[2024-01-24 14:22:01,560] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:22:01,563] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:22:01,563] [INFO] DQC Reference Directory: /var/lib/cwl/stgaf3c56be-24c2-4953-8e94-7004a274ffd2/dqc_reference
[2024-01-24 14:22:02,841] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:22:02,842] [INFO] Task started: Prodigal
[2024-01-24 14:22:02,843] [INFO] Running command: gunzip -c /var/lib/cwl/stg5a8ba81a-daa3-4c16-8647-317dc224151c/GCF_900112355.1_IMG-taxon_2675903061_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900112355.1_IMG-taxon_2675903061_annotated_assembly_genomic.fna/cds.fna -a GCF_900112355.1_IMG-taxon_2675903061_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:22:22,284] [INFO] Task succeeded: Prodigal
[2024-01-24 14:22:22,285] [INFO] Task started: HMMsearch
[2024-01-24 14:22:22,285] [INFO] Running command: hmmsearch --tblout GCF_900112355.1_IMG-taxon_2675903061_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgaf3c56be-24c2-4953-8e94-7004a274ffd2/dqc_reference/reference_markers.hmm GCF_900112355.1_IMG-taxon_2675903061_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:22:22,601] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:22:22,602] [INFO] Found 6/6 markers.
[2024-01-24 14:22:22,656] [INFO] Query marker FASTA was written to GCF_900112355.1_IMG-taxon_2675903061_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 14:22:22,657] [INFO] Task started: Blastn
[2024-01-24 14:22:22,657] [INFO] Running command: blastn -query GCF_900112355.1_IMG-taxon_2675903061_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgaf3c56be-24c2-4953-8e94-7004a274ffd2/dqc_reference/reference_markers.fasta -out GCF_900112355.1_IMG-taxon_2675903061_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:22:23,925] [INFO] Task succeeded: Blastn
[2024-01-24 14:22:23,929] [INFO] Selected 34 target genomes.
[2024-01-24 14:22:23,929] [INFO] Target genome list was writen to GCF_900112355.1_IMG-taxon_2675903061_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 14:22:23,942] [INFO] Task started: fastANI
[2024-01-24 14:22:23,942] [INFO] Running command: fastANI --query /var/lib/cwl/stg5a8ba81a-daa3-4c16-8647-317dc224151c/GCF_900112355.1_IMG-taxon_2675903061_annotated_assembly_genomic.fna.gz --refList GCF_900112355.1_IMG-taxon_2675903061_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900112355.1_IMG-taxon_2675903061_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:23:17,770] [INFO] Task succeeded: fastANI
[2024-01-24 14:23:17,771] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgaf3c56be-24c2-4953-8e94-7004a274ffd2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:23:17,771] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgaf3c56be-24c2-4953-8e94-7004a274ffd2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:23:17,795] [INFO] Found 34 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:23:17,795] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:23:17,796] [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 aidingensis	strain=CGMCC 4.5739	GCA_900112355.1	910347	910347	type	True	100.0	2129	2136	95	conclusive
Streptomyces calidiresistens	strain=DSM 42108	GCA_014141525.1	1485586	1485586	type	True	80.9157	717	2136	95	below_threshold
Streptomyces alkaliphilus	strain=DSM 42118	GCA_014141535.1	1472722	1472722	type	True	80.7346	635	2136	95	below_threshold
Streptomyces pini	strain=PL19	GCA_900114215.1	1520580	1520580	type	True	80.3794	981	2136	95	below_threshold
Streptomyces barkulensis	strain=RC 1831	GCA_002811705.2	1257026	1257026	type	True	80.256	1011	2136	95	below_threshold
Streptomyces taklimakanensis	strain=TRM43335	GCA_009709575.1	2569853	2569853	type	True	80.1675	948	2136	95	below_threshold
Streptomyces triticirhizae	strain=NEAU-YY642	GCA_003696235.1	2483353	2483353	type	True	80.0667	941	2136	95	below_threshold
Streptomyces carminius	strain=TRM SA0054	GCA_002794255.1	2665496	2665496	type	True	80.001	1068	2136	95	below_threshold
Streptomyces mimosae	strain=3MP-10	GCA_006334995.2	2586635	2586635	type	True	79.8784	1051	2136	95	below_threshold
Streptomyces durbertensis	strain=DSM 104538	GCA_014156695.1	2448886	2448886	type	True	79.8401	719	2136	95	below_threshold
Streptomyces alkaliterrae	strain=OF1	GCA_007097205.2	2213162	2213162	type	True	79.7848	778	2136	95	below_threshold
Streptomyces hoynatensis	strain=KCTC 29097	GCA_003626535.1	1141874	1141874	type	True	79.577	1038	2136	95	below_threshold
