[2024-01-24 13:22:11,378] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:22:11,380] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:22:11,380] [INFO] DQC Reference Directory: /var/lib/cwl/stgde3ca226-c6fa-4e35-a0b0-642ce884f22c/dqc_reference
[2024-01-24 13:22:13,354] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:22:13,357] [INFO] Task started: Prodigal
[2024-01-24 13:22:13,357] [INFO] Running command: gunzip -c /var/lib/cwl/stgff8189f3-f3e2-4a58-a9bb-a430d2890df3/GCF_013046785.1_ASM1304678v1_genomic.fna.gz | prodigal -d GCF_013046785.1_ASM1304678v1_genomic.fna/cds.fna -a GCF_013046785.1_ASM1304678v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:22:34,106] [INFO] Task succeeded: Prodigal
[2024-01-24 13:22:34,106] [INFO] Task started: HMMsearch
[2024-01-24 13:22:34,106] [INFO] Running command: hmmsearch --tblout GCF_013046785.1_ASM1304678v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgde3ca226-c6fa-4e35-a0b0-642ce884f22c/dqc_reference/reference_markers.hmm GCF_013046785.1_ASM1304678v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:22:34,532] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:22:34,533] [INFO] Found 6/6 markers.
[2024-01-24 13:22:34,639] [INFO] Query marker FASTA was written to GCF_013046785.1_ASM1304678v1_genomic.fna/markers.fasta
[2024-01-24 13:22:34,639] [INFO] Task started: Blastn
[2024-01-24 13:22:34,639] [INFO] Running command: blastn -query GCF_013046785.1_ASM1304678v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgde3ca226-c6fa-4e35-a0b0-642ce884f22c/dqc_reference/reference_markers.fasta -out GCF_013046785.1_ASM1304678v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:22:35,921] [INFO] Task succeeded: Blastn
[2024-01-24 13:22:35,923] [INFO] Selected 12 target genomes.
[2024-01-24 13:22:35,924] [INFO] Target genome list was writen to GCF_013046785.1_ASM1304678v1_genomic.fna/target_genomes.txt
[2024-01-24 13:22:35,927] [INFO] Task started: fastANI
[2024-01-24 13:22:35,927] [INFO] Running command: fastANI --query /var/lib/cwl/stgff8189f3-f3e2-4a58-a9bb-a430d2890df3/GCF_013046785.1_ASM1304678v1_genomic.fna.gz --refList GCF_013046785.1_ASM1304678v1_genomic.fna/target_genomes.txt --output GCF_013046785.1_ASM1304678v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:23:04,617] [INFO] Task succeeded: fastANI
[2024-01-24 13:23:04,617] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgde3ca226-c6fa-4e35-a0b0-642ce884f22c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:23:04,618] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgde3ca226-c6fa-4e35-a0b0-642ce884f22c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:23:04,626] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:23:04,626] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:23:04,627] [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 spinosus	strain=SBTS01	GCA_020400655.1	2872623	2872623	type	True	99.2047	2437	2605	95	conclusive
Streptomyces corchorusii	strain=DSM 40340	GCA_001514055.1	1903	1903	type	True	94.4637	2267	2605	95	below_threshold
Streptomyces canarius	strain=JCM 4733	GCA_014650735.1	285453	285453	type	True	94.4437	2206	2605	95	below_threshold
Streptomyces olivaceoviridis	strain=JCM 4499	GCA_014650115.1	1921	1921	type	True	94.3945	2227	2605	95	below_threshold
Streptomyces echinatus	strain=JCM4574	GCA_020400685.1	67293	67293	type	True	89.8382	1973	2605	95	below_threshold
Streptomyces achromogenes subsp. achromogenes	strain=NRRL B-2120	GCA_000720835.1	67256	67255	type	True	89.545	1851	2605	95	below_threshold
Streptomyces lavenduligriseus	strain=NRRL ISP-5487	GCA_000718625.1	67315	67315	type	True	89.5301	1848	2605	95	below_threshold
Streptomyces rubradiris	strain=NBRC 14000	GCA_016860525.1	285531	285531	type	True	89.4021	1889	2605	95	below_threshold
Streptomyces barringtoniae	strain=JA03	GCA_020819595.1	2892029	2892029	type	True	88.2325	1897	2605	95	below_threshold
Streptomyces sennicomposti	strain=RCPT1-4	GCA_019890635.1	2873384	2873384	type	True	85.4892	1558	2605	95	below_threshold
