[2024-01-25 19:07:20,652] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:07:20,653] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:07:20,653] [INFO] DQC Reference Directory: /var/lib/cwl/stg84af143e-d8de-44b0-adec-5a95c58b453a/dqc_reference
[2024-01-25 19:07:21,818] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:07:21,818] [INFO] Task started: Prodigal
[2024-01-25 19:07:21,819] [INFO] Running command: gunzip -c /var/lib/cwl/stgaf432c99-a5ff-4df9-8268-9cfb982e2533/GCF_000720455.1_ASM72045v1_genomic.fna.gz | prodigal -d GCF_000720455.1_ASM72045v1_genomic.fna/cds.fna -a GCF_000720455.1_ASM72045v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:07:41,474] [INFO] Task succeeded: Prodigal
[2024-01-25 19:07:41,475] [INFO] Task started: HMMsearch
[2024-01-25 19:07:41,475] [INFO] Running command: hmmsearch --tblout GCF_000720455.1_ASM72045v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg84af143e-d8de-44b0-adec-5a95c58b453a/dqc_reference/reference_markers.hmm GCF_000720455.1_ASM72045v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:07:41,784] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:07:41,785] [INFO] Found 6/6 markers.
[2024-01-25 19:07:41,845] [INFO] Query marker FASTA was written to GCF_000720455.1_ASM72045v1_genomic.fna/markers.fasta
[2024-01-25 19:07:41,845] [INFO] Task started: Blastn
[2024-01-25 19:07:41,845] [INFO] Running command: blastn -query GCF_000720455.1_ASM72045v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg84af143e-d8de-44b0-adec-5a95c58b453a/dqc_reference/reference_markers.fasta -out GCF_000720455.1_ASM72045v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:07:43,106] [INFO] Task succeeded: Blastn
[2024-01-25 19:07:43,109] [INFO] Selected 14 target genomes.
[2024-01-25 19:07:43,109] [INFO] Target genome list was writen to GCF_000720455.1_ASM72045v1_genomic.fna/target_genomes.txt
[2024-01-25 19:07:43,120] [INFO] Task started: fastANI
[2024-01-25 19:07:43,120] [INFO] Running command: fastANI --query /var/lib/cwl/stgaf432c99-a5ff-4df9-8268-9cfb982e2533/GCF_000720455.1_ASM72045v1_genomic.fna.gz --refList GCF_000720455.1_ASM72045v1_genomic.fna/target_genomes.txt --output GCF_000720455.1_ASM72045v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:08:13,734] [INFO] Task succeeded: fastANI
[2024-01-25 19:08:13,735] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg84af143e-d8de-44b0-adec-5a95c58b453a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:08:13,736] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg84af143e-d8de-44b0-adec-5a95c58b453a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:08:13,746] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:08:13,746] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:08:13,746] [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 virginiae	strain=NRRL ISP-5094	GCA_000720455.1	1961	1961	suspected-type	True	100.0	2717	2721	95	conclusive
Streptomyces amritsarensis	strain=MTCC 11845	GCA_001953875.1	681158	681158	type	True	92.55	2062	2721	95	below_threshold
Streptomyces yangpuensis	strain=fd2-tb	GCA_001005295.1	1648182	1648182	type	True	92.4934	2140	2721	95	below_threshold
Streptomyces nojiriensis	strain=JCM 3382	GCA_014648615.1	66374	66374	type	True	89.6118	2093	2721	95	below_threshold
Streptomyces nojiriensis	strain=JCM 3382	GCA_017639205.1	66374	66374	type	True	89.5948	2129	2721	95	below_threshold
Streptomyces spororaveus	strain=NBRC 15456	GCA_016755875.1	284039	284039	type	True	89.5733	2089	2721	95	below_threshold
Streptomyces avidinii	strain=DSM 40526	GCA_017874515.1	1895	1895	type	True	89.3381	2092	2721	95	below_threshold
Streptomyces avidinii	strain=JCM 4726	GCA_014650695.1	1895	1895	type	True	89.3361	2086	2721	95	below_threshold
Streptomyces goshikiensis	strain=JCM 4640	GCA_014650555.1	1942	1942	type	True	87.2294	1812	2721	95	below_threshold
Streptomyces nymphaeiformis	strain=SFB5A	GCA_014203895.1	2663842	2663842	type	True	82.2779	1504	2721	95	below_threshold
Streptomyces sennicomposti	strain=RCPT1-4	GCA_019890635.1	2873384	2873384	type	True	81.265	1255	2721	95	below_threshold
Streptomyces harenosi	strain=PRKS01-65	GCA_011008945.1	2697029	2697029	type	True	81.1558	1179	2721	95	below_threshold
Streptomyces panaciradicis	strain=NBRC 109811	GCA_023516615.1	1470261	1470261	type	True	80.9908	1327	2721	95	below_threshold