Streptomyces thermodiastaticus	strain=DSM 40573	GCA_021394575.1	44061	44061	type	True	79.4483	901	2136	95	below_threshold
Streptomyces oryzae	strain=S16-07	GCA_017676365.1	1434886	1434886	type	True	79.1727	846	2136	95	below_threshold
Actinacidiphila bryophytorum	strain=DSM 42138	GCA_017164735.1	1436133	1436133	type	True	79.0733	822	2136	95	below_threshold
Streptomyces morookaense	strain=JCM 4793	GCA_014656115.1	1970	1970	type	True	79.0112	879	2136	95	below_threshold
Streptomyces sennicomposti	strain=RCPT1-4	GCA_019890635.1	2873384	2873384	type	True	78.9721	965	2136	95	below_threshold
Streptomyces physcomitrii	strain=LD120	GCA_012273655.1	2724184	2724184	type	True	78.9671	931	2136	95	below_threshold
Streptomyces morookaense	strain=DSM 40503	GCA_013030945.1	1970	1970	type	True	78.9386	841	2136	95	below_threshold
Actinacidiphila bryophytorum	strain=DSM 42138	GCA_016916835.1	1436133	1436133	type	True	78.9147	945	2136	95	below_threshold
Streptomyces rimosus	strain=ATCC 10970	GCA_008704655.1	1927	1927	type	True	78.8982	989	2136	95	below_threshold
Streptomyces rimosus subsp. rimosus	strain=NRRL ISP-5260	GCA_000717285.1	132474	1927	type	True	78.8705	992	2136	95	below_threshold
Streptomyces rimosus subsp. rimosus	strain=ATCC 10970	GCA_000331185.2	132474	1927	type	True	78.8686	995	2136	95	below_threshold
Streptomyces rimosus subsp. rimosus	strain=R7	GCA_022760195.1	132474	1927	type	True	78.859	1003	2136	95	below_threshold
Streptomyces roseicoloratus	strain=TRM44457	GCA_004117935.1	2508722	2508722	type	True	78.8325	903	2136	95	below_threshold
Actinacidiphila glaucinigra	strain=CGMCC 4.1858	GCA_900188405.1	235986	235986	type	True	78.8069	984	2136	95	below_threshold
Streptomyces apocyni	strain=TRM 66233	GCA_009739465.1	2654677	2654677	type	True	78.8029	794	2136	95	below_threshold
Streptomyces spinosus	strain=SBTS01	GCA_020400655.1	2872623	2872623	type	True	78.8023	982	2136	95	below_threshold
Streptomyces shenzhenensis subsp. oryzicola	strain=W18L9	GCA_013870495.1	2749088	943815	type	True	78.7046	801	2136	95	below_threshold
Streptomyces microflavus	strain=JCM 4496	GCA_014650075.1	1919	1919	type	True	78.6781	906	2136	95	below_threshold
Streptomyces omiyaensis	strain=JCM 4806	GCA_014650895.1	68247	68247	type	True	78.4593	1000	2136	95	below_threshold
Allostreptomyces psammosilenae	strain=DSM 42178	GCA_013407765.1	1892865	1892865	type	True	78.3931	888	2136	95	below_threshold
Streptomyces shenzhenensis	strain=DSM 42034	GCA_021462265.1	943815	943815	type	True	78.377	1002	2136	95	below_threshold
Kitasatospora paracochleata	strain=DSM 41656	GCA_024172095.1	58354	58354	type	True	78.2018	952	2136	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:23:17,797] [INFO] DFAST Taxonomy check result was written to GCF_900112355.1_IMG-taxon_2675903061_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 14:23:17,797] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:23:17,798] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:23:17,798] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgaf3c56be-24c2-4953-8e94-7004a274ffd2/dqc_reference/checkm_data
[2024-01-24 14:23:17,799] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:23:17,858] [INFO] Task started: CheckM
[2024-01-24 14:23:17,858] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900112355.1_IMG-taxon_2675903061_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900112355.1_IMG-taxon_2675903061_annotated_assembly_genomic.fna/checkm_input GCF_900112355.1_IMG-taxon_2675903061_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 14:24:52,664] [INFO] Task succeeded: CheckM
[2024-01-24 14:24:52,665] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:24:52,685] [INFO] ===== Completeness check finished =====
[2024-01-24 14:24:52,686] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:24:52,686] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900112355.1_IMG-taxon_2675903061_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 14:24:52,686] [INFO] Task started: Blastn
[2024-01-24 14:24:52,686] [INFO] Running command: blastn -query GCF_900112355.1_IMG-taxon_2675903061_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgaf3c56be-24c2-4953-8e94-7004a274ffd2/dqc_reference/reference_markers_gtdb.fasta -out GCF_900112355.1_IMG-taxon_2675903061_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:24:54,645] [INFO] Task succeeded: Blastn
[2024-01-24 14:24:54,649] [INFO] Selected 30 target genomes.
