[2024-01-24 10:47:06,548] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:47:06,555] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:47:06,555] [INFO] DQC Reference Directory: /var/lib/cwl/stgc46d6c9e-508d-4b1e-b7e1-931a25ebcc33/dqc_reference
[2024-01-24 10:47:12,103] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:47:12,104] [INFO] Task started: Prodigal
[2024-01-24 10:47:12,104] [INFO] Running command: gunzip -c /var/lib/cwl/stg418173db-09f4-42a2-93ba-c58be42f9ee6/GCF_016863655.1_ASM1686365v1_genomic.fna.gz | prodigal -d GCF_016863655.1_ASM1686365v1_genomic.fna/cds.fna -a GCF_016863655.1_ASM1686365v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:47:50,806] [INFO] Task succeeded: Prodigal
[2024-01-24 10:47:50,807] [INFO] Task started: HMMsearch
[2024-01-24 10:47:50,807] [INFO] Running command: hmmsearch --tblout GCF_016863655.1_ASM1686365v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc46d6c9e-508d-4b1e-b7e1-931a25ebcc33/dqc_reference/reference_markers.hmm GCF_016863655.1_ASM1686365v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:47:51,305] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:47:51,306] [INFO] Found 6/6 markers.
[2024-01-24 10:47:51,402] [INFO] Query marker FASTA was written to GCF_016863655.1_ASM1686365v1_genomic.fna/markers.fasta
[2024-01-24 10:47:51,402] [INFO] Task started: Blastn
[2024-01-24 10:47:51,402] [INFO] Running command: blastn -query GCF_016863655.1_ASM1686365v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc46d6c9e-508d-4b1e-b7e1-931a25ebcc33/dqc_reference/reference_markers.fasta -out GCF_016863655.1_ASM1686365v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:47:52,708] [INFO] Task succeeded: Blastn
[2024-01-24 10:47:52,715] [INFO] Selected 21 target genomes.
[2024-01-24 10:47:52,716] [INFO] Target genome list was writen to GCF_016863655.1_ASM1686365v1_genomic.fna/target_genomes.txt
[2024-01-24 10:47:52,728] [INFO] Task started: fastANI
[2024-01-24 10:47:52,728] [INFO] Running command: fastANI --query /var/lib/cwl/stg418173db-09f4-42a2-93ba-c58be42f9ee6/GCF_016863655.1_ASM1686365v1_genomic.fna.gz --refList GCF_016863655.1_ASM1686365v1_genomic.fna/target_genomes.txt --output GCF_016863655.1_ASM1686365v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:48:34,250] [INFO] Task succeeded: fastANI
[2024-01-24 10:48:34,251] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc46d6c9e-508d-4b1e-b7e1-931a25ebcc33/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:48:34,251] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc46d6c9e-508d-4b1e-b7e1-931a25ebcc33/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:48:34,267] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 10:48:34,267] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:48:34,267] [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
Virgisporangium ochraceum	strain=NBRC 16418	GCA_016863655.1	65505	65505	type	True	100.0	3708	3715	95	conclusive
Virgisporangium aurantiacum	strain=NBRC 16421	GCA_016863635.1	175570	175570	type	True	85.4859	2552	3715	95	below_threshold
Virgisporangium aliadipatigenens	strain=NBRC 105644	GCA_016863615.1	741659	741659	type	True	78.6119	1581	3715	95	below_threshold
Micromonospora maritima		GCA_902825405.1	986711	986711	type	True	78.0709	883	3715	95	below_threshold
Micromonospora orduensis	strain=S2509	GCA_006228125.1	1420891	1420891	type	True	77.9035	1006	3715	95	below_threshold
Dactylosporangium roseum	strain=NRRL B-16295	GCA_025264685.1	47989	47989	type	True	77.8989	1145	3715	95	below_threshold
Micromonospora humida	strain=MMS20-R1-14	GCA_016901255.1	2809018	2809018	type	True	77.7676	1164	3715	95	below_threshold
Dactylosporangium fulvum	strain=NRRL B-16292	GCA_025137375.1	53359	53359	type	True	77.7573	1342	3715	95	below_threshold
Micromonospora ferruginea	strain=28ISP2-46	GCA_013694245.1	2749844	2749844	type	True	77.7445	1172	3715	95	below_threshold
Micromonospora phytophila	strain=DSM 105363	GCA_023656545.1	709888	709888	type	True	77.7382	837	3715	95	below_threshold
Micromonospora deserti	strain=13K206	GCA_003236335.1	2070366	2070366	type	True	77.723	958	3715	95	below_threshold
Micromonospora chokoriensis	strain=DSM 45160	GCA_900091505.1	356851	356851	type	True	77.6952	1049	3715	95	below_threshold
Micromonospora purpureochromogenes	strain=DSM 43821	GCA_900091515.1	47872	47872	type	True	77.6897	1084	3715	95	below_threshold
Micromonospora coriariae	strain=DSM 44875	GCA_900091455.1	285665	285665	type	True	77.6031	1057	3715	95	below_threshold
Micromonospora rosaria	strain=DSM 803	GCA_001567585.1	47874	47874	type	True	77.575	1083	3715	95	below_threshold
Catellatospora chokoriensis	strain=2-25(1)	GCA_011297315.1	310353	310353	type	True	77.3723	1225	3715	95	below_threshold
Salinispora arenicola	strain=DSM 44819	GCA_006716065.1	168697	168697	type	True	77.1077	627	3715	95	below_threshold
Pilimelia anulata	strain=JCM 3090	GCA_014647895.1	53371	53371	type	True	76.9938	940	3715	95	below_threshold
Rugosimonospora africana	strain=NBRC 104875	GCA_016862975.1	556532	556532	type	True	76.9927	1122	3715	95	below_threshold
Lentzea guizhouensis	strain=DHS C013	GCA_001701025.1	1586287	1586287	type	True	76.2692	985	3715	95	below_threshold
Amycolatopsis thermalba	strain=NRRL B-24845	GCA_003385215.1	944492	944492	type	True	76.2348	834	3715	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:48:34,270] [INFO] DFAST Taxonomy check result was written to GCF_016863655.1_ASM1686365v1_genomic.fna/tc_result.tsv
