[2024-01-24 13:32:32,576] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:32:32,579] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:32:32,579] [INFO] DQC Reference Directory: /var/lib/cwl/stgdd3779f2-7c28-4a3a-8ee6-3e7ed661619d/dqc_reference
[2024-01-24 13:32:33,887] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:32:33,888] [INFO] Task started: Prodigal
[2024-01-24 13:32:33,888] [INFO] Running command: gunzip -c /var/lib/cwl/stgd2881fae-21f9-452d-9fb0-eb56b6c14263/GCF_018316655.1_ASM1831665v1_genomic.fna.gz | prodigal -d GCF_018316655.1_ASM1831665v1_genomic.fna/cds.fna -a GCF_018316655.1_ASM1831665v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:32:55,252] [INFO] Task succeeded: Prodigal
[2024-01-24 13:32:55,252] [INFO] Task started: HMMsearch
[2024-01-24 13:32:55,252] [INFO] Running command: hmmsearch --tblout GCF_018316655.1_ASM1831665v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdd3779f2-7c28-4a3a-8ee6-3e7ed661619d/dqc_reference/reference_markers.hmm GCF_018316655.1_ASM1831665v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:32:55,821] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:32:55,823] [INFO] Found 6/6 markers.
[2024-01-24 13:32:55,900] [INFO] Query marker FASTA was written to GCF_018316655.1_ASM1831665v1_genomic.fna/markers.fasta
[2024-01-24 13:32:55,901] [INFO] Task started: Blastn
[2024-01-24 13:32:55,901] [INFO] Running command: blastn -query GCF_018316655.1_ASM1831665v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdd3779f2-7c28-4a3a-8ee6-3e7ed661619d/dqc_reference/reference_markers.fasta -out GCF_018316655.1_ASM1831665v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:57,434] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:57,438] [INFO] Selected 34 target genomes.
[2024-01-24 13:32:57,438] [INFO] Target genome list was writen to GCF_018316655.1_ASM1831665v1_genomic.fna/target_genomes.txt
[2024-01-24 13:32:57,463] [INFO] Task started: fastANI
[2024-01-24 13:32:57,463] [INFO] Running command: fastANI --query /var/lib/cwl/stgd2881fae-21f9-452d-9fb0-eb56b6c14263/GCF_018316655.1_ASM1831665v1_genomic.fna.gz --refList GCF_018316655.1_ASM1831665v1_genomic.fna/target_genomes.txt --output GCF_018316655.1_ASM1831665v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:33:43,722] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:43,723] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdd3779f2-7c28-4a3a-8ee6-3e7ed661619d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:33:43,724] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdd3779f2-7c28-4a3a-8ee6-3e7ed661619d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:33:43,752] [INFO] Found 34 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:33:43,753] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:33:43,753] [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
Nocardiopsis flavescens	strain=CGMCC 4.5723	GCA_900141985.1	758803	758803	type	True	90.1036	1829	2463	95	below_threshold
Nocardiopsis dassonvillei	strain=ATCC 23218	GCA_012396345.1	2014	2014	type	True	84.1239	1429	2463	95	below_threshold
Nocardiopsis dassonvillei subsp. dassonvillei	strain=DSM 43111	GCA_000092985.1	568208	2014	type	True	84.1154	1513	2463	95	below_threshold
Nocardiopsis dassonvillei	strain=NCTC10488	GCA_900638215.1	2014	2014	type	True	84.0986	1512	2463	95	below_threshold
Nocardiopsis alborubida	strain=NBRC 13392	GCA_001552695.1	146802	146802	type	True	83.9882	1450	2463	95	below_threshold
Nocardiopsis alborubida	strain=ATCC 23612	GCA_012396365.1	146802	146802	type	True	83.937	1488	2463	95	below_threshold
Nocardiopsis algeriensis	strain=CECT 8712	GCA_014203695.1	1478215	1478215	type	True	83.8934	1208	2463	95	below_threshold
Nocardiopsis sinuspersici	strain=UTMC 00102	GCA_001998325.1	501010	501010	type	True	83.8451	1398	2463	95	below_threshold
Nocardiopsis halotolerans	strain=DSM 44410	GCA_000341065.1	124252	124252	type	True	83.5955	1288	2463	95	below_threshold
Nocardiopsis aegyptia	strain=DSM 44442	GCA_013410755.1	220378	220378	type	True	82.9529	1418	2463	95	below_threshold
Nocardiopsis metallicus	strain=DSM 44598	GCA_014201115.1	179819	179819	type	True	82.9057	1423	2463	95	below_threshold
Nocardiopsis terrae	strain=DSM 45157	GCA_014874035.1	372655	372655	type	True	82.8528	1342	2463	95	below_threshold
