[2024-01-24 14:23:04,623] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:23:04,625] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:23:04,625] [INFO] DQC Reference Directory: /var/lib/cwl/stgdc23dcae-bfdf-42a8-b05e-9a5f0e0d6322/dqc_reference
[2024-01-24 14:23:06,011] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:23:06,012] [INFO] Task started: Prodigal
[2024-01-24 14:23:06,012] [INFO] Running command: gunzip -c /var/lib/cwl/stg7a8b7cca-f434-40dd-8d59-7e8b595ba40d/GCF_017874515.1_ASM1787451v1_genomic.fna.gz | prodigal -d GCF_017874515.1_ASM1787451v1_genomic.fna/cds.fna -a GCF_017874515.1_ASM1787451v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:23:30,816] [INFO] Task succeeded: Prodigal
[2024-01-24 14:23:30,816] [INFO] Task started: HMMsearch
[2024-01-24 14:23:30,816] [INFO] Running command: hmmsearch --tblout GCF_017874515.1_ASM1787451v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdc23dcae-bfdf-42a8-b05e-9a5f0e0d6322/dqc_reference/reference_markers.hmm GCF_017874515.1_ASM1787451v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:23:31,340] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:23:31,341] [INFO] Found 6/6 markers.
[2024-01-24 14:23:31,415] [INFO] Query marker FASTA was written to GCF_017874515.1_ASM1787451v1_genomic.fna/markers.fasta
[2024-01-24 14:23:31,415] [INFO] Task started: Blastn
[2024-01-24 14:23:31,415] [INFO] Running command: blastn -query GCF_017874515.1_ASM1787451v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdc23dcae-bfdf-42a8-b05e-9a5f0e0d6322/dqc_reference/reference_markers.fasta -out GCF_017874515.1_ASM1787451v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:23:32,809] [INFO] Task succeeded: Blastn
[2024-01-24 14:23:32,812] [INFO] Selected 16 target genomes.
[2024-01-24 14:23:32,813] [INFO] Target genome list was writen to GCF_017874515.1_ASM1787451v1_genomic.fna/target_genomes.txt
[2024-01-24 14:23:32,819] [INFO] Task started: fastANI
[2024-01-24 14:23:32,819] [INFO] Running command: fastANI --query /var/lib/cwl/stg7a8b7cca-f434-40dd-8d59-7e8b595ba40d/GCF_017874515.1_ASM1787451v1_genomic.fna.gz --refList GCF_017874515.1_ASM1787451v1_genomic.fna/target_genomes.txt --output GCF_017874515.1_ASM1787451v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:24:08,167] [INFO] Task succeeded: fastANI
[2024-01-24 14:24:08,168] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdc23dcae-bfdf-42a8-b05e-9a5f0e0d6322/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:24:08,168] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdc23dcae-bfdf-42a8-b05e-9a5f0e0d6322/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:24:08,191] [INFO] Found 16 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:24:08,191] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:24:08,191] [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 avidinii	strain=DSM 40526	GCA_017874515.1	1895	1895	type	True	100.0	2762	2765	95	conclusive
Streptomyces avidinii	strain=JCM 4726	GCA_014650695.1	1895	1895	type	True	99.9875	2735	2765	95	conclusive
Streptomyces nojiriensis	strain=JCM 3382	GCA_014648615.1	66374	66374	type	True	92.2289	2203	2765	95	below_threshold
Streptomyces nojiriensis	strain=NBRC 13794	GCA_016755855.1	66374	66374	type	True	92.199	2221	2765	95	below_threshold
Streptomyces nojiriensis	strain=JCM 3382	GCA_017639205.1	66374	66374	type	True	92.1493	2239	2765	95	below_threshold
Streptomyces spororaveus	strain=NBRC 15456	GCA_016755875.1	284039	284039	type	True	91.9476	2173	2765	95	below_threshold
Streptomyces virginiae	strain=NRRL ISP-5094	GCA_000720455.1	1961	1961	suspected-type	True	89.3531	2079	2765	95	below_threshold
Streptomyces amritsarensis	strain=MTCC 11845	GCA_001953875.1	681158	681158	type	True	89.0585	1920	2765	95	below_threshold
Streptomyces xanthophaeus	strain=NBRC 12829	GCA_016755895.1	67385	67385	type	True	88.0852	1978	2765	95	below_threshold
Streptomyces xanthophaeus	strain=NRRL B-5414	GCA_000725805.1	67385	67385	type	True	88.0046	1967	2765	95	below_threshold
Streptomyces subrutilus	strain=ATCC 27467	GCA_008704535.1	36818	36818	type	True	87.7094	1772	2765	95	below_threshold
Streptomyces formicae	strain=1H-GS9	GCA_022647665.1	1616117	1616117	type	True	81.7842	1368	2765	95	below_threshold
Streptomyces somaliensis	strain=DSM 40738	GCA_024349285.1	78355	78355	type	True	81.5552	987	2765	95	below_threshold
