[2024-01-25 19:38:35,646] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:38:35,647] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:38:35,647] [INFO] DQC Reference Directory: /var/lib/cwl/stga6d6c811-819c-4991-9be0-32fc04577069/dqc_reference
[2024-01-25 19:38:36,912] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:38:36,913] [INFO] Task started: Prodigal
[2024-01-25 19:38:36,913] [INFO] Running command: gunzip -c /var/lib/cwl/stg85bea19a-5d0c-450c-b2f1-c7829670e3b5/GCF_014647915.1_ASM1464791v1_genomic.fna.gz | prodigal -d GCF_014647915.1_ASM1464791v1_genomic.fna/cds.fna -a GCF_014647915.1_ASM1464791v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:38:47,442] [INFO] Task succeeded: Prodigal
[2024-01-25 19:38:47,443] [INFO] Task started: HMMsearch
[2024-01-25 19:38:47,443] [INFO] Running command: hmmsearch --tblout GCF_014647915.1_ASM1464791v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga6d6c811-819c-4991-9be0-32fc04577069/dqc_reference/reference_markers.hmm GCF_014647915.1_ASM1464791v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:38:47,676] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:38:47,677] [INFO] Found 6/6 markers.
[2024-01-25 19:38:47,723] [INFO] Query marker FASTA was written to GCF_014647915.1_ASM1464791v1_genomic.fna/markers.fasta
[2024-01-25 19:38:47,723] [INFO] Task started: Blastn
[2024-01-25 19:38:47,723] [INFO] Running command: blastn -query GCF_014647915.1_ASM1464791v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga6d6c811-819c-4991-9be0-32fc04577069/dqc_reference/reference_markers.fasta -out GCF_014647915.1_ASM1464791v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:38:48,854] [INFO] Task succeeded: Blastn
[2024-01-25 19:38:48,856] [INFO] Selected 22 target genomes.
[2024-01-25 19:38:48,857] [INFO] Target genome list was writen to GCF_014647915.1_ASM1464791v1_genomic.fna/target_genomes.txt
[2024-01-25 19:38:48,883] [INFO] Task started: fastANI
[2024-01-25 19:38:48,883] [INFO] Running command: fastANI --query /var/lib/cwl/stg85bea19a-5d0c-450c-b2f1-c7829670e3b5/GCF_014647915.1_ASM1464791v1_genomic.fna.gz --refList GCF_014647915.1_ASM1464791v1_genomic.fna/target_genomes.txt --output GCF_014647915.1_ASM1464791v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:39:21,769] [INFO] Task succeeded: fastANI
[2024-01-25 19:39:21,769] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga6d6c811-819c-4991-9be0-32fc04577069/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:39:21,770] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga6d6c811-819c-4991-9be0-32fc04577069/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:39:21,782] [INFO] Found 22 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:39:21,783] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:39:21,783] [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
Pilimelia terevasa	strain=JCM 3091	GCA_014647915.1	53372	53372	type	True	100.0	1488	1490	95	conclusive
Pilimelia anulata	strain=JCM 3090	GCA_014647895.1	53371	53371	type	True	84.1169	1065	1490	95	below_threshold
Micromonospora phytophila	strain=DSM 105363	GCA_023656545.1	709888	709888	type	True	79.204	577	1490	95	below_threshold
Micromonospora kangleipakensis	strain=DSM 45612	GCA_004217615.1	1077942	1077942	type	True	78.9841	718	1490	95	below_threshold
Micromonospora olivasterospora	strain=DSM 43868	GCA_007830265.1	1880	1880	type	True	78.959	725	1490	95	below_threshold
Micromonospora inositola	strain=DSM 43819	GCA_900090285.1	47865	47865	type	True	78.9542	710	1490	95	below_threshold
Micromonospora deserti	strain=13K206	GCA_003236335.1	2070366	2070366	type	True	78.9482	628	1490	95	below_threshold
Micromonospora coxensis	strain=DSM 45161	GCA_900090295.1	356852	356852	type	True	78.9472	759	1490	95	below_threshold
Micromonospora viridifaciens	strain=DSM 43909	GCA_900091545.1	1881	1881	type	True	78.9361	692	1490	95	below_threshold
Micromonospora auratinigra	strain=DSM 44815	GCA_900089595.1	261654	261654	type	True	78.9243	748	1490	95	below_threshold
Micromonospora echinaurantiaca	strain=DSM 43904	GCA_900090235.1	47857	47857	type	True	78.8373	764	1490	95	below_threshold
Micromonospora narathiwatensis	strain=DSM 45248	GCA_900089605.1	299146	299146	type	True	78.8333	719	1490	95	below_threshold
Micromonospora halophytica	strain=DSM 43171	GCA_900090245.1	47864	47864	type	True	78.8311	716	1490	95	below_threshold
Micromonospora veneta	strain=CAP181	GCA_016598485.1	2796464	2796464	type	True	78.8167	703	1490	95	below_threshold
Micromonospora chaiyaphumensis	strain=DSM 45246	GCA_900091435.1	307119	307119	type	True	78.8113	737	1490	95	below_threshold
Micromonospora rifamycinica	strain=DSM 44983	GCA_900090265.1	291594	291594	type	True	78.8096	720	1490	95	below_threshold
Micromonospora rifamycinica	strain=AM105	GCA_001542325.1	291594	291594	type	True	78.7117	680	1490	95	below_threshold
Micromonospora humida	strain=MMS20-R1-14	GCA_016901255.1	2809018	2809018	type	True	78.6478	726	1490	95	below_threshold
Micromonospora wenchangensis	strain=CCTCC AA 2012002	GCA_002210435.1	1185415	1185415	type	True	78.635	733	1490	95	below_threshold
Micromonospora polyrhachis	strain=DSM 45886	GCA_014203835.1	1282883	1282883	type	True	78.2943	546	1490	95	below_threshold
Actinoplanes atraurantiacus	strain=CGMCC 4.6857	GCA_900215205.1	1036182	1036182	type	True	77.6355	705	1490	95	below_threshold
Kibdelosporangium philippinense	strain=ATCC 49844	GCA_021390435.3	211113	211113	type	True	76.3924	268	1490	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:39:21,787] [INFO] DFAST Taxonomy check result was written to GCF_014647915.1_ASM1464791v1_genomic.fna/tc_result.tsv
[2024-01-25 19:39:21,787] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:39:21,788] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:39:21,788] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga6d6c811-819c-4991-9be0-32fc04577069/dqc_reference/checkm_data
