[2024-01-24 13:45:59,232] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:45:59,238] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:45:59,238] [INFO] DQC Reference Directory: /var/lib/cwl/stgfc5c8062-302e-4978-85ef-4171632960fc/dqc_reference
[2024-01-24 13:46:00,519] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:46:00,520] [INFO] Task started: Prodigal
[2024-01-24 13:46:00,520] [INFO] Running command: gunzip -c /var/lib/cwl/stg87198586-25d0-40fd-a11b-cfb5e5e25a96/GCF_014201195.1_ASM1420119v1_genomic.fna.gz | prodigal -d GCF_014201195.1_ASM1420119v1_genomic.fna/cds.fna -a GCF_014201195.1_ASM1420119v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:46:18,690] [INFO] Task succeeded: Prodigal
[2024-01-24 13:46:18,691] [INFO] Task started: HMMsearch
[2024-01-24 13:46:18,691] [INFO] Running command: hmmsearch --tblout GCF_014201195.1_ASM1420119v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfc5c8062-302e-4978-85ef-4171632960fc/dqc_reference/reference_markers.hmm GCF_014201195.1_ASM1420119v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:46:19,030] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:46:19,031] [INFO] Found 6/6 markers.
[2024-01-24 13:46:19,077] [INFO] Query marker FASTA was written to GCF_014201195.1_ASM1420119v1_genomic.fna/markers.fasta
[2024-01-24 13:46:19,078] [INFO] Task started: Blastn
[2024-01-24 13:46:19,078] [INFO] Running command: blastn -query GCF_014201195.1_ASM1420119v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfc5c8062-302e-4978-85ef-4171632960fc/dqc_reference/reference_markers.fasta -out GCF_014201195.1_ASM1420119v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:46:20,493] [INFO] Task succeeded: Blastn
[2024-01-24 13:46:20,496] [INFO] Selected 14 target genomes.
[2024-01-24 13:46:20,496] [INFO] Target genome list was writen to GCF_014201195.1_ASM1420119v1_genomic.fna/target_genomes.txt
[2024-01-24 13:46:20,542] [INFO] Task started: fastANI
[2024-01-24 13:46:20,542] [INFO] Running command: fastANI --query /var/lib/cwl/stg87198586-25d0-40fd-a11b-cfb5e5e25a96/GCF_014201195.1_ASM1420119v1_genomic.fna.gz --refList GCF_014201195.1_ASM1420119v1_genomic.fna/target_genomes.txt --output GCF_014201195.1_ASM1420119v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:46:43,984] [INFO] Task succeeded: fastANI
[2024-01-24 13:46:43,984] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfc5c8062-302e-4978-85ef-4171632960fc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:46:43,985] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfc5c8062-302e-4978-85ef-4171632960fc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:46:44,002] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:46:44,003] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:46:44,003] [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 mwathae	strain=DSM 46659	GCA_014201195.1	1472723	1472723	type	True	100.0	1977	1978	95	conclusive
Nocardiopsis gilva	strain=YIM 90087	GCA_002263495.1	280236	280236	type	True	87.0427	1509	1978	95	below_threshold
Nocardiopsis gilva	strain=YIM 90087	GCA_000341165.1	280236	280236	type	True	87.0197	1310	1978	95	below_threshold
Nocardiopsis composta	strain=DSM 44551	GCA_014200805.1	157465	157465	type	True	81.1682	1132	1978	95	below_threshold
Nocardiopsis chromatogenes	strain=YIM 90109	GCA_000341185.1	280239	280239	type	True	81.0947	995	1978	95	below_threshold
Nocardiopsis potens	strain=DSM 45234	GCA_000341105.1	1246458	1246458	type	True	81.0347	1094	1978	95	below_threshold
Streptomonospora litoralis	strain=M2	GCA_004323735.1	2498135	2498135	type	True	80.7511	938	1978	95	below_threshold
Streptomonospora alba	strain=YIM 90003	GCA_000826685.1	183763	183763	type	True	80.7128	903	1978	95	below_threshold
Thermobifida alba	strain=DSM 43795	GCA_023208015.1	53522	53522	type	True	80.1909	780	1978	95	below_threshold
Thermobifida halotolerans	strain=DSM 44931	GCA_003574835.2	483545	483545	type	True	80.1591	777	1978	95	below_threshold
Nocardiopsis sinuspersici	strain=UTMC 00102	GCA_001998325.1	501010	501010	type	True	80.027	861	1978	95	below_threshold
Thermobifida halotolerans	strain=YIM 90462	GCA_001660385.1	483545	483545	type	True	80.0219	774	1978	95	below_threshold
Nocardiopsis exhalans	strain=JCM11759T	GCA_024134545.1	163604	163604	type	True	79.9359	842	1978	95	below_threshold
Nocardiopsis coralli	strain=HNM0947	GCA_014892575.1	2772213	2772213	type	True	79.5063	773	1978	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:46:44,004] [INFO] DFAST Taxonomy check result was written to GCF_014201195.1_ASM1420119v1_genomic.fna/tc_result.tsv