[2024-01-24 10:48:34,270] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:48:34,270] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:48:34,271] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc46d6c9e-508d-4b1e-b7e1-931a25ebcc33/dqc_reference/checkm_data
[2024-01-24 10:48:34,272] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:48:34,369] [INFO] Task started: CheckM
[2024-01-24 10:48:34,370] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016863655.1_ASM1686365v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016863655.1_ASM1686365v1_genomic.fna/checkm_input GCF_016863655.1_ASM1686365v1_genomic.fna/checkm_result
[2024-01-24 10:50:51,645] [INFO] Task succeeded: CheckM
[2024-01-24 10:50:51,646] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 13.43%
Strain heterogeneity: 22.22%
--------------------------------------------------------------------------------
[2024-01-24 10:50:51,673] [INFO] ===== Completeness check finished =====
[2024-01-24 10:50:51,673] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:50:51,674] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016863655.1_ASM1686365v1_genomic.fna/markers.fasta)
[2024-01-24 10:50:51,674] [INFO] Task started: Blastn
[2024-01-24 10:50:51,674] [INFO] Running command: blastn -query GCF_016863655.1_ASM1686365v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc46d6c9e-508d-4b1e-b7e1-931a25ebcc33/dqc_reference/reference_markers_gtdb.fasta -out GCF_016863655.1_ASM1686365v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:50:53,502] [INFO] Task succeeded: Blastn
[2024-01-24 10:50:53,505] [INFO] Selected 19 target genomes.
[2024-01-24 10:50:53,505] [INFO] Target genome list was writen to GCF_016863655.1_ASM1686365v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:50:53,517] [INFO] Task started: fastANI
[2024-01-24 10:50:53,517] [INFO] Running command: fastANI --query /var/lib/cwl/stg418173db-09f4-42a2-93ba-c58be42f9ee6/GCF_016863655.1_ASM1686365v1_genomic.fna.gz --refList GCF_016863655.1_ASM1686365v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016863655.1_ASM1686365v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:51:27,963] [INFO] Task succeeded: fastANI
[2024-01-24 10:51:27,979] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:51:27,980] [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_016863655.1	s__Virgisporangium ochraceum	100.0	3708	3715	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Virgisporangium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_016863635.1	s__Virgisporangium aurantiacum	85.4342	2564	3715	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Virgisporangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016863615.1	s__Virgisporangium aliadipatigenens	78.6362	1571	3715	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Virgisporangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011947225.1	s__Planosporangium flavigriseum	78.1317	831	3715	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Planosporangium	95.0	99.99	99.99	1.00	1.00	2	-
GCF_902825405.1	s__Micromonospora maritima	78.0373	891	3715	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016863255.1	s__Planosporangium mesophilum	77.8993	1008	3715	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Planosporangium	95.0	100.00	100.00	0.99	0.99	2	-
GCF_006228125.1	s__Micromonospora orduensis	77.8894	1010	3715	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003667505.1	s__Micromonospora sp003667505	77.7548	1000	3715	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	98.83	98.83	0.94	0.94	2	-
GCF_007830265.1	s__Micromonospora olivasterospora	77.7392	989	3715	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018397995.1	s__NBRC-107566 sp018397995	77.7267	983	3715	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_015751765.1	s__Micromonospora ureilytica	77.6618	1030	3715	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	97.52	97.34	0.88	0.87	3	-
GCF_003236335.1	s__Micromonospora deserti	77.6611	978	3715	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900091455.1	s__Micromonospora coriariae	77.5947	1060	3715	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001567585.1	s__Micromonospora rosaria	77.5459	1092	3715	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004217235.1	s__Plantactinospora sp004217235	77.5207	1039	3715	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Plantactinospora	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016880465.1	s__EFPC-2 sp016880465	77.4274	595	3715	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__EFPC-2	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016862975.1	s__Rugosimonospora africana	76.998	1119	3715	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Rugosimonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014647895.1	s__Pilimelia anulata	76.9667	951	3715	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Pilimelia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002904335.1	s__Amycolatopsis sp002904335	75.961	1098	3715	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 10:51:27,982] [INFO] GTDB search result was written to GCF_016863655.1_ASM1686365v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:51:27,982] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:51:27,987] [INFO] DFAST_QC result json was written to GCF_016863655.1_ASM1686365v1_genomic.fna/dqc_result.json
[2024-01-24 10:51:27,987] [INFO] DFAST_QC completed!
[2024-01-24 10:51:27,987] [INFO] Total running time: 0h4m21s