[2024-01-24 14:05:16,128] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:05:16,129] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:05:16,129] [INFO] DQC Reference Directory: /var/lib/cwl/stg790ea226-42af-43be-a9f4-e9a5cb7fc1d8/dqc_reference
[2024-01-24 14:05:17,395] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:05:17,396] [INFO] Task started: Prodigal
[2024-01-24 14:05:17,396] [INFO] Running command: gunzip -c /var/lib/cwl/stgc115e36b-eec2-46b5-b5fd-39d5b0321ad8/GCF_007829815.1_ASM782981v1_genomic.fna.gz | prodigal -d GCF_007829815.1_ASM782981v1_genomic.fna/cds.fna -a GCF_007829815.1_ASM782981v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:05:45,000] [INFO] Task succeeded: Prodigal
[2024-01-24 14:05:45,000] [INFO] Task started: HMMsearch
[2024-01-24 14:05:45,000] [INFO] Running command: hmmsearch --tblout GCF_007829815.1_ASM782981v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg790ea226-42af-43be-a9f4-e9a5cb7fc1d8/dqc_reference/reference_markers.hmm GCF_007829815.1_ASM782981v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:05:45,509] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:05:45,511] [INFO] Found 6/6 markers.
[2024-01-24 14:05:45,615] [INFO] Query marker FASTA was written to GCF_007829815.1_ASM782981v1_genomic.fna/markers.fasta
[2024-01-24 14:05:45,615] [INFO] Task started: Blastn
[2024-01-24 14:05:45,615] [INFO] Running command: blastn -query GCF_007829815.1_ASM782981v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg790ea226-42af-43be-a9f4-e9a5cb7fc1d8/dqc_reference/reference_markers.fasta -out GCF_007829815.1_ASM782981v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:05:47,042] [INFO] Task succeeded: Blastn
[2024-01-24 14:05:47,046] [INFO] Selected 11 target genomes.
[2024-01-24 14:05:47,047] [INFO] Target genome list was writen to GCF_007829815.1_ASM782981v1_genomic.fna/target_genomes.txt
[2024-01-24 14:05:47,052] [INFO] Task started: fastANI
[2024-01-24 14:05:47,053] [INFO] Running command: fastANI --query /var/lib/cwl/stgc115e36b-eec2-46b5-b5fd-39d5b0321ad8/GCF_007829815.1_ASM782981v1_genomic.fna.gz --refList GCF_007829815.1_ASM782981v1_genomic.fna/target_genomes.txt --output GCF_007829815.1_ASM782981v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:06:18,113] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:18,113] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg790ea226-42af-43be-a9f4-e9a5cb7fc1d8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:06:18,114] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg790ea226-42af-43be-a9f4-e9a5cb7fc1d8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:06:18,130] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:06:18,130] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:06:18,130] [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 viridis	strain=DSM 44826	GCA_007829815.1	281105	281105	type	True	100.0	3357	3360	95	conclusive
Kitasatospora acidiphila	strain=MMS16-CNU292	GCA_006636205.1	2567942	2567942	type	True	86.2864	1870	3360	95	below_threshold
Kitasatospora humi	strain=RB6PN24	GCA_020907985.1	2893891	2893891	type	True	85.839	1775	3360	95	below_threshold
Kitasatospora azatica	strain=KCTC 9699	GCA_000744785.1	58347	58347	type	True	85.5535	1776	3360	95	below_threshold
Kitasatospora kifunensis	strain=DSM 41654	GCA_014203855.1	58351	58351	type	True	84.8018	1871	3360	95	below_threshold
Kitasatospora mediocidica	strain=KCTC 9733	GCA_000744225.1	58352	58352	type	True	83.8402	1740	3360	95	below_threshold
Kitasatospora paracochleata	strain=DSM 41656	GCA_024172095.1	58354	58354	type	True	82.6109	1638	3360	95	below_threshold
Kitasatospora gansuensis	strain=DSM 44786	GCA_014203705.1	258050	258050	type	True	82.4518	1609	3360	95	below_threshold
Kitasatospora purpeofusca	strain=NRRL B-1817	GCA_000718025.1	67352	67352	type	True	82.2219	1705	3360	95	below_threshold
Streptomyces rubrisoli	strain=DSM 42083	GCA_024436055.1	1387313	1387313	type	True	79.1233	1082	3360	95	below_threshold
Streptomyces lichenis	strain=LCR6-01	GCA_023218175.1	2306967	2306967	type	True	78.9577	1193	3360	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:06:18,132] [INFO] DFAST Taxonomy check result was written to GCF_007829815.1_ASM782981v1_genomic.fna/tc_result.tsv
[2024-01-24 14:06:18,132] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:06:18,132] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:06:18,133] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg790ea226-42af-43be-a9f4-e9a5cb7fc1d8/dqc_reference/checkm_data
[2024-01-24 14:06:18,134] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:06:18,223] [INFO] Task started: CheckM
[2024-01-24 14:06:18,223] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007829815.1_ASM782981v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007829815.1_ASM782981v1_genomic.fna/checkm_input GCF_007829815.1_ASM782981v1_genomic.fna/checkm_result
[2024-01-24 14:08:49,341] [INFO] Task succeeded: CheckM
[2024-01-24 14:08:49,342] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 5.21%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:08:49,374] [INFO] ===== Completeness check finished =====
[2024-01-24 14:08:49,375] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:08:49,376] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007829815.1_ASM782981v1_genomic.fna/markers.fasta)
[2024-01-24 14:08:49,376] [INFO] Task started: Blastn
[2024-01-24 14:08:49,376] [INFO] Running command: blastn -query GCF_007829815.1_ASM782981v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg790ea226-42af-43be-a9f4-e9a5cb7fc1d8/dqc_reference/reference_markers_gtdb.fasta -out GCF_007829815.1_ASM782981v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:08:51,741] [INFO] Task succeeded: Blastn
[2024-01-24 14:08:51,747] [INFO] Selected 7 target genomes.
[2024-01-24 14:08:51,747] [INFO] Target genome list was writen to GCF_007829815.1_ASM782981v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:08:51,753] [INFO] Task started: fastANI
[2024-01-24 14:08:51,753] [INFO] Running command: fastANI --query /var/lib/cwl/stgc115e36b-eec2-46b5-b5fd-39d5b0321ad8/GCF_007829815.1_ASM782981v1_genomic.fna.gz --refList GCF_007829815.1_ASM782981v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007829815.1_ASM782981v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:09:14,823] [INFO] Task succeeded: fastANI
[2024-01-24 14:09:14,837] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:09:14,838] [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_007829815.1	s__Kitasatospora viridis	100.0	3359	3360	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_002846355.1	s__Kitasatospora sp002846355	86.0803	1877	3360	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Kitasatospora	95.0	96.05	96.05	0.83	0.83	2	-
GCF_003205575.1	s__Kitasatospora tateyamensis	85.6417	1647	3360	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Kitasatospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000744785.1	s__Kitasatospora azatica	85.5522	1773	3360	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	84.7909	1872	3360	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	83.8359	1737	3360	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Kitasatospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014203705.1	s__Kitasatospora gansuensis	82.5309	1594	3360	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 14:09:14,840] [INFO] GTDB search result was written to GCF_007829815.1_ASM782981v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:09:14,841] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:09:14,846] [INFO] DFAST_QC result json was written to GCF_007829815.1_ASM782981v1_genomic.fna/dqc_result.json
[2024-01-24 14:09:14,847] [INFO] DFAST_QC completed!
[2024-01-24 14:09:14,847] [INFO] Total running time: 0h3m59s