[2024-01-24 11:43:42,397] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:43:42,399] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:43:42,400] [INFO] DQC Reference Directory: /var/lib/cwl/stg95cb411d-0527-45cf-89be-615364dc27d5/dqc_reference
[2024-01-24 11:43:43,834] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:43:43,835] [INFO] Task started: Prodigal
[2024-01-24 11:43:43,836] [INFO] Running command: gunzip -c /var/lib/cwl/stg041bc7d8-65e8-4c38-a53e-2cc286b1a1c4/GCF_014650075.1_ASM1465007v1_genomic.fna.gz | prodigal -d GCF_014650075.1_ASM1465007v1_genomic.fna/cds.fna -a GCF_014650075.1_ASM1465007v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:44:08,726] [INFO] Task succeeded: Prodigal
[2024-01-24 11:44:08,727] [INFO] Task started: HMMsearch
[2024-01-24 11:44:08,727] [INFO] Running command: hmmsearch --tblout GCF_014650075.1_ASM1465007v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg95cb411d-0527-45cf-89be-615364dc27d5/dqc_reference/reference_markers.hmm GCF_014650075.1_ASM1465007v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:44:09,239] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:44:09,241] [INFO] Found 6/6 markers.
[2024-01-24 11:44:09,331] [INFO] Query marker FASTA was written to GCF_014650075.1_ASM1465007v1_genomic.fna/markers.fasta
[2024-01-24 11:44:09,331] [INFO] Task started: Blastn
[2024-01-24 11:44:09,331] [INFO] Running command: blastn -query GCF_014650075.1_ASM1465007v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg95cb411d-0527-45cf-89be-615364dc27d5/dqc_reference/reference_markers.fasta -out GCF_014650075.1_ASM1465007v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:44:10,777] [INFO] Task succeeded: Blastn
[2024-01-24 11:44:10,780] [INFO] Selected 17 target genomes.
[2024-01-24 11:44:10,781] [INFO] Target genome list was writen to GCF_014650075.1_ASM1465007v1_genomic.fna/target_genomes.txt
[2024-01-24 11:44:10,784] [INFO] Task started: fastANI
[2024-01-24 11:44:10,785] [INFO] Running command: fastANI --query /var/lib/cwl/stg041bc7d8-65e8-4c38-a53e-2cc286b1a1c4/GCF_014650075.1_ASM1465007v1_genomic.fna.gz --refList GCF_014650075.1_ASM1465007v1_genomic.fna/target_genomes.txt --output GCF_014650075.1_ASM1465007v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:44:44,525] [INFO] Task succeeded: fastANI
[2024-01-24 11:44:44,526] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg95cb411d-0527-45cf-89be-615364dc27d5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:44:44,526] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg95cb411d-0527-45cf-89be-615364dc27d5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:44:44,542] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:44:44,542] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:44:44,542] [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
Streptomyces microflavus	strain=JCM 4496	GCA_014650075.1	1919	1919	type	True	100.0	2817	2819	95	conclusive
Streptomyces cavourensis	strain=JCM 4298	GCA_014649215.1	67258	67258	type	True	91.6392	2120	2819	95	below_threshold
Streptomyces rhizosphaericola	strain=1AS2c	GCA_004794175.1	2564098	2564098	type	True	91.2053	1731	2819	95	below_threshold
Streptomyces anulatus	strain=JCM 4721	GCA_014650675.1	1892	1892	type	True	89.8249	2083	2819	95	below_threshold
Streptomyces parvus	strain=NRRL B-1455	GCA_008632535.1	66428	66428	type	True	89.5156	1833	2819	95	below_threshold
Streptomyces parvus	strain=JCM 4069	GCA_014648875.1	66428	66428	type	True	89.4715	2041	2819	95	below_threshold
Streptomyces sindenensis	strain=JCM 4164	GCA_014649035.1	67363	67363	type	True	89.445	1932	2819	95	below_threshold
Streptomyces griseus	strain=NCTC13033	GCA_900460065.1	1911	1911	type	True	89.3423	2024	2819	95	below_threshold
Streptomyces griseus	strain=DSM 40236	GCA_900105705.1	1911	1911	type	True	89.2827	2061	2819	95	below_threshold
Streptomyces badius	strain=JCM 4350	GCA_014649415.1	1941	1941	type	True	89.2344	1927	2819	95	below_threshold
Streptomyces fulvorobeus	strain=DSM 41455	GCA_013409565.1	284028	284028	type	True	85.1913	1496	2819	95	below_threshold
[Kitasatospora] papulosa	strain=NRRL B-16504	GCA_000717245.1	1464011	1464011	type	True	84.7243	1657	2819	95	below_threshold
Streptomyces formicae	strain=1H-GS9	GCA_022647665.1	1616117	1616117	type	True	82.6166	1459	2819	95	below_threshold
Streptomyces genisteinicus	strain=CRPJ-33	GCA_014489615.1	2768068	2768068	type	True	82.4453	1479	2819	95	below_threshold
Streptomyces sudanensis	strain=SD 504	GCA_023614315.1	436397	436397	type	True	82.0148	1074	2819	95	below_threshold
Streptomyces durmitorensis	strain=MS405	GCA_023498005.1	319947	319947	type	True	81.6008	1511	2819	95	below_threshold
Streptomyces zagrosensis	strain=CECT 8305	GCA_014203645.1	1042984	1042984	type	True	79.6678	1075	2819	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:44:44,544] [INFO] DFAST Taxonomy check result was written to GCF_014650075.1_ASM1465007v1_genomic.fna/tc_result.tsv
