[2024-01-24 13:49:45,551] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:49:45,553] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:49:45,553] [INFO] DQC Reference Directory: /var/lib/cwl/stgf82b7593-bb59-42b6-a667-82206cd732b7/dqc_reference
[2024-01-24 13:49:46,903] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:46,906] [INFO] Task started: Prodigal
[2024-01-24 13:49:46,906] [INFO] Running command: gunzip -c /var/lib/cwl/stg4f1e393c-1abc-46fc-9f39-17e6e8d3e67f/GCF_031458235.1_ASM3145823v1_genomic.fna.gz | prodigal -d GCF_031458235.1_ASM3145823v1_genomic.fna/cds.fna -a GCF_031458235.1_ASM3145823v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:50:17,900] [INFO] Task succeeded: Prodigal
[2024-01-24 13:50:17,900] [INFO] Task started: HMMsearch
[2024-01-24 13:50:17,901] [INFO] Running command: hmmsearch --tblout GCF_031458235.1_ASM3145823v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf82b7593-bb59-42b6-a667-82206cd732b7/dqc_reference/reference_markers.hmm GCF_031458235.1_ASM3145823v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:50:18,301] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:50:18,302] [INFO] Found 6/6 markers.
[2024-01-24 13:50:18,371] [INFO] Query marker FASTA was written to GCF_031458235.1_ASM3145823v1_genomic.fna/markers.fasta
[2024-01-24 13:50:18,372] [INFO] Task started: Blastn
[2024-01-24 13:50:18,372] [INFO] Running command: blastn -query GCF_031458235.1_ASM3145823v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf82b7593-bb59-42b6-a667-82206cd732b7/dqc_reference/reference_markers.fasta -out GCF_031458235.1_ASM3145823v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:19,651] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:19,655] [INFO] Selected 34 target genomes.
[2024-01-24 13:50:19,655] [INFO] Target genome list was writen to GCF_031458235.1_ASM3145823v1_genomic.fna/target_genomes.txt
[2024-01-24 13:50:19,678] [INFO] Task started: fastANI
[2024-01-24 13:50:19,679] [INFO] Running command: fastANI --query /var/lib/cwl/stg4f1e393c-1abc-46fc-9f39-17e6e8d3e67f/GCF_031458235.1_ASM3145823v1_genomic.fna.gz --refList GCF_031458235.1_ASM3145823v1_genomic.fna/target_genomes.txt --output GCF_031458235.1_ASM3145823v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:51:20,292] [INFO] Task succeeded: fastANI
[2024-01-24 13:51:20,292] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf82b7593-bb59-42b6-a667-82206cd732b7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:51:20,293] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf82b7593-bb59-42b6-a667-82206cd732b7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:51:20,327] [INFO] Found 34 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:51:20,327] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:51:20,327] [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 marina	strain=DSM 45555	GCA_900091565.1	307120	307120	type	True	79.484	1060	2968	95	below_threshold
Micromonospora sediminicola	strain=DSM 45794	GCA_900089585.1	946078	946078	type	True	79.4501	1220	2968	95	below_threshold
Micromonospora aurantiaca	strain=ATCC 27029	GCA_000145235.1	47850	47850	type	True	79.4149	1215	2968	95	below_threshold
Micromonospora tulbaghiae	strain=DSM 45142	GCA_900091605.1	479978	479978	type	True	79.3948	1195	2968	95	below_threshold
Micromonospora pattaloongensis	strain=DSM 45245	GCA_900107255.1	405436	405436	type	True	79.3792	1018	2968	95	below_threshold
Micromonospora acroterricola	strain=5R2A7	GCA_003172955.1	2202421	2202421	type	True	79.3681	1011	2968	95	below_threshold
Micromonospora mirobrigensis	strain=DSM 44830	GCA_900091555.1	262898	262898	type	True	79.307	1097	2968	95	below_threshold
Micromonospora humi	strain=DSM 45647	GCA_900090105.1	745366	745366	type	True	79.2776	1223	2968	95	below_threshold
Micromonospora terminaliae	strain=DSM 101760	GCA_009671205.1	1914461	1914461	type	True	79.2558	1162	2968	95	below_threshold
Micromonospora siamensis	strain=DSM 45097	GCA_900090305.1	299152	299152	type	True	79.2544	1135	2968	95	below_threshold
Micromonospora terminaliae	strain=TMS7	GCA_010671825.1	1914461	1914461	type	True	79.2166	1160	2968	95	below_threshold
Micromonospora chersina	strain=DSM 44151	GCA_900091475.1	47854	47854	type	True	79.1649	1197	2968	95	below_threshold
