[2024-01-24 13:57:32,234] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:57:32,237] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:57:32,237] [INFO] DQC Reference Directory: /var/lib/cwl/stg50d91901-02db-4302-be01-7b39763bbbb6/dqc_reference
[2024-01-24 13:57:33,711] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:57:33,712] [INFO] Task started: Prodigal
[2024-01-24 13:57:33,712] [INFO] Running command: gunzip -c /var/lib/cwl/stgf4b01a11-542a-406d-9f3a-eb315ac6b3a2/GCF_031458255.1_ASM3145825v1_genomic.fna.gz | prodigal -d GCF_031458255.1_ASM3145825v1_genomic.fna/cds.fna -a GCF_031458255.1_ASM3145825v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:58:04,139] [INFO] Task succeeded: Prodigal
[2024-01-24 13:58:04,139] [INFO] Task started: HMMsearch
[2024-01-24 13:58:04,139] [INFO] Running command: hmmsearch --tblout GCF_031458255.1_ASM3145825v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg50d91901-02db-4302-be01-7b39763bbbb6/dqc_reference/reference_markers.hmm GCF_031458255.1_ASM3145825v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:58:04,488] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:58:04,489] [INFO] Found 6/6 markers.
[2024-01-24 13:58:04,567] [INFO] Query marker FASTA was written to GCF_031458255.1_ASM3145825v1_genomic.fna/markers.fasta
[2024-01-24 13:58:04,568] [INFO] Task started: Blastn
[2024-01-24 13:58:04,568] [INFO] Running command: blastn -query GCF_031458255.1_ASM3145825v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg50d91901-02db-4302-be01-7b39763bbbb6/dqc_reference/reference_markers.fasta -out GCF_031458255.1_ASM3145825v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:05,788] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:05,792] [INFO] Selected 29 target genomes.
[2024-01-24 13:58:05,792] [INFO] Target genome list was writen to GCF_031458255.1_ASM3145825v1_genomic.fna/target_genomes.txt
[2024-01-24 13:58:05,808] [INFO] Task started: fastANI
[2024-01-24 13:58:05,808] [INFO] Running command: fastANI --query /var/lib/cwl/stgf4b01a11-542a-406d-9f3a-eb315ac6b3a2/GCF_031458255.1_ASM3145825v1_genomic.fna.gz --refList GCF_031458255.1_ASM3145825v1_genomic.fna/target_genomes.txt --output GCF_031458255.1_ASM3145825v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:59:04,728] [INFO] Task succeeded: fastANI
[2024-01-24 13:59:04,729] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg50d91901-02db-4302-be01-7b39763bbbb6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:59:04,729] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg50d91901-02db-4302-be01-7b39763bbbb6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:59:04,751] [INFO] Found 29 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:59:04,751] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:59:04,751] [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 pattaloongensis	strain=DSM 45245	GCA_900107255.1	405436	405436	type	True	79.3817	1026	3247	95	below_threshold
Micromonospora chalcea	strain=DSM 43026	GCA_002926165.1	1874	1874	type	True	79.3495	1213	3247	95	below_threshold
Micromonospora acroterricola	strain=5R2A7	GCA_003172955.1	2202421	2202421	type	True	79.2591	1067	3247	95	below_threshold
Micromonospora aurantiaca	strain=ATCC 27029	GCA_000145235.1	47850	47850	type	True	79.2509	1298	3247	95	below_threshold
Micromonospora tulbaghiae	strain=DSM 45142	GCA_900091605.1	479978	479978	type	True	79.247	1245	3247	95	below_threshold
Micromonospora siamensis	strain=DSM 45097	GCA_900090305.1	299152	299152	type	True	79.1926	1132	3247	95	below_threshold
Micromonospora narathiwatensis	strain=DSM 45248	GCA_900089605.1	299146	299146	type	True	79.1661	1144	3247	95	below_threshold
Micromonospora mirobrigensis	strain=DSM 44830	GCA_900091555.1	262898	262898	type	True	79.1636	1158	3247	95	below_threshold
Micromonospora kangleipakensis	strain=DSM 45612	GCA_004217615.1	1077942	1077942	type	True	79.146	1179	3247	95	below_threshold
Micromonospora chersina	strain=DSM 44151	GCA_900091475.1	47854	47854	type	True	79.1359	1223	3247	95	below_threshold
