[2024-01-25 18:54:35,450] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:54:35,452] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:54:35,452] [INFO] DQC Reference Directory: /var/lib/cwl/stg5c309f45-2847-450d-89af-5565d5c4fe38/dqc_reference
[2024-01-25 18:54:36,606] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:54:36,606] [INFO] Task started: Prodigal
[2024-01-25 18:54:36,607] [INFO] Running command: gunzip -c /var/lib/cwl/stg2686bbe3-225b-4a40-b464-607fa4d374f5/GCF_027706745.1_ASM2770674v1_genomic.fna.gz | prodigal -d GCF_027706745.1_ASM2770674v1_genomic.fna/cds.fna -a GCF_027706745.1_ASM2770674v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:54:53,064] [INFO] Task succeeded: Prodigal
[2024-01-25 18:54:53,064] [INFO] Task started: HMMsearch
[2024-01-25 18:54:53,064] [INFO] Running command: hmmsearch --tblout GCF_027706745.1_ASM2770674v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5c309f45-2847-450d-89af-5565d5c4fe38/dqc_reference/reference_markers.hmm GCF_027706745.1_ASM2770674v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:54:53,399] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:54:53,401] [INFO] Found 6/6 markers.
[2024-01-25 18:54:53,452] [INFO] Query marker FASTA was written to GCF_027706745.1_ASM2770674v1_genomic.fna/markers.fasta
[2024-01-25 18:54:53,453] [INFO] Task started: Blastn
[2024-01-25 18:54:53,453] [INFO] Running command: blastn -query GCF_027706745.1_ASM2770674v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5c309f45-2847-450d-89af-5565d5c4fe38/dqc_reference/reference_markers.fasta -out GCF_027706745.1_ASM2770674v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:54:54,667] [INFO] Task succeeded: Blastn
[2024-01-25 18:54:54,671] [INFO] Selected 14 target genomes.
[2024-01-25 18:54:54,671] [INFO] Target genome list was writen to GCF_027706745.1_ASM2770674v1_genomic.fna/target_genomes.txt
[2024-01-25 18:54:54,681] [INFO] Task started: fastANI
[2024-01-25 18:54:54,681] [INFO] Running command: fastANI --query /var/lib/cwl/stg2686bbe3-225b-4a40-b464-607fa4d374f5/GCF_027706745.1_ASM2770674v1_genomic.fna.gz --refList GCF_027706745.1_ASM2770674v1_genomic.fna/target_genomes.txt --output GCF_027706745.1_ASM2770674v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:55:15,640] [INFO] Task succeeded: fastANI
[2024-01-25 18:55:15,641] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5c309f45-2847-450d-89af-5565d5c4fe38/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:55:15,641] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5c309f45-2847-450d-89af-5565d5c4fe38/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:55:15,650] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 18:55:15,650] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 18:55:15,651] [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
Nocardiopsis chromatogenes	strain=YIM 90109	GCA_000341185.1	280239	280239	type	True	93.1725	1782	2248	95	below_threshold
Nocardiopsis potens	strain=DSM 45234	GCA_000341105.1	1246458	1246458	type	True	82.8349	1369	2248	95	below_threshold
Nocardiopsis composta	strain=DSM 44551	GCA_014200805.1	157465	157465	type	True	82.7186	1397	2248	95	below_threshold
Nocardiopsis mwathae	strain=DSM 46659	GCA_014201195.1	1472723	1472723	type	True	81.039	1029	2248	95	below_threshold
Nocardiopsis gilva	strain=YIM 90087	GCA_000341165.1	280236	280236	type	True	80.8678	907	2248	95	below_threshold
Streptomonospora alba	strain=YIM 90003	GCA_000826685.1	183763	183763	type	True	80.4706	973	2248	95	below_threshold
Streptomonospora litoralis	strain=M2	GCA_004323735.1	2498135	2498135	type	True	80.3397	1003	2248	95	below_threshold
Nocardiopsis sinuspersici	strain=UTMC 00102	GCA_001998325.1	501010	501010	type	True	79.9898	958	2248	95	below_threshold
Thermobifida halotolerans	strain=DSM 44931	GCA_003574835.2	483545	483545	type	True	79.835	802	2248	95	below_threshold
Thermobifida alba	strain=DSM 43795	GCA_023208015.1	53522	53522	type	True	79.7844	817	2248	95	below_threshold
Nocardiopsis flavescens	strain=CGMCC 4.5723	GCA_900141985.1	758803	758803	type	True	79.6724	1065	2248	95	below_threshold
Nocardiopsis exhalans	strain=JCM11759T	GCA_024134545.1	163604	163604	type	True	79.6022	928	2248	95	below_threshold
Nocardiopsis coralli	strain=HNM0947	GCA_014892575.1	2772213	2772213	type	True	79.4678	879	2248	95	below_threshold
