[2024-01-24 13:40:29,228] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:29,230] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:29,230] [INFO] DQC Reference Directory: /var/lib/cwl/stgd70fd95f-90f0-4e41-bce1-891bd46f24e8/dqc_reference
[2024-01-24 13:40:30,541] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:30,542] [INFO] Task started: Prodigal
[2024-01-24 13:40:30,542] [INFO] Running command: gunzip -c /var/lib/cwl/stg232cd91f-c594-4b7d-a825-a4b2cf46ee64/GCF_017592555.1_ASM1759255v1_genomic.fna.gz | prodigal -d GCF_017592555.1_ASM1759255v1_genomic.fna/cds.fna -a GCF_017592555.1_ASM1759255v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:40:59,982] [INFO] Task succeeded: Prodigal
[2024-01-24 13:40:59,983] [INFO] Task started: HMMsearch
[2024-01-24 13:40:59,983] [INFO] Running command: hmmsearch --tblout GCF_017592555.1_ASM1759255v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd70fd95f-90f0-4e41-bce1-891bd46f24e8/dqc_reference/reference_markers.hmm GCF_017592555.1_ASM1759255v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:41:00,501] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:41:00,502] [INFO] Found 6/6 markers.
[2024-01-24 13:41:00,576] [INFO] Query marker FASTA was written to GCF_017592555.1_ASM1759255v1_genomic.fna/markers.fasta
[2024-01-24 13:41:00,576] [INFO] Task started: Blastn
[2024-01-24 13:41:00,576] [INFO] Running command: blastn -query GCF_017592555.1_ASM1759255v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd70fd95f-90f0-4e41-bce1-891bd46f24e8/dqc_reference/reference_markers.fasta -out GCF_017592555.1_ASM1759255v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:01,880] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:01,884] [INFO] Selected 12 target genomes.
[2024-01-24 13:41:01,885] [INFO] Target genome list was writen to GCF_017592555.1_ASM1759255v1_genomic.fna/target_genomes.txt
[2024-01-24 13:41:01,890] [INFO] Task started: fastANI
[2024-01-24 13:41:01,891] [INFO] Running command: fastANI --query /var/lib/cwl/stg232cd91f-c594-4b7d-a825-a4b2cf46ee64/GCF_017592555.1_ASM1759255v1_genomic.fna.gz --refList GCF_017592555.1_ASM1759255v1_genomic.fna/target_genomes.txt --output GCF_017592555.1_ASM1759255v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:32,924] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:32,924] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd70fd95f-90f0-4e41-bce1-891bd46f24e8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:32,925] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd70fd95f-90f0-4e41-bce1-891bd46f24e8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:32,938] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:41:32,939] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:41:32,939] [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 flavus	strain=NEAU-H7	GCA_017592555.1	2820290	2820290	type	True	100.0	3169	3184	95	conclusive
Actinoplanes campanulatus	strain=NBRC 12511	GCA_016862035.1	113559	113559	type	True	93.9882	2657	3184	95	below_threshold
Actinoplanes hulinensis	strain=NEAU-M9	GCA_019429605.1	1144547	1144547	type	True	93.9812	2606	3184	95	below_threshold
Actinoplanes campanulatus	strain=JCM 3059	GCA_014647795.1	113559	113559	type	True	93.9635	2702	3184	95	below_threshold
Actinoplanes capillaceus	strain=NBRC 16408	GCA_016862055.1	76756	76756	type	True	93.8624	2586	3184	95	below_threshold
Actinoplanes lobatus	strain=JCM 3061	GCA_014647815.1	113568	113568	type	True	93.789	2631	3184	95	below_threshold
Actinoplanes lobatus	strain=NBRC 12513	GCA_016862255.1	113568	113568	type	True	93.762	2575	3184	95	below_threshold
Actinoplanes lobatus	strain=DSM 43150	GCA_014205215.1	113568	113568	type	True	93.7387	2654	3184	95	below_threshold
Micromonospora phytophila	strain=DSM 105363	GCA_023656545.1	709888	709888	type	True	79.1419	835	3184	95	below_threshold
Micromonospora acroterricola	strain=5R2A7	GCA_003172955.1	2202421	2202421	type	True	78.8818	974	3184	95	below_threshold
Dactylosporangium fulvum	strain=NRRL B-16292	GCA_025137375.1	53359	53359	type	True	77.2946	1101	3184	95	below_threshold