[2024-01-24 11:44:44,544] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:44:44,544] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:44:44,545] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg95cb411d-0527-45cf-89be-615364dc27d5/dqc_reference/checkm_data
[2024-01-24 11:44:44,546] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:44:44,620] [INFO] Task started: CheckM
[2024-01-24 11:44:44,620] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014650075.1_ASM1465007v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014650075.1_ASM1465007v1_genomic.fna/checkm_input GCF_014650075.1_ASM1465007v1_genomic.fna/checkm_result
[2024-01-24 11:46:01,814] [INFO] Task succeeded: CheckM
[2024-01-24 11:46:01,816] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 9.38%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:46:01,844] [INFO] ===== Completeness check finished =====
[2024-01-24 11:46:01,844] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:46:01,845] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014650075.1_ASM1465007v1_genomic.fna/markers.fasta)
[2024-01-24 11:46:01,845] [INFO] Task started: Blastn
[2024-01-24 11:46:01,845] [INFO] Running command: blastn -query GCF_014650075.1_ASM1465007v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg95cb411d-0527-45cf-89be-615364dc27d5/dqc_reference/reference_markers_gtdb.fasta -out GCF_014650075.1_ASM1465007v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:46:03,965] [INFO] Task succeeded: Blastn
[2024-01-24 11:46:03,970] [INFO] Selected 18 target genomes.
[2024-01-24 11:46:03,970] [INFO] Target genome list was writen to GCF_014650075.1_ASM1465007v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:46:03,978] [INFO] Task started: fastANI
[2024-01-24 11:46:03,978] [INFO] Running command: fastANI --query /var/lib/cwl/stg041bc7d8-65e8-4c38-a53e-2cc286b1a1c4/GCF_014650075.1_ASM1465007v1_genomic.fna.gz --refList GCF_014650075.1_ASM1465007v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014650075.1_ASM1465007v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:46:39,006] [INFO] Task succeeded: fastANI
[2024-01-24 11:46:39,027] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:46:39,027] [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_014650075.1	s__Streptomyces microflavus	100.0	2817	2819	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.25	97.27	0.91	0.85	13	conclusive
GCF_000718135.1	s__Streptomyces cyaneofuscatus	93.3322	2183	2819	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.78	95.81	0.91	0.85	12	-
GCF_001905595.1	s__Streptomyces sp001905595	92.9097	1993	2819	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.40	99.32	0.92	0.90	4	-
GCF_003610995.1	s__Streptomyces sp003116725	92.8284	2064	2819	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.40	95.27	0.92	0.85	7	-
GCF_002082585.1	s__Streptomyces albolongus	92.0213	2041	2819	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002154345.1	s__Streptomyces fimicarius	89.8806	1712	2819	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.88	95.22	0.89	0.81	11	-
GCF_014650675.1	s__Streptomyces anulatus	89.8185	2084	2819	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.62	96.42	0.89	0.81	27	-
GCA_002551355.1	s__Streptomyces sp002551355	89.8125	1971	2819	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014649875.1	s__Streptomyces rubiginosohelvolus	89.7774	2026	2819	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	96.2941	98.09	96.67	0.91	0.87	22	-
GCF_002910905.1	s__Streptomyces sp002910905	89.6561	1809	2819	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014649555.1	s__Streptomyces globisporus	89.6499	2074	2819	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	96.2941	98.88	97.57	0.92	0.86	14	-
GCF_003501885.1	s__Streptomyces globisporus_D	89.623	1781	2819	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.6693	N/A	N/A	N/A	N/A	1	-
GCF_016901035.1	s__Streptomyces sp016901035	89.5604	1777	2819	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014648875.1	s__Streptomyces parvus	89.486	2039	2819	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.2347	97.39	96.11	0.86	0.79	24	-
GCF_002551245.1	s__Streptomyces sp002551245	89.4613	1759	2819	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000470535.1	s__Streptomyces sp000470535	84.8793	1524	2819	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001905365.1	s__Streptomyces sp001905365	84.8662	1721	2819	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002941025.1	s__Streptomyces sp002941025	84.7356	1717	2819	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:46:39,029] [INFO] GTDB search result was written to GCF_014650075.1_ASM1465007v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:46:39,030] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:46:39,033] [INFO] DFAST_QC result json was written to GCF_014650075.1_ASM1465007v1_genomic.fna/dqc_result.json
[2024-01-24 11:46:39,034] [INFO] DFAST_QC completed!
[2024-01-24 11:46:39,034] [INFO] Total running time: 0h2m57s