[2024-01-24 13:31:44,224] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:31:44,226] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:31:44,227] [INFO] DQC Reference Directory: /var/lib/cwl/stg30046498-60aa-4f84-8ed2-360c0f668518/dqc_reference
[2024-01-24 13:31:45,597] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:31:45,597] [INFO] Task started: Prodigal
[2024-01-24 13:31:45,598] [INFO] Running command: gunzip -c /var/lib/cwl/stg86bf2a33-9d1b-44fc-8ea2-16f5d8a46b12/GCF_900113865.1_IMG-taxon_2667527412_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900113865.1_IMG-taxon_2667527412_annotated_assembly_genomic.fna/cds.fna -a GCF_900113865.1_IMG-taxon_2667527412_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:32:12,116] [INFO] Task succeeded: Prodigal
[2024-01-24 13:32:12,117] [INFO] Task started: HMMsearch
[2024-01-24 13:32:12,118] [INFO] Running command: hmmsearch --tblout GCF_900113865.1_IMG-taxon_2667527412_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg30046498-60aa-4f84-8ed2-360c0f668518/dqc_reference/reference_markers.hmm GCF_900113865.1_IMG-taxon_2667527412_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:32:12,532] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:32:12,534] [INFO] Found 6/6 markers.
[2024-01-24 13:32:12,607] [INFO] Query marker FASTA was written to GCF_900113865.1_IMG-taxon_2667527412_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 13:32:12,608] [INFO] Task started: Blastn
[2024-01-24 13:32:12,608] [INFO] Running command: blastn -query GCF_900113865.1_IMG-taxon_2667527412_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg30046498-60aa-4f84-8ed2-360c0f668518/dqc_reference/reference_markers.fasta -out GCF_900113865.1_IMG-taxon_2667527412_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:13,991] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:13,996] [INFO] Selected 16 target genomes.
[2024-01-24 13:32:13,996] [INFO] Target genome list was writen to GCF_900113865.1_IMG-taxon_2667527412_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 13:32:14,010] [INFO] Task started: fastANI
[2024-01-24 13:32:14,010] [INFO] Running command: fastANI --query /var/lib/cwl/stg86bf2a33-9d1b-44fc-8ea2-16f5d8a46b12/GCF_900113865.1_IMG-taxon_2667527412_annotated_assembly_genomic.fna.gz --refList GCF_900113865.1_IMG-taxon_2667527412_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900113865.1_IMG-taxon_2667527412_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:32:51,715] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:51,716] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg30046498-60aa-4f84-8ed2-360c0f668518/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:32:51,717] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg30046498-60aa-4f84-8ed2-360c0f668518/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:32:51,741] [INFO] Found 16 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:32:51,741] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 13:32:51,741] [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	100.0	3040	3047	95	inconclusive
Streptosporangium minutum	strain=M26	GCA_002149035.1	569862	569862	type	True	95.7178	2386	3047	95	inconclusive
Streptosporangium roseum	strain=DSM 43021	GCA_000024865.1	2001	2001	type	True	94.917	2584	3047	95	below_threshold
Streptosporangium album	strain=DSM 43023	GCA_014203795.1	47479	47479	type	True	88.4407	1927	3047	95	below_threshold
Streptosporangium amethystogenes	strain=NRRL B-2639	GCA_000721075.1	2002	2002	type	True	85.3993	1854	3047	95	below_threshold
Streptosporangium sandarakinum	strain=DSM 45763	GCA_013409935.1	1260955	1260955	type	True	85.1127	1757	3047	95	below_threshold
Planomonospora parontospora subsp. antibiotica	strain=NBRC 15869	GCA_016863235.1	97193	58119	type	True	84.6407	1610	3047	95	below_threshold
Planobispora takensis	strain=NBRC 109077	GCA_016863195.1	1367882	1367882	type	True	84.5363	1713	3047	95	below_threshold
Planobispora siamensis	strain=NBRC 107568	GCA_016863175.1	936338	936338	type	True	84.4454	1723	3047	95	below_threshold
Planobispora longispora	strain=NBRC 13918	GCA_016863135.1	28887	28887	type	True	84.4402	1716	3047	95	below_threshold
Planobispora rosea	strain=NBRC 15558	GCA_016863155.1	35762	35762	type	True	84.4087	1656	3047	95	below_threshold
Nonomuraea roseoviolacea subsp. carminata	strain=DSM 44170	GCA_024172185.1	160689	103837	type	True	80.4992	1555	3047	95	below_threshold
Nonomuraea rhizosphaerae	strain=CGMCC 4.7431	GCA_019396405.1	2665663	2665663	type	True	80.4629	1020	3047	95	below_threshold
Nonomuraea phyllanthi	strain=PA1-10	GCA_006334985.2	2219224	2219224	type	True	80.1667	1453	3047	95	below_threshold
Nonomuraea phyllanthi	strain=WYY166	GCA_009497075.1	2219224	2219224	type	True	80.1591	1466	3047	95	below_threshold
