[2024-01-24 14:30:17,165] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:30:17,167] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:30:17,168] [INFO] DQC Reference Directory: /var/lib/cwl/stg67d01ad0-5170-4336-95c9-a0f082214366/dqc_reference
[2024-01-24 14:30:18,559] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:30:18,559] [INFO] Task started: Prodigal
[2024-01-24 14:30:18,560] [INFO] Running command: gunzip -c /var/lib/cwl/stg250a8cd1-354d-4681-8271-7eb4e410a2ea/GCF_014203835.1_ASM1420383v1_genomic.fna.gz | prodigal -d GCF_014203835.1_ASM1420383v1_genomic.fna/cds.fna -a GCF_014203835.1_ASM1420383v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:30:46,429] [INFO] Task succeeded: Prodigal
[2024-01-24 14:30:46,429] [INFO] Task started: HMMsearch
[2024-01-24 14:30:46,429] [INFO] Running command: hmmsearch --tblout GCF_014203835.1_ASM1420383v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg67d01ad0-5170-4336-95c9-a0f082214366/dqc_reference/reference_markers.hmm GCF_014203835.1_ASM1420383v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:30:46,865] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:30:46,866] [INFO] Found 6/6 markers.
[2024-01-24 14:30:46,932] [INFO] Query marker FASTA was written to GCF_014203835.1_ASM1420383v1_genomic.fna/markers.fasta
[2024-01-24 14:30:46,932] [INFO] Task started: Blastn
[2024-01-24 14:30:46,932] [INFO] Running command: blastn -query GCF_014203835.1_ASM1420383v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg67d01ad0-5170-4336-95c9-a0f082214366/dqc_reference/reference_markers.fasta -out GCF_014203835.1_ASM1420383v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:30:48,081] [INFO] Task succeeded: Blastn
[2024-01-24 14:30:48,085] [INFO] Selected 26 target genomes.
[2024-01-24 14:30:48,086] [INFO] Target genome list was writen to GCF_014203835.1_ASM1420383v1_genomic.fna/target_genomes.txt
[2024-01-24 14:30:48,098] [INFO] Task started: fastANI
[2024-01-24 14:30:48,098] [INFO] Running command: fastANI --query /var/lib/cwl/stg250a8cd1-354d-4681-8271-7eb4e410a2ea/GCF_014203835.1_ASM1420383v1_genomic.fna.gz --refList GCF_014203835.1_ASM1420383v1_genomic.fna/target_genomes.txt --output GCF_014203835.1_ASM1420383v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:31:29,630] [INFO] Task succeeded: fastANI
[2024-01-24 14:31:29,631] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg67d01ad0-5170-4336-95c9-a0f082214366/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:31:29,631] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg67d01ad0-5170-4336-95c9-a0f082214366/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:31:29,653] [INFO] Found 26 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:31:29,654] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:31:29,654] [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
Micromonospora polyrhachis	strain=DSM 45886	GCA_014203835.1	1282883	1282883	type	True	100.0	2382	2384	95	conclusive
Micromonospora phytophila	strain=DSM 105363	GCA_023656545.1	709888	709888	type	True	81.7505	834	2384	95	below_threshold
Micromonospora inositola	strain=DSM 43819	GCA_900090285.1	47865	47865	type	True	81.5147	998	2384	95	below_threshold
Micromonospora echinaurantiaca	strain=DSM 43904	GCA_900090235.1	47857	47857	type	True	81.4748	1146	2384	95	below_threshold
Micromonospora sagamiensis	strain=DSM 43912	GCA_007829995.1	47875	47875	type	True	81.4007	1059	2384	95	below_threshold
Micromonospora rhizosphaerae	strain=DSM 45431	GCA_900091465.1	568872	568872	type	True	81.33	1012	2384	95	below_threshold
Micromonospora peucetia	strain=DSM 43363	GCA_900091625.1	47871	47871	type	True	81.3135	1159	2384	95	below_threshold
Micromonospora inyonensis	strain=DSM 46123	GCA_900091415.1	47866	47866	type	True	81.2982	1013	2384	95	below_threshold