Streptomyces sudanensis	strain=SD 504	GCA_023614315.1	436397	436397	type	True	81.2871	1054	2765	95	below_threshold
Streptomyces harenosi	strain=PRKS01-65	GCA_011008945.1	2697029	2697029	type	True	81.0353	1167	2765	95	below_threshold
Streptomyces glomeratus	strain=DSM 41457	GCA_021462825.1	284452	284452	type	True	80.7745	1211	2765	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:24:08,193] [INFO] DFAST Taxonomy check result was written to GCF_017874515.1_ASM1787451v1_genomic.fna/tc_result.tsv
[2024-01-24 14:24:08,194] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:24:08,194] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:24:08,195] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdc23dcae-bfdf-42a8-b05e-9a5f0e0d6322/dqc_reference/checkm_data
[2024-01-24 14:24:08,196] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:24:08,272] [INFO] Task started: CheckM
[2024-01-24 14:24:08,272] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017874515.1_ASM1787451v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017874515.1_ASM1787451v1_genomic.fna/checkm_input GCF_017874515.1_ASM1787451v1_genomic.fna/checkm_result
[2024-01-24 14:25:53,322] [INFO] Task succeeded: CheckM
[2024-01-24 14:25:53,324] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 5.21%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:25:53,350] [INFO] ===== Completeness check finished =====
[2024-01-24 14:25:53,350] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:25:53,351] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017874515.1_ASM1787451v1_genomic.fna/markers.fasta)
[2024-01-24 14:25:53,351] [INFO] Task started: Blastn
[2024-01-24 14:25:53,351] [INFO] Running command: blastn -query GCF_017874515.1_ASM1787451v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdc23dcae-bfdf-42a8-b05e-9a5f0e0d6322/dqc_reference/reference_markers_gtdb.fasta -out GCF_017874515.1_ASM1787451v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:25:55,461] [INFO] Task succeeded: Blastn
[2024-01-24 14:25:55,464] [INFO] Selected 9 target genomes.
[2024-01-24 14:25:55,464] [INFO] Target genome list was writen to GCF_017874515.1_ASM1787451v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:25:55,490] [INFO] Task started: fastANI
[2024-01-24 14:25:55,490] [INFO] Running command: fastANI --query /var/lib/cwl/stg7a8b7cca-f434-40dd-8d59-7e8b595ba40d/GCF_017874515.1_ASM1787451v1_genomic.fna.gz --refList GCF_017874515.1_ASM1787451v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017874515.1_ASM1787451v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:26:16,860] [INFO] Task succeeded: fastANI
[2024-01-24 14:26:16,872] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:26:16,872] [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_014650695.1	s__Streptomyces avidinii	99.9875	2735	2765	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.99	99.99	1.00	1.00	2	conclusive
GCF_002080455.1	s__Streptomyces sp002080455	94.4956	2312	2765	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.34	98.21	0.92	0.90	7	-
GCF_017639205.1	s__Streptomyces nojiriensis	92.199	2232	2765	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	100.00	100.00	1.00	1.00	3	-
GCF_016755875.1	s__Streptomyces spororaveus	91.9569	2171	2765	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000716685.1	s__Streptomyces virginiae_A	91.8024	2246	2765	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.46	95.91	0.89	0.84	3	-
GCF_003148825.1	s__Streptomyces sp003148825	91.713	2242	2765	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.84	95.84	0.87	0.86	3	-
GCF_008642275.1	s__Streptomyces venezuelae_E	91.7064	2101	2765	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	90.2789	2047	2765	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000725805.1	s__Streptomyces xanthophaeus	88.0196	1965	2765	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.79	99.60	0.97	0.96	3	-
--------------------------------------------------------------------------------
[2024-01-24 14:26:16,874] [INFO] GTDB search result was written to GCF_017874515.1_ASM1787451v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:26:16,875] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:26:16,878] [INFO] DFAST_QC result json was written to GCF_017874515.1_ASM1787451v1_genomic.fna/dqc_result.json
[2024-01-24 14:26:16,879] [INFO] DFAST_QC completed!
[2024-01-24 14:26:16,879] [INFO] Total running time: 0h3m12s