[2024-01-24 13:01:33,244] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:01:33,246] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:01:33,246] [INFO] DQC Reference Directory: /var/lib/cwl/stgfad3d366-1eea-47c5-8a29-c56bc8e420d8/dqc_reference
[2024-01-24 13:01:34,544] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:01:34,545] [INFO] Task started: Prodigal
[2024-01-24 13:01:34,545] [INFO] Running command: gunzip -c /var/lib/cwl/stg19ff457b-4a4e-409b-9a06-9378cc08c011/GCF_000024545.1_ASM2454v1_genomic.fna.gz | prodigal -d GCF_000024545.1_ASM2454v1_genomic.fna/cds.fna -a GCF_000024545.1_ASM2454v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:01:56,430] [INFO] Task succeeded: Prodigal
[2024-01-24 13:01:56,431] [INFO] Task started: HMMsearch
[2024-01-24 13:01:56,431] [INFO] Running command: hmmsearch --tblout GCF_000024545.1_ASM2454v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfad3d366-1eea-47c5-8a29-c56bc8e420d8/dqc_reference/reference_markers.hmm GCF_000024545.1_ASM2454v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:01:56,783] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:01:56,784] [INFO] Found 6/6 markers.
[2024-01-24 13:01:56,845] [INFO] Query marker FASTA was written to GCF_000024545.1_ASM2454v1_genomic.fna/markers.fasta
[2024-01-24 13:01:56,846] [INFO] Task started: Blastn
[2024-01-24 13:01:56,846] [INFO] Running command: blastn -query GCF_000024545.1_ASM2454v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfad3d366-1eea-47c5-8a29-c56bc8e420d8/dqc_reference/reference_markers.fasta -out GCF_000024545.1_ASM2454v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:01:58,050] [INFO] Task succeeded: Blastn
[2024-01-24 13:01:58,054] [INFO] Selected 22 target genomes.
[2024-01-24 13:01:58,055] [INFO] Target genome list was writen to GCF_000024545.1_ASM2454v1_genomic.fna/target_genomes.txt
[2024-01-24 13:01:58,065] [INFO] Task started: fastANI
[2024-01-24 13:01:58,065] [INFO] Running command: fastANI --query /var/lib/cwl/stg19ff457b-4a4e-409b-9a06-9378cc08c011/GCF_000024545.1_ASM2454v1_genomic.fna.gz --refList GCF_000024545.1_ASM2454v1_genomic.fna/target_genomes.txt --output GCF_000024545.1_ASM2454v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:02:23,137] [INFO] Task succeeded: fastANI
[2024-01-24 13:02:23,138] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfad3d366-1eea-47c5-8a29-c56bc8e420d8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:02:23,139] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfad3d366-1eea-47c5-8a29-c56bc8e420d8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:02:23,159] [INFO] Found 22 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:02:23,159] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:02:23,159] [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
Stackebrandtia nassauensis	strain=DSM 44728	GCA_000024545.1	283811	283811	type	True	100.0	2280	2280	95	conclusive
Stackebrandtia albiflava	strain=DSM 45044	GCA_007994225.1	406432	406432	type	True	79.0967	716	2280	95	below_threshold
Stackebrandtia endophytica	strain=DSM 45928	GCA_006716355.1	1496996	1496996	type	True	78.5825	610	2280	95	below_threshold
Glycomyces arizonensis	strain=DSM 44726	GCA_000482705.1	256035	256035	type	True	77.7019	513	2280	95	below_threshold
Glycomyces xiaoerkulensis	strain=TRM 41368	GCA_002798405.1	2038139	2038139	type	True	77.6503	468	2280	95	below_threshold
Phytomonospora endophytica	strain=YIM 65646	GCA_014202425.1	714109	714109	type	True	77.5515	740	2280	95	below_threshold
Micromonospora veneta	strain=CAP181	GCA_016598485.1	2796464	2796464	type	True	77.1551	513	2280	95	below_threshold
Glycomyces paridis	strain=CPCC 204357	GCA_004912155.1	2126555	2126555	type	True	77.1279	518	2280	95	below_threshold
Micromonospora acroterricola	strain=5R2A7	GCA_003172955.1	2202421	2202421	type	True	77.1133	481	2280	95	below_threshold
Catellatospora chokoriensis	strain=2-25(1)	GCA_011297315.1	310353	310353	type	True	76.9821	623	2280	95	below_threshold
Catellatospora paridis	strain=NEAU-CL2	GCA_009720365.1	1617086	1617086	type	True	76.9137	631	2280	95	below_threshold
Catellatospora tritici	strain=NEAU-YM18	GCA_019083965.1	2851566	2851566	type	True	76.8665	609	2280	95	below_threshold
Micromonospora carbonacea	strain=DSM 43815	GCA_014205165.1	47853	47853	type	True	76.8095	621	2280	95	below_threshold
Catellatospora vulcania	strain=NEAU-JM1	GCA_009720385.1	1460450	1460450	type	True	76.8087	639	2280	95	below_threshold
Catellatospora methionotrophica	strain=IMSNU 22006	GCA_011297335.1	121620	121620	type	True	76.8084	630	2280	95	below_threshold
Micromonospora carbonacea	strain=aurantiaca	GCA_013389765.1	47853	47853	type	True	76.802	617	2280	95	below_threshold
Catellatospora methionotrophica	strain=NBRC 14553	GCA_016862655.1	121620	121620	type	True	76.7746	631	2280	95	below_threshold
Inhella inkyongensis	strain=IMCC1713	GCA_005952805.1	392593	392593	type	True	75.0514	81	2280	95	below_threshold
Acidovorax anthurii	strain=CFPB 3232	GCA_003269065.1	78229	78229	type	True	74.9748	129	2280	95	below_threshold
Inhella inkyongensis	strain=DSM 23958	GCA_014202795.1	392593	392593	type	True	74.9608	82	2280	95	below_threshold
Acidovorax citrulli	strain=DSM 17060	GCA_900100305.1	80869	80869	type	True	74.9241	119	2280	95	below_threshold
Acidovorax avenae subsp. avenae	strain=ATCC 19860	GCA_000176855.2	80870	80867	suspected-type	True	74.8961	133	2280	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:02:23,161] [INFO] DFAST Taxonomy check result was written to GCF_000024545.1_ASM2454v1_genomic.fna/tc_result.tsv
[2024-01-24 13:02:23,162] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:02:23,162] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:02:23,163] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfad3d366-1eea-47c5-8a29-c56bc8e420d8/dqc_reference/checkm_data