Micromonospora fulviviridis	strain=JCM 3259	GCA_014648395.1	47860	47860	type	True	79.0854	1245	3247	95	below_threshold
Micromonospora endolithica	strain=DSM 44398	GCA_007994185.1	230091	230091	type	True	79.0798	1150	3247	95	below_threshold
Micromonospora endolithica	strain=JCM 12677	GCA_003626595.1	230091	230091	type	True	79.0229	1155	3247	95	below_threshold
Micromonospora eburnea	strain=DSM 44814	GCA_900090225.1	227316	227316	type	True	78.9808	1161	3247	95	below_threshold
Micromonospora saelicesensis	strain=DSM 44871	GCA_900091575.1	285676	285676	type	True	78.8288	1138	3247	95	below_threshold
Actinoplanes nipponensis	strain=NBRC 14063	GCA_016862275.1	135950	135950	type	True	78.753	1433	3247	95	below_threshold
Actinoplanes ianthinogenes	strain=NBRC 13996	GCA_018324205.1	122358	122358	type	True	78.6516	1458	3247	95	below_threshold
Actinoplanes ianthinogenes	strain=JCM 3249	GCA_014648375.1	122358	122358	type	True	78.6196	1442	3247	95	below_threshold
Phytohabitans suffuscus	strain=NBRC 105367	GCA_011764565.1	624315	624315	type	True	78.6148	1400	3247	95	below_threshold
Micromonospora polyrhachis	strain=DSM 45886	GCA_014203835.1	1282883	1282883	type	True	78.5904	879	3247	95	below_threshold
Actinoplanes deccanensis	strain=NBRC 13994	GCA_016862115.1	113561	113561	type	True	78.5339	1468	3247	95	below_threshold
Phytohabitans rumicis	strain=NBRC 108638	GCA_011764445.1	1076125	1076125	type	True	78.5173	1405	3247	95	below_threshold
Actinoplanes atraurantiacus	strain=CGMCC 4.6857	GCA_900215205.1	1036182	1036182	type	True	78.3385	1426	3247	95	below_threshold
Phytohabitans houttuyneae	strain=NBRC 108639	GCA_011764425.1	1076126	1076126	type	True	78.3076	1449	3247	95	below_threshold
Dactylosporangium roseum	strain=NRRL B-16295	GCA_025264685.1	47989	47989	type	True	77.6989	1076	3247	95	below_threshold
Pilimelia terevasa	strain=JCM 3091	GCA_014647915.1	53372	53372	type	True	77.6308	831	3247	95	below_threshold
Dactylosporangium aurantiacum	strain=NRRL B-8018	GCA_025264705.1	35754	35754	type	True	77.4594	1523	3247	95	below_threshold
Dactylosporangium fulvum	strain=NRRL B-16292	GCA_025137375.1	53359	53359	type	True	77.4339	1255	3247	95	below_threshold
Dactylosporangium matsuzakiense	strain=NRRL B-16293	GCA_025264725.1	53360	53360	type	True	77.3465	1300	3247	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:59:04,753] [INFO] DFAST Taxonomy check result was written to GCF_031458255.1_ASM3145825v1_genomic.fna/tc_result.tsv
[2024-01-24 13:59:04,754] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:59:04,754] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:59:04,754] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg50d91901-02db-4302-be01-7b39763bbbb6/dqc_reference/checkm_data
[2024-01-24 13:59:04,755] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:59:04,847] [INFO] Task started: CheckM
[2024-01-24 13:59:04,847] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_031458255.1_ASM3145825v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_031458255.1_ASM3145825v1_genomic.fna/checkm_input GCF_031458255.1_ASM3145825v1_genomic.fna/checkm_result
[2024-01-24 14:01:17,188] [INFO] Task succeeded: CheckM
[2024-01-24 14:01:17,189] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:01:17,211] [INFO] ===== Completeness check finished =====
[2024-01-24 14:01:17,211] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:01:17,212] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_031458255.1_ASM3145825v1_genomic.fna/markers.fasta)
[2024-01-24 14:01:17,212] [INFO] Task started: Blastn
[2024-01-24 14:01:17,212] [INFO] Running command: blastn -query GCF_031458255.1_ASM3145825v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg50d91901-02db-4302-be01-7b39763bbbb6/dqc_reference/reference_markers_gtdb.fasta -out GCF_031458255.1_ASM3145825v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:01:19,088] [INFO] Task succeeded: Blastn
[2024-01-24 14:01:19,092] [INFO] Selected 27 target genomes.
