[2024-01-25 18:33:20,573] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:33:20,575] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:33:20,575] [INFO] DQC Reference Directory: /var/lib/cwl/stg5c9413b6-f35d-49f7-a3ce-087dc9570a45/dqc_reference
[2024-01-25 18:33:21,805] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:33:21,806] [INFO] Task started: Prodigal
[2024-01-25 18:33:21,806] [INFO] Running command: gunzip -c /var/lib/cwl/stg1658063e-9897-4d51-aa88-da2e0f4b60cd/GCF_001005295.1_ASM100529v1_genomic.fna.gz | prodigal -d GCF_001005295.1_ASM100529v1_genomic.fna/cds.fna -a GCF_001005295.1_ASM100529v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:33:41,515] [INFO] Task succeeded: Prodigal
[2024-01-25 18:33:41,515] [INFO] Task started: HMMsearch
[2024-01-25 18:33:41,515] [INFO] Running command: hmmsearch --tblout GCF_001005295.1_ASM100529v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5c9413b6-f35d-49f7-a3ce-087dc9570a45/dqc_reference/reference_markers.hmm GCF_001005295.1_ASM100529v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:33:41,821] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:33:41,822] [INFO] Found 6/6 markers.
[2024-01-25 18:33:41,885] [INFO] Query marker FASTA was written to GCF_001005295.1_ASM100529v1_genomic.fna/markers.fasta
[2024-01-25 18:33:41,885] [INFO] Task started: Blastn
[2024-01-25 18:33:41,885] [INFO] Running command: blastn -query GCF_001005295.1_ASM100529v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5c9413b6-f35d-49f7-a3ce-087dc9570a45/dqc_reference/reference_markers.fasta -out GCF_001005295.1_ASM100529v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:33:43,171] [INFO] Task succeeded: Blastn
[2024-01-25 18:33:43,173] [INFO] Selected 21 target genomes.
[2024-01-25 18:33:43,174] [INFO] Target genome list was writen to GCF_001005295.1_ASM100529v1_genomic.fna/target_genomes.txt
[2024-01-25 18:33:43,187] [INFO] Task started: fastANI
[2024-01-25 18:33:43,188] [INFO] Running command: fastANI --query /var/lib/cwl/stg1658063e-9897-4d51-aa88-da2e0f4b60cd/GCF_001005295.1_ASM100529v1_genomic.fna.gz --refList GCF_001005295.1_ASM100529v1_genomic.fna/target_genomes.txt --output GCF_001005295.1_ASM100529v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:34:25,727] [INFO] Task succeeded: fastANI
[2024-01-25 18:34:25,728] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5c9413b6-f35d-49f7-a3ce-087dc9570a45/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:34:25,729] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5c9413b6-f35d-49f7-a3ce-087dc9570a45/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:34:25,741] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:34:25,741] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:34:25,741] [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 yangpuensis	strain=fd2-tb	GCA_001005295.1	1648182	1648182	type	True	100.0	2542	2543	95	conclusive
Streptomyces amritsarensis	strain=MTCC 11845	GCA_001953875.1	681158	681158	type	True	92.7377	2074	2543	95	below_threshold
Streptomyces virginiae	strain=NRRL ISP-5094	GCA_000720455.1	1961	1961	suspected-type	True	92.5191	2132	2543	95	below_threshold
Streptomyces nojiriensis	strain=NBRC 13794	GCA_016755855.1	66374	66374	type	True	89.2939	1991	2543	95	below_threshold
Streptomyces spororaveus	strain=NBRC 15456	GCA_016755875.1	284039	284039	type	True	89.2736	1968	2543	95	below_threshold
Streptomyces nojiriensis	strain=JCM 3382	GCA_017639205.1	66374	66374	type	True	89.2663	1991	2543	95	below_threshold
Streptomyces nojiriensis	strain=JCM 3382	GCA_014648615.1	66374	66374	type	True	89.231	2005	2543	95	below_threshold
Streptomyces avidinii	strain=DSM 40526	GCA_017874515.1	1895	1895	type	True	89.1094	1971	2543	95	below_threshold
Streptomyces goshikiensis	strain=JCM 4640	GCA_014650555.1	1942	1942	type	True	87.0522	1749	2543	95	below_threshold
Streptomyces vinaceus	strain=JCM 4849	GCA_014656155.1	1960	1960	type	True	86.987	1772	2543	95	below_threshold
Streptomyces katrae	strain=NRRL ISP-5550	GCA_000966975.1	68223	68223	type	True	86.6598	1324	2543	95	below_threshold
Streptomyces nymphaeiformis	strain=SFB5A	GCA_014203895.1	2663842	2663842	type	True	82.2685	1471	2543	95	below_threshold
Streptomyces sudanensis	strain=SD 504	GCA_023614315.1	436397	436397	type	True	81.6851	1061	2543	95	below_threshold
Streptomyces genisteinicus	strain=CRPJ-33	GCA_014489615.1	2768068	2768068	type	True	81.5065	1346	2543	95	below_threshold
Streptomyces sennicomposti	strain=RCPT1-4	GCA_019890635.1	2873384	2873384	type	True	81.3721	1208	2543	95	below_threshold
Streptomyces harenosi	strain=PRKS01-65	GCA_011008945.1	2697029	2697029	type	True	81.3485	1154	2543	95	below_threshold
Streptomyces fumanus	strain=JCM 4477	GCA_014655295.1	67302	67302	type	True	80.9943	1268	2543	95	below_threshold
Streptomyces fragilis	strain=NBRC 12862	GCA_003112515.1	67301	67301	type	True	80.8521	1121	2543	95	below_threshold
