[2024-01-24 14:19:45,765] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:19:45,768] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:19:45,769] [INFO] DQC Reference Directory: /var/lib/cwl/stg7457506c-d206-4307-9a4a-4ada37241896/dqc_reference
[2024-01-24 14:19:47,133] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:19:47,134] [INFO] Task started: Prodigal
[2024-01-24 14:19:47,135] [INFO] Running command: gunzip -c /var/lib/cwl/stg508adf40-3cde-47f7-b771-be83f3e644b6/GCF_005786655.1_ASM578665v1_genomic.fna.gz | prodigal -d GCF_005786655.1_ASM578665v1_genomic.fna/cds.fna -a GCF_005786655.1_ASM578665v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:20:16,539] [INFO] Task succeeded: Prodigal
[2024-01-24 14:20:16,539] [INFO] Task started: HMMsearch
[2024-01-24 14:20:16,539] [INFO] Running command: hmmsearch --tblout GCF_005786655.1_ASM578665v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7457506c-d206-4307-9a4a-4ada37241896/dqc_reference/reference_markers.hmm GCF_005786655.1_ASM578665v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:20:16,988] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:20:16,990] [INFO] Found 6/6 markers.
[2024-01-24 14:20:17,073] [INFO] Query marker FASTA was written to GCF_005786655.1_ASM578665v1_genomic.fna/markers.fasta
[2024-01-24 14:20:17,073] [INFO] Task started: Blastn
[2024-01-24 14:20:17,073] [INFO] Running command: blastn -query GCF_005786655.1_ASM578665v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7457506c-d206-4307-9a4a-4ada37241896/dqc_reference/reference_markers.fasta -out GCF_005786655.1_ASM578665v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:20:18,333] [INFO] Task succeeded: Blastn
[2024-01-24 14:20:18,336] [INFO] Selected 16 target genomes.
[2024-01-24 14:20:18,336] [INFO] Target genome list was writen to GCF_005786655.1_ASM578665v1_genomic.fna/target_genomes.txt
[2024-01-24 14:20:18,344] [INFO] Task started: fastANI
[2024-01-24 14:20:18,345] [INFO] Running command: fastANI --query /var/lib/cwl/stg508adf40-3cde-47f7-b771-be83f3e644b6/GCF_005786655.1_ASM578665v1_genomic.fna.gz --refList GCF_005786655.1_ASM578665v1_genomic.fna/target_genomes.txt --output GCF_005786655.1_ASM578665v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:20:56,218] [INFO] Task succeeded: fastANI
[2024-01-24 14:20:56,219] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7457506c-d206-4307-9a4a-4ada37241896/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:20:56,219] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7457506c-d206-4307-9a4a-4ada37241896/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:20:56,232] [INFO] Found 16 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 14:20:56,232] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 14:20:56,233] [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 montanus	strain=NEAU-C151	GCA_005786655.1	2580423	2580423	type	True	100.0	3326	3332	95	inconclusive
Streptomyces sporangiiformans	strain=NEAU-SSA 1	GCA_003568675.1	2315329	2315329	type	True	95.8538	2686	3332	95	inconclusive
Streptomyces sporangiiformans	strain=NEAU-SSA 1	GCA_005768555.2	2315329	2315329	type	True	95.8449	2686	3332	95	inconclusive
Streptomyces scabichelini	strain=HC44	GCA_011045015.1	2711217	2711217	type	True	88.2929	2118	3332	95	below_threshold
Streptomyces umbrinus	strain=JCM 4521	GCA_014650195.1	67370	67370	type	True	86.1251	2193	3332	95	below_threshold
Streptomyces phaeochromogenes	strain=NRRL B-1248	GCA_001418655.1	1923	1923	type	True	85.9951	1934	3332	95	below_threshold
Streptomyces aurantiacus	strain=NRRL ISP-5412	GCA_001418335.1	47760	47760	type	True	85.1472	1598	3332	95	below_threshold
Streptomyces dengpaensis	strain=XZHG99	GCA_002946835.1	2049881	2049881	type	True	84.9689	1684	3332	95	below_threshold
Streptomyces swartbergensis	strain=HMC13	GCA_002148965.1	487165	487165	type	True	83.8459	1633	3332	95	below_threshold
Streptomyces violarus	strain=CECT 3237	GCA_014191845.1	67380	67380	type	True	83.7996	1901	3332	95	below_threshold
Streptomyces blattellae	strain=TRM63209	GCA_009709555.1	2569855	2569855	type	True	83.7901	1677	3332	95	below_threshold
Streptomyces janthinus	strain=JCM 4387	GCA_014649675.1	67308	67308	type	True	83.6634	1939	3332	95	below_threshold
Streptomyces deccanensis	strain=KCTC 19241	GCA_022385335.1	424188	424188	type	True	83.6133	1909	3332	95	below_threshold
Streptomyces glomeratus	strain=DSM 41457	GCA_021462825.1	284452	284452	type	True	83.5068	1515	3332	95	below_threshold
Streptomyces caniscabiei	strain=NE06-02D	GCA_014930365.1	2746961	2746961	type	True	83.3756	1945	3332	95	below_threshold
Streptomyces hokutonensis	strain=R1-NS-10	GCA_000376565.1	1306990	1306990	type	True	83.1963	1825	3332	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:20:56,234] [INFO] DFAST Taxonomy check result was written to GCF_005786655.1_ASM578665v1_genomic.fna/tc_result.tsv
