[2024-01-24 12:54:21,858] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:54:21,860] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:54:21,861] [INFO] DQC Reference Directory: /var/lib/cwl/stg01859f58-8da2-4ca7-bb9e-e5c4c79702c4/dqc_reference
[2024-01-24 12:54:23,879] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:54:23,880] [INFO] Task started: Prodigal
[2024-01-24 12:54:23,880] [INFO] Running command: gunzip -c /var/lib/cwl/stgb7da39e3-8da2-4902-b4d3-39dd1a128ec3/GCF_900111245.1_IMG-taxon_2675903055_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900111245.1_IMG-taxon_2675903055_annotated_assembly_genomic.fna/cds.fna -a GCF_900111245.1_IMG-taxon_2675903055_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:54:45,159] [INFO] Task succeeded: Prodigal
[2024-01-24 12:54:45,159] [INFO] Task started: HMMsearch
[2024-01-24 12:54:45,159] [INFO] Running command: hmmsearch --tblout GCF_900111245.1_IMG-taxon_2675903055_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg01859f58-8da2-4ca7-bb9e-e5c4c79702c4/dqc_reference/reference_markers.hmm GCF_900111245.1_IMG-taxon_2675903055_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:54:45,483] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:54:45,484] [INFO] Found 6/6 markers.
[2024-01-24 12:54:45,542] [INFO] Query marker FASTA was written to GCF_900111245.1_IMG-taxon_2675903055_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 12:54:45,542] [INFO] Task started: Blastn
[2024-01-24 12:54:45,543] [INFO] Running command: blastn -query GCF_900111245.1_IMG-taxon_2675903055_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg01859f58-8da2-4ca7-bb9e-e5c4c79702c4/dqc_reference/reference_markers.fasta -out GCF_900111245.1_IMG-taxon_2675903055_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:54:46,871] [INFO] Task succeeded: Blastn
[2024-01-24 12:54:46,878] [INFO] Selected 11 target genomes.
[2024-01-24 12:54:46,879] [INFO] Target genome list was writen to GCF_900111245.1_IMG-taxon_2675903055_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 12:54:46,888] [INFO] Task started: fastANI
[2024-01-24 12:54:46,888] [INFO] Running command: fastANI --query /var/lib/cwl/stgb7da39e3-8da2-4902-b4d3-39dd1a128ec3/GCF_900111245.1_IMG-taxon_2675903055_annotated_assembly_genomic.fna.gz --refList GCF_900111245.1_IMG-taxon_2675903055_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900111245.1_IMG-taxon_2675903055_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:55:08,320] [INFO] Task succeeded: fastANI
[2024-01-24 12:55:08,321] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg01859f58-8da2-4ca7-bb9e-e5c4c79702c4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:55:08,321] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg01859f58-8da2-4ca7-bb9e-e5c4c79702c4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:55:08,330] [INFO] Found 11 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:55:08,330] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:55:08,331] [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 qinglanensis	strain=CGMCC 4.6825	GCA_900111245.1	943816	943816	type	True	100.0	2368	2371	95	conclusive
Streptomyces qinglanensis	strain=172205	GCA_003265665.1	943816	943816	type	True	99.9806	2353	2371	95	conclusive
Streptomyces smyrnaeus	strain=DSM 42105	GCA_017676345.1	1387713	1387713	type	True	87.4919	1778	2371	95	below_threshold
Streptomyces oryzae	strain=S16-07	GCA_017676365.1	1434886	1434886	type	True	86.9907	1614	2371	95	below_threshold
Streptomyces spirodelae	strain=DW4-2	GCA_017676385.1	2812904	2812904	type	True	86.8814	1749	2371	95	below_threshold
Streptomyces reniochalinae	strain=LHW50302	GCA_003323735.1	2250578	2250578	type	True	84.6761	1587	2371	95	below_threshold
Streptomyces paromomycinus	strain=NBRC 15454	GCA_003865155.1	92743	92743	type	True	80.2932	1186	2371	95	below_threshold
Streptomyces gobiensis	strain=1_25	GCA_021216675.1	2875706	2875706	type	True	80.2639	876	2371	95	below_threshold
Streptomyces monomycini	strain=NRRL B-24309	GCA_022271435.1	371720	371720	type	True	80.1236	1179	2371	95	below_threshold
