[2024-01-25 19:08:20,873] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:08:20,874] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:08:20,874] [INFO] DQC Reference Directory: /var/lib/cwl/stg45f3a8e6-2a33-4059-9fbd-8abd9e6ec268/dqc_reference
[2024-01-25 19:08:21,994] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:08:21,995] [INFO] Task started: Prodigal
[2024-01-25 19:08:21,995] [INFO] Running command: gunzip -c /var/lib/cwl/stg0a24c64f-08cb-4625-85af-79a8d2ec9432/GCF_000787855.1_ASM78785v1_genomic.fna.gz | prodigal -d GCF_000787855.1_ASM78785v1_genomic.fna/cds.fna -a GCF_000787855.1_ASM78785v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:08:44,220] [INFO] Task succeeded: Prodigal
[2024-01-25 19:08:44,221] [INFO] Task started: HMMsearch
[2024-01-25 19:08:44,221] [INFO] Running command: hmmsearch --tblout GCF_000787855.1_ASM78785v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg45f3a8e6-2a33-4059-9fbd-8abd9e6ec268/dqc_reference/reference_markers.hmm GCF_000787855.1_ASM78785v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:08:44,566] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:08:44,567] [INFO] Found 6/6 markers.
[2024-01-25 19:08:44,633] [INFO] Query marker FASTA was written to GCF_000787855.1_ASM78785v1_genomic.fna/markers.fasta
[2024-01-25 19:08:44,633] [INFO] Task started: Blastn
[2024-01-25 19:08:44,633] [INFO] Running command: blastn -query GCF_000787855.1_ASM78785v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg45f3a8e6-2a33-4059-9fbd-8abd9e6ec268/dqc_reference/reference_markers.fasta -out GCF_000787855.1_ASM78785v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:08:46,005] [INFO] Task succeeded: Blastn
[2024-01-25 19:08:46,007] [INFO] Selected 13 target genomes.
[2024-01-25 19:08:46,008] [INFO] Target genome list was writen to GCF_000787855.1_ASM78785v1_genomic.fna/target_genomes.txt
[2024-01-25 19:08:46,016] [INFO] Task started: fastANI
[2024-01-25 19:08:46,016] [INFO] Running command: fastANI --query /var/lib/cwl/stg0a24c64f-08cb-4625-85af-79a8d2ec9432/GCF_000787855.1_ASM78785v1_genomic.fna.gz --refList GCF_000787855.1_ASM78785v1_genomic.fna/target_genomes.txt --output GCF_000787855.1_ASM78785v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:09:17,179] [INFO] Task succeeded: fastANI
[2024-01-25 19:09:17,179] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg45f3a8e6-2a33-4059-9fbd-8abd9e6ec268/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:09:17,179] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg45f3a8e6-2a33-4059-9fbd-8abd9e6ec268/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:09:17,188] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:09:17,188] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:09:17,188] [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
Streptacidiphilus anmyonensis	strain=NBRC 103185	GCA_000787855.1	405782	405782	type	True	100.0	3034	3050	95	conclusive
Streptacidiphilus melanogenes	strain=NBRC 103184	GCA_000787835.1	411235	411235	type	True	91.4993	2244	3050	95	below_threshold
Streptacidiphilus neutrinimicus	strain=NBRC 100921	GCA_000787815.1	105420	105420	type	True	91.0899	2116	3050	95	below_threshold
Streptacidiphilus pinicola	strain=MMS16-CNU450	GCA_003258295.1	2219663	2219663	type	True	88.0857	1852	3050	95	below_threshold
Streptacidiphilus jiangxiensis	strain=NBRC 100920	GCA_000787795.1	235985	235985	type	True	86.9049	2008	3050	95	below_threshold
Streptacidiphilus jiangxiensis	strain=CGMCC 4.1857	GCA_900109465.1	235985	235985	type	True	86.8835	2031	3050	95	below_threshold
Streptacidiphilus rugosus	strain=AM-16	GCA_000744655.1	405783	405783	type	True	84.5024	1825	3050	95	below_threshold
Streptomyces rubellomurinus	strain=ATCC 31215	GCA_000961885.1	359131	359131	type	True	79.9997	1247	3050	95	below_threshold
Kitasatospora humi	strain=RB6PN24	GCA_020907985.1	2893891	2893891	type	True	79.9586	1167	3050	95	below_threshold
Kitasatospora purpeofusca	strain=NRRL B-1817	GCA_000718025.1	67352	67352	type	True	79.6929	1275	3050	95	below_threshold
Streptomyces griseocarneus	strain=JCM 4580	GCA_014655595.1	51201	51201	type	True	79.0437	1018	3050	95	below_threshold
