[2024-01-25 19:44:51,725] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:44:51,731] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:44:51,731] [INFO] DQC Reference Directory: /var/lib/cwl/stg49b81535-7ee6-480b-a822-ea6b8fb556fc/dqc_reference
[2024-01-25 19:44:52,922] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:44:52,922] [INFO] Task started: Prodigal
[2024-01-25 19:44:52,923] [INFO] Running command: gunzip -c /var/lib/cwl/stgb5d7820c-9175-4b9e-8d9e-4ce631cd1fa8/GCF_015704865.1_ASM1570486v1_genomic.fna.gz | prodigal -d GCF_015704865.1_ASM1570486v1_genomic.fna/cds.fna -a GCF_015704865.1_ASM1570486v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:45:19,731] [INFO] Task succeeded: Prodigal
[2024-01-25 19:45:19,731] [INFO] Task started: HMMsearch
[2024-01-25 19:45:19,731] [INFO] Running command: hmmsearch --tblout GCF_015704865.1_ASM1570486v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg49b81535-7ee6-480b-a822-ea6b8fb556fc/dqc_reference/reference_markers.hmm GCF_015704865.1_ASM1570486v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:45:20,173] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:45:20,174] [INFO] Found 6/6 markers.
[2024-01-25 19:45:20,257] [INFO] Query marker FASTA was written to GCF_015704865.1_ASM1570486v1_genomic.fna/markers.fasta
[2024-01-25 19:45:20,257] [INFO] Task started: Blastn
[2024-01-25 19:45:20,257] [INFO] Running command: blastn -query GCF_015704865.1_ASM1570486v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg49b81535-7ee6-480b-a822-ea6b8fb556fc/dqc_reference/reference_markers.fasta -out GCF_015704865.1_ASM1570486v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:45:21,438] [INFO] Task succeeded: Blastn
[2024-01-25 19:45:21,440] [INFO] Selected 25 target genomes.
[2024-01-25 19:45:21,441] [INFO] Target genome list was writen to GCF_015704865.1_ASM1570486v1_genomic.fna/target_genomes.txt
[2024-01-25 19:45:21,451] [INFO] Task started: fastANI
[2024-01-25 19:45:21,451] [INFO] Running command: fastANI --query /var/lib/cwl/stgb5d7820c-9175-4b9e-8d9e-4ce631cd1fa8/GCF_015704865.1_ASM1570486v1_genomic.fna.gz --refList GCF_015704865.1_ASM1570486v1_genomic.fna/target_genomes.txt --output GCF_015704865.1_ASM1570486v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:46:15,449] [INFO] Task succeeded: fastANI
[2024-01-25 19:46:15,449] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg49b81535-7ee6-480b-a822-ea6b8fb556fc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:46:15,451] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg49b81535-7ee6-480b-a822-ea6b8fb556fc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:46:15,464] [INFO] Found 25 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 19:46:15,465] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 19:46:15,465] [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 missouriensis	strain=431	GCA_000284295.1	1866	1866	type	True	83.9051	1935	3525	95	below_threshold
Actinoplanes hulinensis	strain=NEAU-M9	GCA_019429605.1	1144547	1144547	type	True	83.8698	1935	3525	95	below_threshold
Actinoplanes campanulatus	strain=NBRC 12511	GCA_016862035.1	113559	113559	type	True	83.7794	1958	3525	95	below_threshold
Actinoplanes capillaceus	strain=NBRC 16408	GCA_016862055.1	76756	76756	type	True	83.72	1912	3525	95	below_threshold
Actinoplanes flavus	strain=NEAU-H7	GCA_017592555.1	2820290	2820290	type	True	83.6991	1955	3525	95	below_threshold
Actinoplanes lobatus	strain=NBRC 12513	GCA_016862255.1	113568	113568	type	True	83.6844	1935	3525	95	below_threshold
Actinoplanes lobatus	strain=JCM 3061	GCA_014647815.1	113568	113568	type	True	83.6547	1964	3525	95	below_threshold
Actinoplanes lobatus	strain=DSM 43150	GCA_014205215.1	113568	113568	type	True	83.6515	1988	3525	95	below_threshold
Actinoplanes utahensis	strain=NBRC 13244	GCA_016862455.1	1869	1869	type	True	83.3583	1899	3525	95	below_threshold
Actinoplanes teichomyceticus	strain=NBRC 13999	GCA_016862415.1	1867	1867	type	True	83.2847	1635	3525	95	below_threshold
Actinoplanes teichomyceticus	strain=DSM 43866	GCA_007829915.1	1867	1867	type	True	83.2018	1678	3525	95	below_threshold
Actinoplanes teichomyceticus	strain=ATCC 31121	GCA_003711105.1	1867	1867	type	True	83.1353	1705	3525	95	below_threshold
Actinoplanes philippinensis	strain=NBRC 13878	GCA_016862335.1	35752	35752	type	True	83.131	1925	3525	95	below_threshold
Actinoplanes philippinensis	strain=DSM 43019	GCA_900113015.1	35752	35752	type	True	83.0692	1974	3525	95	below_threshold
Actinoplanes ianthinogenes	strain=NBRC 13996	GCA_018324205.1	122358	122358	type	True	82.9415	1909	3525	95	below_threshold
Actinoplanes ianthinogenes	strain=JCM 3249	GCA_014648375.1	122358	122358	type	True	82.9276	1915	3525	95	below_threshold
Actinoplanes italicus	strain=DSM 43146	GCA_003001815.1	113567	113567	type	True	82.8726	2091	3525	95	below_threshold
Actinoplanes regularis	strain=DSM 43151	GCA_900188005.1	52697	52697	type	True	82.6149	1822	3525	95	below_threshold
Actinoplanes regularis	strain=NBRC 12514	GCA_016862355.1	52697	52697	type	True	82.6007	1792	3525	95	below_threshold
Actinoplanes atraurantiacus	strain=CGMCC 4.6857	GCA_900215205.1	1036182	1036182	type	True	80.7036	1738	3525	95	below_threshold
Couchioplanes caeruleus	strain=DSM 43634	GCA_003751945.1	56438	56438	type	True	80.353	1372	3525	95	below_threshold