Streptomyces rimosus subsp. rimosus	strain=R7	GCA_022760195.1	132474	1927	type	True	80.0796	1216	2371	95	below_threshold
Streptomyces rapamycinicus	strain=NRRL 5491	GCA_024298965.1	1226757	1226757	type	True	79.8371	1276	2371	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:55:08,332] [INFO] DFAST Taxonomy check result was written to GCF_900111245.1_IMG-taxon_2675903055_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 12:55:08,333] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:55:08,333] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:55:08,333] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg01859f58-8da2-4ca7-bb9e-e5c4c79702c4/dqc_reference/checkm_data
[2024-01-24 12:55:08,334] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:55:08,404] [INFO] Task started: CheckM
[2024-01-24 12:55:08,404] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900111245.1_IMG-taxon_2675903055_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900111245.1_IMG-taxon_2675903055_annotated_assembly_genomic.fna/checkm_input GCF_900111245.1_IMG-taxon_2675903055_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 12:56:58,832] [INFO] Task succeeded: CheckM
[2024-01-24 12:56:58,834] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 5.21%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:56:58,862] [INFO] ===== Completeness check finished =====
[2024-01-24 12:56:58,862] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:56:58,863] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900111245.1_IMG-taxon_2675903055_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 12:56:58,863] [INFO] Task started: Blastn
[2024-01-24 12:56:58,863] [INFO] Running command: blastn -query GCF_900111245.1_IMG-taxon_2675903055_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg01859f58-8da2-4ca7-bb9e-e5c4c79702c4/dqc_reference/reference_markers_gtdb.fasta -out GCF_900111245.1_IMG-taxon_2675903055_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:57:00,929] [INFO] Task succeeded: Blastn
[2024-01-24 12:57:00,934] [INFO] Selected 7 target genomes.
[2024-01-24 12:57:00,934] [INFO] Target genome list was writen to GCF_900111245.1_IMG-taxon_2675903055_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:57:00,943] [INFO] Task started: fastANI
[2024-01-24 12:57:00,943] [INFO] Running command: fastANI --query /var/lib/cwl/stgb7da39e3-8da2-4902-b4d3-39dd1a128ec3/GCF_900111245.1_IMG-taxon_2675903055_annotated_assembly_genomic.fna.gz --refList GCF_900111245.1_IMG-taxon_2675903055_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900111245.1_IMG-taxon_2675903055_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:57:14,487] [INFO] Task succeeded: fastANI
[2024-01-24 12:57:14,499] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:57:14,499] [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_900111245.1	s__Streptomyces qinglanensis	100.0	2368	2371	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.98	99.98	0.99	0.99	2	conclusive
GCF_000424765.1	s__Streptomyces sp000424765	94.5081	2065	2371	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.13	98.98	0.93	0.92	5	-
GCF_017676345.1	s__Streptomyces smyrnaeus	87.4975	1777	2371	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.11	97.08	0.90	0.88	5	-
GCF_017676365.1	s__Streptomyces oryzae	86.9686	1618	2371	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017676385.1	s__Streptomyces sp017676385	86.8675	1751	2371	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013302895.1	s__Streptomyces chlorinus	85.3661	1612	2371	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003323735.1	s__Streptomyces reniochalinae	84.6969	1584	2371	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 12:57:14,501] [INFO] GTDB search result was written to GCF_900111245.1_IMG-taxon_2675903055_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 12:57:14,501] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:57:14,504] [INFO] DFAST_QC result json was written to GCF_900111245.1_IMG-taxon_2675903055_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 12:57:14,504] [INFO] DFAST_QC completed!
[2024-01-24 12:57:14,504] [INFO] Total running time: 0h2m53s