Streptomyces blattellae	strain=TRM63209	GCA_009709555.1	2569855	2569855	type	True	80.6764	1179	2721	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:08:13,752] [INFO] DFAST Taxonomy check result was written to GCF_000720455.1_ASM72045v1_genomic.fna/tc_result.tsv
[2024-01-25 19:08:13,752] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:08:13,753] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:08:13,753] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg84af143e-d8de-44b0-adec-5a95c58b453a/dqc_reference/checkm_data
[2024-01-25 19:08:13,754] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:08:13,835] [INFO] Task started: CheckM
[2024-01-25 19:08:13,835] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000720455.1_ASM72045v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000720455.1_ASM72045v1_genomic.fna/checkm_input GCF_000720455.1_ASM72045v1_genomic.fna/checkm_result
[2024-01-25 19:10:00,965] [INFO] Task succeeded: CheckM
[2024-01-25 19:10:00,966] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 5.21%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:10:00,995] [INFO] ===== Completeness check finished =====
[2024-01-25 19:10:00,995] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:10:00,996] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000720455.1_ASM72045v1_genomic.fna/markers.fasta)
[2024-01-25 19:10:00,996] [INFO] Task started: Blastn
[2024-01-25 19:10:00,996] [INFO] Running command: blastn -query GCF_000720455.1_ASM72045v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg84af143e-d8de-44b0-adec-5a95c58b453a/dqc_reference/reference_markers_gtdb.fasta -out GCF_000720455.1_ASM72045v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:10:03,158] [INFO] Task succeeded: Blastn
[2024-01-25 19:10:03,161] [INFO] Selected 10 target genomes.
[2024-01-25 19:10:03,161] [INFO] Target genome list was writen to GCF_000720455.1_ASM72045v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:10:03,173] [INFO] Task started: fastANI
[2024-01-25 19:10:03,174] [INFO] Running command: fastANI --query /var/lib/cwl/stgaf432c99-a5ff-4df9-8268-9cfb982e2533/GCF_000720455.1_ASM72045v1_genomic.fna.gz --refList GCF_000720455.1_ASM72045v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000720455.1_ASM72045v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:10:27,151] [INFO] Task succeeded: fastANI
[2024-01-25 19:10:27,158] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:10:27,158] [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_014648795.1	s__Streptomyces cinnamonensis	96.7054	2438	2721	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.18	96.61	0.93	0.87	24	conclusive
GCF_000725555.1	s__Streptomyces erythrochromogenes	93.607	2074	2721	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.80	95.80	0.85	0.85	2	-
GCF_001941845.1	s__Streptomyces sp001941845	93.4266	2083	2721	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.45	99.45	0.96	0.96	2	-
GCF_001953875.1	s__Streptomyces amritsarensis	92.5589	2061	2721	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.17	98.97	0.95	0.93	4	-
GCF_001005295.1	s__Streptomyces yangpuensis	92.5114	2138	2721	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.05	95.28	0.86	0.84	3	-
GCF_000719345.1	s__Streptomyces sp000719345	92.1621	2079	2721	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000612545.1	s__Streptomyces sp000612545	91.7042	1992	2721	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000720115.1	s__Streptomyces sp000720115	89.8645	2068	2721	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008642275.1	s__Streptomyces venezuelae_E	89.6568	1957	2721	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016755875.1	s__Streptomyces spororaveus	89.6057	2084	2721	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:10:27,159] [INFO] GTDB search result was written to GCF_000720455.1_ASM72045v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:10:27,160] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:10:27,163] [INFO] DFAST_QC result json was written to GCF_000720455.1_ASM72045v1_genomic.fna/dqc_result.json
[2024-01-25 19:10:27,163] [INFO] DFAST_QC completed!
[2024-01-25 19:10:27,163] [INFO] Total running time: 0h3m7s