[2024-01-24 13:46:44,005] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:46:44,005] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:46:44,005] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfc5c8062-302e-4978-85ef-4171632960fc/dqc_reference/checkm_data
[2024-01-24 13:46:44,007] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:46:44,076] [INFO] Task started: CheckM
[2024-01-24 13:46:44,076] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014201195.1_ASM1420119v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014201195.1_ASM1420119v1_genomic.fna/checkm_input GCF_014201195.1_ASM1420119v1_genomic.fna/checkm_result
[2024-01-24 13:47:51,342] [INFO] Task succeeded: CheckM
[2024-01-24 13:47:51,344] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 2.31%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2024-01-24 13:47:51,367] [INFO] ===== Completeness check finished =====
[2024-01-24 13:47:51,367] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:47:51,368] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014201195.1_ASM1420119v1_genomic.fna/markers.fasta)
[2024-01-24 13:47:51,368] [INFO] Task started: Blastn
[2024-01-24 13:47:51,369] [INFO] Running command: blastn -query GCF_014201195.1_ASM1420119v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfc5c8062-302e-4978-85ef-4171632960fc/dqc_reference/reference_markers_gtdb.fasta -out GCF_014201195.1_ASM1420119v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:47:53,490] [INFO] Task succeeded: Blastn
[2024-01-24 13:47:53,493] [INFO] Selected 13 target genomes.
[2024-01-24 13:47:53,494] [INFO] Target genome list was writen to GCF_014201195.1_ASM1420119v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:47:53,508] [INFO] Task started: fastANI
[2024-01-24 13:47:53,509] [INFO] Running command: fastANI --query /var/lib/cwl/stg87198586-25d0-40fd-a11b-cfb5e5e25a96/GCF_014201195.1_ASM1420119v1_genomic.fna.gz --refList GCF_014201195.1_ASM1420119v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014201195.1_ASM1420119v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:48:12,293] [INFO] Task succeeded: fastANI
[2024-01-24 13:48:12,309] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:48:12,309] [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_014201195.1	s__Nocardiopsis_C mwathae	100.0	1976	1978	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis_C	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002263495.1	s__Nocardiopsis_C gilva	87.0445	1509	1978	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis_C	95.0	99.97	99.97	1.00	1.00	2	-
GCF_013408795.1	s__Spinactinospora alkalitolerans	81.6158	1017	1978	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spinactinospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001552555.1	s__Nocardiopsis_B trehalosi	81.5353	1001	1978	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013410565.1	s__Streptomonospora nanhaiensis	81.4496	1002	1978	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Streptomonospora	95.0	99.69	99.69	0.95	0.95	2	-
GCF_009728995.1	s__Streptomonospora sp009728995	81.2677	932	1978	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Streptomonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014200805.1	s__Nocardiopsis_A composta	81.235	1126	1978	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_000341245.1	s__Nocardiopsis_A halophila	81.2121	966	1978	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis_A	95.0	98.23	98.23	0.90	0.90	2	-
GCF_000341185.1	s__Nocardiopsis_A chromatogenes	81.1145	992	1978	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_000341105.1	s__Nocardiopsis_A potens	81.0423	1094	1978	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_000826685.1	s__Streptomonospora alba	80.6747	909	1978	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Streptomonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018316655.1	s__Nocardiopsis sp018316655	80.1573	925	1978	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001660385.1	s__Thermobifida halotolerans	80.0022	777	1978	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Thermobifida	95.0	99.91	99.91	0.97	0.97	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:48:12,311] [INFO] GTDB search result was written to GCF_014201195.1_ASM1420119v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:48:12,311] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:48:12,314] [INFO] DFAST_QC result json was written to GCF_014201195.1_ASM1420119v1_genomic.fna/dqc_result.json
[2024-01-24 13:48:12,315] [INFO] DFAST_QC completed!
[2024-01-24 13:48:12,315] [INFO] Total running time: 0h2m13s