Nocardiopsis exhalans	strain=JCM11759T	GCA_024134545.1	163604	163604	type	True	82.7457	1410	2463	95	below_threshold
Nocardiopsis terrae	strain=KCTC 19431	GCA_014651695.1	372655	372655	type	True	82.6856	1346	2463	95	below_threshold
Nocardiopsis prasina	strain=DSM 43845	GCA_000341265.1	2015	2015	type	True	82.6648	1254	2463	95	below_threshold
Nocardiopsis lucentensis	strain=DSM 44048	GCA_000341125.1	53441	53441	type	True	82.4526	1058	2463	95	below_threshold
Nocardiopsis coralli	strain=HNM0947	GCA_014892575.1	2772213	2772213	type	True	81.9195	1176	2463	95	below_threshold
Nocardiopsis kunsanensis	strain=DSM 44524	GCA_000340965.1	141693	141693	type	True	81.3853	1001	2463	95	below_threshold
Nocardiopsis mwathae	strain=DSM 46659	GCA_014201195.1	1472723	1472723	type	True	80.1754	959	2463	95	below_threshold
Nocardiopsis potens	strain=DSM 45234	GCA_000341105.1	1246458	1246458	type	True	79.839	1161	2463	95	below_threshold
Thermobifida alba	strain=DSM 43795	GCA_023208015.1	53522	53522	type	True	79.8061	855	2463	95	below_threshold
Streptomonospora litoralis	strain=M2	GCA_004323735.1	2498135	2498135	type	True	79.4753	932	2463	95	below_threshold
Actinomadura nitritigenes	strain=L46	GCA_017573545.1	134602	134602	type	True	76.9016	931	2463	95	below_threshold
Nocardioides okcheonensis	strain=MMS20-HV4-12	GCA_020991065.1	2894081	2894081	type	True	76.5556	488	2463	95	below_threshold
Nocardioides marinisabuli	strain=DSM 18965	GCA_013409965.1	419476	419476	type	True	76.529	530	2463	95	below_threshold
Nocardioides sediminis	strain=KCTC 19271	GCA_003047295.1	433648	433648	type	True	76.5225	476	2463	95	below_threshold
Nocardioides marinisabuli	strain=DSM 18965	GCA_013466785.1	419476	419476	type	True	76.4895	527	2463	95	below_threshold
Nocardioides rubriscoriae	strain=DSM 23986	GCA_008087085.1	642762	642762	type	True	76.4698	494	2463	95	below_threshold
Klenkia taihuensis	strain=CGMCC 1.12303	GCA_014653095.1	1225127	1225127	type	True	76.4396	604	2463	95	below_threshold
Klenkia taihuensis	strain=DSM 45962	GCA_900112525.1	1225127	1225127	type	True	76.4367	614	2463	95	below_threshold
Modestobacter roseus	strain=DSM 45764	GCA_007994135.1	1181884	1181884	type	True	76.3876	574	2463	95	below_threshold
Klenkia soli	strain=DSM 45843	GCA_900103975.1	1052260	1052260	type	True	76.3572	603	2463	95	below_threshold
Klenkia marina	strain=DSM 45722	GCA_900101025.1	1960309	1960309	type	True	76.2537	596	2463	95	below_threshold
Georgenia soli	strain=DSM 21838	GCA_002563695.1	638953	638953	type	True	76.2398	428	2463	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:33:43,755] [INFO] DFAST Taxonomy check result was written to GCF_018316655.1_ASM1831665v1_genomic.fna/tc_result.tsv
[2024-01-24 13:33:43,755] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:33:43,755] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:33:43,756] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdd3779f2-7c28-4a3a-8ee6-3e7ed661619d/dqc_reference/checkm_data
[2024-01-24 13:33:43,757] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:33:43,828] [INFO] Task started: CheckM
[2024-01-24 13:33:43,828] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_018316655.1_ASM1831665v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_018316655.1_ASM1831665v1_genomic.fna/checkm_input GCF_018316655.1_ASM1831665v1_genomic.fna/checkm_result
[2024-01-24 13:35:41,449] [INFO] Task succeeded: CheckM
[2024-01-24 13:35:41,450] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:35:41,475] [INFO] ===== Completeness check finished =====
[2024-01-24 13:35:41,476] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:35:41,476] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_018316655.1_ASM1831665v1_genomic.fna/markers.fasta)
[2024-01-24 13:35:41,476] [INFO] Task started: Blastn
[2024-01-24 13:35:41,477] [INFO] Running command: blastn -query GCF_018316655.1_ASM1831665v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdd3779f2-7c28-4a3a-8ee6-3e7ed661619d/dqc_reference/reference_markers_gtdb.fasta -out GCF_018316655.1_ASM1831665v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:35:43,514] [INFO] Task succeeded: Blastn
[2024-01-24 13:35:43,519] [INFO] Selected 19 target genomes.
