[2024-01-24 11:44:23,602] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:44:23,606] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:44:23,607] [INFO] DQC Reference Directory: /var/lib/cwl/stga41ff770-8a98-40d7-b86a-35d46a8e621a/dqc_reference
[2024-01-24 11:44:26,341] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:44:26,342] [INFO] Task started: Prodigal
[2024-01-24 11:44:26,342] [INFO] Running command: gunzip -c /var/lib/cwl/stgd0930a7a-e519-44ee-9bd7-9770114da7af/GCF_015910445.1_ASM1591044v1_genomic.fna.gz | prodigal -d GCF_015910445.1_ASM1591044v1_genomic.fna/cds.fna -a GCF_015910445.1_ASM1591044v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:44:47,875] [INFO] Task succeeded: Prodigal
[2024-01-24 11:44:47,876] [INFO] Task started: HMMsearch
[2024-01-24 11:44:47,876] [INFO] Running command: hmmsearch --tblout GCF_015910445.1_ASM1591044v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga41ff770-8a98-40d7-b86a-35d46a8e621a/dqc_reference/reference_markers.hmm GCF_015910445.1_ASM1591044v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:44:48,234] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:44:48,236] [INFO] Found 6/6 markers.
[2024-01-24 11:44:48,295] [INFO] Query marker FASTA was written to GCF_015910445.1_ASM1591044v1_genomic.fna/markers.fasta
[2024-01-24 11:44:48,296] [INFO] Task started: Blastn
[2024-01-24 11:44:48,296] [INFO] Running command: blastn -query GCF_015910445.1_ASM1591044v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga41ff770-8a98-40d7-b86a-35d46a8e621a/dqc_reference/reference_markers.fasta -out GCF_015910445.1_ASM1591044v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:44:49,534] [INFO] Task succeeded: Blastn
[2024-01-24 11:44:49,539] [INFO] Selected 20 target genomes.
[2024-01-24 11:44:49,540] [INFO] Target genome list was writen to GCF_015910445.1_ASM1591044v1_genomic.fna/target_genomes.txt
[2024-01-24 11:44:49,550] [INFO] Task started: fastANI
[2024-01-24 11:44:49,550] [INFO] Running command: fastANI --query /var/lib/cwl/stgd0930a7a-e519-44ee-9bd7-9770114da7af/GCF_015910445.1_ASM1591044v1_genomic.fna.gz --refList GCF_015910445.1_ASM1591044v1_genomic.fna/target_genomes.txt --output GCF_015910445.1_ASM1591044v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:45:20,058] [INFO] Task succeeded: fastANI
[2024-01-24 11:45:20,059] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga41ff770-8a98-40d7-b86a-35d46a8e621a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:45:20,059] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga41ff770-8a98-40d7-b86a-35d46a8e621a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:45:20,078] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:45:20,078] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:45:20,078] [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 bathyalis	strain=ASO4wet	GCA_015910445.1	2710756	2710756	type	True	100.0	2459	2459	95	conclusive
Streptomyces albidus (ex Kaewkla and Franco 2021)	strain=CAP215	GCA_013870515.1	722709	722709	type	True	84.4315	1496	2459	95	below_threshold
Streptomyces daqingensis	strain=CGMCC 4.7178	GCA_014645895.1	1472640	1472640	type	True	83.5782	1569	2459	95	below_threshold
Streptomyces oryzae	strain=S16-07	GCA_017676365.1	1434886	1434886	type	True	80.6964	1056	2459	95	below_threshold
Streptomyces boncukensis	strain=SB3404	GCA_011045075.1	2711219	2711219	type	True	80.6896	950	2459	95	below_threshold
Streptomyces spirodelae	strain=DW4-2	GCA_017676385.1	2812904	2812904	type	True	80.6604	1080	2459	95	below_threshold
Streptomyces smyrnaeus	strain=DSM 42105	GCA_017676345.1	1387713	1387713	type	True	80.616	1117	2459	95	below_threshold
Streptomyces pathocidini	strain=NRRL B-24287	GCA_001418495.1	1650571	1650571	type	True	80.5748	769	2459	95	below_threshold
Streptomyces albus subsp. albus	strain=NRRL B-1811	GCA_000725885.1	67257	1888	suspected-type	True	80.5529	1065	2459	95	below_threshold
Streptomyces albus	strain=NBRC 13014	GCA_000813365.1	1888	1888	suspected-type	True	80.5451	1054	2459	95	below_threshold
Streptomyces qinglanensis	strain=172205	GCA_003265665.1	943816	943816	type	True	80.5256	1084	2459	95	below_threshold
Streptomyces qinglanensis	strain=CGMCC 4.6825	GCA_900111245.1	943816	943816	type	True	80.4964	1106	2459	95	below_threshold
Streptomyces cacaoi	strain=NRRL B-1220	GCA_002154495.1	1898	1898	type	True	80.4604	980	2459	95	below_threshold
Streptomyces taklimakanensis	strain=TRM43335	GCA_009709575.1	2569853	2569853	type	True	80.3205	928	2459	95	below_threshold
Streptomyces megasporus	strain=NRRL B-16372	GCA_000718985.1	44060	44060	type	True	80.3126	897	2459	95	below_threshold
Streptomyces gobiensis	strain=1_25	GCA_021216675.1	2875706	2875706	type	True	80.0264	800	2459	95	below_threshold
