[2024-01-25 19:38:05,873] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:38:05,874] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:38:05,875] [INFO] DQC Reference Directory: /var/lib/cwl/stgeebf437d-1e86-45f5-9fea-59a48bdf12ea/dqc_reference
[2024-01-25 19:38:07,026] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:38:07,026] [INFO] Task started: Prodigal
[2024-01-25 19:38:07,027] [INFO] Running command: gunzip -c /var/lib/cwl/stg67d4aece-63dc-41ad-a247-5555817d4c3a/GCF_016862855.1_ASM1686285v1_genomic.fna.gz | prodigal -d GCF_016862855.1_ASM1686285v1_genomic.fna/cds.fna -a GCF_016862855.1_ASM1686285v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:38:26,751] [INFO] Task succeeded: Prodigal
[2024-01-25 19:38:26,751] [INFO] Task started: HMMsearch
[2024-01-25 19:38:26,751] [INFO] Running command: hmmsearch --tblout GCF_016862855.1_ASM1686285v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgeebf437d-1e86-45f5-9fea-59a48bdf12ea/dqc_reference/reference_markers.hmm GCF_016862855.1_ASM1686285v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:38:27,104] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:38:27,105] [INFO] Found 6/6 markers.
[2024-01-25 19:38:27,170] [INFO] Query marker FASTA was written to GCF_016862855.1_ASM1686285v1_genomic.fna/markers.fasta
[2024-01-25 19:38:27,170] [INFO] Task started: Blastn
[2024-01-25 19:38:27,170] [INFO] Running command: blastn -query GCF_016862855.1_ASM1686285v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgeebf437d-1e86-45f5-9fea-59a48bdf12ea/dqc_reference/reference_markers.fasta -out GCF_016862855.1_ASM1686285v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:38:28,277] [INFO] Task succeeded: Blastn
[2024-01-25 19:38:28,279] [INFO] Selected 21 target genomes.
[2024-01-25 19:38:28,280] [INFO] Target genome list was writen to GCF_016862855.1_ASM1686285v1_genomic.fna/target_genomes.txt
[2024-01-25 19:38:28,294] [INFO] Task started: fastANI
[2024-01-25 19:38:28,294] [INFO] Running command: fastANI --query /var/lib/cwl/stg67d4aece-63dc-41ad-a247-5555817d4c3a/GCF_016862855.1_ASM1686285v1_genomic.fna.gz --refList GCF_016862855.1_ASM1686285v1_genomic.fna/target_genomes.txt --output GCF_016862855.1_ASM1686285v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:39:04,707] [INFO] Task succeeded: fastANI
[2024-01-25 19:39:04,707] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgeebf437d-1e86-45f5-9fea-59a48bdf12ea/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:39:04,708] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgeebf437d-1e86-45f5-9fea-59a48bdf12ea/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:39:04,720] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:39:04,720] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:39:04,720] [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
Phytomonospora endophytica	strain=YIM 65646	GCA_014202425.1	714109	714109	type	True	99.9987	2703	2704	95	conclusive
Stackebrandtia nassauensis	strain=DSM 44728	GCA_000024545.1	283811	283811	type	True	77.5908	727	2704	95	below_threshold
Stackebrandtia albiflava	strain=DSM 45044	GCA_007994225.1	406432	406432	type	True	77.3228	636	2704	95	below_threshold
Glycomyces arizonensis	strain=DSM 44726	GCA_000482705.1	256035	256035	type	True	77.2491	641	2704	95	below_threshold
Micromonospora acroterricola	strain=5R2A7	GCA_003172955.1	2202421	2202421	type	True	76.9661	609	2704	95	below_threshold
Micromonospora palomenae	strain=DSM 102131	GCA_007829925.1	1461247	1461247	type	True	76.9117	720	2704	95	below_threshold
Glycomyces artemisiae	strain=CGMCC 4.7067	GCA_003002955.1	1076443	1076443	type	True	76.8694	755	2704	95	below_threshold
Micromonospora polyrhachis	strain=DSM 45886	GCA_014203835.1	1282883	1282883	type	True	76.8219	501	2704	95	below_threshold
Catellatospora chokoriensis	strain=2-25(1)	GCA_011297315.1	310353	310353	type	True	76.8098	803	2704	95	below_threshold
Micromonospora kangleipakensis	strain=DSM 45612	GCA_004217615.1	1077942	1077942	type	True	76.7802	698	2704	95	below_threshold
Catellatospora citrea	strain=NBRC 14495	GCA_016862615.1	53366	53366	type	True	76.7729	827	2704	95	below_threshold
Catellatospora tritici	strain=NEAU-YM18	GCA_019083965.1	2851566	2851566	type	True	76.7703	789	2704	95	below_threshold
Catellatospora sichuanensis	strain=H14505	GCA_007483665.1	1969805	1969805	type	True	76.7649	794	2704	95	below_threshold
Catellatospora vulcania	strain=NEAU-JM1	GCA_009720385.1	1460450	1460450	type	True	76.7507	806	2704	95	below_threshold
Actinoplanes nipponensis	strain=NBRC 14063	GCA_016862275.1	135950	135950	type	True	76.6414	771	2704	95	below_threshold
Pilimelia anulata	strain=JCM 3090	GCA_014647895.1	53371	53371	type	True	76.5645	631	2704	95	below_threshold
Phytohabitans houttuyneae	strain=NBRC 108639	GCA_011764425.1	1076126	1076126	type	True	76.4015	841	2704	95	below_threshold
Virgisporangium aurantiacum	strain=NBRC 16421	GCA_016863635.1	175570	175570	type	True	76.2668	952	2704	95	below_threshold
Actinoplanes humidus	strain=NBRC 14915	GCA_016862215.1	113566	113566	type	True	76.243	708	2704	95	below_threshold
Actinomadura rubrisoli	strain=H3C3	GCA_004349215.1	2530368	2530368	type	True	75.864	664	2704	95	below_threshold
Amycolatopsis vancoresmycina	strain=DSM 44592	GCA_000388135.1	208444	208444	type	True	75.8532	646	2704	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:39:04,721] [INFO] DFAST Taxonomy check result was written to GCF_016862855.1_ASM1686285v1_genomic.fna/tc_result.tsv
[2024-01-25 19:39:04,722] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:39:04,722] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:39:04,722] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgeebf437d-1e86-45f5-9fea-59a48bdf12ea/dqc_reference/checkm_data