Nonomuraea typhae	strain=p1410	GCA_009760925.1	2603600	2603600	type	True	80.1091	1527	3047	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:32:51,743] [INFO] DFAST Taxonomy check result was written to GCF_900113865.1_IMG-taxon_2667527412_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 13:32:51,743] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:32:51,743] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:32:51,744] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg30046498-60aa-4f84-8ed2-360c0f668518/dqc_reference/checkm_data
[2024-01-24 13:32:51,744] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:32:51,834] [INFO] Task started: CheckM
[2024-01-24 13:32:51,834] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900113865.1_IMG-taxon_2667527412_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900113865.1_IMG-taxon_2667527412_annotated_assembly_genomic.fna/checkm_input GCF_900113865.1_IMG-taxon_2667527412_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 13:34:09,758] [INFO] Task succeeded: CheckM
[2024-01-24 13:34:09,760] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:34:09,786] [INFO] ===== Completeness check finished =====
[2024-01-24 13:34:09,787] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:34:09,787] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900113865.1_IMG-taxon_2667527412_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 13:34:09,788] [INFO] Task started: Blastn
[2024-01-24 13:34:09,788] [INFO] Running command: blastn -query GCF_900113865.1_IMG-taxon_2667527412_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg30046498-60aa-4f84-8ed2-360c0f668518/dqc_reference/reference_markers_gtdb.fasta -out GCF_900113865.1_IMG-taxon_2667527412_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:34:11,987] [INFO] Task succeeded: Blastn
[2024-01-24 13:34:11,991] [INFO] Selected 12 target genomes.
[2024-01-24 13:34:11,991] [INFO] Target genome list was writen to GCF_900113865.1_IMG-taxon_2667527412_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:34:12,001] [INFO] Task started: fastANI
[2024-01-24 13:34:12,002] [INFO] Running command: fastANI --query /var/lib/cwl/stg86bf2a33-9d1b-44fc-8ea2-16f5d8a46b12/GCF_900113865.1_IMG-taxon_2667527412_annotated_assembly_genomic.fna.gz --refList GCF_900113865.1_IMG-taxon_2667527412_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900113865.1_IMG-taxon_2667527412_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:34:40,080] [INFO] Task succeeded: fastANI
[2024-01-24 13:34:40,095] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:34:40,095] [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_900113865.1	s__Streptosporangium canum	100.0	3040	3047	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Streptosporangium	95.8736	96.48	96.48	0.86	0.86	2	conclusive
GCF_002149035.1	s__Streptosporangium minutum	95.7313	2384	3047	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Streptosporangium	95.8736	N/A	N/A	N/A	N/A	1	-
GCF_000024865.1	s__Streptosporangium roseum	94.8763	2590	3047	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Streptosporangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014203795.1	s__Streptosporangium album	88.4878	1922	3047	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Streptosporangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900188345.1	s__Streptosporangium subroseum	86.0521	1856	3047	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Streptosporangium	95.0	95.81	95.81	0.87	0.87	2	-
GCF_000721075.1	s__Streptosporangium amethystogenes	85.3862	1856	3047	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Streptosporangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014203605.1	s__Planomonospora_A venezuelensis	84.9015	1694	3047	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_015711605.1	s__Planomonospora_A sp015711605	84.894	1704	3047	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Planomonospora_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014647935.1	s__Planomonospora parontospora	84.5762	1641	3047	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Planomonospora	95.0	97.40	95.90	0.89	0.84	6	-
GCF_016863195.1	s__Planobispora takensis	84.5352	1712	3047	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Planobispora	95.117	N/A	N/A	N/A	N/A	1	-
GCF_016863175.1	s__Planobispora siamensis	84.4532	1722	3047	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	84.3373	1682	3047	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Planobispora	95.0	99.82	99.64	0.97	0.95	3	-
--------------------------------------------------------------------------------
[2024-01-24 13:34:40,097] [INFO] GTDB search result was written to GCF_900113865.1_IMG-taxon_2667527412_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 13:34:40,097] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:34:40,101] [INFO] DFAST_QC result json was written to GCF_900113865.1_IMG-taxon_2667527412_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 13:34:40,101] [INFO] DFAST_QC completed!
[2024-01-24 13:34:40,101] [INFO] Total running time: 0h2m56s