[2024-01-25 19:39:21,789] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:39:21,834] [INFO] Task started: CheckM
[2024-01-25 19:39:21,834] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014647915.1_ASM1464791v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014647915.1_ASM1464791v1_genomic.fna/checkm_input GCF_014647915.1_ASM1464791v1_genomic.fna/checkm_result
[2024-01-25 19:40:01,137] [INFO] Task succeeded: CheckM
[2024-01-25 19:40:01,138] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 8.33%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:40:01,155] [INFO] ===== Completeness check finished =====
[2024-01-25 19:40:01,155] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:40:01,156] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014647915.1_ASM1464791v1_genomic.fna/markers.fasta)
[2024-01-25 19:40:01,156] [INFO] Task started: Blastn
[2024-01-25 19:40:01,156] [INFO] Running command: blastn -query GCF_014647915.1_ASM1464791v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga6d6c811-819c-4991-9be0-32fc04577069/dqc_reference/reference_markers_gtdb.fasta -out GCF_014647915.1_ASM1464791v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:40:02,790] [INFO] Task succeeded: Blastn
[2024-01-25 19:40:02,793] [INFO] Selected 25 target genomes.
[2024-01-25 19:40:02,793] [INFO] Target genome list was writen to GCF_014647915.1_ASM1464791v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:40:02,812] [INFO] Task started: fastANI
[2024-01-25 19:40:02,812] [INFO] Running command: fastANI --query /var/lib/cwl/stg85bea19a-5d0c-450c-b2f1-c7829670e3b5/GCF_014647915.1_ASM1464791v1_genomic.fna.gz --refList GCF_014647915.1_ASM1464791v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014647915.1_ASM1464791v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:40:38,640] [INFO] Task succeeded: fastANI
[2024-01-25 19:40:38,656] [INFO] Found 25 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:40:38,657] [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_014647915.1	s__Pilimelia terevasa	100.0	1488	1490	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Pilimelia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014647895.1	s__Pilimelia anulata	84.1759	1059	1490	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Pilimelia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900090285.1	s__Micromonospora inositola	79.0246	699	1490	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007830265.1	s__Micromonospora olivasterospora	78.971	724	1490	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004217615.1	s__Micromonospora kangleipakensis	78.9482	723	1490	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004348595.1	s__Micromonospora sp004348595	78.9426	654	1490	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900090245.1	s__Micromonospora halophytica	78.8927	705	1490	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900090295.1	s__Micromonospora coxensis	78.8925	768	1490	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900089595.1	s__Micromonospora auratinigra	78.8924	754	1490	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014205165.1	s__Micromonospora carbonacea	78.8898	802	1490	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.5545	99.19	98.38	0.95	0.91	3	-
GCF_004345505.1	s__Micromonospora sp004345505	78.8852	734	1490	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	96.85	96.85	0.87	0.87	2	-
GCF_016598485.1	s__Micromonospora veneta	78.8742	694	1490	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000982955.1	s__Micromonospora sp000982955	78.8696	725	1490	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900090235.1	s__Micromonospora echinaurantiaca	78.8379	764	1490	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	95.93	95.22	0.84	0.83	3	-
GCF_900091435.1	s__Micromonospora chaiyaphumensis	78.785	741	1490	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	95.16	95.15	0.86	0.86	3	-
GCF_900090265.1	s__Micromonospora rifamycinica	78.7801	723	1490	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	100.00	100.00	1.00	1.00	2	-
GCF_016863535.1	s__Micromonospora lutea	78.5285	564	1490	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	78.4173	724	1490	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Polymorphospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002846275.1	s__Plantactinospora sp002846275	78.3582	694	1490	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Plantactinospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003030345.1	s__Plantactinospora sp003030345	78.339	737	1490	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Plantactinospora	95.0	98.72	98.72	0.95	0.95	2	-
GCF_014203835.1	s__Micromonospora_H polyrhachis	78.295	544	1490	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora_H	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004522235.1	s__Amycolatopsis nivea	76.2387	409	1490	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	97.97	97.28	0.91	0.88	6	-
GCA_019239965.1	s__Kutzneria sp019239965	76.1656	204	1490	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Kutzneria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015356825.1	s__Catenulispora rubra	76.1181	560	1490	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Catenulisporaceae;g__Catenulispora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000411975.1	s__Amycolatopsis orientalis_D	76.1057	448	1490	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:40:38,658] [INFO] GTDB search result was written to GCF_014647915.1_ASM1464791v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:40:38,659] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:40:38,662] [INFO] DFAST_QC result json was written to GCF_014647915.1_ASM1464791v1_genomic.fna/dqc_result.json
[2024-01-25 19:40:38,662] [INFO] DFAST_QC completed!
[2024-01-25 19:40:38,662] [INFO] Total running time: 0h2m3s