[2024-01-25 18:15:35,477] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:15:35,480] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:15:35,480] [INFO] DQC Reference Directory: /var/lib/cwl/stg23cbaf54-569e-4d0b-8fef-3038d9d6bae0/dqc_reference
[2024-01-25 18:15:36,678] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:15:36,678] [INFO] Task started: Prodigal
[2024-01-25 18:15:36,679] [INFO] Running command: gunzip -c /var/lib/cwl/stg84592812-4234-44f6-9dd9-e5fc41528378/GCF_024172095.1_ASM2417209v1_genomic.fna.gz | prodigal -d GCF_024172095.1_ASM2417209v1_genomic.fna/cds.fna -a GCF_024172095.1_ASM2417209v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:15:57,465] [INFO] Task succeeded: Prodigal
[2024-01-25 18:15:57,466] [INFO] Task started: HMMsearch
[2024-01-25 18:15:57,466] [INFO] Running command: hmmsearch --tblout GCF_024172095.1_ASM2417209v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg23cbaf54-569e-4d0b-8fef-3038d9d6bae0/dqc_reference/reference_markers.hmm GCF_024172095.1_ASM2417209v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:15:57,885] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:15:57,886] [INFO] Found 6/6 markers.
[2024-01-25 18:15:57,966] [INFO] Query marker FASTA was written to GCF_024172095.1_ASM2417209v1_genomic.fna/markers.fasta
[2024-01-25 18:15:57,967] [INFO] Task started: Blastn
[2024-01-25 18:15:57,967] [INFO] Running command: blastn -query GCF_024172095.1_ASM2417209v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg23cbaf54-569e-4d0b-8fef-3038d9d6bae0/dqc_reference/reference_markers.fasta -out GCF_024172095.1_ASM2417209v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:15:59,365] [INFO] Task succeeded: Blastn
[2024-01-25 18:15:59,367] [INFO] Selected 15 target genomes.
[2024-01-25 18:15:59,367] [INFO] Target genome list was writen to GCF_024172095.1_ASM2417209v1_genomic.fna/target_genomes.txt
[2024-01-25 18:15:59,378] [INFO] Task started: fastANI
[2024-01-25 18:15:59,378] [INFO] Running command: fastANI --query /var/lib/cwl/stg84592812-4234-44f6-9dd9-e5fc41528378/GCF_024172095.1_ASM2417209v1_genomic.fna.gz --refList GCF_024172095.1_ASM2417209v1_genomic.fna/target_genomes.txt --output GCF_024172095.1_ASM2417209v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:16:36,287] [INFO] Task succeeded: fastANI
[2024-01-25 18:16:36,288] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg23cbaf54-569e-4d0b-8fef-3038d9d6bae0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:16:36,289] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg23cbaf54-569e-4d0b-8fef-3038d9d6bae0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:16:36,298] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:16:36,298] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:16:36,298] [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
Kitasatospora paracochleata	strain=DSM 41656	GCA_024172095.1	58354	58354	type	True	100.0	2872	2876	95	conclusive
Kitasatospora atroaurantiaca	strain=DSM 41649	GCA_007828955.1	285545	285545	type	True	84.7157	1606	2876	95	below_threshold
Kitasatospora phosalacinea	strain=NRRL B-16230	GCA_000716545.1	2065	2065	type	True	84.4441	1580	2876	95	below_threshold
Kitasatospora cheerisanensis	strain=KCTC 2395	GCA_000696185.1	81942	81942	type	True	84.399	1650	2876	95	below_threshold
Kitasatospora setae	strain=KM-6054	GCA_000269985.1	2066	2066	type	True	84.3582	1671	2876	95	below_threshold
Kitasatospora setae	strain=NRRL B-16185	GCA_000716965.1	2066	2066	type	True	84.3434	1613	2876	95	below_threshold
Kitasatospora griseola	strain=JCM 3339	GCA_014648555.1	2064	2064	type	True	84.2307	1601	2876	95	below_threshold
Kitasatospora gansuensis	strain=DSM 44786	GCA_014203705.1	258050	258050	type	True	83.963	1663	2876	95	below_threshold
Streptomyces rubellomurinus	strain=ATCC 31215	GCA_000961885.1	359131	359131	type	True	83.8031	1563	2876	95	below_threshold
Kitasatospora aureofaciens	strain=NRRL 2209	GCA_000978515.1	1894	1894	type	True	83.6063	1395	2876	95	below_threshold
Kitasatospora aureofaciens	strain=ATCC 10762	GCA_001188955.3	1894	1894	type	True	83.5655	1620	2876	95	below_threshold
Kitasatospora purpeofusca	strain=NRRL B-1817	GCA_000718025.1	67352	67352	type	True	83.3076	1664	2876	95	below_threshold
Kitasatospora humi	strain=RB6PN24	GCA_020907985.1	2893891	2893891	type	True	82.5794	1396	2876	95	below_threshold
Streptomyces sudanensis	strain=SD 504	GCA_023614315.1	436397	436397	type	True	79.2971	888	2876	95	below_threshold
Streptomyces smaragdinus	strain=RB5	GCA_009604385.1	2585196	2585196	type	True	78.4272	998	2876	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:16:36,301] [INFO] DFAST Taxonomy check result was written to GCF_024172095.1_ASM2417209v1_genomic.fna/tc_result.tsv
[2024-01-25 18:16:36,302] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:16:36,302] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:16:36,302] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg23cbaf54-569e-4d0b-8fef-3038d9d6bae0/dqc_reference/checkm_data
[2024-01-25 18:16:36,303] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:16:36,380] [INFO] Task started: CheckM
[2024-01-25 18:16:36,380] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024172095.1_ASM2417209v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024172095.1_ASM2417209v1_genomic.fna/checkm_input GCF_024172095.1_ASM2417209v1_genomic.fna/checkm_result
[2024-01-25 18:18:45,678] [INFO] Task succeeded: CheckM
[2024-01-25 18:18:45,679] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:18:45,703] [INFO] ===== Completeness check finished =====
[2024-01-25 18:18:45,703] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:18:45,704] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024172095.1_ASM2417209v1_genomic.fna/markers.fasta)
[2024-01-25 18:18:45,704] [INFO] Task started: Blastn
[2024-01-25 18:18:45,704] [INFO] Running command: blastn -query GCF_024172095.1_ASM2417209v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg23cbaf54-569e-4d0b-8fef-3038d9d6bae0/dqc_reference/reference_markers_gtdb.fasta -out GCF_024172095.1_ASM2417209v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:18:47,800] [INFO] Task succeeded: Blastn
[2024-01-25 18:18:47,803] [INFO] Selected 21 target genomes.
