[2024-01-24 11:43:52,740] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:43:52,742] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:43:52,742] [INFO] DQC Reference Directory: /var/lib/cwl/stgcd99a4bf-34ad-4163-bfb7-62db20f4277a/dqc_reference
[2024-01-24 11:43:54,039] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:43:54,040] [INFO] Task started: Prodigal
[2024-01-24 11:43:54,040] [INFO] Running command: gunzip -c /var/lib/cwl/stgb62386ad-d3fe-4a19-a429-bbf898191864/GCF_024134545.1_ASM2413454v1_genomic.fna.gz | prodigal -d GCF_024134545.1_ASM2413454v1_genomic.fna/cds.fna -a GCF_024134545.1_ASM2413454v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:44:16,104] [INFO] Task succeeded: Prodigal
[2024-01-24 11:44:16,105] [INFO] Task started: HMMsearch
[2024-01-24 11:44:16,105] [INFO] Running command: hmmsearch --tblout GCF_024134545.1_ASM2413454v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcd99a4bf-34ad-4163-bfb7-62db20f4277a/dqc_reference/reference_markers.hmm GCF_024134545.1_ASM2413454v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:44:16,397] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:44:16,399] [INFO] Found 6/6 markers.
[2024-01-24 11:44:16,457] [INFO] Query marker FASTA was written to GCF_024134545.1_ASM2413454v1_genomic.fna/markers.fasta
[2024-01-24 11:44:16,457] [INFO] Task started: Blastn
[2024-01-24 11:44:16,457] [INFO] Running command: blastn -query GCF_024134545.1_ASM2413454v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcd99a4bf-34ad-4163-bfb7-62db20f4277a/dqc_reference/reference_markers.fasta -out GCF_024134545.1_ASM2413454v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:44:17,666] [INFO] Task succeeded: Blastn
[2024-01-24 11:44:17,670] [INFO] Selected 13 target genomes.
[2024-01-24 11:44:17,670] [INFO] Target genome list was writen to GCF_024134545.1_ASM2413454v1_genomic.fna/target_genomes.txt
[2024-01-24 11:44:17,713] [INFO] Task started: fastANI
[2024-01-24 11:44:17,713] [INFO] Running command: fastANI --query /var/lib/cwl/stgb62386ad-d3fe-4a19-a429-bbf898191864/GCF_024134545.1_ASM2413454v1_genomic.fna.gz --refList GCF_024134545.1_ASM2413454v1_genomic.fna/target_genomes.txt --output GCF_024134545.1_ASM2413454v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:44:38,506] [INFO] Task succeeded: fastANI
[2024-01-24 11:44:38,506] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcd99a4bf-34ad-4163-bfb7-62db20f4277a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:44:38,507] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcd99a4bf-34ad-4163-bfb7-62db20f4277a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:44:38,518] [INFO] Found 13 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 11:44:38,519] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 11:44:38,519] [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 exhalans	strain=JCM11759T	GCA_024134545.1	163604	163604	type	True	100.0	2532	2532	95	inconclusive
Nocardiopsis valliformis	strain=DSM 45023	GCA_000340985.1	239974	239974	type	True	96.211	1981	2532	95	inconclusive
Nocardiopsis metallicus	strain=DSM 44598	GCA_014201115.1	179819	179819	type	True	95.4653	2083	2532	95	inconclusive
Nocardiopsis ganjiahuensis	strain=DSM 45031	GCA_000341085.1	239984	239984	type	True	89.5183	1750	2532	95	below_threshold
Nocardiopsis terrae	strain=KCTC 19431	GCA_014651695.1	372655	372655	type	True	87.6885	1570	2532	95	below_threshold
Nocardiopsis terrae	strain=DSM 45157	GCA_014874035.1	372655	372655	type	True	87.6817	1582	2532	95	below_threshold
Nocardiopsis prasina	strain=DSM 43845	GCA_000341265.1	2015	2015	type	True	87.2434	1467	2532	95	below_threshold
Nocardiopsis sinuspersici	strain=UTMC 00102	GCA_001998325.1	501010	501010	type	True	83.727	1327	2532	95	below_threshold
Nocardiopsis lucentensis	strain=DSM 44048	GCA_000341125.1	53441	53441	type	True	82.8366	1046	2532	95	below_threshold
Nocardiopsis salina	strain=YIM 90010	GCA_000341025.1	245836	245836	type	True	81.6553	1063	2532	95	below_threshold
Nocardiopsis kunsanensis	strain=DSM 44524	GCA_000340965.1	141693	141693	type	True	81.4877	1018	2532	95	below_threshold
Thermobifida alba	strain=DSM 43795	GCA_023208015.1	53522	53522	type	True	79.624	732	2532	95	below_threshold