Streptomyces harenosi	strain=PRKS01-65	GCA_011008945.1	2697029	2697029	type	True	78.774	988	3050	95	below_threshold
Streptomyces albireticuli	strain=NRRL B1670	GCA_021228125.1	1940	1940	type	True	78.6714	1039	3050	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:09:17,189] [INFO] DFAST Taxonomy check result was written to GCF_000787855.1_ASM78785v1_genomic.fna/tc_result.tsv
[2024-01-25 19:09:17,190] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:09:17,190] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:09:17,190] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg45f3a8e6-2a33-4059-9fbd-8abd9e6ec268/dqc_reference/checkm_data
[2024-01-25 19:09:17,191] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:09:17,274] [INFO] Task started: CheckM
[2024-01-25 19:09:17,275] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000787855.1_ASM78785v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000787855.1_ASM78785v1_genomic.fna/checkm_input GCF_000787855.1_ASM78785v1_genomic.fna/checkm_result
[2024-01-25 19:11:06,250] [INFO] Task succeeded: CheckM
[2024-01-25 19:11:06,251] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 97.92%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:11:06,295] [INFO] ===== Completeness check finished =====
[2024-01-25 19:11:06,295] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:11:06,296] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000787855.1_ASM78785v1_genomic.fna/markers.fasta)
[2024-01-25 19:11:06,296] [INFO] Task started: Blastn
[2024-01-25 19:11:06,297] [INFO] Running command: blastn -query GCF_000787855.1_ASM78785v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg45f3a8e6-2a33-4059-9fbd-8abd9e6ec268/dqc_reference/reference_markers_gtdb.fasta -out GCF_000787855.1_ASM78785v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:11:08,461] [INFO] Task succeeded: Blastn
[2024-01-25 19:11:08,464] [INFO] Selected 7 target genomes.
[2024-01-25 19:11:08,464] [INFO] Target genome list was writen to GCF_000787855.1_ASM78785v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:11:08,469] [INFO] Task started: fastANI
[2024-01-25 19:11:08,470] [INFO] Running command: fastANI --query /var/lib/cwl/stg0a24c64f-08cb-4625-85af-79a8d2ec9432/GCF_000787855.1_ASM78785v1_genomic.fna.gz --refList GCF_000787855.1_ASM78785v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000787855.1_ASM78785v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:11:27,751] [INFO] Task succeeded: fastANI
[2024-01-25 19:11:27,757] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:11:27,757] [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_000787855.1	s__Streptacidiphilus anmyonensis	100.0	3034	3050	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptacidiphilus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000787835.1	s__Streptacidiphilus melanogenes	91.5054	2243	3050	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptacidiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000787815.1	s__Streptacidiphilus neutrinimicus	91.1045	2114	3050	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptacidiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003258295.1	s__Streptacidiphilus pinicola	88.065	1854	3050	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptacidiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109465.1	s__Streptacidiphilus jiangxiensis	86.896	2028	3050	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptacidiphilus	95.0	99.97	99.97	0.98	0.98	2	-
GCF_000744655.1	s__Streptacidiphilus rugosus	84.4684	1830	3050	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptacidiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014084125.1	s__Streptacidiphilus sp014084125	81.2599	1389	3050	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptacidiphilus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:11:27,758] [INFO] GTDB search result was written to GCF_000787855.1_ASM78785v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:11:27,759] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:11:27,761] [INFO] DFAST_QC result json was written to GCF_000787855.1_ASM78785v1_genomic.fna/dqc_result.json
[2024-01-25 19:11:27,761] [INFO] DFAST_QC completed!
[2024-01-25 19:11:27,761] [INFO] Total running time: 0h3m7s