[2024-01-25 18:18:47,803] [INFO] Target genome list was writen to GCF_024172095.1_ASM2417209v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:18:47,818] [INFO] Task started: fastANI
[2024-01-25 18:18:47,818] [INFO] Running command: fastANI --query /var/lib/cwl/stg84592812-4234-44f6-9dd9-e5fc41528378/GCF_024172095.1_ASM2417209v1_genomic.fna.gz --refList GCF_024172095.1_ASM2417209v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024172095.1_ASM2417209v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:19:38,649] [INFO] Task succeeded: fastANI
[2024-01-25 18:19:38,662] [INFO] Found 21 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 18:19:38,662] [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_000717715.1	s__Kitasatospora sp000717715	84.9365	1781	2876	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Kitasatospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002300355.1	s__Kitasatospora sp002300355	84.8524	1815	2876	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Kitasatospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002813365.1	s__Kitasatospora sp002813365	84.73	1775	2876	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Kitasatospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002754615.1	s__Kitasatospora sp002754615	84.6743	1688	2876	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Kitasatospora	95.0	100.00	100.00	0.99	0.99	2	-
GCF_002813165.1	s__Kitasatospora sp002813165	84.5619	1653	2876	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Kitasatospora	95.0	97.28	97.28	0.90	0.90	2	-
GCF_000716545.1	s__Kitasatospora phosalacinea	84.5047	1569	2876	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Kitasatospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003751605.1	s__Kitasatospora cineracea	84.4732	1695	2876	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Kitasatospora	95.0	97.58	96.37	0.89	0.86	4	-
GCF_013364235.1	s__Kitasatospora sp013364235	84.4504	1656	2876	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Kitasatospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000717185.1	s__Kitasatospora phosalacinea_A	84.4124	1597	2876	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Kitasatospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000696185.1	s__Kitasatospora cheerisanensis	84.4106	1651	2876	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Kitasatospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001905465.1	s__Kitasatospora sp001905465	84.3182	1573	2876	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Kitasatospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014648555.1	s__Kitasatospora griseola	84.1694	1613	2876	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Kitasatospora	95.0	97.80	97.68	0.89	0.89	3	-
GCF_000716875.1	s__Kitasatospora novaecaesareae	83.9741	1449	2876	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Kitasatospora	95.0	99.97	99.97	0.97	0.97	2	-
GCF_000961885.1	s__Kitasatospora rubellomurina	83.8419	1556	2876	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Kitasatospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009569385.1	s__Kitasatospora kaniharaensis	83.7967	1572	2876	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Kitasatospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002953255.1	s__Kitasatospora sp002953255	83.7239	1628	2876	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Kitasatospora	95.0	98.26	96.53	0.79	0.78	3	-
GCA_019192735.1	s__Kitasatospora aureofaciens_A	83.6591	1580	2876	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Kitasatospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001188955.3	s__Kitasatospora aureofaciens	83.606	1613	2876	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Kitasatospora	95.0	99.54	97.86	0.95	0.85	10	-
GCF_000719705.1	s__Kitasatospora sp000719705	83.5724	1551	2876	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Kitasatospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001625365.1	s__Kitasatospora sp001625365	83.5631	1615	2876	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Kitasatospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000720635.1	s__Kitasatospora sp000720635	83.1906	1546	2876	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Kitasatospora	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:19:38,663] [INFO] GTDB search result was written to GCF_024172095.1_ASM2417209v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:19:38,664] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:19:38,668] [INFO] DFAST_QC result json was written to GCF_024172095.1_ASM2417209v1_genomic.fna/dqc_result.json
[2024-01-25 18:19:38,668] [INFO] DFAST_QC completed!
[2024-01-25 18:19:38,668] [INFO] Total running time: 0h4m3s