[2024-01-24 12:30:49,608] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:30:49,610] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:30:49,610] [INFO] DQC Reference Directory: /var/lib/cwl/stgc7003236-ed87-40a8-9f49-6aaec822102d/dqc_reference
[2024-01-24 12:30:50,831] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:30:50,832] [INFO] Task started: Prodigal
[2024-01-24 12:30:50,832] [INFO] Running command: gunzip -c /var/lib/cwl/stg61212314-b1de-458e-957a-66e0119cc30d/GCF_900188345.1_IMG-taxon_2671180041_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900188345.1_IMG-taxon_2671180041_annotated_assembly_genomic.fna/cds.fna -a GCF_900188345.1_IMG-taxon_2671180041_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:31:21,867] [INFO] Task succeeded: Prodigal
[2024-01-24 12:31:21,868] [INFO] Task started: HMMsearch
[2024-01-24 12:31:21,868] [INFO] Running command: hmmsearch --tblout GCF_900188345.1_IMG-taxon_2671180041_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc7003236-ed87-40a8-9f49-6aaec822102d/dqc_reference/reference_markers.hmm GCF_900188345.1_IMG-taxon_2671180041_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:31:22,271] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:31:22,272] [INFO] Found 6/6 markers.
[2024-01-24 12:31:22,351] [INFO] Query marker FASTA was written to GCF_900188345.1_IMG-taxon_2671180041_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 12:31:22,351] [INFO] Task started: Blastn
[2024-01-24 12:31:22,351] [INFO] Running command: blastn -query GCF_900188345.1_IMG-taxon_2671180041_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgc7003236-ed87-40a8-9f49-6aaec822102d/dqc_reference/reference_markers.fasta -out GCF_900188345.1_IMG-taxon_2671180041_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:31:23,658] [INFO] Task succeeded: Blastn
[2024-01-24 12:31:23,662] [INFO] Selected 22 target genomes.
[2024-01-24 12:31:23,663] [INFO] Target genome list was writen to GCF_900188345.1_IMG-taxon_2671180041_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 12:31:23,684] [INFO] Task started: fastANI
[2024-01-24 12:31:23,684] [INFO] Running command: fastANI --query /var/lib/cwl/stg61212314-b1de-458e-957a-66e0119cc30d/GCF_900188345.1_IMG-taxon_2671180041_annotated_assembly_genomic.fna.gz --refList GCF_900188345.1_IMG-taxon_2671180041_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900188345.1_IMG-taxon_2671180041_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:32:04,421] [INFO] Task succeeded: fastANI
[2024-01-24 12:32:04,421] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc7003236-ed87-40a8-9f49-6aaec822102d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:32:04,422] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc7003236-ed87-40a8-9f49-6aaec822102d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:32:04,443] [INFO] Found 22 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:32:04,443] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:32:04,443] [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
Streptosporangium canum	strain=CGMCC 4.2126	GCA_900113865.1	324952	324952	type	True	86.006	1846	3500	95	below_threshold
Streptosporangium roseum	strain=DSM 43021	GCA_000024865.1	2001	2001	type	True	85.9098	2017	3500	95	below_threshold
Streptosporangium minutum	strain=M26	GCA_002149035.1	569862	569862	type	True	85.6979	1813	3500	95	below_threshold
Streptosporangium album	strain=DSM 43023	GCA_014203795.1	47479	47479	type	True	85.3137	1784	3500	95	below_threshold
Streptosporangium amethystogenes	strain=NRRL B-2639	GCA_000721075.1	2002	2002	type	True	84.7563	1807	3500	95	below_threshold
Planomonospora parontospora subsp. antibiotica	strain=NBRC 15869	GCA_016863235.1	97193	58119	type	True	83.2851	1514	3500	95	below_threshold
Planobispora takensis	strain=NBRC 109077	GCA_016863195.1	1367882	1367882	type	True	83.2317	1653	3500	95	below_threshold
Planomonospora parontospora subsp. antibiotica	strain=JCM 3094	GCA_014647955.1	97193	58119	type	True	83.2109	1534	3500	95	below_threshold
Planobispora rosea	strain=JCM 3166	GCA_014648175.1	35762	35762	type	True	83.1649	1564	3500	95	below_threshold
Planomonospora sphaerica	strain=JCM 9374	GCA_001653075.1	161355	161355	type	True	83.1161	1574	3500	95	below_threshold
Planobispora rosea	strain=NBRC 15558	GCA_016863155.1	35762	35762	type	True	83.0903	1563	3500	95	below_threshold
Planobispora longispora	strain=NBRC 13918	GCA_016863135.1	28887	28887	type	True	83.061	1661	3500	95	below_threshold
Nonomuraea rhizosphaerae	strain=CGMCC 4.7431	GCA_019396405.1	2665663	2665663	type	True	79.8913	928	3500	95	below_threshold
Nonomuraea aurantiaca	strain=NEAU-L178	GCA_020215705.1	2878562	2878562	type	True	79.8819	1495	3500	95	below_threshold
Nonomuraea basaltis	strain=160415	GCA_005893125.1	2495887	2495887	type	True	79.6641	1441	3500	95	below_threshold
Nonomuraea roseoviolacea subsp. carminata	strain=DSM 44170	GCA_024172185.1	160689	103837	type	True	79.5867	1433	3500	95	below_threshold
Nonomuraea phyllanthi	strain=WYY166	GCA_009497075.1	2219224	2219224	type	True	79.5531	1486	3500	95	below_threshold
Kitasatospora phosalacinea	strain=NRRL B-16230	GCA_000716545.1	2065	2065	type	True	76.6377	764	3500	95	below_threshold
Geodermatophilus pulveris	strain=DSM 46839	GCA_900188375.1	1564159	1564159	type	True	76.4458	492	3500	95	below_threshold
Streptomyces capitiformicae	strain=CGMCC 4.7403	GCA_014653855.1	2014920	2014920	type	True	76.4118	657	3500	95	below_threshold
