[2024-01-25 19:24:45,022] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:24:45,024] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:24:45,024] [INFO] DQC Reference Directory: /var/lib/cwl/stg082960b0-6794-4a0a-9348-3835821c9b31/dqc_reference
[2024-01-25 19:24:48,242] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:24:48,242] [INFO] Task started: Prodigal
[2024-01-25 19:24:48,243] [INFO] Running command: gunzip -c /var/lib/cwl/stg25e28dcf-e053-4e28-bacb-d7eb875343ec/GCF_900107255.1_IMG-taxon_2693429860_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900107255.1_IMG-taxon_2693429860_annotated_assembly_genomic.fna/cds.fna -a GCF_900107255.1_IMG-taxon_2693429860_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:25:01,209] [INFO] Task succeeded: Prodigal
[2024-01-25 19:25:01,209] [INFO] Task started: HMMsearch
[2024-01-25 19:25:01,209] [INFO] Running command: hmmsearch --tblout GCF_900107255.1_IMG-taxon_2693429860_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg082960b0-6794-4a0a-9348-3835821c9b31/dqc_reference/reference_markers.hmm GCF_900107255.1_IMG-taxon_2693429860_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:25:01,441] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:25:01,442] [INFO] Found 6/6 markers.
[2024-01-25 19:25:01,485] [INFO] Query marker FASTA was written to GCF_900107255.1_IMG-taxon_2693429860_annotated_assembly_genomic.fna/markers.fasta
[2024-01-25 19:25:01,486] [INFO] Task started: Blastn
[2024-01-25 19:25:01,486] [INFO] Running command: blastn -query GCF_900107255.1_IMG-taxon_2693429860_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg082960b0-6794-4a0a-9348-3835821c9b31/dqc_reference/reference_markers.fasta -out GCF_900107255.1_IMG-taxon_2693429860_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:25:02,715] [INFO] Task succeeded: Blastn
[2024-01-25 19:25:02,718] [INFO] Selected 26 target genomes.
[2024-01-25 19:25:02,719] [INFO] Target genome list was writen to GCF_900107255.1_IMG-taxon_2693429860_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-25 19:25:02,726] [INFO] Task started: fastANI
[2024-01-25 19:25:02,726] [INFO] Running command: fastANI --query /var/lib/cwl/stg25e28dcf-e053-4e28-bacb-d7eb875343ec/GCF_900107255.1_IMG-taxon_2693429860_annotated_assembly_genomic.fna.gz --refList GCF_900107255.1_IMG-taxon_2693429860_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900107255.1_IMG-taxon_2693429860_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:25:42,348] [INFO] Task succeeded: fastANI
[2024-01-25 19:25:42,348] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg082960b0-6794-4a0a-9348-3835821c9b31/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:25:42,350] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg082960b0-6794-4a0a-9348-3835821c9b31/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:25:42,365] [INFO] Found 26 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:25:42,365] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:25:42,365] [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	100.0	1769	1771	95	conclusive
Micromonospora phytophila	strain=DSM 105363	GCA_023656545.1	709888	709888	type	True	82.0513	860	1771	95	below_threshold
Micromonospora coxensis	strain=DSM 45161	GCA_900090295.1	356852	356852	type	True	81.92	1070	1771	95	below_threshold
Micromonospora citrea	strain=DSM 43903	GCA_900090315.1	47855	47855	type	True	81.8087	1086	1771	95	below_threshold
Micromonospora echinofusca	strain=DSM 43913	GCA_900091445.1	47858	47858	type	True	81.7538	1071	1771	95	below_threshold
Micromonospora veneta	strain=CAP181	GCA_016598485.1	2796464	2796464	type	True	81.7336	1033	1771	95	below_threshold
Micromonospora terminaliae	strain=TMS7	GCA_010671825.1	1914461	1914461	type	True	81.7032	1051	1771	95	below_threshold
Micromonospora narathiwatensis	strain=DSM 45248	GCA_900089605.1	299146	299146	type	True	81.6776	1013	1771	95	below_threshold
