[2024-01-25 17:34:07,123] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:34:07,127] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:34:07,127] [INFO] DQC Reference Directory: /var/lib/cwl/stg2ac0f0a7-915b-41fc-9e50-f7b492517471/dqc_reference
[2024-01-25 17:34:09,025] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:34:09,026] [INFO] Task started: Prodigal
[2024-01-25 17:34:09,026] [INFO] Running command: gunzip -c /var/lib/cwl/stgca277c78-32e4-4102-bdbc-e13456f6588f/GCF_016862135.1_ASM1686213v1_genomic.fna.gz | prodigal -d GCF_016862135.1_ASM1686213v1_genomic.fna/cds.fna -a GCF_016862135.1_ASM1686213v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:34:39,551] [INFO] Task succeeded: Prodigal
[2024-01-25 17:34:39,552] [INFO] Task started: HMMsearch
[2024-01-25 17:34:39,552] [INFO] Running command: hmmsearch --tblout GCF_016862135.1_ASM1686213v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2ac0f0a7-915b-41fc-9e50-f7b492517471/dqc_reference/reference_markers.hmm GCF_016862135.1_ASM1686213v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:34:40,059] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:34:40,061] [INFO] Found 6/6 markers.
[2024-01-25 17:34:40,138] [INFO] Query marker FASTA was written to GCF_016862135.1_ASM1686213v1_genomic.fna/markers.fasta
[2024-01-25 17:34:40,139] [INFO] Task started: Blastn
[2024-01-25 17:34:40,139] [INFO] Running command: blastn -query GCF_016862135.1_ASM1686213v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2ac0f0a7-915b-41fc-9e50-f7b492517471/dqc_reference/reference_markers.fasta -out GCF_016862135.1_ASM1686213v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:34:41,373] [INFO] Task succeeded: Blastn
[2024-01-25 17:34:41,375] [INFO] Selected 16 target genomes.
[2024-01-25 17:34:41,376] [INFO] Target genome list was writen to GCF_016862135.1_ASM1686213v1_genomic.fna/target_genomes.txt
[2024-01-25 17:34:41,386] [INFO] Task started: fastANI
[2024-01-25 17:34:41,386] [INFO] Running command: fastANI --query /var/lib/cwl/stgca277c78-32e4-4102-bdbc-e13456f6588f/GCF_016862135.1_ASM1686213v1_genomic.fna.gz --refList GCF_016862135.1_ASM1686213v1_genomic.fna/target_genomes.txt --output GCF_016862135.1_ASM1686213v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:35:18,744] [INFO] Task succeeded: fastANI
[2024-01-25 17:35:18,745] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2ac0f0a7-915b-41fc-9e50-f7b492517471/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:35:18,745] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2ac0f0a7-915b-41fc-9e50-f7b492517471/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:35:18,755] [INFO] Found 16 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 17:35:18,755] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:35:18,756] [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
Actinoplanes derwentensis	strain=NBRC 14935	GCA_016862135.1	113562	113562	type	True	100.0	3387	3398	95	conclusive
Actinoplanes derwentensis	strain=DSM 43941	GCA_900104725.1	113562	113562	type	True	99.9997	3398	3398	95	conclusive
Actinoplanes utahensis	strain=NBRC 13244	GCA_016862455.1	1869	1869	type	True	84.4555	1927	3398	95	below_threshold
Actinoplanes xinjiangensis	strain=DSM 45184	GCA_003148685.1	512350	512350	type	True	84.2243	2100	3398	95	below_threshold
Actinoplanes philippinensis	strain=NBRC 13878	GCA_016862335.1	35752	35752	type	True	84.1521	2095	3398	95	below_threshold
Actinoplanes flavus	strain=NEAU-H7	GCA_017592555.1	2820290	2820290	type	True	84.0384	1888	3398	95	below_threshold
Actinoplanes hulinensis	strain=NEAU-M9	GCA_019429605.1	1144547	1144547	type	True	83.95	1907	3398	95	below_threshold
Actinoplanes lobatus	strain=NBRC 12513	GCA_016862255.1	113568	113568	type	True	83.911	1896	3398	95	below_threshold
Actinoplanes campanulatus	strain=NBRC 12511	GCA_016862035.1	113559	113559	type	True	83.8813	1928	3398	95	below_threshold
Actinoplanes italicus	strain=NBRC 13911	GCA_016862235.1	113567	113567	type	True	83.851	2026	3398	95	below_threshold
Actinoplanes italicus	strain=DSM 43146	GCA_003001815.1	113567	113567	type	True	83.7558	2063	3398	95	below_threshold
Actinoplanes subtropicus	strain=NRRL B-24665	GCA_000721705.1	543632	543632	type	True	79.9223	1490	3398	95	below_threshold
Micromonospora phytophila	strain=DSM 105363	GCA_023656545.1	709888	709888	type	True	78.7979	759	3398	95	below_threshold