Micromonospora citrea	strain=DSM 43903	GCA_900090315.1	47855	47855	type	True	79.1563	1193	2968	95	below_threshold
Micromonospora eburnea	strain=DSM 44814	GCA_900090225.1	227316	227316	type	True	79.1171	1092	2968	95	below_threshold
Micromonospora endolithica	strain=JCM 12677	GCA_003626595.1	230091	230091	type	True	79.0939	1121	2968	95	below_threshold
Micromonospora sagamiensis	strain=DSM 43912	GCA_007829995.1	47875	47875	type	True	79.0444	1102	2968	95	below_threshold
Micromonospora fulviviridis	strain=JCM 3259	GCA_014648395.1	47860	47860	type	True	79.0289	1234	2968	95	below_threshold
Micromonospora wenchangensis	strain=CCTCC AA 2012002	GCA_002210435.1	1185415	1185415	type	True	78.9888	1164	2968	95	below_threshold
Actinoplanes nipponensis	strain=NBRC 14063	GCA_016862275.1	135950	135950	type	True	78.9502	1368	2968	95	below_threshold
Actinoplanes auranticolor	strain=NBRC 12245	GCA_018332655.1	47988	47988	type	True	78.8739	1385	2968	95	below_threshold
Micromonospora yangpuensis	strain=DSM 45577	GCA_900091615.1	683228	683228	type	True	78.7195	1038	2968	95	below_threshold
Micromonospora yangpuensis	strain=CGMCC 4.5736	GCA_014645775.1	683228	683228	type	True	78.6977	1015	2968	95	below_threshold
Actinoplanes utahensis	strain=NBRC 13244	GCA_016862455.1	1869	1869	type	True	78.627	1246	2968	95	below_threshold
Actinoplanes deccanensis	strain=NBRC 13994	GCA_016862115.1	113561	113561	type	True	78.5915	1409	2968	95	below_threshold
Phytohabitans rumicis	strain=NBRC 108638	GCA_011764445.1	1076125	1076125	type	True	78.5747	1348	2968	95	below_threshold
Phytohabitans houttuyneae	strain=NBRC 108639	GCA_011764425.1	1076126	1076126	type	True	78.544	1384	2968	95	below_threshold
Asanoa iriomotensis	strain=NBRC 100142	GCA_016862515.1	234613	234613	type	True	78.5031	1168	2968	95	below_threshold
Actinoplanes ferrugineus	strain=NBRC 15555	GCA_016862195.1	113564	113564	type	True	78.4145	1215	2968	95	below_threshold
Salinispora oceanensis	strain=CNT-138	GCA_000514455.1	1050199	1050199	type	True	78.2291	684	2968	95	below_threshold
Salinispora oceanensis	strain=DSM 45547	GCA_000383575.1	1050199	1050199	type	True	78.2161	698	2968	95	below_threshold
Dactylosporangium aurantiacum	strain=NRRL B-8018	GCA_025264705.1	35754	35754	type	True	77.6598	1448	2968	95	below_threshold
Dactylosporangium roseum	strain=NRRL B-16295	GCA_025264685.1	47989	47989	type	True	77.6009	1009	2968	95	below_threshold
Dactylosporangium fulvum	strain=NRRL B-16292	GCA_025137375.1	53359	53359	type	True	77.5628	1186	2968	95	below_threshold
Dactylosporangium matsuzakiense	strain=NRRL B-16293	GCA_025264725.1	53360	53360	type	True	77.4758	1253	2968	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:51:20,329] [INFO] DFAST Taxonomy check result was written to GCF_031458235.1_ASM3145823v1_genomic.fna/tc_result.tsv
[2024-01-24 13:51:20,329] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:51:20,330] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:51:20,330] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf82b7593-bb59-42b6-a667-82206cd732b7/dqc_reference/checkm_data
[2024-01-24 13:51:20,331] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:51:20,413] [INFO] Task started: CheckM
[2024-01-24 13:51:20,414] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_031458235.1_ASM3145823v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_031458235.1_ASM3145823v1_genomic.fna/checkm_input GCF_031458235.1_ASM3145823v1_genomic.fna/checkm_result
[2024-01-24 13:53:08,684] [INFO] Task succeeded: CheckM
[2024-01-24 13:53:08,685] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:53:08,710] [INFO] ===== Completeness check finished =====
[2024-01-24 13:53:08,711] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:53:08,711] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_031458235.1_ASM3145823v1_genomic.fna/markers.fasta)
[2024-01-24 13:53:08,712] [INFO] Task started: Blastn
[2024-01-24 13:53:08,712] [INFO] Running command: blastn -query GCF_031458235.1_ASM3145823v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf82b7593-bb59-42b6-a667-82206cd732b7/dqc_reference/reference_markers_gtdb.fasta -out GCF_031458235.1_ASM3145823v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:53:10,674] [INFO] Task succeeded: Blastn
[2024-01-24 13:53:10,678] [INFO] Selected 29 target genomes.
