[2024-01-24 12:45:10,290] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:45:10,293] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:45:10,293] [INFO] DQC Reference Directory: /var/lib/cwl/stgfde6095d-af64-45e3-88d6-0ed766e6881c/dqc_reference
[2024-01-24 12:45:13,084] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:45:13,086] [INFO] Task started: Prodigal
[2024-01-24 12:45:13,086] [INFO] Running command: gunzip -c /var/lib/cwl/stg887ba6a1-3166-4264-ad8a-d3aa832f49c5/GCF_002891295.1_ASM289129v1_genomic.fna.gz | prodigal -d GCF_002891295.1_ASM289129v1_genomic.fna/cds.fna -a GCF_002891295.1_ASM289129v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:45:38,744] [INFO] Task succeeded: Prodigal
[2024-01-24 12:45:38,745] [INFO] Task started: HMMsearch
[2024-01-24 12:45:38,745] [INFO] Running command: hmmsearch --tblout GCF_002891295.1_ASM289129v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfde6095d-af64-45e3-88d6-0ed766e6881c/dqc_reference/reference_markers.hmm GCF_002891295.1_ASM289129v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:45:39,078] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:45:39,080] [INFO] Found 6/6 markers.
[2024-01-24 12:45:39,147] [INFO] Query marker FASTA was written to GCF_002891295.1_ASM289129v1_genomic.fna/markers.fasta
[2024-01-24 12:45:39,147] [INFO] Task started: Blastn
[2024-01-24 12:45:39,148] [INFO] Running command: blastn -query GCF_002891295.1_ASM289129v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfde6095d-af64-45e3-88d6-0ed766e6881c/dqc_reference/reference_markers.fasta -out GCF_002891295.1_ASM289129v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:45:40,503] [INFO] Task succeeded: Blastn
[2024-01-24 12:45:40,506] [INFO] Selected 9 target genomes.
[2024-01-24 12:45:40,507] [INFO] Target genome list was writen to GCF_002891295.1_ASM289129v1_genomic.fna/target_genomes.txt
[2024-01-24 12:45:40,514] [INFO] Task started: fastANI
[2024-01-24 12:45:40,514] [INFO] Running command: fastANI --query /var/lib/cwl/stg887ba6a1-3166-4264-ad8a-d3aa832f49c5/GCF_002891295.1_ASM289129v1_genomic.fna.gz --refList GCF_002891295.1_ASM289129v1_genomic.fna/target_genomes.txt --output GCF_002891295.1_ASM289129v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:46:05,241] [INFO] Task succeeded: fastANI
[2024-01-24 12:46:05,242] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfde6095d-af64-45e3-88d6-0ed766e6881c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:46:05,242] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfde6095d-af64-45e3-88d6-0ed766e6881c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:46:05,251] [INFO] Found 9 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 12:46:05,252] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:46:05,252] [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 eurocidicus	strain=ATCC 27428	GCA_002891295.1	66423	66423	type	True	100.0	2633	2635	95	conclusive
Streptomyces eurocidicus	strain=CECT 3259	GCA_014203505.1	66423	66423	type	True	99.9745	2584	2635	95	conclusive
Streptomyces eurocidicus	strain=NRRL ISP-5604	GCA_015475845.1	66423	66423	type	True	99.9606	2568	2635	95	conclusive
Streptomyces albireticuli	strain=NRRL B1670	GCA_021228125.1	1940	1940	type	True	93.0025	2236	2635	95	below_threshold
Streptomyces albireticuli	strain=NRRL B-1670	GCA_002286695.1	1940	1940	type	True	92.9709	1912	2635	95	below_threshold
Streptomyces rapamycinicus	strain=NRRL 5491	GCA_024298965.1	1226757	1226757	type	True	81.256	1423	2635	95	below_threshold
Streptomyces harenosi	strain=PRKS01-65	GCA_011008945.1	2697029	2697029	type	True	80.899	1160	2635	95	below_threshold
Streptomyces spinosus	strain=SBTS01	GCA_020400655.1	2872623	2872623	type	True	80.7473	1262	2635	95	below_threshold
Streptomyces justiciae	strain=3R004	GCA_015163075.1	2780140	2780140	type	True	80.453	1276	2635	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:46:05,254] [INFO] DFAST Taxonomy check result was written to GCF_002891295.1_ASM289129v1_genomic.fna/tc_result.tsv
