[2024-01-24 13:13:10,789] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:13:10,792] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:13:10,793] [INFO] DQC Reference Directory: /var/lib/cwl/stg3fa4af04-4659-42f1-8fe7-14df1652a799/dqc_reference
[2024-01-24 13:13:12,090] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:13:12,091] [INFO] Task started: Prodigal
[2024-01-24 13:13:12,091] [INFO] Running command: gunzip -c /var/lib/cwl/stg46cabee3-65b9-4a5b-9cbd-5315d1e983a8/GCF_014203705.1_ASM1420370v1_genomic.fna.gz | prodigal -d GCF_014203705.1_ASM1420370v1_genomic.fna/cds.fna -a GCF_014203705.1_ASM1420370v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:13:36,470] [INFO] Task succeeded: Prodigal
[2024-01-24 13:13:36,470] [INFO] Task started: HMMsearch
[2024-01-24 13:13:36,470] [INFO] Running command: hmmsearch --tblout GCF_014203705.1_ASM1420370v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3fa4af04-4659-42f1-8fe7-14df1652a799/dqc_reference/reference_markers.hmm GCF_014203705.1_ASM1420370v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:13:36,887] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:13:36,889] [INFO] Found 6/6 markers.
[2024-01-24 13:13:36,963] [INFO] Query marker FASTA was written to GCF_014203705.1_ASM1420370v1_genomic.fna/markers.fasta
[2024-01-24 13:13:36,963] [INFO] Task started: Blastn
[2024-01-24 13:13:36,964] [INFO] Running command: blastn -query GCF_014203705.1_ASM1420370v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3fa4af04-4659-42f1-8fe7-14df1652a799/dqc_reference/reference_markers.fasta -out GCF_014203705.1_ASM1420370v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:13:38,431] [INFO] Task succeeded: Blastn
[2024-01-24 13:13:38,434] [INFO] Selected 15 target genomes.
[2024-01-24 13:13:38,435] [INFO] Target genome list was writen to GCF_014203705.1_ASM1420370v1_genomic.fna/target_genomes.txt
[2024-01-24 13:13:38,479] [INFO] Task started: fastANI
[2024-01-24 13:13:38,480] [INFO] Running command: fastANI --query /var/lib/cwl/stg46cabee3-65b9-4a5b-9cbd-5315d1e983a8/GCF_014203705.1_ASM1420370v1_genomic.fna.gz --refList GCF_014203705.1_ASM1420370v1_genomic.fna/target_genomes.txt --output GCF_014203705.1_ASM1420370v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:14:13,265] [INFO] Task succeeded: fastANI
[2024-01-24 13:14:13,266] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3fa4af04-4659-42f1-8fe7-14df1652a799/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:14:13,266] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3fa4af04-4659-42f1-8fe7-14df1652a799/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:14:13,278] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:14:13,279] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:14:13,279] [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 gansuensis	strain=DSM 44786	GCA_014203705.1	258050	258050	type	True	100.0	2761	2764	95	conclusive
Kitasatospora atroaurantiaca	strain=DSM 41649	GCA_007828955.1	285545	285545	type	True	85.3504	1636	2764	95	below_threshold
Kitasatospora paracochleata	strain=DSM 41656	GCA_024172095.1	58354	58354	type	True	84.0402	1639	2764	95	below_threshold
Kitasatospora indigofera	strain=JCM 4646	GCA_014655955.1	67307	67307	type	True	83.9255	1684	2764	95	below_threshold
Kitasatospora herbaricolor	strain=JCM 4138	GCA_014648975.1	68217	68217	type	True	83.8672	1695	2764	95	below_threshold
Kitasatospora azatica	strain=KCTC 9699	GCA_000744785.1	58347	58347	type	True	83.6076	1477	2764	95	below_threshold
Kitasatospora mediocidica	strain=KCTC 9733	GCA_000744225.1	58352	58352	type	True	83.3998	1497	2764	95	below_threshold
Kitasatospora aureofaciens	strain=NRRL 2209	GCA_000978515.1	1894	1894	type	True	83.3175	1301	2764	95	below_threshold
Kitasatospora phosalacinea	strain=NRRL B-16230	GCA_000716545.1	2065	2065	type	True	83.2827	1503	2764	95	below_threshold
Kitasatospora purpeofusca	strain=NRRL B-1817	GCA_000718025.1	67352	67352	type	True	83.2538	1603	2764	95	below_threshold
Streptomyces rubellomurinus	strain=ATCC 31215	GCA_000961885.1	359131	359131	type	True	83.161	1493	2764	95	below_threshold
Kitasatospora kifunensis	strain=DSM 41654	GCA_014203855.1	58351	58351	type	True	82.741	1453	2764	95	below_threshold
Kitasatospora humi	strain=RB6PN24	GCA_020907985.1	2893891	2893891	type	True	82.4054	1306	2764	95	below_threshold
Streptomyces rubrisoli	strain=DSM 42083	GCA_024436055.1	1387313	1387313	type	True	79.1113	932	2764	95	below_threshold
Streptomyces sudanensis	strain=SD 504	GCA_023614315.1	436397	436397	type	True	78.9293	810	2764	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:14:13,281] [INFO] DFAST Taxonomy check result was written to GCF_014203705.1_ASM1420370v1_genomic.fna/tc_result.tsv