[2024-01-25 19:39:04,723] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:39:04,800] [INFO] Task started: CheckM
[2024-01-25 19:39:04,800] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016862855.1_ASM1686285v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016862855.1_ASM1686285v1_genomic.fna/checkm_input GCF_016862855.1_ASM1686285v1_genomic.fna/checkm_result
[2024-01-25 19:40:32,683] [INFO] Task succeeded: CheckM
[2024-01-25 19:40:32,684] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 8.33%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:40:32,707] [INFO] ===== Completeness check finished =====
[2024-01-25 19:40:32,708] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:40:32,709] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016862855.1_ASM1686285v1_genomic.fna/markers.fasta)
[2024-01-25 19:40:32,709] [INFO] Task started: Blastn
[2024-01-25 19:40:32,709] [INFO] Running command: blastn -query GCF_016862855.1_ASM1686285v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgeebf437d-1e86-45f5-9fea-59a48bdf12ea/dqc_reference/reference_markers_gtdb.fasta -out GCF_016862855.1_ASM1686285v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:40:34,460] [INFO] Task succeeded: Blastn
[2024-01-25 19:40:34,462] [INFO] Selected 21 target genomes.
[2024-01-25 19:40:34,463] [INFO] Target genome list was writen to GCF_016862855.1_ASM1686285v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:40:34,494] [INFO] Task started: fastANI
[2024-01-25 19:40:34,494] [INFO] Running command: fastANI --query /var/lib/cwl/stg67d4aece-63dc-41ad-a247-5555817d4c3a/GCF_016862855.1_ASM1686285v1_genomic.fna.gz --refList GCF_016862855.1_ASM1686285v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016862855.1_ASM1686285v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:41:06,743] [INFO] Task succeeded: fastANI
[2024-01-25 19:41:06,757] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:41:06,757] [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_014202425.1	s__Phytomonospora endophytica	99.9987	2703	2704	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Phytomonospora	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_000024545.1	s__Stackebrandtia nassauensis	77.5951	727	2704	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Stackebrandtia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007994225.1	s__Stackebrandtia albiflava	77.3003	641	2704	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Stackebrandtia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000482705.1	s__Glycomyces arizonensis	77.2429	642	2704	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Glycomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016918015.1	s__Glycomyces sp016918015	76.9875	590	2704	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Glycomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009707425.1	s__Micromonospora sp009707425	76.9542	646	2704	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014648395.1	s__Micromonospora fulviviridis	76.9538	742	2704	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	95.01	95.01	0.74	0.74	2	-
GCF_004345505.1	s__Micromonospora sp004345505	76.8731	781	2704	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	96.85	96.85	0.87	0.87	2	-
GCF_003002955.1	s__Glycomyces artemisiae	76.8602	756	2704	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Glycomyces	95.0	97.80	97.80	0.92	0.92	2	-
GCF_004217615.1	s__Micromonospora kangleipakensis	76.7909	695	2704	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003610235.1	s__Catellatospora citrea	76.7752	830	2704	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Catellatospora	95.0	97.34	95.99	0.88	0.83	4	-
GCF_019083965.1	s__Catellatospora sp019083965	76.7493	792	2704	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Catellatospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004348525.1	s__Micromonospora sp004348525	76.7489	657	2704	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018324255.1	s__Polymorphospora rubra	76.672	755	2704	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Polymorphospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016862275.1	s__Actinoplanes nipponensis	76.6324	775	2704	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014647895.1	s__Pilimelia anulata	76.5659	630	2704	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Pilimelia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018397995.1	s__NBRC-107566 sp018397995	76.5426	604	2704	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__NBRC-107566	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011764425.1	s__Phytohabitans houttuyneae	76.4133	836	2704	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Phytohabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016863635.1	s__Virgisporangium aurantiacum	76.2498	961	2704	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Virgisporangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004349215.1	s__Spirillospora rubrisoli	75.8682	660	2704	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000716785.1	s__Amycolatopsis vancoresmycina	75.7729	753	2704	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	99.98	99.98	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-25 19:41:06,759] [INFO] GTDB search result was written to GCF_016862855.1_ASM1686285v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:41:06,759] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:41:06,763] [INFO] DFAST_QC result json was written to GCF_016862855.1_ASM1686285v1_genomic.fna/dqc_result.json
[2024-01-25 19:41:06,764] [INFO] DFAST_QC completed!
[2024-01-25 19:41:06,764] [INFO] Total running time: 0h3m1s