Dactylosporangium matsuzakiense	strain=NRRL B-16293	GCA_025264725.1	53360	53360	type	True	77.1553	1231	3184	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:32,942] [INFO] DFAST Taxonomy check result was written to GCF_017592555.1_ASM1759255v1_genomic.fna/tc_result.tsv
[2024-01-24 13:41:32,942] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:32,942] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:32,943] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd70fd95f-90f0-4e41-bce1-891bd46f24e8/dqc_reference/checkm_data
[2024-01-24 13:41:32,944] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:33,035] [INFO] Task started: CheckM
[2024-01-24 13:41:33,035] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017592555.1_ASM1759255v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017592555.1_ASM1759255v1_genomic.fna/checkm_input GCF_017592555.1_ASM1759255v1_genomic.fna/checkm_result
[2024-01-24 13:43:09,647] [INFO] Task succeeded: CheckM
[2024-01-24 13:43:09,649] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:43:09,678] [INFO] ===== Completeness check finished =====
[2024-01-24 13:43:09,678] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:43:09,679] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017592555.1_ASM1759255v1_genomic.fna/markers.fasta)
[2024-01-24 13:43:09,679] [INFO] Task started: Blastn
[2024-01-24 13:43:09,679] [INFO] Running command: blastn -query GCF_017592555.1_ASM1759255v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd70fd95f-90f0-4e41-bce1-891bd46f24e8/dqc_reference/reference_markers_gtdb.fasta -out GCF_017592555.1_ASM1759255v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:43:11,549] [INFO] Task succeeded: Blastn
[2024-01-24 13:43:11,554] [INFO] Selected 11 target genomes.
[2024-01-24 13:43:11,554] [INFO] Target genome list was writen to GCF_017592555.1_ASM1759255v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:43:11,602] [INFO] Task started: fastANI
[2024-01-24 13:43:11,602] [INFO] Running command: fastANI --query /var/lib/cwl/stg232cd91f-c594-4b7d-a825-a4b2cf46ee64/GCF_017592555.1_ASM1759255v1_genomic.fna.gz --refList GCF_017592555.1_ASM1759255v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017592555.1_ASM1759255v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:43:42,123] [INFO] Task succeeded: fastANI
[2024-01-24 13:43:42,138] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:43:42,138] [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_017592555.1	s__Actinoplanes sp017592555	100.0	3170	3184	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014647795.1	s__Actinoplanes campanulatus	93.9691	2701	3184	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	93.7309	2655	3184	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0428	99.99	99.99	1.00	1.00	3	-
GCF_016862455.1	s__Actinoplanes utahensis	85.0998	1995	3184	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	99.99	99.99	0.99	0.99	2	-
GCF_900113015.1	s__Actinoplanes philippinensis	85.0026	2099	3184	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003148685.1	s__Actinoplanes xinjiangensis	84.9871	2090	3184	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900104725.1	s__Actinoplanes derwentensis	83.8925	1955	3184	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000284295.1	s__Actinoplanes missouriensis	83.428	1806	3184	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014205225.1	s__Actinoplanes octamycinicus	82.8963	1886	3184	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	100.00	100.00	1.00	1.00	2	-
GCF_016862395.1	s__Actinoplanes siamensis	82.7671	1573	3184	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018324205.1	s__Actinoplanes ianthinogenes	82.7342	1853	3184	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	99.99	99.99	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:43:42,141] [INFO] GTDB search result was written to GCF_017592555.1_ASM1759255v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:43:42,141] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:43:42,147] [INFO] DFAST_QC result json was written to GCF_017592555.1_ASM1759255v1_genomic.fna/dqc_result.json
[2024-01-24 13:43:42,147] [INFO] DFAST_QC completed!
[2024-01-24 13:43:42,147] [INFO] Total running time: 0h3m13s