Streptomyces sparsogenes	strain=ATCC 25498	GCA_001704635.1	67365	67365	type	True	80.5365	1189	2543	95	below_threshold
Actinacidiphila bryophytorum	strain=DSM 42138	GCA_017164735.1	1436133	1436133	type	True	79.888	920	2543	95	below_threshold
Actinacidiphila bryophytorum	strain=DSM 42138	GCA_016916835.1	1436133	1436133	type	True	79.7133	1074	2543	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:34:25,743] [INFO] DFAST Taxonomy check result was written to GCF_001005295.1_ASM100529v1_genomic.fna/tc_result.tsv
[2024-01-25 18:34:25,744] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:34:25,744] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:34:25,744] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5c9413b6-f35d-49f7-a3ce-087dc9570a45/dqc_reference/checkm_data
[2024-01-25 18:34:25,745] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:34:25,815] [INFO] Task started: CheckM
[2024-01-25 18:34:25,815] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001005295.1_ASM100529v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001005295.1_ASM100529v1_genomic.fna/checkm_input GCF_001005295.1_ASM100529v1_genomic.fna/checkm_result
[2024-01-25 18:36:05,258] [INFO] Task succeeded: CheckM
[2024-01-25 18:36:05,269] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.15%
Contamintation: 5.21%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:36:05,311] [INFO] ===== Completeness check finished =====
[2024-01-25 18:36:05,311] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:36:05,312] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001005295.1_ASM100529v1_genomic.fna/markers.fasta)
[2024-01-25 18:36:05,312] [INFO] Task started: Blastn
[2024-01-25 18:36:05,312] [INFO] Running command: blastn -query GCF_001005295.1_ASM100529v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5c9413b6-f35d-49f7-a3ce-087dc9570a45/dqc_reference/reference_markers_gtdb.fasta -out GCF_001005295.1_ASM100529v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:36:07,589] [INFO] Task succeeded: Blastn
[2024-01-25 18:36:07,592] [INFO] Selected 12 target genomes.
[2024-01-25 18:36:07,592] [INFO] Target genome list was writen to GCF_001005295.1_ASM100529v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:36:07,670] [INFO] Task started: fastANI
[2024-01-25 18:36:07,670] [INFO] Running command: fastANI --query /var/lib/cwl/stg1658063e-9897-4d51-aa88-da2e0f4b60cd/GCF_001005295.1_ASM100529v1_genomic.fna.gz --refList GCF_001005295.1_ASM100529v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001005295.1_ASM100529v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:36:34,324] [INFO] Task succeeded: fastANI
[2024-01-25 18:36:34,332] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:36:34,333] [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_001005295.1	s__Streptomyces yangpuensis	100.0	2542	2543	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.05	95.28	0.86	0.84	3	conclusive
GCF_000725555.1	s__Streptomyces erythrochromogenes	93.225	1969	2543	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.80	95.80	0.85	0.85	2	-
GCF_001953875.1	s__Streptomyces amritsarensis	92.7348	2075	2543	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.17	98.97	0.95	0.93	4	-
GCF_014648795.1	s__Streptomyces cinnamonensis	92.5925	2128	2543	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.18	96.61	0.93	0.87	24	-
GCF_001941845.1	s__Streptomyces sp001941845	91.8659	2023	2543	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.45	99.45	0.96	0.96	2	-
GCF_000612545.1	s__Streptomyces sp000612545	91.5765	1985	2543	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000719345.1	s__Streptomyces sp000719345	91.3971	1953	2543	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017639205.1	s__Streptomyces nojiriensis	89.2813	1989	2543	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	100.00	100.00	1.00	1.00	3	-
GCF_005795905.1	s__Streptomyces marianii	81.4178	1321	2543	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014655295.1	s__Streptomyces fumanus	80.9846	1268	2543	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000242715.1	s__Streptomyces acidiscabies	80.0282	1178	2543	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.11	97.67	0.95	0.89	7	-
GCF_016916835.1	s__Streptomyces bryophytorum	79.7264	1070	2543	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.96	99.96	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-25 18:36:34,334] [INFO] GTDB search result was written to GCF_001005295.1_ASM100529v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:36:34,336] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:36:34,340] [INFO] DFAST_QC result json was written to GCF_001005295.1_ASM100529v1_genomic.fna/dqc_result.json
[2024-01-25 18:36:34,340] [INFO] DFAST_QC completed!
[2024-01-25 18:36:34,340] [INFO] Total running time: 0h3m14s