[2024-01-24 13:53:10,678] [INFO] Target genome list was writen to GCF_031458235.1_ASM3145823v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:53:10,740] [INFO] Task started: fastANI
[2024-01-24 13:53:10,741] [INFO] Running command: fastANI --query /var/lib/cwl/stg4f1e393c-1abc-46fc-9f39-17e6e8d3e67f/GCF_031458235.1_ASM3145823v1_genomic.fna.gz --refList GCF_031458235.1_ASM3145823v1_genomic.fna/target_genomes_gtdb.txt --output GCF_031458235.1_ASM3145823v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:54:09,443] [INFO] Task succeeded: fastANI
[2024-01-24 13:54:09,477] [INFO] Found 29 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:54:09,477] [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	86.5644	2148	2968	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Catenuloplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004217615.1	s__Micromonospora kangleipakensis	79.3256	1155	2968	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	79.2869	1100	2968	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	79.2452	1065	2968	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003434305.1	s__Micromonospora sp003434305	79.2265	1132	2968	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	79.2256	1107	2968	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	79.1762	1058	2968	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	79.1757	1202	2968	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	95.87	95.82	0.87	0.87	3	-
GCF_900090315.1	s__Micromonospora citrea	79.1609	1192	2968	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002140155.1	s__Micromonospora sp002140155	79.1529	1169	2968	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016862395.1	s__Actinoplanes siamensis	79.1343	1206	2968	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016863475.1	s__Spirilliplanes yamanashiensis	79.1001	1208	2968	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Spirilliplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014648395.1	s__Micromonospora fulviviridis	79.0887	1221	2968	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	95.01	95.01	0.74	0.74	2	-
GCF_002210435.1	s__Micromonospora wenchangensis	78.9448	1177	2968	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	95.84	95.43	0.85	0.83	5	-
GCF_016862275.1	s__Actinoplanes nipponensis	78.9088	1378	2968	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018332655.1	s__Actinoplanes auranticolor	78.8714	1385	2968	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001905095.1	s__Micromonospora sp001905095	78.7999	1179	2968	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004217545.1	s__Actinoplanes cinnamomeus	78.7621	1072	2968	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000389965.1	s__Actinoplanes sp000389965	78.6321	1264	2968	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011764445.1	s__Phytohabitans rumicis	78.5808	1341	2968	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Phytohabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018324255.1	s__Polymorphospora rubra	78.5566	1191	2968	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Polymorphospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011764425.1	s__Phytohabitans houttuyneae	78.5398	1387	2968	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Phytohabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003751085.1	s__Micromonospora_E sp003751085	78.448	1088	2968	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016862515.1	s__Asanoa iriomotensis	78.4319	1190	2968	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Asanoa	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000383575.1	s__Micromonospora oceanensis	78.2052	703	2968	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	97.54	95.98	0.89	0.84	12	-
GCF_012933445.1	s__Actinoplanes sp012933445	78.0901	1190	2968	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000716715.1	s__Dactylosporangium aurantiacum	77.6197	1419	2968	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Dactylosporangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014647515.1	s__Dactylosporangium sucinum	77.586	1342	2968	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	77.4372	1332	2968	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 13:54:09,479] [INFO] GTDB search result was written to GCF_031458235.1_ASM3145823v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:54:09,479] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:54:09,485] [INFO] DFAST_QC result json was written to GCF_031458235.1_ASM3145823v1_genomic.fna/dqc_result.json
[2024-01-24 13:54:09,485] [INFO] DFAST_QC completed!
[2024-01-24 13:54:09,485] [INFO] Total running time: 0h4m24s