Micromonospora acroterricola	strain=5R2A7	GCA_003172955.1	2202421	2202421	type	True	79.0973	1005	3525	95	below_threshold
Micromonospora phaseoli	strain=NBRC 110907	GCA_016863675.1	1144548	1144548	type	True	78.7929	1018	3525	95	below_threshold
Micromonospora humida	strain=MMS20-R1-14	GCA_016901255.1	2809018	2809018	type	True	78.6172	1171	3525	95	below_threshold
Dactylosporangium fulvum	strain=NRRL B-16292	GCA_025137375.1	53359	53359	type	True	77.3628	1161	3525	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:46:15,466] [INFO] DFAST Taxonomy check result was written to GCF_015704865.1_ASM1570486v1_genomic.fna/tc_result.tsv
[2024-01-25 19:46:15,467] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:46:15,467] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:46:15,467] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg49b81535-7ee6-480b-a822-ea6b8fb556fc/dqc_reference/checkm_data
[2024-01-25 19:46:15,468] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:46:15,561] [INFO] Task started: CheckM
[2024-01-25 19:46:15,561] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_015704865.1_ASM1570486v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_015704865.1_ASM1570486v1_genomic.fna/checkm_input GCF_015704865.1_ASM1570486v1_genomic.fna/checkm_result
[2024-01-25 19:47:49,758] [INFO] Task succeeded: CheckM
[2024-01-25 19:47:49,759] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:47:49,817] [INFO] ===== Completeness check finished =====
[2024-01-25 19:47:49,818] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:47:49,818] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_015704865.1_ASM1570486v1_genomic.fna/markers.fasta)
[2024-01-25 19:47:49,818] [INFO] Task started: Blastn
[2024-01-25 19:47:49,818] [INFO] Running command: blastn -query GCF_015704865.1_ASM1570486v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg49b81535-7ee6-480b-a822-ea6b8fb556fc/dqc_reference/reference_markers_gtdb.fasta -out GCF_015704865.1_ASM1570486v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:47:51,716] [INFO] Task succeeded: Blastn
[2024-01-25 19:47:51,719] [INFO] Selected 18 target genomes.
[2024-01-25 19:47:51,719] [INFO] Target genome list was writen to GCF_015704865.1_ASM1570486v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:47:51,729] [INFO] Task started: fastANI
[2024-01-25 19:47:51,729] [INFO] Running command: fastANI --query /var/lib/cwl/stgb5d7820c-9175-4b9e-8d9e-4ce631cd1fa8/GCF_015704865.1_ASM1570486v1_genomic.fna.gz --refList GCF_015704865.1_ASM1570486v1_genomic.fna/target_genomes_gtdb.txt --output GCF_015704865.1_ASM1570486v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:48:37,894] [INFO] Task succeeded: fastANI
[2024-01-25 19:48:37,906] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:48:37,906] [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_015704865.1	s__Actinoplanes sp015704865	100.0	3513	3525	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_000284295.1	s__Actinoplanes missouriensis	83.9209	1931	3525	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017592555.1	s__Actinoplanes sp017592555	83.7176	1954	3525	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	83.6801	1980	3525	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	83.6793	1983	3525	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0428	99.99	99.99	1.00	1.00	3	-
GCF_004001265.1	s__Actinoplanes sp004001265	83.5065	1921	3525	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	83.3407	1902	3525	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	99.99	99.99	0.99	0.99	2	-
GCF_003711105.1	s__Actinoplanes teichomyceticus	83.14	1704	3525	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	100.00	99.99	1.00	1.00	4	-
GCF_900113015.1	s__Actinoplanes philippinensis	83.1026	1965	3525	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014205225.1	s__Actinoplanes octamycinicus	83.0641	1961	3525	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	100.00	100.00	1.00	1.00	2	-
GCF_018324205.1	s__Actinoplanes ianthinogenes	82.9243	1914	3525	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	99.99	99.99	0.99	0.99	2	-
GCF_016862395.1	s__Actinoplanes siamensis	82.8098	1630	3525	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016862315.1	s__Actinoplanes palleronii	82.5128	1937	3525	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	97.70	97.70	0.89	0.89	2	-
GCF_000962825.1	s__Actinoplanes rectilineatus	82.4482	1816	3525	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900119315.1	s__Actinoplanes sp900119315	82.2509	1700	3525	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	100.00	100.00	1.00	1.00	3	-
GCF_900215205.1	s__Actinoplanes atraurantiacus	80.7134	1734	3525	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003751945.1	s__Actinoplanes caeruleus	80.3976	1363	3525	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	99.99	99.99	0.98	0.98	2	-
GCF_001553785.1	s__Actinoplanes sp001553785	79.8053	1168	3525	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 19:48:37,908] [INFO] GTDB search result was written to GCF_015704865.1_ASM1570486v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:48:37,908] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:48:37,912] [INFO] DFAST_QC result json was written to GCF_015704865.1_ASM1570486v1_genomic.fna/dqc_result.json
[2024-01-25 19:48:37,912] [INFO] DFAST_QC completed!
[2024-01-25 19:48:37,912] [INFO] Total running time: 0h3m46s