Micromonospora acroterricola	strain=5R2A7	GCA_003172955.1	2202421	2202421	type	True	78.6035	862	3398	95	below_threshold
Dactylosporangium aurantiacum	strain=NRRL B-8018	GCA_025264705.1	35754	35754	type	True	77.1993	1192	3398	95	below_threshold
Dactylosporangium fulvum	strain=NRRL B-16292	GCA_025137375.1	53359	53359	type	True	77.0491	966	3398	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:35:18,757] [INFO] DFAST Taxonomy check result was written to GCF_016862135.1_ASM1686213v1_genomic.fna/tc_result.tsv
[2024-01-25 17:35:18,757] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:35:18,757] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:35:18,757] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2ac0f0a7-915b-41fc-9e50-f7b492517471/dqc_reference/checkm_data
[2024-01-25 17:35:18,758] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:35:18,848] [INFO] Task started: CheckM
[2024-01-25 17:35:18,848] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016862135.1_ASM1686213v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016862135.1_ASM1686213v1_genomic.fna/checkm_input GCF_016862135.1_ASM1686213v1_genomic.fna/checkm_result
[2024-01-25 17:37:03,590] [INFO] Task succeeded: CheckM
[2024-01-25 17:37:03,593] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:37:03,634] [INFO] ===== Completeness check finished =====
[2024-01-25 17:37:03,634] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:37:03,635] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016862135.1_ASM1686213v1_genomic.fna/markers.fasta)
[2024-01-25 17:37:03,635] [INFO] Task started: Blastn
[2024-01-25 17:37:03,636] [INFO] Running command: blastn -query GCF_016862135.1_ASM1686213v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2ac0f0a7-915b-41fc-9e50-f7b492517471/dqc_reference/reference_markers_gtdb.fasta -out GCF_016862135.1_ASM1686213v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:37:05,624] [INFO] Task succeeded: Blastn
[2024-01-25 17:37:05,627] [INFO] Selected 10 target genomes.
[2024-01-25 17:37:05,627] [INFO] Target genome list was writen to GCF_016862135.1_ASM1686213v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:37:05,632] [INFO] Task started: fastANI
[2024-01-25 17:37:05,633] [INFO] Running command: fastANI --query /var/lib/cwl/stgca277c78-32e4-4102-bdbc-e13456f6588f/GCF_016862135.1_ASM1686213v1_genomic.fna.gz --refList GCF_016862135.1_ASM1686213v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016862135.1_ASM1686213v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:37:33,656] [INFO] Task succeeded: fastANI
[2024-01-25 17:37:33,663] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:37:33,663] [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_900104725.1	s__Actinoplanes derwentensis	99.9997	3398	3398	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_016862075.1	s__Actinoplanes couchii	87.9273	2461	3398	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016862455.1	s__Actinoplanes utahensis	84.4524	1927	3398	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	99.99	99.99	0.99	0.99	2	-
GCF_003148685.1	s__Actinoplanes xinjiangensis	84.2475	2095	3398	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900113015.1	s__Actinoplanes philippinensis	84.0864	2112	3398	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	100.00	100.00	1.00	1.00	2	-
GCF_017592555.1	s__Actinoplanes sp017592555	84.0296	1889	3398	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014647795.1	s__Actinoplanes campanulatus	83.9723	1910	3398	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0428	98.93	96.79	0.95	0.87	4	-
GCF_014205215.1	s__Actinoplanes lobatus	83.9012	1946	3398	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0428	99.99	99.99	1.00	1.00	3	-
GCF_003001815.1	s__Actinoplanes italicus	83.7074	2074	3398	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	99.99	99.99	1.00	1.00	2	-
GCF_000721705.1	s__Actinoplanes subtropicus	79.904	1496	3398	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:37:33,665] [INFO] GTDB search result was written to GCF_016862135.1_ASM1686213v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:37:33,665] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:37:33,669] [INFO] DFAST_QC result json was written to GCF_016862135.1_ASM1686213v1_genomic.fna/dqc_result.json
[2024-01-25 17:37:33,670] [INFO] DFAST_QC completed!
[2024-01-25 17:37:33,670] [INFO] Total running time: 0h3m27s