[2024-01-24 14:03:07,956] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:03:07,958] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:03:07,958] [INFO] DQC Reference Directory: /var/lib/cwl/stg1e31cad1-b50d-4429-9d1e-689e6cf4e5eb/dqc_reference
[2024-01-24 14:03:09,282] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:03:09,283] [INFO] Task started: Prodigal
[2024-01-24 14:03:09,283] [INFO] Running command: gunzip -c /var/lib/cwl/stgafad5814-0b9d-4c38-a2a6-785c2685f848/GCF_014650115.1_ASM1465011v1_genomic.fna.gz | prodigal -d GCF_014650115.1_ASM1465011v1_genomic.fna/cds.fna -a GCF_014650115.1_ASM1465011v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:03:41,474] [INFO] Task succeeded: Prodigal
[2024-01-24 14:03:41,475] [INFO] Task started: HMMsearch
[2024-01-24 14:03:41,475] [INFO] Running command: hmmsearch --tblout GCF_014650115.1_ASM1465011v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1e31cad1-b50d-4429-9d1e-689e6cf4e5eb/dqc_reference/reference_markers.hmm GCF_014650115.1_ASM1465011v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:03:41,863] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:03:41,865] [INFO] Found 6/6 markers.
[2024-01-24 14:03:41,943] [INFO] Query marker FASTA was written to GCF_014650115.1_ASM1465011v1_genomic.fna/markers.fasta
[2024-01-24 14:03:41,944] [INFO] Task started: Blastn
[2024-01-24 14:03:41,944] [INFO] Running command: blastn -query GCF_014650115.1_ASM1465011v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1e31cad1-b50d-4429-9d1e-689e6cf4e5eb/dqc_reference/reference_markers.fasta -out GCF_014650115.1_ASM1465011v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:03:43,320] [INFO] Task succeeded: Blastn
[2024-01-24 14:03:43,325] [INFO] Selected 12 target genomes.
[2024-01-24 14:03:43,326] [INFO] Target genome list was writen to GCF_014650115.1_ASM1465011v1_genomic.fna/target_genomes.txt
[2024-01-24 14:03:43,333] [INFO] Task started: fastANI
[2024-01-24 14:03:43,333] [INFO] Running command: fastANI --query /var/lib/cwl/stgafad5814-0b9d-4c38-a2a6-785c2685f848/GCF_014650115.1_ASM1465011v1_genomic.fna.gz --refList GCF_014650115.1_ASM1465011v1_genomic.fna/target_genomes.txt --output GCF_014650115.1_ASM1465011v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:04:14,048] [INFO] Task succeeded: fastANI
[2024-01-24 14:04:14,049] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1e31cad1-b50d-4429-9d1e-689e6cf4e5eb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:04:14,050] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1e31cad1-b50d-4429-9d1e-689e6cf4e5eb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:04:14,060] [INFO] Found 12 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 14:04:14,060] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 14:04:14,060] [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 olivaceoviridis	strain=JCM 4499	GCA_014650115.1	1921	1921	type	True	100.0	3186	3190	95	inconclusive
Streptomyces canarius	strain=JCM 4733	GCA_014650735.1	285453	285453	type	True	97.3276	2844	3190	95	inconclusive
Streptomyces corchorusii	strain=DSM 40340	GCA_001514055.1	1903	1903	type	True	96.7142	2738	3190	95	inconclusive
Streptomyces spinosus	strain=SBTS01	GCA_020400655.1	2872623	2872623	type	True	93.8648	2430	3190	95	below_threshold
Streptomyces musisoli	strain=CH5-8	GCA_016741855.1	2802280	2802280	type	True	89.7245	2099	3190	95	below_threshold
Streptomyces echinatus	strain=JCM4574	GCA_020400685.1	67293	67293	type	True	89.709	2072	3190	95	below_threshold
Streptomyces achromogenes subsp. achromogenes	strain=NRRL B-2120	GCA_000720835.1	67256	67255	type	True	89.3243	1942	3190	95	below_threshold
Streptomyces lavenduligriseus	strain=NRRL ISP-5487	GCA_000718625.1	67315	67315	type	True	89.1254	1976	3190	95	below_threshold
Streptomyces barringtoniae	strain=JA03	GCA_020819595.1	2892029	2892029	type	True	88.0107	2007	3190	95	below_threshold
Streptomyces shenzhenensis subsp. oryzicola	strain=W18L9	GCA_013870495.1	2749088	943815	type	True	85.3506	1458	3190	95	below_threshold