Streptomyces lomondensis	strain=DSM 41428	GCA_021440105.1	68229	68229	type	True	85.077	1700	2605	95	below_threshold
Streptomyces harenosi	strain=PRKS01-65	GCA_011008945.1	2697029	2697029	type	True	84.9496	1432	2605	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:23:04,630] [INFO] DFAST Taxonomy check result was written to GCF_013046785.1_ASM1304678v1_genomic.fna/tc_result.tsv
[2024-01-24 13:23:04,630] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:23:04,630] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:23:04,631] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgde3ca226-c6fa-4e35-a0b0-642ce884f22c/dqc_reference/checkm_data
[2024-01-24 13:23:04,631] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:23:04,704] [INFO] Task started: CheckM
[2024-01-24 13:23:04,704] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013046785.1_ASM1304678v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013046785.1_ASM1304678v1_genomic.fna/checkm_input GCF_013046785.1_ASM1304678v1_genomic.fna/checkm_result
[2024-01-24 13:25:27,158] [INFO] Task succeeded: CheckM
[2024-01-24 13:25:27,159] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 5.21%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:25:27,175] [INFO] ===== Completeness check finished =====
[2024-01-24 13:25:27,176] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:25:27,176] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013046785.1_ASM1304678v1_genomic.fna/markers.fasta)
[2024-01-24 13:25:27,176] [INFO] Task started: Blastn
[2024-01-24 13:25:27,176] [INFO] Running command: blastn -query GCF_013046785.1_ASM1304678v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgde3ca226-c6fa-4e35-a0b0-642ce884f22c/dqc_reference/reference_markers_gtdb.fasta -out GCF_013046785.1_ASM1304678v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:25:29,276] [INFO] Task succeeded: Blastn
[2024-01-24 13:25:29,278] [INFO] Selected 8 target genomes.
[2024-01-24 13:25:29,278] [INFO] Target genome list was writen to GCF_013046785.1_ASM1304678v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:25:29,282] [INFO] Task started: fastANI
[2024-01-24 13:25:29,282] [INFO] Running command: fastANI --query /var/lib/cwl/stgff8189f3-f3e2-4a58-a9bb-a430d2890df3/GCF_013046785.1_ASM1304678v1_genomic.fna.gz --refList GCF_013046785.1_ASM1304678v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013046785.1_ASM1304678v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:25:49,235] [INFO] Task succeeded: fastANI
[2024-01-24 13:25:49,242] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:25:49,242] [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_013046785.1	s__Streptomyces sp013046785	100.0	2605	2605	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002920615.1	s__Streptomyces sp002920615	94.4459	2193	2605	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.01	97.01	0.88	0.88	2	-
GCF_014650115.1	s__Streptomyces olivaceoviridis	94.4047	2226	2605	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.78	96.54	0.86	0.85	6	-
GCF_000716535.1	s__Streptomyces flaveolus_A	93.8521	2198	2605	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.26	98.84	0.94	0.91	9	-
GCF_017526105.1	s__Streptomyces cyanogenus	90.9067	2008	2605	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014648635.1	s__Streptomyces cinerochromogenes	90.7229	2056	2605	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014649295.1	s__Streptomyces libani_A	90.3639	1933	2605	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014203595.1	s__Streptomyces echinatus	89.832	2009	2605	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 13:25:49,243] [INFO] GTDB search result was written to GCF_013046785.1_ASM1304678v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:25:49,243] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:25:49,246] [INFO] DFAST_QC result json was written to GCF_013046785.1_ASM1304678v1_genomic.fna/dqc_result.json
[2024-01-24 13:25:49,246] [INFO] DFAST_QC completed!
[2024-01-24 13:25:49,246] [INFO] Total running time: 0h3m38s