Thermomonospora catenispora	strain=3-22-3	GCA_006363815.1	2493090	2493090	type	True	77.7629	684	2248	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:55:15,652] [INFO] DFAST Taxonomy check result was written to GCF_027706745.1_ASM2770674v1_genomic.fna/tc_result.tsv
[2024-01-25 18:55:15,652] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:55:15,653] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:55:15,653] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5c309f45-2847-450d-89af-5565d5c4fe38/dqc_reference/checkm_data
[2024-01-25 18:55:15,654] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:55:15,720] [INFO] Task started: CheckM
[2024-01-25 18:55:15,720] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_027706745.1_ASM2770674v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_027706745.1_ASM2770674v1_genomic.fna/checkm_input GCF_027706745.1_ASM2770674v1_genomic.fna/checkm_result
[2024-01-25 18:56:14,951] [INFO] Task succeeded: CheckM
[2024-01-25 18:56:14,952] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:56:14,967] [INFO] ===== Completeness check finished =====
[2024-01-25 18:56:14,967] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:56:14,968] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_027706745.1_ASM2770674v1_genomic.fna/markers.fasta)
[2024-01-25 18:56:14,968] [INFO] Task started: Blastn
[2024-01-25 18:56:14,968] [INFO] Running command: blastn -query GCF_027706745.1_ASM2770674v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5c309f45-2847-450d-89af-5565d5c4fe38/dqc_reference/reference_markers_gtdb.fasta -out GCF_027706745.1_ASM2770674v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:56:16,913] [INFO] Task succeeded: Blastn
[2024-01-25 18:56:16,916] [INFO] Selected 11 target genomes.
[2024-01-25 18:56:16,916] [INFO] Target genome list was writen to GCF_027706745.1_ASM2770674v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:56:16,935] [INFO] Task started: fastANI
[2024-01-25 18:56:16,935] [INFO] Running command: fastANI --query /var/lib/cwl/stg2686bbe3-225b-4a40-b464-607fa4d374f5/GCF_027706745.1_ASM2770674v1_genomic.fna.gz --refList GCF_027706745.1_ASM2770674v1_genomic.fna/target_genomes_gtdb.txt --output GCF_027706745.1_ASM2770674v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:56:35,753] [INFO] Task succeeded: fastANI
[2024-01-25 18:56:35,760] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 18:56:35,761] [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_000341185.1	s__Nocardiopsis_A chromatogenes	93.1472	1785	2248	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_000341245.1	s__Nocardiopsis_A halophila	88.642	1614	2248	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis_A	95.0	98.23	98.23	0.90	0.90	2	-
GCF_000341105.1	s__Nocardiopsis_A potens	82.8166	1372	2248	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_014200805.1	s__Nocardiopsis_A composta	82.7783	1386	2248	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_014201195.1	s__Nocardiopsis_C mwathae	81.0584	1026	2248	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_001552555.1	s__Nocardiopsis_B trehalosi	80.8476	1098	2248	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_013410565.1	s__Streptomonospora nanhaiensis	80.8269	1122	2248	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Streptomonospora	95.0	99.69	99.69	0.95	0.95	2	-
GCF_009830945.1	s__Nocardiopsis sp009830945	80.0981	978	2248	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	99.72	99.66	0.93	0.93	3	-
GCA_018316655.1	s__Nocardiopsis sp018316655	79.7248	1114	2248	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000515115.1	s__Nocardiopsis sp000515115	79.3762	769	2248	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014203805.1	s__Lipingzhangella halophila	79.1443	864	2248	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Lipingzhangella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:56:35,762] [INFO] GTDB search result was written to GCF_027706745.1_ASM2770674v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:56:35,763] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:56:35,767] [INFO] DFAST_QC result json was written to GCF_027706745.1_ASM2770674v1_genomic.fna/dqc_result.json
[2024-01-25 18:56:35,767] [INFO] DFAST_QC completed!
[2024-01-25 18:56:35,767] [INFO] Total running time: 0h2m0s