[2024-01-25 20:17:50,593] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:17:50,594] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:17:50,594] [INFO] DQC Reference Directory: /var/lib/cwl/stg3776cfec-abbd-4e3c-9860-c61776b437ec/dqc_reference
[2024-01-25 20:17:51,716] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:17:51,717] [INFO] Task started: Prodigal
[2024-01-25 20:17:51,717] [INFO] Running command: gunzip -c /var/lib/cwl/stgb5bbf0c8-2ca8-43ce-b942-e1ba94657bfa/GCF_015356865.1_ASM1535686v1_genomic.fna.gz | prodigal -d GCF_015356865.1_ASM1535686v1_genomic.fna/cds.fna -a GCF_015356865.1_ASM1535686v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:18:24,318] [INFO] Task succeeded: Prodigal
[2024-01-25 20:18:24,318] [INFO] Task started: HMMsearch
[2024-01-25 20:18:24,318] [INFO] Running command: hmmsearch --tblout GCF_015356865.1_ASM1535686v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3776cfec-abbd-4e3c-9860-c61776b437ec/dqc_reference/reference_markers.hmm GCF_015356865.1_ASM1535686v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:18:24,958] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:18:24,959] [INFO] Found 6/6 markers.
[2024-01-25 20:18:25,057] [INFO] Query marker FASTA was written to GCF_015356865.1_ASM1535686v1_genomic.fna/markers.fasta
[2024-01-25 20:18:25,057] [INFO] Task started: Blastn
[2024-01-25 20:18:25,057] [INFO] Running command: blastn -query GCF_015356865.1_ASM1535686v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3776cfec-abbd-4e3c-9860-c61776b437ec/dqc_reference/reference_markers.fasta -out GCF_015356865.1_ASM1535686v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:18:26,453] [INFO] Task succeeded: Blastn
[2024-01-25 20:18:26,457] [INFO] Selected 14 target genomes.
[2024-01-25 20:18:26,457] [INFO] Target genome list was writen to GCF_015356865.1_ASM1535686v1_genomic.fna/target_genomes.txt
[2024-01-25 20:18:26,465] [INFO] Task started: fastANI
[2024-01-25 20:18:26,465] [INFO] Running command: fastANI --query /var/lib/cwl/stgb5bbf0c8-2ca8-43ce-b942-e1ba94657bfa/GCF_015356865.1_ASM1535686v1_genomic.fna.gz --refList GCF_015356865.1_ASM1535686v1_genomic.fna/target_genomes.txt --output GCF_015356865.1_ASM1535686v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:18:57,089] [INFO] Task succeeded: fastANI
[2024-01-25 20:18:57,090] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3776cfec-abbd-4e3c-9860-c61776b437ec/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:18:57,090] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3776cfec-abbd-4e3c-9860-c61776b437ec/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:18:57,099] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:18:57,100] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:18:57,100] [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
Catenulispora pinisilvae	strain=NH11	GCA_015356865.1	2705253	2705253	type	True	100.0	3511	3535	95	conclusive
Catenulispora pinistramenti	strain=NL8	GCA_018274385.1	2705254	2705254	type	True	94.7514	2809	3535	95	below_threshold
Catenulispora rubra	strain=DSM 44948	GCA_015356825.1	280293	280293	type	True	86.9882	2221	3535	95	below_threshold
Catenulispora acidiphila	strain=DSM 44928	GCA_000024025.1	304895	304895	type	True	86.4572	2185	3535	95	below_threshold
Actinocrinis puniceicyclus	strain=DSM 45618	GCA_018283645.1	977794	977794	type	True	77.6668	708	3535	95	below_threshold
Streptomyces parmotrematis	strain=Ptm05	GCA_019890615.1	2873249	2873249	type	True	77.4189	798	3535	95	below_threshold
Streptacidiphilus jiangxiensis	strain=CGMCC 4.1857	GCA_900109465.1	235985	235985	type	True	77.1325	952	3535	95	below_threshold
Kitasatospora setae	strain=KM-6054	GCA_000269985.1	2066	2066	type	True	76.9989	1039	3535	95	below_threshold
Streptomyces barringtoniae	strain=JA03	GCA_020819595.1	2892029	2892029	type	True	76.8926	824	3535	95	below_threshold
Streptomyces spinosus	strain=SBTS01	GCA_020400655.1	2872623	2872623	type	True	76.886	826	3535	95	below_threshold
Streptomyces sparsogenes	strain=ATCC 25498	GCA_001704635.1	67365	67365	type	True	76.8565	803	3535	95	below_threshold
Streptomyces justiciae	strain=3R004	GCA_015163075.1	2780140	2780140	type	True	76.5539	828	3535	95	below_threshold
