[2024-01-25 20:00:05,912] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:00:05,914] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:00:05,914] [INFO] DQC Reference Directory: /var/lib/cwl/stg8bba109c-f9f1-42e9-864c-c7e1e8a90c51/dqc_reference
[2024-01-25 20:00:07,124] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:00:07,125] [INFO] Task started: Prodigal
[2024-01-25 20:00:07,125] [INFO] Running command: gunzip -c /var/lib/cwl/stg0508fb26-51f4-4d86-8d55-c8588565bd55/GCF_900167435.1_IMG-taxon_2524614583_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900167435.1_IMG-taxon_2524614583_annotated_assembly_genomic.fna/cds.fna -a GCF_900167435.1_IMG-taxon_2524614583_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:00:21,048] [INFO] Task succeeded: Prodigal
[2024-01-25 20:00:21,048] [INFO] Task started: HMMsearch
[2024-01-25 20:00:21,048] [INFO] Running command: hmmsearch --tblout GCF_900167435.1_IMG-taxon_2524614583_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8bba109c-f9f1-42e9-864c-c7e1e8a90c51/dqc_reference/reference_markers.hmm GCF_900167435.1_IMG-taxon_2524614583_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:00:21,421] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:00:21,423] [INFO] Found 6/6 markers.
[2024-01-25 20:00:21,488] [INFO] Query marker FASTA was written to GCF_900167435.1_IMG-taxon_2524614583_annotated_assembly_genomic.fna/markers.fasta
[2024-01-25 20:00:21,488] [INFO] Task started: Blastn
[2024-01-25 20:00:21,488] [INFO] Running command: blastn -query GCF_900167435.1_IMG-taxon_2524614583_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg8bba109c-f9f1-42e9-864c-c7e1e8a90c51/dqc_reference/reference_markers.fasta -out GCF_900167435.1_IMG-taxon_2524614583_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:00:22,680] [INFO] Task succeeded: Blastn
[2024-01-25 20:00:22,683] [INFO] Selected 17 target genomes.
[2024-01-25 20:00:22,683] [INFO] Target genome list was writen to GCF_900167435.1_IMG-taxon_2524614583_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-25 20:00:22,703] [INFO] Task started: fastANI
[2024-01-25 20:00:22,704] [INFO] Running command: fastANI --query /var/lib/cwl/stg0508fb26-51f4-4d86-8d55-c8588565bd55/GCF_900167435.1_IMG-taxon_2524614583_annotated_assembly_genomic.fna.gz --refList GCF_900167435.1_IMG-taxon_2524614583_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900167435.1_IMG-taxon_2524614583_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:00:44,281] [INFO] Task succeeded: fastANI
[2024-01-25 20:00:44,282] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8bba109c-f9f1-42e9-864c-c7e1e8a90c51/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:00:44,282] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8bba109c-f9f1-42e9-864c-c7e1e8a90c51/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:00:44,293] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 20:00:44,294] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 20:00:44,294] [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
Thermobifida cellulosilytica	strain=TB100	GCA_001517975.1	144786	144786	type	True	80.7316	799	1871	95	below_threshold
Nocardiopsis gilva	strain=YIM 90087	GCA_000341165.1	280236	280236	type	True	80.7083	767	1871	95	below_threshold
Nocardiopsis mwathae	strain=DSM 46659	GCA_014201195.1	1472723	1472723	type	True	80.6734	876	1871	95	below_threshold
Thermobifida halotolerans	strain=DSM 44931	GCA_003574835.2	483545	483545	type	True	80.6315	849	1871	95	below_threshold
Nocardiopsis gilva	strain=YIM 90087	GCA_002263495.1	280236	280236	type	True	80.6105	837	1871	95	below_threshold
Thermobifida halotolerans	strain=YIM 90462	GCA_001660385.1	483545	483545	type	True	80.5961	838	1871	95	below_threshold
Thermobifida alba	strain=DSM 43795	GCA_023208015.1	53522	53522	type	True	80.5741	829	1871	95	below_threshold
Nocardiopsis composta	strain=DSM 44551	GCA_014200805.1	157465	157465	type	True	80.366	1011	1871	95	below_threshold
Streptomonospora litoralis	strain=M2	GCA_004323735.1	2498135	2498135	type	True	80.1426	843	1871	95	below_threshold
Nocardiopsis chromatogenes	strain=YIM 90109	GCA_000341185.1	280239	280239	type	True	80.1299	866	1871	95	below_threshold
Nocardiopsis potens	strain=DSM 45234	GCA_000341105.1	1246458	1246458	type	True	80.1215	990	1871	95	below_threshold
Nocardiopsis dassonvillei subsp. crassaminis	strain=D1	GCA_902825375.1	2580523	2014	type	True	79.8248	792	1871	95	below_threshold
Nocardiopsis sinuspersici	strain=UTMC 00102	GCA_001998325.1	501010	501010	type	True	79.6536	812	1871	95	below_threshold
Nocardiopsis alborubida	strain=ATCC 23612	GCA_012396365.1	146802	146802	type	True	79.647	886	1871	95	below_threshold
Nocardiopsis exhalans	strain=JCM11759T	GCA_024134545.1	163604	163604	type	True	79.3653	753	1871	95	below_threshold
Nocardiopsis flavescens	strain=CGMCC 4.5723	GCA_900141985.1	758803	758803	type	True	79.2983	874	1871	95	below_threshold