Micromonospora terminaliae	strain=DSM 101760	GCA_009671205.1	1914461	1914461	type	True	81.6622	1075	1771	95	below_threshold
Micromonospora olivasterospora	strain=DSM 43868	GCA_007830265.1	1880	1880	type	True	81.6417	1010	1771	95	below_threshold
Micromonospora eburnea	strain=DSM 44814	GCA_900090225.1	227316	227316	type	True	81.5713	1033	1771	95	below_threshold
Micromonospora acroterricola	strain=5R2A7	GCA_003172955.1	2202421	2202421	type	True	81.5534	966	1771	95	below_threshold
Micromonospora chaiyaphumensis	strain=DSM 45246	GCA_900091435.1	307119	307119	type	True	81.5465	1072	1771	95	below_threshold
Micromonospora chersina	strain=DSM 44151	GCA_900091475.1	47854	47854	type	True	81.5397	1064	1771	95	below_threshold
Micromonospora ferruginea	strain=28ISP2-46	GCA_013694245.1	2749844	2749844	type	True	81.4913	1055	1771	95	below_threshold
Micromonospora cremea	strain=DSM 45599	GCA_900143515.1	709881	709881	type	True	81.2943	1075	1771	95	below_threshold
Micromonospora orduensis	strain=S2509	GCA_006228125.1	1420891	1420891	type	True	81.2604	973	1771	95	below_threshold
Micromonospora echinospora	strain=ATCC 15837	GCA_002266845.1	1877	1877	type	True	81.2127	1024	1771	95	below_threshold
Micromonospora humida	strain=MMS20-R1-14	GCA_016901255.1	2809018	2809018	type	True	81.1914	1034	1771	95	below_threshold
Micromonospora phaseoli	strain=NBRC 110907	GCA_016863675.1	1144548	1144548	type	True	81.0634	933	1771	95	below_threshold
Phytohabitans suffuscus	strain=NBRC 105367	GCA_011764565.1	624315	624315	type	True	80.4874	1048	1771	95	below_threshold
Phytohabitans rumicis	strain=NBRC 108638	GCA_011764445.1	1076125	1076125	type	True	80.4662	1047	1771	95	below_threshold
Phytohabitans flavus	strain=NBRC 107702	GCA_011764545.1	1076124	1076124	type	True	80.1147	976	1771	95	below_threshold
Phytohabitans houttuyneae	strain=NBRC 108639	GCA_011764425.1	1076126	1076126	type	True	79.9712	1072	1771	95	below_threshold
Asanoa ishikariensis	strain=DSM 44718	GCA_900107455.1	137265	137265	type	True	79.8384	957	1771	95	below_threshold
Amycolatopsis thermalba	strain=NRRL B-24845	GCA_003385215.1	944492	944492	type	True	76.8576	514	1771	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:25:42,366] [INFO] DFAST Taxonomy check result was written to GCF_900107255.1_IMG-taxon_2693429860_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-25 19:25:42,368] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:25:42,368] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:25:42,369] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg082960b0-6794-4a0a-9348-3835821c9b31/dqc_reference/checkm_data
[2024-01-25 19:25:42,369] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:25:42,421] [INFO] Task started: CheckM
[2024-01-25 19:25:42,421] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900107255.1_IMG-taxon_2693429860_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900107255.1_IMG-taxon_2693429860_annotated_assembly_genomic.fna/checkm_input GCF_900107255.1_IMG-taxon_2693429860_annotated_assembly_genomic.fna/checkm_result
[2024-01-25 19:26:28,805] [INFO] Task succeeded: CheckM
[2024-01-25 19:26:28,806] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:26:28,824] [INFO] ===== Completeness check finished =====
[2024-01-25 19:26:28,824] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:26:28,825] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900107255.1_IMG-taxon_2693429860_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-25 19:26:28,825] [INFO] Task started: Blastn
[2024-01-25 19:26:28,825] [INFO] Running command: blastn -query GCF_900107255.1_IMG-taxon_2693429860_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg082960b0-6794-4a0a-9348-3835821c9b31/dqc_reference/reference_markers_gtdb.fasta -out GCF_900107255.1_IMG-taxon_2693429860_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:26:30,783] [INFO] Task succeeded: Blastn
[2024-01-25 19:26:30,786] [INFO] Selected 26 target genomes.
