[2024-01-24 11:44:05,456] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:44:05,457] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:44:05,457] [INFO] DQC Reference Directory: /var/lib/cwl/stg2bf15a93-526d-484a-bb4f-e725502a8e35/dqc_reference
[2024-01-24 11:44:08,847] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:44:08,848] [INFO] Task started: Prodigal
[2024-01-24 11:44:08,849] [INFO] Running command: gunzip -c /var/lib/cwl/stg56d0a6d4-067e-4f9e-acc7-7eaa14c72245/GCF_018324685.1_ASM1832468v1_genomic.fna.gz | prodigal -d GCF_018324685.1_ASM1832468v1_genomic.fna/cds.fna -a GCF_018324685.1_ASM1832468v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:44:34,717] [INFO] Task succeeded: Prodigal
[2024-01-24 11:44:34,717] [INFO] Task started: HMMsearch
[2024-01-24 11:44:34,717] [INFO] Running command: hmmsearch --tblout GCF_018324685.1_ASM1832468v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2bf15a93-526d-484a-bb4f-e725502a8e35/dqc_reference/reference_markers.hmm GCF_018324685.1_ASM1832468v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:44:35,022] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:44:35,023] [INFO] Found 6/6 markers.
[2024-01-24 11:44:35,079] [INFO] Query marker FASTA was written to GCF_018324685.1_ASM1832468v1_genomic.fna/markers.fasta
[2024-01-24 11:44:35,079] [INFO] Task started: Blastn
[2024-01-24 11:44:35,079] [INFO] Running command: blastn -query GCF_018324685.1_ASM1832468v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2bf15a93-526d-484a-bb4f-e725502a8e35/dqc_reference/reference_markers.fasta -out GCF_018324685.1_ASM1832468v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:44:36,477] [INFO] Task succeeded: Blastn
[2024-01-24 11:44:36,480] [INFO] Selected 15 target genomes.
[2024-01-24 11:44:36,480] [INFO] Target genome list was writen to GCF_018324685.1_ASM1832468v1_genomic.fna/target_genomes.txt
[2024-01-24 11:44:36,486] [INFO] Task started: fastANI
[2024-01-24 11:44:36,486] [INFO] Running command: fastANI --query /var/lib/cwl/stg56d0a6d4-067e-4f9e-acc7-7eaa14c72245/GCF_018324685.1_ASM1832468v1_genomic.fna.gz --refList GCF_018324685.1_ASM1832468v1_genomic.fna/target_genomes.txt --output GCF_018324685.1_ASM1832468v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:45:02,276] [INFO] Task succeeded: fastANI
[2024-01-24 11:45:02,277] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2bf15a93-526d-484a-bb4f-e725502a8e35/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:45:02,277] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2bf15a93-526d-484a-bb4f-e725502a8e35/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:45:02,289] [INFO] Found 15 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:45:02,289] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:45:02,290] [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
Actinocatenispora sera	strain=NBRC 101916	GCA_018324685.1	390989	390989	type	True	100.0	2341	2348	95	conclusive
Actinocatenispora sera	strain=NRRL B-24477	GCA_000720965.1	390989	390989	type	True	99.9657	2286	2348	95	conclusive
Actinocatenispora comari	strain=NUM-2625	GCA_017312725.1	2807577	2807577	type	True	92.7349	1997	2348	95	below_threshold
Micromonospora radicis	strain=AZ1-13	GCA_003583405.1	1894971	1894971	type	True	77.7111	715	2348	95	below_threshold
Micromonospora palomenae	strain=DSM 102131	GCA_007829925.1	1461247	1461247	type	True	77.6833	904	2348	95	below_threshold
Micromonospora rifamycinica	strain=DSM 44983	GCA_900090265.1	291594	291594	type	True	77.6779	863	2348	95	below_threshold
Micromonospora maris	strain=NRRL B-24793	GCA_001507315.1	1003110	1003110	type	True	77.6128	722	2348	95	below_threshold
Micromonospora maris	strain=AB-18-032	GCA_000204155.1	1003110	1003110	type	True	77.5674	739	2348	95	below_threshold
Micromonospora wenchangensis	strain=CCTCC AA 2012002	GCA_002210435.1	1185415	1185415	type	True	77.5542	875	2348	95	below_threshold
Micromonospora polyrhachis	strain=DSM 45886	GCA_014203835.1	1282883	1282883	type	True	77.3701	625	2348	95	below_threshold
Longispora albida	strain=DSM 44784	GCA_000379825.1	203523	203523	type	True	77.2559	634	2348	95	below_threshold
Catellatospora citrea	strain=NBRC 14495	GCA_016862615.1	53366	53366	type	True	77.193	884	2348	95	below_threshold
Catellatospora methionotrophica	strain=NBRC 14553	GCA_016862655.1	121620	121620	type	True	77.0926	872	2348	95	below_threshold
Couchioplanes caeruleus	strain=DSM 43634	GCA_003751945.1	56438	56438	type	True	76.9071	760	2348	95	below_threshold