Streptomyces deccanensis	strain=KCTC 19241	GCA_022385335.1	424188	424188	type	True	76.5434	742	3535	95	below_threshold
Actinokineospora enzanensis	strain=DSM 44649	GCA_000374445.1	155975	155975	type	True	76.2137	662	3535	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:18:57,101] [INFO] DFAST Taxonomy check result was written to GCF_015356865.1_ASM1535686v1_genomic.fna/tc_result.tsv
[2024-01-25 20:18:57,101] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:18:57,101] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:18:57,102] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3776cfec-abbd-4e3c-9860-c61776b437ec/dqc_reference/checkm_data
[2024-01-25 20:18:57,102] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:18:57,204] [INFO] Task started: CheckM
[2024-01-25 20:18:57,204] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_015356865.1_ASM1535686v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_015356865.1_ASM1535686v1_genomic.fna/checkm_input GCF_015356865.1_ASM1535686v1_genomic.fna/checkm_result
[2024-01-25 20:20:32,632] [INFO] Task succeeded: CheckM
[2024-01-25 20:20:32,633] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 9.38%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:20:32,661] [INFO] ===== Completeness check finished =====
[2024-01-25 20:20:32,661] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:20:32,662] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_015356865.1_ASM1535686v1_genomic.fna/markers.fasta)
[2024-01-25 20:20:32,662] [INFO] Task started: Blastn
[2024-01-25 20:20:32,662] [INFO] Running command: blastn -query GCF_015356865.1_ASM1535686v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3776cfec-abbd-4e3c-9860-c61776b437ec/dqc_reference/reference_markers_gtdb.fasta -out GCF_015356865.1_ASM1535686v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:20:34,786] [INFO] Task succeeded: Blastn
[2024-01-25 20:20:34,789] [INFO] Selected 6 target genomes.
[2024-01-25 20:20:34,789] [INFO] Target genome list was writen to GCF_015356865.1_ASM1535686v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:20:34,796] [INFO] Task started: fastANI
[2024-01-25 20:20:34,796] [INFO] Running command: fastANI --query /var/lib/cwl/stgb5bbf0c8-2ca8-43ce-b942-e1ba94657bfa/GCF_015356865.1_ASM1535686v1_genomic.fna.gz --refList GCF_015356865.1_ASM1535686v1_genomic.fna/target_genomes_gtdb.txt --output GCF_015356865.1_ASM1535686v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:20:54,233] [INFO] Task succeeded: fastANI
[2024-01-25 20:20:54,239] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:20:54,239] [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_015356865.1	s__Catenulispora pinisilvae	100.0	3511	3535	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Catenulisporaceae;g__Catenulispora	95.0	99.32	99.32	0.94	0.94	2	conclusive
GCF_018274385.1	s__Catenulispora sp018274385	94.7516	2811	3535	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Catenulisporaceae;g__Catenulispora	95.0	99.51	99.51	0.94	0.94	2	-
GCF_015356825.1	s__Catenulispora rubra	86.9643	2226	3535	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Catenulisporaceae;g__Catenulispora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000024025.1	s__Catenulispora acidiphila	86.4462	2187	3535	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Catenulisporaceae;g__Catenulispora	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013361685.1	s__Catenulispora sp013361685	83.6187	1504	3535	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Catenulisporaceae;g__Catenulispora	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013362315.1	s__Catenulispora sp013362315	83.0295	1340	3535	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Catenulisporaceae;g__Catenulispora	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:20:54,240] [INFO] GTDB search result was written to GCF_015356865.1_ASM1535686v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:20:54,245] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:20:54,248] [INFO] DFAST_QC result json was written to GCF_015356865.1_ASM1535686v1_genomic.fna/dqc_result.json
[2024-01-25 20:20:54,248] [INFO] DFAST_QC completed!
[2024-01-25 20:20:54,248] [INFO] Total running time: 0h3m4s