[2024-01-24 12:13:29,237] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:13:29,238] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:13:29,239] [INFO] DQC Reference Directory: /var/lib/cwl/stgad6928b3-cbac-44f1-839d-860b1b45020d/dqc_reference
[2024-01-24 12:13:30,497] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:13:30,498] [INFO] Task started: Prodigal
[2024-01-24 12:13:30,498] [INFO] Running command: gunzip -c /var/lib/cwl/stg6a451aa4-d1f6-4bd2-ab03-a1eb057f9dbb/GCF_001570545.1_ASM157054v1_genomic.fna.gz | prodigal -d GCF_001570545.1_ASM157054v1_genomic.fna/cds.fna -a GCF_001570545.1_ASM157054v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:13:56,430] [INFO] Task succeeded: Prodigal
[2024-01-24 12:13:56,431] [INFO] Task started: HMMsearch
[2024-01-24 12:13:56,431] [INFO] Running command: hmmsearch --tblout GCF_001570545.1_ASM157054v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgad6928b3-cbac-44f1-839d-860b1b45020d/dqc_reference/reference_markers.hmm GCF_001570545.1_ASM157054v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:13:56,916] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:13:56,918] [INFO] Found 6/6 markers.
[2024-01-24 12:13:56,991] [INFO] Query marker FASTA was written to GCF_001570545.1_ASM157054v1_genomic.fna/markers.fasta
[2024-01-24 12:13:56,991] [INFO] Task started: Blastn
[2024-01-24 12:13:56,991] [INFO] Running command: blastn -query GCF_001570545.1_ASM157054v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgad6928b3-cbac-44f1-839d-860b1b45020d/dqc_reference/reference_markers.fasta -out GCF_001570545.1_ASM157054v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:13:58,395] [INFO] Task succeeded: Blastn
[2024-01-24 12:13:58,399] [INFO] Selected 12 target genomes.
[2024-01-24 12:13:58,400] [INFO] Target genome list was writen to GCF_001570545.1_ASM157054v1_genomic.fna/target_genomes.txt
[2024-01-24 12:13:58,409] [INFO] Task started: fastANI
[2024-01-24 12:13:58,410] [INFO] Running command: fastANI --query /var/lib/cwl/stg6a451aa4-d1f6-4bd2-ab03-a1eb057f9dbb/GCF_001570545.1_ASM157054v1_genomic.fna.gz --refList GCF_001570545.1_ASM157054v1_genomic.fna/target_genomes.txt --output GCF_001570545.1_ASM157054v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:14:25,808] [INFO] Task succeeded: fastANI
[2024-01-24 12:14:25,809] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgad6928b3-cbac-44f1-839d-860b1b45020d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:14:25,810] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgad6928b3-cbac-44f1-839d-860b1b45020d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:14:25,826] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:14:25,826] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:14:25,826] [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
Herbidospora mongoliensis	strain=NBRC 105882	GCA_001570545.1	688067	688067	type	True	100.0	3000	3004	95	conclusive
Herbidospora cretacea	strain=NBRC 15474	GCA_001570605.1	28444	28444	type	True	90.5639	2339	3004	95	below_threshold
Herbidospora galbida	strain=NEAU-GS14	GCA_005233835.1	2575442	2575442	type	True	89.9607	2207	3004	95	below_threshold
Herbidospora solisilvae	strain=NEAU-GS84	GCA_009901565.1	2696284	2696284	type	True	89.5336	2242	3004	95	below_threshold
Herbidospora sakaeratensis	strain=NBRC 102641	GCA_001570525.1	564415	564415	type	True	89.2651	2290	3004	95	below_threshold
Acrocarpospora catenulata	strain=H8750	GCA_018476525.1	2836182	2836182	type	True	80.7901	1491	3004	95	below_threshold
Microbispora rosea subsp. rosea	strain=NBRC 14044	GCA_016863055.1	58118	58117	type	True	79.6685	1192	3004	95	below_threshold
Microbispora rosea	strain=ATCC 12950	GCA_900156315.1	58117	58117	type	True	79.6562	1215	3004	95	below_threshold
Microbispora oryzae	strain=RL4-1S	GCA_017896165.1	2806554	2806554	type	True	79.6078	1115	3004	95	below_threshold
Sphaerisporangium corydalis	strain=NEAU-YHS15	GCA_025506355.1	1441875	1441875	type	True	79.5061	1257	3004	95	below_threshold
Sphaerimonospora thailandensis	strain=NBRC 107569	GCA_016863115.1	795644	795644	type	True	79.2573	858	3004	95	below_threshold