Actinokineospora enzanensis	strain=DSM 44649	GCA_000374445.1	155975	155975	type	True	76.4323	596	2348	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:45:02,291] [INFO] DFAST Taxonomy check result was written to GCF_018324685.1_ASM1832468v1_genomic.fna/tc_result.tsv
[2024-01-24 11:45:02,291] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:45:02,292] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:45:02,292] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2bf15a93-526d-484a-bb4f-e725502a8e35/dqc_reference/checkm_data
[2024-01-24 11:45:02,293] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:45:02,355] [INFO] Task started: CheckM
[2024-01-24 11:45:02,356] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_018324685.1_ASM1832468v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_018324685.1_ASM1832468v1_genomic.fna/checkm_input GCF_018324685.1_ASM1832468v1_genomic.fna/checkm_result
[2024-01-24 11:47:22,044] [INFO] Task succeeded: CheckM
[2024-01-24 11:47:22,045] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:47:22,073] [INFO] ===== Completeness check finished =====
[2024-01-24 11:47:22,073] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:47:22,074] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_018324685.1_ASM1832468v1_genomic.fna/markers.fasta)
[2024-01-24 11:47:22,074] [INFO] Task started: Blastn
[2024-01-24 11:47:22,074] [INFO] Running command: blastn -query GCF_018324685.1_ASM1832468v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2bf15a93-526d-484a-bb4f-e725502a8e35/dqc_reference/reference_markers_gtdb.fasta -out GCF_018324685.1_ASM1832468v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:47:24,363] [INFO] Task succeeded: Blastn
[2024-01-24 11:47:24,368] [INFO] Selected 10 target genomes.
[2024-01-24 11:47:24,368] [INFO] Target genome list was writen to GCF_018324685.1_ASM1832468v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:47:24,380] [INFO] Task started: fastANI
[2024-01-24 11:47:24,380] [INFO] Running command: fastANI --query /var/lib/cwl/stg56d0a6d4-067e-4f9e-acc7-7eaa14c72245/GCF_018324685.1_ASM1832468v1_genomic.fna.gz --refList GCF_018324685.1_ASM1832468v1_genomic.fna/target_genomes_gtdb.txt --output GCF_018324685.1_ASM1832468v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:47:43,268] [INFO] Task succeeded: fastANI
[2024-01-24 11:47:43,282] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:47:43,282] [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_018324685.1	s__Actinocatenispora sera	100.0	2343	2348	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinocatenispora	95.0	99.99	99.99	1.00	1.00	2	conclusive
GCF_017312725.1	s__Actinocatenispora sp017312725	92.7305	1999	2348	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinocatenispora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016865425.1	s__Actinocatenispora thailandica	89.8085	1979	2348	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinocatenispora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016861975.1	s__Actinocatenispora rupis	82.1643	1461	2348	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinocatenispora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003583405.1	s__Micromonospora radicis	77.7233	713	2348	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002210435.1	s__Micromonospora wenchangensis	77.5372	878	2348	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	95.84	95.43	0.85	0.83	5	-
GCF_014203835.1	s__Micromonospora_H polyrhachis	77.3549	623	2348	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora_H	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003610235.1	s__Catellatospora citrea	77.1979	907	2348	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Catellatospora	95.0	97.34	95.99	0.88	0.83	4	-
GCF_016863475.1	s__Spirilliplanes yamanashiensis	77.1634	917	2348	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Spirilliplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000374445.1	s__Actinokineospora enzanensis	76.4249	598	2348	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinokineospora	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:47:43,284] [INFO] GTDB search result was written to GCF_018324685.1_ASM1832468v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:47:43,285] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:47:43,288] [INFO] DFAST_QC result json was written to GCF_018324685.1_ASM1832468v1_genomic.fna/dqc_result.json
[2024-01-24 11:47:43,289] [INFO] DFAST_QC completed!
[2024-01-24 11:47:43,289] [INFO] Total running time: 0h3m38s