Micromonospora olivasterospora	strain=DSM 43868	GCA_007830265.1	1880	1880	type	True	81.261	1031	2384	95	below_threshold
Micromonospora narathiwatensis	strain=DSM 45248	GCA_900089605.1	299146	299146	type	True	81.2329	1032	2384	95	below_threshold
Micromonospora fulviviridis	strain=JCM 3259	GCA_014648395.1	47860	47860	type	True	81.1873	1089	2384	95	below_threshold
Micromonospora auratinigra	strain=DSM 44815	GCA_900089595.1	261654	261654	type	True	81.1808	1060	2384	95	below_threshold
Micromonospora haikouensis	strain=DSM 45626	GCA_900091595.1	686309	686309	type	True	81.1159	1065	2384	95	below_threshold
Micromonospora cremea	strain=DSM 45599	GCA_900143515.1	709881	709881	type	True	81.0808	1057	2384	95	below_threshold
Micromonospora acroterricola	strain=5R2A7	GCA_003172955.1	2202421	2202421	type	True	81.0771	945	2384	95	below_threshold
Micromonospora terminaliae	strain=TMS7	GCA_010671825.1	1914461	1914461	type	True	80.99	1036	2384	95	below_threshold
Micromonospora maris	strain=AB-18-032	GCA_000204155.1	1003110	1003110	type	True	80.9722	969	2384	95	below_threshold
Micromonospora maris	strain=NRRL B-24793	GCA_001507315.1	1003110	1003110	type	True	80.9716	958	2384	95	below_threshold
Micromonospora humida	strain=MMS20-R1-14	GCA_016901255.1	2809018	2809018	type	True	80.8951	1074	2384	95	below_threshold
Micromonospora parathelypteridis	strain=DSM 103125	GCA_014201145.1	1839617	1839617	type	True	80.8783	981	2384	95	below_threshold
Micromonospora ferruginea	strain=28ISP2-46	GCA_013694245.1	2749844	2749844	type	True	80.8593	1039	2384	95	below_threshold
Micromonospora parathelypteridis	strain=CGMCC 4.7347	GCA_014646315.1	1839617	1839617	type	True	80.7909	983	2384	95	below_threshold
Micromonospora inaquosa	strain=LB39	GCA_003857055.1	2203716	2203716	type	True	80.7164	929	2384	95	below_threshold
Phytohabitans suffuscus	strain=NBRC 105367	GCA_011764565.1	624315	624315	type	True	79.197	921	2384	95	below_threshold
Phytohabitans flavus	strain=NBRC 107702	GCA_011764545.1	1076124	1076124	type	True	78.9486	863	2384	95	below_threshold
Actinoplanes flavus	strain=NEAU-H7	GCA_017592555.1	2820290	2820290	type	True	78.3947	813	2384	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:31:29,656] [INFO] DFAST Taxonomy check result was written to GCF_014203835.1_ASM1420383v1_genomic.fna/tc_result.tsv
[2024-01-24 14:31:29,657] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:31:29,657] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:31:29,657] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg67d01ad0-5170-4336-95c9-a0f082214366/dqc_reference/checkm_data
[2024-01-24 14:31:29,659] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:31:29,730] [INFO] Task started: CheckM
[2024-01-24 14:31:29,731] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014203835.1_ASM1420383v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014203835.1_ASM1420383v1_genomic.fna/checkm_input GCF_014203835.1_ASM1420383v1_genomic.fna/checkm_result
[2024-01-24 14:32:49,962] [INFO] Task succeeded: CheckM
[2024-01-24 14:32:49,964] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:32:49,989] [INFO] ===== Completeness check finished =====
[2024-01-24 14:32:49,990] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:32:49,990] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014203835.1_ASM1420383v1_genomic.fna/markers.fasta)
[2024-01-24 14:32:49,991] [INFO] Task started: Blastn
[2024-01-24 14:32:49,991] [INFO] Running command: blastn -query GCF_014203835.1_ASM1420383v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg67d01ad0-5170-4336-95c9-a0f082214366/dqc_reference/reference_markers_gtdb.fasta -out GCF_014203835.1_ASM1420383v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:32:51,632] [INFO] Task succeeded: Blastn
[2024-01-24 14:32:51,638] [INFO] Selected 25 target genomes.