Nonomuraea roseoviolacea subsp. carminata	strain=DSM 44170	GCA_024172185.1	160689	103837	type	True	79.0136	1218	3004	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:14:25,832] [INFO] DFAST Taxonomy check result was written to GCF_001570545.1_ASM157054v1_genomic.fna/tc_result.tsv
[2024-01-24 12:14:25,832] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:14:25,832] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:14:25,833] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgad6928b3-cbac-44f1-839d-860b1b45020d/dqc_reference/checkm_data
[2024-01-24 12:14:25,834] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:14:25,915] [INFO] Task started: CheckM
[2024-01-24 12:14:25,915] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001570545.1_ASM157054v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001570545.1_ASM157054v1_genomic.fna/checkm_input GCF_001570545.1_ASM157054v1_genomic.fna/checkm_result
[2024-01-24 12:15:52,918] [INFO] Task succeeded: CheckM
[2024-01-24 12:15:52,921] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:15:52,946] [INFO] ===== Completeness check finished =====
[2024-01-24 12:15:52,946] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:15:52,946] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001570545.1_ASM157054v1_genomic.fna/markers.fasta)
[2024-01-24 12:15:52,947] [INFO] Task started: Blastn
[2024-01-24 12:15:52,947] [INFO] Running command: blastn -query GCF_001570545.1_ASM157054v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgad6928b3-cbac-44f1-839d-860b1b45020d/dqc_reference/reference_markers_gtdb.fasta -out GCF_001570545.1_ASM157054v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:55,045] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:55,051] [INFO] Selected 8 target genomes.
[2024-01-24 12:15:55,051] [INFO] Target genome list was writen to GCF_001570545.1_ASM157054v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:15:55,058] [INFO] Task started: fastANI
[2024-01-24 12:15:55,058] [INFO] Running command: fastANI --query /var/lib/cwl/stg6a451aa4-d1f6-4bd2-ab03-a1eb057f9dbb/GCF_001570545.1_ASM157054v1_genomic.fna.gz --refList GCF_001570545.1_ASM157054v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001570545.1_ASM157054v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:16:15,313] [INFO] Task succeeded: fastANI
[2024-01-24 12:16:15,325] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:16:15,326] [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_001570545.1	s__Herbidospora mongoliensis	100.0	3000	3004	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Herbidospora	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001570605.1	s__Herbidospora cretacea	90.5554	2341	3004	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Herbidospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005233835.1	s__Herbidospora galbida	89.942	2210	3004	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Herbidospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001570565.1	s__Herbidospora yilanensis	89.6386	2150	3004	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Herbidospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009901565.1	s__Herbidospora solisilvae	89.5154	2244	3004	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Herbidospora	95.0	95.93	95.93	0.91	0.91	2	-
GCF_001570585.1	s__Herbidospora daliensis	89.3111	2270	3004	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Herbidospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001570525.1	s__Herbidospora sakaeratensis	89.2741	2288	3004	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Herbidospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900156315.1	s__Microbispora rosea	79.671	1210	3004	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Microbispora	95.0	99.16	98.33	0.97	0.94	3	-
--------------------------------------------------------------------------------
[2024-01-24 12:16:15,327] [INFO] GTDB search result was written to GCF_001570545.1_ASM157054v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:16:15,328] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:16:15,331] [INFO] DFAST_QC result json was written to GCF_001570545.1_ASM157054v1_genomic.fna/dqc_result.json
[2024-01-24 12:16:15,331] [INFO] DFAST_QC completed!
[2024-01-24 12:16:15,331] [INFO] Total running time: 0h2m46s