Blastococcus aggregatus	strain=DSM 4725	GCA_900221005.1	38502	38502	type	True	76.4117	441	3500	95	below_threshold
Streptomyces capitiformicae	strain=1H-SSA4	GCA_002214185.1	2014920	2014920	type	True	76.4061	674	3500	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:32:04,444] [INFO] DFAST Taxonomy check result was written to GCF_900188345.1_IMG-taxon_2671180041_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 12:32:04,447] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:32:04,447] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:32:04,447] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc7003236-ed87-40a8-9f49-6aaec822102d/dqc_reference/checkm_data
[2024-01-24 12:32:04,448] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:32:04,547] [INFO] Task started: CheckM
[2024-01-24 12:32:04,547] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900188345.1_IMG-taxon_2671180041_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900188345.1_IMG-taxon_2671180041_annotated_assembly_genomic.fna/checkm_input GCF_900188345.1_IMG-taxon_2671180041_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 12:33:37,558] [INFO] Task succeeded: CheckM
[2024-01-24 12:33:37,560] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:33:37,590] [INFO] ===== Completeness check finished =====
[2024-01-24 12:33:37,590] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:33:37,591] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900188345.1_IMG-taxon_2671180041_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 12:33:37,591] [INFO] Task started: Blastn
[2024-01-24 12:33:37,591] [INFO] Running command: blastn -query GCF_900188345.1_IMG-taxon_2671180041_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgc7003236-ed87-40a8-9f49-6aaec822102d/dqc_reference/reference_markers_gtdb.fasta -out GCF_900188345.1_IMG-taxon_2671180041_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:33:39,613] [INFO] Task succeeded: Blastn
[2024-01-24 12:33:39,618] [INFO] Selected 13 target genomes.
[2024-01-24 12:33:39,618] [INFO] Target genome list was writen to GCF_900188345.1_IMG-taxon_2671180041_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:33:39,628] [INFO] Task started: fastANI
[2024-01-24 12:33:39,629] [INFO] Running command: fastANI --query /var/lib/cwl/stg61212314-b1de-458e-957a-66e0119cc30d/GCF_900188345.1_IMG-taxon_2671180041_annotated_assembly_genomic.fna.gz --refList GCF_900188345.1_IMG-taxon_2671180041_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900188345.1_IMG-taxon_2671180041_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:34:06,455] [INFO] Task succeeded: fastANI
[2024-01-24 12:34:06,473] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:34:06,474] [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_900188345.1	s__Streptosporangium subroseum	100.0	3490	3500	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Streptosporangium	95.0	95.81	95.81	0.87	0.87	2	conclusive
GCF_900113865.1	s__Streptosporangium canum	85.9771	1850	3500	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Streptosporangium	95.8736	96.48	96.48	0.86	0.86	2	-
GCF_000024865.1	s__Streptosporangium roseum	85.8965	2019	3500	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Streptosporangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002149035.1	s__Streptosporangium minutum	85.6876	1815	3500	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Streptosporangium	95.8736	N/A	N/A	N/A	N/A	1	-
GCF_014203795.1	s__Streptosporangium album	85.3299	1783	3500	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Streptosporangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000721075.1	s__Streptosporangium amethystogenes	84.7867	1802	3500	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Streptosporangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015711605.1	s__Planomonospora_A sp015711605	83.3692	1632	3500	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Planomonospora_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016863195.1	s__Planobispora takensis	83.2069	1657	3500	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Planobispora	95.117	N/A	N/A	N/A	N/A	1	-
GCF_014648175.1	s__Planobispora rosea	83.1783	1562	3500	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Planobispora	95.0	99.82	99.64	0.97	0.95	3	-
GCF_900105415.1	s__Streptomyces sp900105415	76.6729	697	3500	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.65	95.65	0.85	0.85	2	-
GCF_014649755.1	s__Streptomyces litmocidini	76.5841	684	3500	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.07	95.07	0.85	0.85	2	-
GCF_000717185.1	s__Kitasatospora phosalacinea_A	76.5182	818	3500	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Kitasatospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002953255.1	s__Kitasatospora sp002953255	76.4884	780	3500	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Kitasatospora	95.0	98.26	96.53	0.79	0.78	3	-
--------------------------------------------------------------------------------
[2024-01-24 12:34:06,475] [INFO] GTDB search result was written to GCF_900188345.1_IMG-taxon_2671180041_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 12:34:06,476] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:34:06,480] [INFO] DFAST_QC result json was written to GCF_900188345.1_IMG-taxon_2671180041_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 12:34:06,480] [INFO] DFAST_QC completed!
[2024-01-24 12:34:06,480] [INFO] Total running time: 0h3m17s