Nocardiopsis metallicus	strain=DSM 44598	GCA_014201115.1	179819	179819	type	True	79.0911	782	1871	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:00:44,298] [INFO] DFAST Taxonomy check result was written to GCF_900167435.1_IMG-taxon_2524614583_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-25 20:00:44,299] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:00:44,299] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:00:44,299] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8bba109c-f9f1-42e9-864c-c7e1e8a90c51/dqc_reference/checkm_data
[2024-01-25 20:00:44,300] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:00:44,355] [INFO] Task started: CheckM
[2024-01-25 20:00:44,355] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900167435.1_IMG-taxon_2524614583_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900167435.1_IMG-taxon_2524614583_annotated_assembly_genomic.fna/checkm_input GCF_900167435.1_IMG-taxon_2524614583_annotated_assembly_genomic.fna/checkm_result
[2024-01-25 20:01:33,732] [INFO] Task succeeded: CheckM
[2024-01-25 20:01:33,733] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:01:33,751] [INFO] ===== Completeness check finished =====
[2024-01-25 20:01:33,751] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:01:33,752] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900167435.1_IMG-taxon_2524614583_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-25 20:01:33,752] [INFO] Task started: Blastn
[2024-01-25 20:01:33,752] [INFO] Running command: blastn -query GCF_900167435.1_IMG-taxon_2524614583_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg8bba109c-f9f1-42e9-864c-c7e1e8a90c51/dqc_reference/reference_markers_gtdb.fasta -out GCF_900167435.1_IMG-taxon_2524614583_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:01:35,732] [INFO] Task succeeded: Blastn
[2024-01-25 20:01:35,735] [INFO] Selected 15 target genomes.
[2024-01-25 20:01:35,735] [INFO] Target genome list was writen to GCF_900167435.1_IMG-taxon_2524614583_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:01:35,750] [INFO] Task started: fastANI
[2024-01-25 20:01:35,751] [INFO] Running command: fastANI --query /var/lib/cwl/stg0508fb26-51f4-4d86-8d55-c8588565bd55/GCF_900167435.1_IMG-taxon_2524614583_annotated_assembly_genomic.fna.gz --refList GCF_900167435.1_IMG-taxon_2524614583_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900167435.1_IMG-taxon_2524614583_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:01:55,830] [INFO] Task succeeded: fastANI
[2024-01-25 20:01:55,839] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:01:55,840] [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_900167435.1	s__Marinactinospora thermotolerans	100.0	1869	1871	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Marinactinospora	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_013408795.1	s__Spinactinospora alkalitolerans	82.2938	1125	1871	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spinactinospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003336425.1	s__Marinitenerispora sediminis	81.1382	977	1871	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Marinitenerispora	95.0	99.95	99.94	0.96	0.96	3	-
GCF_001552555.1	s__Nocardiopsis_B trehalosi	80.9482	989	1871	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004363075.1	s__Actinorugispora endophytica	80.9362	933	1871	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Actinorugispora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013410565.1	s__Streptomonospora nanhaiensis	80.7632	998	1871	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Streptomonospora	95.0	99.69	99.69	0.95	0.95	2	-
GCF_001517975.1	s__Thermobifida cellulosilytica	80.738	797	1871	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Thermobifida	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014201195.1	s__Nocardiopsis_C mwathae	80.666	877	1871	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001660385.1	s__Thermobifida halotolerans	80.591	839	1871	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Thermobifida	95.0	99.91	99.91	0.97	0.97	2	-
GCF_014200805.1	s__Nocardiopsis_A composta	80.3653	1011	1871	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009728995.1	s__Streptomonospora sp009728995	80.3278	910	1871	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Streptomonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000341105.1	s__Nocardiopsis_A potens	80.1026	993	1871	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000341185.1	s__Nocardiopsis_A chromatogenes	80.1011	871	1871	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018316655.1	s__Nocardiopsis sp018316655	79.5198	897	1871	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900141985.1	s__Nocardiopsis flavescens	79.2951	872	1871	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:01:55,841] [INFO] GTDB search result was written to GCF_900167435.1_IMG-taxon_2524614583_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-25 20:01:55,842] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:01:55,845] [INFO] DFAST_QC result json was written to GCF_900167435.1_IMG-taxon_2524614583_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-25 20:01:55,845] [INFO] DFAST_QC completed!
[2024-01-25 20:01:55,845] [INFO] Total running time: 0h1m50s