Streptomyces rimosus subsp. rimosus	strain=R7	GCA_022760195.1	132474	1927	type	True	79.9698	1064	2459	95	below_threshold
Streptomyces formicae	strain=1H-GS9	GCA_022647665.1	1616117	1616117	type	True	79.7691	1044	2459	95	below_threshold
Streptomyces monomycini	strain=NRRL B-24309	GCA_022271435.1	371720	371720	type	True	79.7505	1047	2459	95	below_threshold
Streptomyces rapamycinicus	strain=NRRL 5491	GCA_024298965.1	1226757	1226757	type	True	79.4973	1150	2459	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:45:20,080] [INFO] DFAST Taxonomy check result was written to GCF_015910445.1_ASM1591044v1_genomic.fna/tc_result.tsv
[2024-01-24 11:45:20,080] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:45:20,081] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:45:20,081] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga41ff770-8a98-40d7-b86a-35d46a8e621a/dqc_reference/checkm_data
[2024-01-24 11:45:20,082] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:45:20,153] [INFO] Task started: CheckM
[2024-01-24 11:45:20,153] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_015910445.1_ASM1591044v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_015910445.1_ASM1591044v1_genomic.fna/checkm_input GCF_015910445.1_ASM1591044v1_genomic.fna/checkm_result
[2024-01-24 11:47:28,324] [INFO] Task succeeded: CheckM
[2024-01-24 11:47:28,326] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:47:28,350] [INFO] ===== Completeness check finished =====
[2024-01-24 11:47:28,350] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:47:28,351] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_015910445.1_ASM1591044v1_genomic.fna/markers.fasta)
[2024-01-24 11:47:28,351] [INFO] Task started: Blastn
[2024-01-24 11:47:28,351] [INFO] Running command: blastn -query GCF_015910445.1_ASM1591044v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga41ff770-8a98-40d7-b86a-35d46a8e621a/dqc_reference/reference_markers_gtdb.fasta -out GCF_015910445.1_ASM1591044v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:47:30,294] [INFO] Task succeeded: Blastn
[2024-01-24 11:47:30,298] [INFO] Selected 12 target genomes.
[2024-01-24 11:47:30,298] [INFO] Target genome list was writen to GCF_015910445.1_ASM1591044v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:47:30,307] [INFO] Task started: fastANI
[2024-01-24 11:47:30,307] [INFO] Running command: fastANI --query /var/lib/cwl/stgd0930a7a-e519-44ee-9bd7-9770114da7af/GCF_015910445.1_ASM1591044v1_genomic.fna.gz --refList GCF_015910445.1_ASM1591044v1_genomic.fna/target_genomes_gtdb.txt --output GCF_015910445.1_ASM1591044v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:47:52,108] [INFO] Task succeeded: fastANI
[2024-01-24 11:47:52,128] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:47:52,128] [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_015910445.1	s__Streptomyces bathyalis	100.0	2459	2459	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000426165.1	s__Streptomyces sp000426165	94.7626	2089	2459	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001418285.1	s__Streptomyces sp001418285	89.8543	1848	2459	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.71	95.43	0.94	0.89	3	-
GCF_001751365.1	s__Streptomyces abyssalis	87.6051	1816	2459	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.91	99.91	0.99	0.99	2	-
GCF_014204855.1	s__Streptomyces haliclonae	86.8519	1712	2459	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012726265.1	s__Streptomyces sp012726265	86.4791	1782	2459	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001751255.1	s__Streptomyces nanshensis_A	86.3641	1495	2459	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.85	97.85	0.86	0.86	2	-
GCF_013870515.1	s__Streptomyces albidus	84.4199	1497	2459	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000718985.1	s__Streptomyces megasporus	80.3506	892	2459	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009709575.1	s__Streptomyces taklimakanensis	80.3267	927	2459	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002847285.1	s__Streptomyces sp002847285	79.3161	1029	2459	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.16	95.03	0.85	0.85	4	-
GCF_002797655.1	s__Streptomyces sp002797655	79.0879	1057	2459	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.99	97.30	0.92	0.88	9	-
--------------------------------------------------------------------------------
[2024-01-24 11:47:52,130] [INFO] GTDB search result was written to GCF_015910445.1_ASM1591044v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:47:52,131] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:47:52,134] [INFO] DFAST_QC result json was written to GCF_015910445.1_ASM1591044v1_genomic.fna/dqc_result.json
[2024-01-24 11:47:52,135] [INFO] DFAST_QC completed!
[2024-01-24 11:47:52,135] [INFO] Total running time: 0h3m29s