[2024-01-24 14:01:19,092] [INFO] Target genome list was writen to GCF_031458255.1_ASM3145825v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:01:19,112] [INFO] Task started: fastANI
[2024-01-24 14:01:19,112] [INFO] Running command: fastANI --query /var/lib/cwl/stgf4b01a11-542a-406d-9f3a-eb315ac6b3a2/GCF_031458255.1_ASM3145825v1_genomic.fna.gz --refList GCF_031458255.1_ASM3145825v1_genomic.fna/target_genomes_gtdb.txt --output GCF_031458255.1_ASM3145825v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:02:13,715] [INFO] Task succeeded: fastANI
[2024-01-24 14:02:13,735] [INFO] Found 27 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 14:02:13,735] [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_000717135.1	s__Catenuloplanes japonicus	86.4837	2341	3247	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Catenuloplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902825405.1	s__Micromonospora maritima	79.5805	948	3247	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002926165.1	s__Micromonospora chalcea	79.3703	1207	3247	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	97.52	95.31	0.89	0.84	18	-
GCF_008868175.1	s__Micromonospora sp008868175	79.3639	1099	3247	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000145235.1	s__Micromonospora aurantiaca	79.2687	1300	3247	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.1942	98.37	95.58	0.90	0.84	15	-
GCF_900090305.1	s__Micromonospora siamensis	79.1607	1142	3247	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900091555.1	s__Micromonospora mirobrigensis	79.1412	1161	3247	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	79.1389	1232	3247	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	95.01	95.01	0.74	0.74	2	-
GCF_900089605.1	s__Micromonospora narathiwatensis	79.1259	1148	3247	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900090225.1	s__Micromonospora eburnea	78.9828	1160	3247	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000297395.2	s__Micromonospora lupini	78.9372	1161	3247	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	78.936	1188	3247	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016863475.1	s__Spirilliplanes yamanashiensis	78.8323	1271	3247	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Spirilliplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900091575.1	s__Micromonospora saelicesensis	78.8314	1139	3247	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	96.6221	98.85	97.77	0.96	0.92	6	-
GCF_016862275.1	s__Actinoplanes nipponensis	78.7583	1438	3247	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004217545.1	s__Actinoplanes cinnamomeus	78.6199	1119	3247	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011764565.1	s__Phytohabitans suffuscus	78.5829	1409	3247	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Phytohabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014203835.1	s__Micromonospora_H polyrhachis	78.5707	879	3247	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_016862115.1	s__Actinoplanes deccanensis	78.5305	1466	3247	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018324255.1	s__Polymorphospora rubra	78.5256	1257	3247	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Polymorphospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011764445.1	s__Phytohabitans rumicis	78.5033	1413	3247	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Phytohabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000389965.1	s__Actinoplanes sp000389965	78.4352	1305	3247	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900215205.1	s__Actinoplanes atraurantiacus	78.358	1415	3247	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011764425.1	s__Phytohabitans houttuyneae	78.2951	1452	3247	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Phytohabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014647515.1	s__Dactylosporangium sucinum	77.4977	1429	3247	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Dactylosporangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000716715.1	s__Dactylosporangium aurantiacum	77.4372	1501	3247	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Dactylosporangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016862795.1	s__Dactylosporangium siamense	77.312	1444	3247	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Dactylosporangium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:02:13,737] [INFO] GTDB search result was written to GCF_031458255.1_ASM3145825v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:02:13,737] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:02:13,742] [INFO] DFAST_QC result json was written to GCF_031458255.1_ASM3145825v1_genomic.fna/dqc_result.json
[2024-01-24 14:02:13,742] [INFO] DFAST_QC completed!
[2024-01-24 14:02:13,743] [INFO] Total running time: 0h4m42s