[2024-01-24 14:24:54,649] [INFO] Target genome list was writen to GCF_900112355.1_IMG-taxon_2675903061_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:24:54,685] [INFO] Task started: fastANI
[2024-01-24 14:24:54,686] [INFO] Running command: fastANI --query /var/lib/cwl/stg5a8ba81a-daa3-4c16-8647-317dc224151c/GCF_900112355.1_IMG-taxon_2675903061_annotated_assembly_genomic.fna.gz --refList GCF_900112355.1_IMG-taxon_2675903061_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900112355.1_IMG-taxon_2675903061_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:25:41,060] [INFO] Task succeeded: fastANI
[2024-01-24 14:25:41,085] [INFO] Found 30 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:25:41,085] [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_900112355.1	s__Streptomyces aidingensis	100.0	2128	2136	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_011421595.1	s__Streptomyces sp011421595	89.8398	1499	2136	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114215.1	s__Streptomyces pini	80.4063	976	2136	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	96.765	N/A	N/A	N/A	N/A	1	-
GCF_017114865.1	s__Streptomyces verrucosisporus	80.2823	976	2136	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.1585	N/A	N/A	N/A	N/A	1	-
GCF_002843305.1	s__Streptomyces barkulensis	80.2382	1006	2136	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	96.765	99.92	99.92	0.99	0.99	2	-
GCF_009709575.1	s__Streptomyces taklimakanensis	80.1893	945	2136	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002794255.1	s__Streptomyces carminius	80.0539	1059	2136	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003696235.1	s__Streptomyces triticirhizae	80.0503	943	2136	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.38	95.35	0.89	0.89	3	-
GCF_004348315.1	s__Streptomyces sp004348315	80.0036	938	2136	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016741785.1	s__Streptomyces sp016741785	79.8757	888	2136	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000974485.1	s__Streptomyces sp000974485	79.8121	1018	2136	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900230195.1	s__Streptomyces zhaozhouensis	79.7732	965	2136	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003626535.1	s__Streptomyces hoynatensis	79.6311	1027	2136	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003144095.1	s__Streptomyces sp003144095	79.4367	850	2136	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000240165.1	s__Streptomyces cattleya	79.4041	982	2136	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.99	99.99	1.00	1.00	3	-
GCF_000424845.1	s__Streptomyces sp000424845	79.3629	834	2136	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017676365.1	s__Streptomyces oryzae	79.1919	842	2136	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013364155.1	s__Streptomyces sp013364155	79.1524	994	2136	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012273655.1	s__Streptomyces physcomitrii	78.9677	933	2136	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.15	97.14	0.94	0.93	4	-
GCF_013030945.1	s__Streptomyces morookaense	78.9562	840	2136	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	100.00	100.00	0.99	0.99	2	-
GCF_008704655.1	s__Streptomyces rimosus	78.914	988	2136	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.17	96.53	0.95	0.89	49	-
GCF_016916835.1	s__Streptomyces bryophytorum	78.9107	948	2136	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.96	99.96	0.99	0.99	2	-
GCF_000424965.1	s__Streptomyces sp000424965	78.9001	809	2136	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	78.8923	908	2136	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	78.8387	911	2136	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900188405.1	s__Streptomyces glauciniger	78.8033	986	2136	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.09	95.09	0.86	0.86	3	-
GCF_002797655.1	s__Streptomyces sp002797655	78.5414	989	2136	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.99	97.30	0.92	0.88	9	-
GCF_013407765.1	s__Allostreptomyces psammosilenae	78.3568	896	2136	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Allostreptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004348995.1	s__Nonomuraea terrae	76.3251	642	2136	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000718255.1	s__Spirillospora albida	76.2088	524	2136	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:25:41,087] [INFO] GTDB search result was written to GCF_900112355.1_IMG-taxon_2675903061_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 14:25:41,090] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:25:41,096] [INFO] DFAST_QC result json was written to GCF_900112355.1_IMG-taxon_2675903061_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 14:25:41,096] [INFO] DFAST_QC completed!
[2024-01-24 14:25:41,096] [INFO] Total running time: 0h3m40s