[2024-01-24 14:20:56,235] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:20:56,235] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:20:56,235] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7457506c-d206-4307-9a4a-4ada37241896/dqc_reference/checkm_data
[2024-01-24 14:20:56,237] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:20:56,325] [INFO] Task started: CheckM
[2024-01-24 14:20:56,326] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_005786655.1_ASM578665v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_005786655.1_ASM578665v1_genomic.fna/checkm_input GCF_005786655.1_ASM578665v1_genomic.fna/checkm_result
[2024-01-24 14:22:34,998] [INFO] Task succeeded: CheckM
[2024-01-24 14:22:35,000] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:22:35,025] [INFO] ===== Completeness check finished =====
[2024-01-24 14:22:35,025] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:22:35,025] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_005786655.1_ASM578665v1_genomic.fna/markers.fasta)
[2024-01-24 14:22:35,026] [INFO] Task started: Blastn
[2024-01-24 14:22:35,026] [INFO] Running command: blastn -query GCF_005786655.1_ASM578665v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7457506c-d206-4307-9a4a-4ada37241896/dqc_reference/reference_markers_gtdb.fasta -out GCF_005786655.1_ASM578665v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:22:37,149] [INFO] Task succeeded: Blastn
[2024-01-24 14:22:37,153] [INFO] Selected 18 target genomes.
[2024-01-24 14:22:37,153] [INFO] Target genome list was writen to GCF_005786655.1_ASM578665v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:22:37,167] [INFO] Task started: fastANI
[2024-01-24 14:22:37,167] [INFO] Running command: fastANI --query /var/lib/cwl/stg508adf40-3cde-47f7-b771-be83f3e644b6/GCF_005786655.1_ASM578665v1_genomic.fna.gz --refList GCF_005786655.1_ASM578665v1_genomic.fna/target_genomes_gtdb.txt --output GCF_005786655.1_ASM578665v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:23:20,818] [INFO] Task succeeded: fastANI
[2024-01-24 14:23:20,833] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:23:20,833] [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_005768555.2	s__Streptomyces sporangiiformans	95.8527	2685	3332	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.93	95.85	0.91	0.82	3	conclusive
GCF_011045015.1	s__Streptomyces scabichelini	88.2631	2123	3332	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014647675.1	s__Streptomyces flaveus	87.869	2153	3332	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.63	96.63	0.83	0.83	2	-
GCF_011045025.1	s__Streptomyces ureilyticus	87.2745	2005	3332	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008905045.1	s__Streptomyces albicerus	86.8789	2214	3332	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	86.208	2170	3332	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	86.1028	2146	3332	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	86.0307	1930	3332	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.97	95.89	0.88	0.87	3	-
GCF_019090165.1	s__Streptomyces sp019090165	85.7006	1966	3332	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019219825.1	s__Streptomyces sp019219825	83.8475	1690	3332	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004023625.1	s__Streptomyces cavernae	83.847	1964	3332	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002148965.1	s__Streptomyces swartbergensis	83.7931	1644	3332	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015712165.1	s__Streptomyces spinoverrucosus_A	83.7557	1746	3332	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000317595.1	s__Streptomyces ipomoeae	83.6629	1759	3332	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.29	98.81	0.89	0.87	4	-
GCF_000717875.1	s__Streptomyces sp000717875	83.6349	1702	3332	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.70	99.70	0.96	0.96	2	-
GCA_000715635.1	s__Streptomyces violaceus	83.5957	1938	3332	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.39	95.19	0.85	0.83	5	-
GCF_000376565.1	s__Streptomyces hokutonensis	83.2402	1816	3332	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.37	96.37	0.82	0.82	2	-
GCF_002920535.1	s__Streptomyces sp002920535	83.1228	1607	3332	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 14:23:20,836] [INFO] GTDB search result was written to GCF_005786655.1_ASM578665v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:23:20,836] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:23:20,840] [INFO] DFAST_QC result json was written to GCF_005786655.1_ASM578665v1_genomic.fna/dqc_result.json
[2024-01-24 14:23:20,840] [INFO] DFAST_QC completed!
[2024-01-24 14:23:20,840] [INFO] Total running time: 0h3m35s