[2024-01-24 12:46:05,254] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:46:05,254] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:46:05,255] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfde6095d-af64-45e3-88d6-0ed766e6881c/dqc_reference/checkm_data
[2024-01-24 12:46:05,256] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:46:05,328] [INFO] Task started: CheckM
[2024-01-24 12:46:05,329] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002891295.1_ASM289129v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002891295.1_ASM289129v1_genomic.fna/checkm_input GCF_002891295.1_ASM289129v1_genomic.fna/checkm_result
[2024-01-24 12:47:27,005] [INFO] Task succeeded: CheckM
[2024-01-24 12:47:27,006] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 9.38%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:47:27,037] [INFO] ===== Completeness check finished =====
[2024-01-24 12:47:27,037] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:47:27,038] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002891295.1_ASM289129v1_genomic.fna/markers.fasta)
[2024-01-24 12:47:27,038] [INFO] Task started: Blastn
[2024-01-24 12:47:27,038] [INFO] Running command: blastn -query GCF_002891295.1_ASM289129v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfde6095d-af64-45e3-88d6-0ed766e6881c/dqc_reference/reference_markers_gtdb.fasta -out GCF_002891295.1_ASM289129v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:47:29,232] [INFO] Task succeeded: Blastn
[2024-01-24 12:47:29,237] [INFO] Selected 9 target genomes.
[2024-01-24 12:47:29,237] [INFO] Target genome list was writen to GCF_002891295.1_ASM289129v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:47:29,245] [INFO] Task started: fastANI
[2024-01-24 12:47:29,245] [INFO] Running command: fastANI --query /var/lib/cwl/stg887ba6a1-3166-4264-ad8a-d3aa832f49c5/GCF_002891295.1_ASM289129v1_genomic.fna.gz --refList GCF_002891295.1_ASM289129v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002891295.1_ASM289129v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:47:53,490] [INFO] Task succeeded: fastANI
[2024-01-24 12:47:53,503] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:47:53,503] [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_002891295.1	s__Streptomyces eurocidicus	100.0	2633	2635	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.99	99.98	1.00	1.00	3	conclusive
GCF_002192455.1	s__Streptomyces albireticuli_B	93.3329	2231	2635	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002286695.1	s__Streptomyces albireticuli	92.9709	1912	2635	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018614525.1	s__Streptomyces sp018614525	87.489	1588	2635	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003391135.1	s__Streptomyces olivoreticuli	86.593	1781	2635	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001445655.1	s__Streptomyces roseifaciens	85.9233	1762	2635	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.65	95.65	0.88	0.88	2	-
GCF_017876625.1	s__Streptomyces syringium	85.5792	1660	2635	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.60	99.60	0.98	0.98	2	-
GCF_014203545.1	s__Streptomyces netropsis	85.5744	1659	2635	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.99	99.99	1.00	1.00	2	-
GCF_017916255.1	s__Streptomyces mobaraensis	83.3269	1510	2635	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.59	99.19	0.96	0.92	3	-
--------------------------------------------------------------------------------
[2024-01-24 12:47:53,505] [INFO] GTDB search result was written to GCF_002891295.1_ASM289129v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:47:53,505] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:47:53,509] [INFO] DFAST_QC result json was written to GCF_002891295.1_ASM289129v1_genomic.fna/dqc_result.json
[2024-01-24 12:47:53,509] [INFO] DFAST_QC completed!
[2024-01-24 12:47:53,509] [INFO] Total running time: 0h2m43s