[2024-01-24 13:35:43,519] [INFO] Target genome list was writen to GCF_018316655.1_ASM1831665v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:35:43,642] [INFO] Task started: fastANI
[2024-01-24 13:35:43,643] [INFO] Running command: fastANI --query /var/lib/cwl/stgd2881fae-21f9-452d-9fb0-eb56b6c14263/GCF_018316655.1_ASM1831665v1_genomic.fna.gz --refList GCF_018316655.1_ASM1831665v1_genomic.fna/target_genomes_gtdb.txt --output GCF_018316655.1_ASM1831665v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:36:13,049] [INFO] Task succeeded: fastANI
[2024-01-24 13:36:13,070] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:36:13,070] [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
GCA_018316655.1	s__Nocardiopsis sp018316655	100.0	2463	2463	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900141985.1	s__Nocardiopsis flavescens	90.0827	1831	2463	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002529455.1	s__Nocardiopsis fusca	84.1881	1476	2463	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000092985.1	s__Nocardiopsis dassonvillei	84.0844	1513	2463	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	97.80	95.11	0.93	0.87	11	-
GCF_009830945.1	s__Nocardiopsis sp009830945	84.0651	1361	2463	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	99.72	99.66	0.93	0.93	3	-
GCF_001905145.1	s__Nocardiopsis sp001905145	84.0301	1371	2463	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012396365.1	s__Nocardiopsis alborubida	83.9634	1485	2463	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	96.95	95.06	0.88	0.80	4	-
GCF_014203695.1	s__Nocardiopsis algeriensis	83.8976	1207	2463	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000341065.1	s__Nocardiopsis halotolerans	83.6088	1285	2463	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013410755.1	s__Nocardiopsis aegyptia	82.9849	1413	2463	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014201115.1	s__Nocardiopsis metallicus	82.9065	1420	2463	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001279585.1	s__Nocardiopsis sp001279585	82.8489	1384	2463	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003386285.1	s__Nocardiopsis sp003386285	82.7794	1258	2463	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018388625.1	s__Nocardiopsis sp018388625	82.6951	1324	2463	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014201195.1	s__Nocardiopsis_C mwathae	80.2034	955	2463	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000341105.1	s__Nocardiopsis_A potens	79.8404	1160	2463	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014083985.1	s__SCUT-3 sp014083985	77.1283	757	2463	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__SCUT-3	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008087085.1	s__Nocardioides rubriscoriae	76.4584	497	2463	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009846865.1	s__Xylanimonas puerhi	76.1115	502	2463	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Xylanimonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:36:13,072] [INFO] GTDB search result was written to GCF_018316655.1_ASM1831665v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:36:13,072] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:36:13,080] [INFO] DFAST_QC result json was written to GCF_018316655.1_ASM1831665v1_genomic.fna/dqc_result.json
[2024-01-24 13:36:13,081] [INFO] DFAST_QC completed!
[2024-01-24 13:36:13,081] [INFO] Total running time: 0h3m41s