Streptomyces shenzhenensis	strain=DSM 42034	GCA_021462265.1	943815	943815	type	True	85.1167	1952	3190	95	below_threshold
Streptomyces harenosi	strain=PRKS01-65	GCA_011008945.1	2697029	2697029	type	True	84.6827	1485	3190	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:04:14,062] [INFO] DFAST Taxonomy check result was written to GCF_014650115.1_ASM1465011v1_genomic.fna/tc_result.tsv
[2024-01-24 14:04:14,062] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:04:14,063] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:04:14,063] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1e31cad1-b50d-4429-9d1e-689e6cf4e5eb/dqc_reference/checkm_data
[2024-01-24 14:04:14,064] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:04:14,152] [INFO] Task started: CheckM
[2024-01-24 14:04:14,152] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014650115.1_ASM1465011v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014650115.1_ASM1465011v1_genomic.fna/checkm_input GCF_014650115.1_ASM1465011v1_genomic.fna/checkm_result
[2024-01-24 14:06:44,142] [INFO] Task succeeded: CheckM
[2024-01-24 14:06:44,143] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:06:44,185] [INFO] ===== Completeness check finished =====
[2024-01-24 14:06:44,186] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:06:44,186] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014650115.1_ASM1465011v1_genomic.fna/markers.fasta)
[2024-01-24 14:06:44,186] [INFO] Task started: Blastn
[2024-01-24 14:06:44,186] [INFO] Running command: blastn -query GCF_014650115.1_ASM1465011v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1e31cad1-b50d-4429-9d1e-689e6cf4e5eb/dqc_reference/reference_markers_gtdb.fasta -out GCF_014650115.1_ASM1465011v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:46,594] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:46,598] [INFO] Selected 8 target genomes.
[2024-01-24 14:06:46,598] [INFO] Target genome list was writen to GCF_014650115.1_ASM1465011v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:06:46,606] [INFO] Task started: fastANI
[2024-01-24 14:06:46,606] [INFO] Running command: fastANI --query /var/lib/cwl/stgafad5814-0b9d-4c38-a2a6-785c2685f848/GCF_014650115.1_ASM1465011v1_genomic.fna.gz --refList GCF_014650115.1_ASM1465011v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014650115.1_ASM1465011v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:07:07,333] [INFO] Task succeeded: fastANI
[2024-01-24 14:07:07,345] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:07:07,345] [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_014650115.1	s__Streptomyces olivaceoviridis	100.0	3186	3190	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.78	96.54	0.86	0.85	6	conclusive
GCF_002920615.1	s__Streptomyces sp002920615	94.7472	2423	3190	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.01	97.01	0.88	0.88	2	-
GCF_013046785.1	s__Streptomyces sp013046785	94.272	2241	3190	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000716535.1	s__Streptomyces flaveolus_A	93.8916	2507	3190	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	90.8597	2072	3190	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002155905.1	s__Streptomyces tricolor	90.6241	1765	3190	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.81	98.00	0.86	0.72	5	-
GCF_000718775.1	s__Streptomyces sp000718775	89.5187	2018	3190	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016741775.1	s__Streptomyces actinomycinicus	89.1426	2044	3190	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 14:07:07,347] [INFO] GTDB search result was written to GCF_014650115.1_ASM1465011v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:07:07,347] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:07:07,350] [INFO] DFAST_QC result json was written to GCF_014650115.1_ASM1465011v1_genomic.fna/dqc_result.json
[2024-01-24 14:07:07,351] [INFO] DFAST_QC completed!
[2024-01-24 14:07:07,351] [INFO] Total running time: 0h3m59s