[2024-01-24 13:14:13,282] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:14:13,282] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:14:13,283] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3fa4af04-4659-42f1-8fe7-14df1652a799/dqc_reference/checkm_data
[2024-01-24 13:14:13,285] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:14:13,360] [INFO] Task started: CheckM
[2024-01-24 13:14:13,360] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014203705.1_ASM1420370v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014203705.1_ASM1420370v1_genomic.fna/checkm_input GCF_014203705.1_ASM1420370v1_genomic.fna/checkm_result
[2024-01-24 13:15:49,716] [INFO] Task succeeded: CheckM
[2024-01-24 13:15:49,718] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 5.21%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:15:49,740] [INFO] ===== Completeness check finished =====
[2024-01-24 13:15:49,740] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:15:49,741] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014203705.1_ASM1420370v1_genomic.fna/markers.fasta)
[2024-01-24 13:15:49,741] [INFO] Task started: Blastn
[2024-01-24 13:15:49,741] [INFO] Running command: blastn -query GCF_014203705.1_ASM1420370v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3fa4af04-4659-42f1-8fe7-14df1652a799/dqc_reference/reference_markers_gtdb.fasta -out GCF_014203705.1_ASM1420370v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:15:51,883] [INFO] Task succeeded: Blastn
[2024-01-24 13:15:51,886] [INFO] Selected 12 target genomes.
[2024-01-24 13:15:51,887] [INFO] Target genome list was writen to GCF_014203705.1_ASM1420370v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:15:51,916] [INFO] Task started: fastANI
[2024-01-24 13:15:51,917] [INFO] Running command: fastANI --query /var/lib/cwl/stg46cabee3-65b9-4a5b-9cbd-5315d1e983a8/GCF_014203705.1_ASM1420370v1_genomic.fna.gz --refList GCF_014203705.1_ASM1420370v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014203705.1_ASM1420370v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:16:22,710] [INFO] Task succeeded: fastANI
[2024-01-24 13:16:22,725] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:16:22,725] [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_014203705.1	s__Kitasatospora gansuensis	100.0	2762	2764	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Kitasatospora	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001424875.1	s__Kitasatospora sp001424875	92.9646	2123	2764	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Kitasatospora	95.0	99.95	99.95	0.99	0.99	2	-
GCF_007828955.1	s__Kitasatospora atroaurantiaca	85.3355	1637	2764	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Kitasatospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002943525.1	s__Kitasatospora sp002943525	84.1971	1663	2764	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Kitasatospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014655955.1	s__Kitasatospora indigofera	83.9729	1675	2764	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Kitasatospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014648975.1	s__Kitasatospora herbaricolor	83.8694	1694	2764	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Kitasatospora	95.0	96.20	96.20	0.86	0.86	2	-
GCF_000744785.1	s__Kitasatospora azatica	83.5259	1485	2764	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	83.4981	1580	2764	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Kitasatospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000744225.1	s__Kitasatospora mediocidica	83.4068	1499	2764	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Kitasatospora	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019192735.1	s__Kitasatospora aureofaciens_A	83.3828	1497	2764	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Kitasatospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000961885.1	s__Kitasatospora rubellomurina	83.1934	1488	2764	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Kitasatospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014203855.1	s__Kitasatospora kifunensis	82.772	1449	2764	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Kitasatospora	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:16:22,728] [INFO] GTDB search result was written to GCF_014203705.1_ASM1420370v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:16:22,729] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:16:22,736] [INFO] DFAST_QC result json was written to GCF_014203705.1_ASM1420370v1_genomic.fna/dqc_result.json
[2024-01-24 13:16:22,736] [INFO] DFAST_QC completed!
[2024-01-24 13:16:22,736] [INFO] Total running time: 0h3m12s