[2024-01-24 14:32:51,638] [INFO] Target genome list was writen to GCF_014203835.1_ASM1420383v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:32:51,657] [INFO] Task started: fastANI
[2024-01-24 14:32:51,658] [INFO] Running command: fastANI --query /var/lib/cwl/stg250a8cd1-354d-4681-8271-7eb4e410a2ea/GCF_014203835.1_ASM1420383v1_genomic.fna.gz --refList GCF_014203835.1_ASM1420383v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014203835.1_ASM1420383v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:33:32,080] [INFO] Task succeeded: fastANI
[2024-01-24 14:33:32,099] [INFO] Found 25 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:33:32,099] [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_014203835.1	s__Micromonospora_H polyrhachis	100.0	2384	2384	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora_H	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900090235.1	s__Micromonospora echinaurantiaca	81.4499	1140	2384	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	95.93	95.22	0.84	0.83	3	-
GCF_017614955.1	s__Micromonospora echinofusca_A	81.4499	1034	2384	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900091465.1	s__Micromonospora rhizosphaerae	81.3245	1014	2384	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900091625.1	s__Micromonospora peucetia	81.3227	1161	2384	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003725545.1	s__Micromonospora sp003725545	81.3176	952	2384	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	99.98	99.95	0.98	0.97	4	-
GCF_900089605.1	s__Micromonospora narathiwatensis	81.2936	1022	2384	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	81.2452	1028	2384	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008868175.1	s__Micromonospora sp008868175	81.2382	982	2384	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003030345.1	s__Plantactinospora sp003030345	81.2286	1159	2384	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Plantactinospora	95.0	98.72	98.72	0.95	0.95	2	-
GCF_014648395.1	s__Micromonospora fulviviridis	81.151	1095	2384	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	95.01	95.01	0.74	0.74	2	-
GCF_008868155.1	s__Micromonospora sp008868155	81.1218	915	2384	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900091595.1	s__Micromonospora haikouensis	81.1052	1066	2384	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.5545	97.81	97.42	0.87	0.87	3	-
GCF_900143515.1	s__Micromonospora cremea	81.0777	1057	2384	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002846275.1	s__Plantactinospora sp002846275	81.0499	1114	2384	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Plantactinospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004217235.1	s__Plantactinospora sp004217235	80.986	1109	2384	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Plantactinospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016862935.1	s__Plantactinospora mayteni	80.931	1182	2384	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Plantactinospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018070325.1	s__Micromonospora sp018070325	80.9074	961	2384	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.6333	N/A	N/A	N/A	N/A	1	-
GCF_016862915.1	s__Plantactinospora endophytica	80.8874	1212	2384	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Plantactinospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014874095.1	s__Plantactinospora soyae	80.8854	1159	2384	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Plantactinospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015690345.1	s__Plantactinospora sp015690345	80.5336	1025	2384	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Plantactinospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003762835.1	s__Plantactinospora sp003762835	80.5273	1012	2384	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Plantactinospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011764565.1	s__Phytohabitans suffuscus	79.2064	919	2384	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Phytohabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011764545.1	s__Phytohabitans flavus	78.9708	860	2384	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Phytohabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011764425.1	s__Phytohabitans houttuyneae	78.8829	920	2384	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Phytohabitans	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:33:32,101] [INFO] GTDB search result was written to GCF_014203835.1_ASM1420383v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:33:32,101] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:33:32,106] [INFO] DFAST_QC result json was written to GCF_014203835.1_ASM1420383v1_genomic.fna/dqc_result.json
[2024-01-24 14:33:32,107] [INFO] DFAST_QC completed!
[2024-01-24 14:33:32,107] [INFO] Total running time: 0h3m15s