[2024-01-24 13:02:23,164] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:02:23,225] [INFO] Task started: CheckM
[2024-01-24 13:02:23,225] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000024545.1_ASM2454v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000024545.1_ASM2454v1_genomic.fna/checkm_input GCF_000024545.1_ASM2454v1_genomic.fna/checkm_result
[2024-01-24 13:03:33,375] [INFO] Task succeeded: CheckM
[2024-01-24 13:03:33,377] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 2.78%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:03:33,405] [INFO] ===== Completeness check finished =====
[2024-01-24 13:03:33,405] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:03:33,406] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000024545.1_ASM2454v1_genomic.fna/markers.fasta)
[2024-01-24 13:03:33,406] [INFO] Task started: Blastn
[2024-01-24 13:03:33,406] [INFO] Running command: blastn -query GCF_000024545.1_ASM2454v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfad3d366-1eea-47c5-8a29-c56bc8e420d8/dqc_reference/reference_markers_gtdb.fasta -out GCF_000024545.1_ASM2454v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:03:35,061] [INFO] Task succeeded: Blastn
[2024-01-24 13:03:35,068] [INFO] Selected 22 target genomes.
[2024-01-24 13:03:35,068] [INFO] Target genome list was writen to GCF_000024545.1_ASM2454v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:03:35,083] [INFO] Task started: fastANI
[2024-01-24 13:03:35,084] [INFO] Running command: fastANI --query /var/lib/cwl/stg19ff457b-4a4e-409b-9a06-9378cc08c011/GCF_000024545.1_ASM2454v1_genomic.fna.gz --refList GCF_000024545.1_ASM2454v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000024545.1_ASM2454v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:03:58,795] [INFO] Task succeeded: fastANI
[2024-01-24 13:03:58,818] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:03:58,818] [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_000024545.1	s__Stackebrandtia nassauensis	100.0	2279	2280	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Stackebrandtia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_007994225.1	s__Stackebrandtia albiflava	79.0637	722	2280	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Stackebrandtia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006716355.1	s__Stackebrandtia endophytica	78.5452	610	2280	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Stackebrandtia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016428645.1	s__Glycomyces sp016428645	77.8827	503	2280	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Glycomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000482705.1	s__Glycomyces arizonensis	77.7386	508	2280	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Glycomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002798405.1	s__Glycomyces xiaoerkulensis	77.6535	464	2280	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Glycomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014202425.1	s__Phytomonospora endophytica	77.5076	750	2280	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Phytomonospora	95.0	100.00	100.00	1.00	1.00	2	-
GCA_019112895.1	s__Stackebrandtia faecavium	77.3606	266	2280	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Stackebrandtia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019113825.1	s__Stackebrandtia excrementipullorum	77.3342	352	2280	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Stackebrandtia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003172955.1	s__Micromonospora sp003172955	77.1575	475	2280	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900107255.1	s__Micromonospora_E pattaloongensis	77.1122	451	2280	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_004217615.1	s__Micromonospora kangleipakensis	77.0564	553	2280	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003583405.1	s__Micromonospora radicis	76.903	491	2280	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016862575.1	s__Catellatospora bangladeshensis	76.8887	642	2280	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Catellatospora	95.0	95.24	95.24	0.85	0.85	2	-
GCF_019083965.1	s__Catellatospora sp019083965	76.8509	616	2280	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Catellatospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018327705.1	s__Catellatospora sp018327705	76.818	664	2280	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Catellatospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014205165.1	s__Micromonospora carbonacea	76.8157	619	2280	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.5545	99.19	98.38	0.95	0.91	3	-
GCF_011297335.1	s__Catellatospora methionotrophica	76.8033	630	2280	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Catellatospora	95.0	99.99	99.99	0.99	0.99	2	-
GCF_016428875.1	s__Xylophilus sp016428875	74.9573	139	2280	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Xylophilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000176855.2	s__Acidovorax_A avenae	74.9238	134	2280	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax_A	95.2137	96.92	95.92	0.74	0.51	18	-
GCA_019232985.1	s__JAFAMW01 sp019232985	74.9044	126	2280	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__JAFAMW01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002397315.1	s__Acidovorax_A sp002397315	74.78	108	2280	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:03:58,820] [INFO] GTDB search result was written to GCF_000024545.1_ASM2454v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:03:58,820] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:03:58,825] [INFO] DFAST_QC result json was written to GCF_000024545.1_ASM2454v1_genomic.fna/dqc_result.json
[2024-01-24 13:03:58,825] [INFO] DFAST_QC completed!
[2024-01-24 13:03:58,825] [INFO] Total running time: 0h2m26s