GCF_009709575.1_ASM970957v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:22:22,857] [INFO] Task succeeded: Prodigal
[2024-01-24 14:22:22,857] [INFO] Task started: HMMsearch
[2024-01-24 14:22:22,858] [INFO] Running command: hmmsearch --tblout GCF_009709575.1_ASM970957v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4d8660b2-ba22-450f-9957-4db04da31ff5/dqc_reference/reference_markers.hmm GCF_009709575.1_ASM970957v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:22:23,199] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:22:23,200] [INFO] Found 6/6 markers.
[2024-01-24 14:22:23,250] [INFO] Query marker FASTA was written to GCF_009709575.1_ASM970957v1_genomic.fna/markers.fasta
[2024-01-24 14:22:23,250] [INFO] Task started: Blastn
[2024-01-24 14:22:23,250] [INFO] Running command: blastn -query GCF_009709575.1_ASM970957v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4d8660b2-ba22-450f-9957-4db04da31ff5/dqc_reference/reference_markers.fasta -out GCF_009709575.1_ASM970957v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:22:24,868] [INFO] Task succeeded: Blastn
[2024-01-24 14:22:24,871] [INFO] Selected 18 target genomes.
[2024-01-24 14:22:24,871] [INFO] Target genome list was writen to GCF_009709575.1_ASM970957v1_genomic.fna/target_genomes.txt
[2024-01-24 14:22:24,877] [INFO] Task started: fastANI
[2024-01-24 14:22:24,877] [INFO] Running command: fastANI --query /var/lib/cwl/stg01a8ae43-6e85-4658-8ca4-aa57173e2adf/GCF_009709575.1_ASM970957v1_genomic.fna.gz --refList GCF_009709575.1_ASM970957v1_genomic.fna/target_genomes.txt --output GCF_009709575.1_ASM970957v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:22:54,919] [INFO] Task succeeded: fastANI
[2024-01-24 14:22:54,919] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4d8660b2-ba22-450f-9957-4db04da31ff5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:22:54,920] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4d8660b2-ba22-450f-9957-4db04da31ff5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:22:54,933] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:22:54,934] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:22:54,934] [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 taklimakanensis	strain=TRM43335	GCA_009709575.1	2569853	2569853	type	True	100.0	2044	2045	95	conclusive
Streptomyces radiopugnans	strain=CGMCC 4.3519	GCA_900110735.1	403935	403935	type	True	88.1226	1481	2045	95	below_threshold
Streptomyces barkulensis	strain=RC 1831	GCA_002811705.2	1257026	1257026	type	True	87.5429	1436	2045	95	below_threshold
Streptomyces megasporus	strain=NRRL B-16372	GCA_000718985.1	44060	44060	type	True	87.5061	1385	2045	95	below_threshold
Streptomyces barkulensis	strain=RC 1831	GCA_002843305.1	1257026	1257026	type	True	87.4798	1471	2045	95	below_threshold
Streptomyces verrucosisporus	strain=CPB1-1	GCA_017114865.1	1695161	1695161	type	True	87.4607	1441	2045	95	below_threshold
Streptomyces pini	strain=PL19	GCA_900114215.1	1520580	1520580	type	True	87.4455	1465	2045	95	below_threshold
Streptomyces carminius	strain=TRM SA0054	GCA_002794255.1	2665496	2665496	type	True	86.1843	1415	2045	95	below_threshold
Streptomyces griseocarneus	strain=JCM 4580	GCA_014655595.1	51201	51201	type	True	80.9786	1012	2045	95	below_threshold
Streptomyces griseocarneus	strain=CGMCC4.1088	GCA_020093395.1	51201	51201	type	True	80.8991	1010	2045	95	below_threshold
Streptomyces rimosus subsp. rimosus	strain=R7	GCA_022760195.1	132474	1927	type	True	80.7494	1090	2045	95	below_threshold
Streptomyces albus	strain=NBRC 13014	GCA_000813365.1	1888	1888	suspected-type	True	80.7208	995	2045	95	below_threshold
Streptomyces albus subsp. albus	strain=NRRL B-1811	GCA_000725885.1	67257	1888	suspected-type	True	80.6808	1011	2045	95	below_threshold
Streptomyces sennicomposti	strain=RCPT1-4	GCA_019890635.1	2873384	2873384	type	True	80.6249	1044	2045	95	below_threshold
Streptomyces rapamycinicus	strain=NRRL 5491	GCA_024298965.1	1226757	1226757	type	True	80.6021	1157	2045	95	below_threshold
Actinacidiphila yeochonensis	strain=CN732	GCA_000745345.1	89050	89050	type	True	80.1886	953	2045	95	below_threshold
Actinacidiphila paucisporea	strain=CGMCC 4.2025	GCA_900142575.1	310782	310782	type	True	79.9937	966	2045	95	below_threshold