Streptomonospora litoralis	strain=M2	GCA_004323735.1	2498135	2498135	type	True	79.3381	784	2532	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:44:38,520] [INFO] DFAST Taxonomy check result was written to GCF_024134545.1_ASM2413454v1_genomic.fna/tc_result.tsv
[2024-01-24 11:44:38,521] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:44:38,521] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:44:38,521] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcd99a4bf-34ad-4163-bfb7-62db20f4277a/dqc_reference/checkm_data
[2024-01-24 11:44:38,522] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:44:38,589] [INFO] Task started: CheckM
[2024-01-24 11:44:38,589] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024134545.1_ASM2413454v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024134545.1_ASM2413454v1_genomic.fna/checkm_input GCF_024134545.1_ASM2413454v1_genomic.fna/checkm_result
[2024-01-24 11:45:51,013] [INFO] Task succeeded: CheckM
[2024-01-24 11:45:51,014] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:45:51,033] [INFO] ===== Completeness check finished =====
[2024-01-24 11:45:51,034] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:45:51,034] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024134545.1_ASM2413454v1_genomic.fna/markers.fasta)
[2024-01-24 11:45:51,034] [INFO] Task started: Blastn
[2024-01-24 11:45:51,034] [INFO] Running command: blastn -query GCF_024134545.1_ASM2413454v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcd99a4bf-34ad-4163-bfb7-62db20f4277a/dqc_reference/reference_markers_gtdb.fasta -out GCF_024134545.1_ASM2413454v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:45:52,883] [INFO] Task succeeded: Blastn
[2024-01-24 11:45:52,886] [INFO] Selected 11 target genomes.
[2024-01-24 11:45:52,886] [INFO] Target genome list was writen to GCF_024134545.1_ASM2413454v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:45:52,893] [INFO] Task started: fastANI
[2024-01-24 11:45:52,893] [INFO] Running command: fastANI --query /var/lib/cwl/stgb62386ad-d3fe-4a19-a429-bbf898191864/GCF_024134545.1_ASM2413454v1_genomic.fna.gz --refList GCF_024134545.1_ASM2413454v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024134545.1_ASM2413454v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:46:10,070] [INFO] Task succeeded: fastANI
[2024-01-24 11:46:10,080] [INFO] Found 11 fastANI hits (2 hits with ANI > circumscription radius)
[2024-01-24 11:46:10,080] [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_000340985.1	s__Nocardiopsis valliformis	96.1903	1983	2532	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	N/A	N/A	N/A	N/A	1	inconclusive
GCF_014201115.1	s__Nocardiopsis metallicus	95.4791	2085	2532	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	N/A	N/A	N/A	N/A	1	inconclusive
GCF_000341085.1	s__Nocardiopsis ganjiahuensis	89.507	1750	2532	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014651695.1	s__Nocardiopsis terrae	87.6695	1572	2532	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000341265.1	s__Nocardiopsis prasina	87.2516	1466	2532	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	96.74	95.74	0.91	0.87	4	-
GCA_018388625.1	s__Nocardiopsis sp018388625	87.0871	1533	2532	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000341225.1	s__Nocardiopsis alba	84.4233	1331	2532	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	98.86	98.56	0.95	0.95	4	-
GCF_000092985.1	s__Nocardiopsis dassonvillei	83.6419	1382	2532	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	97.80	95.11	0.93	0.87	11	-
GCF_000341125.1	s__Nocardiopsis lucentensis	82.847	1045	2532	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000341025.1	s__Nocardiopsis salina	81.6713	1061	2532	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003336425.1	s__Marinitenerispora sediminis	79.1595	738	2532	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Marinitenerispora	95.0	99.95	99.94	0.96	0.96	3	-
--------------------------------------------------------------------------------
[2024-01-24 11:46:10,081] [INFO] GTDB search result was written to GCF_024134545.1_ASM2413454v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:46:10,082] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:46:10,160] [INFO] DFAST_QC result json was written to GCF_024134545.1_ASM2413454v1_genomic.fna/dqc_result.json
[2024-01-24 11:46:10,161] [INFO] DFAST_QC completed!
[2024-01-24 11:46:10,161] [INFO] Total running time: 0h2m17s