[2024-01-25 19:26:30,786] [INFO] Target genome list was writen to GCF_900107255.1_IMG-taxon_2693429860_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:26:30,798] [INFO] Task started: fastANI
[2024-01-25 19:26:30,798] [INFO] Running command: fastANI --query /var/lib/cwl/stg25e28dcf-e053-4e28-bacb-d7eb875343ec/GCF_900107255.1_IMG-taxon_2693429860_annotated_assembly_genomic.fna.gz --refList GCF_900107255.1_IMG-taxon_2693429860_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900107255.1_IMG-taxon_2693429860_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:27:14,833] [INFO] Task succeeded: fastANI
[2024-01-25 19:27:14,853] [INFO] Found 26 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:27:14,853] [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_900107255.1	s__Micromonospora_E pattaloongensis	100.0	1769	1771	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora_E	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900090295.1	s__Micromonospora coxensis	81.947	1066	1771	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	81.921	951	1771	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	99.98	99.95	0.98	0.97	4	-
GCF_900090315.1	s__Micromonospora citrea	81.8074	1088	1771	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016598485.1	s__Micromonospora veneta	81.7271	1033	1771	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900091445.1	s__Micromonospora echinofusca	81.7165	1077	1771	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	97.23	97.23	0.90	0.90	2	-
GCF_900089605.1	s__Micromonospora narathiwatensis	81.7066	1009	1771	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900091545.1	s__Micromonospora viridifaciens	81.7057	1021	1771	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	81.6552	1013	1771	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018070575.1	s__Micromonospora sp018070575	81.652	1035	1771	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	81.6173	1013	1771	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900091475.1	s__Micromonospora chersina	81.5865	1057	1771	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	95.87	95.82	0.87	0.87	3	-
GCF_003172955.1	s__Micromonospora sp003172955	81.5732	963	1771	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001905095.1	s__Micromonospora sp001905095	81.5324	1071	1771	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012034245.1	s__Micromonospora sp012034245	81.4654	1014	1771	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006228125.1	s__Micromonospora orduensis	81.2624	972	1771	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	81.1982	1049	1771	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Polymorphospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900091495.1	s__Micromonospora echinospora	81.1906	1018	1771	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	98.77	97.55	0.96	0.91	3	-
GCF_016803395.1	s__Micromonospora sp016803395	81.0949	916	1771	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016862915.1	s__Plantactinospora endophytica	81.0256	1101	1771	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Plantactinospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011764445.1	s__Phytohabitans rumicis	80.506	1040	1771	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Phytohabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011764565.1	s__Phytohabitans suffuscus	80.5012	1045	1771	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	80.1209	975	1771	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	80.0018	1066	1771	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Phytohabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900107455.1	s__Asanoa ishikariensis	79.8928	949	1771	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Asanoa	95.0	100.00	100.00	1.00	1.00	2	-
GCF_011947195.1	s__Planosporangium thailandense	79.2665	827	1771	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Planosporangium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:27:14,859] [INFO] GTDB search result was written to GCF_900107255.1_IMG-taxon_2693429860_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-25 19:27:14,860] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:27:14,866] [INFO] DFAST_QC result json was written to GCF_900107255.1_IMG-taxon_2693429860_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-25 19:27:14,866] [INFO] DFAST_QC completed!
[2024-01-25 19:27:14,866] [INFO] Total running time: 0h2m30s