Actinacidiphila acididurans	strain=KK5PA1	GCA_016918855.1	2784346	2784346	type	True	79.8719	1017	2045	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:22:54,935] [INFO] DFAST Taxonomy check result was written to GCF_009709575.1_ASM970957v1_genomic.fna/tc_result.tsv
[2024-01-24 14:22:54,936] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:22:54,936] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:22:54,936] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4d8660b2-ba22-450f-9957-4db04da31ff5/dqc_reference/checkm_data
[2024-01-24 14:22:54,937] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:22:54,997] [INFO] Task started: CheckM
[2024-01-24 14:22:54,997] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009709575.1_ASM970957v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009709575.1_ASM970957v1_genomic.fna/checkm_input GCF_009709575.1_ASM970957v1_genomic.fna/checkm_result
[2024-01-24 14:24:51,902] [INFO] Task succeeded: CheckM
[2024-01-24 14:24:51,903] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:24:51,922] [INFO] ===== Completeness check finished =====
[2024-01-24 14:24:51,923] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:24:51,923] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009709575.1_ASM970957v1_genomic.fna/markers.fasta)
[2024-01-24 14:24:51,923] [INFO] Task started: Blastn
[2024-01-24 14:24:51,923] [INFO] Running command: blastn -query GCF_009709575.1_ASM970957v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4d8660b2-ba22-450f-9957-4db04da31ff5/dqc_reference/reference_markers_gtdb.fasta -out GCF_009709575.1_ASM970957v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:24:54,321] [INFO] Task succeeded: Blastn
[2024-01-24 14:24:54,324] [INFO] Selected 12 target genomes.
[2024-01-24 14:24:54,324] [INFO] Target genome list was writen to GCF_009709575.1_ASM970957v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:24:54,349] [INFO] Task started: fastANI
[2024-01-24 14:24:54,349] [INFO] Running command: fastANI --query /var/lib/cwl/stg01a8ae43-6e85-4658-8ca4-aa57173e2adf/GCF_009709575.1_ASM970957v1_genomic.fna.gz --refList GCF_009709575.1_ASM970957v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009709575.1_ASM970957v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:25:14,392] [INFO] Task succeeded: fastANI
[2024-01-24 14:25:14,403] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:25:14,404] [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_009709575.1	s__Streptomyces taklimakanensis	100.0	2045	2045	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_900110735.1	s__Streptomyces radiopugnans	88.1163	1482	2045	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000718985.1	s__Streptomyces megasporus	87.4975	1386	2045	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002843305.1	s__Streptomyces barkulensis	87.4885	1470	2045	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	96.765	99.92	99.92	0.99	0.99	2	-
GCF_017114865.1	s__Streptomyces verrucosisporus	87.4817	1438	2045	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.1585	N/A	N/A	N/A	N/A	1	-
GCF_900114215.1	s__Streptomyces pini	87.4058	1470	2045	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	96.765	N/A	N/A	N/A	N/A	1	-
GCF_002794255.1	s__Streptomyces carminius	86.189	1414	2045	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013302895.1	s__Streptomyces chlorinus	80.839	1043	2045	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000725885.1	s__Streptomyces albus	80.653	1016	2045	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.54	97.77	0.97	0.92	14	-
GCF_000745345.1	s__Streptomyces yeochonensis	80.1829	955	2045	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000701325.1	s__Streptomyces sp000701325	80.0395	961	2045	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142575.1	s__Streptomyces paucisporeus	79.9767	971	2045	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 14:25:14,405] [INFO] GTDB search result was written to GCF_009709575.1_ASM970957v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:25:14,406] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:25:14,409] [INFO] DFAST_QC result json was written to GCF_009709575.1_ASM970957v1_genomic.fna/dqc_result.json
[2024-01-24 14:25:14,410] [INFO] DFAST_QC completed!
[2024-01-24 14:25:14,410] [INFO] Total running time: 0h3m13s