[2024-01-24 12:30:48,830] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:30:48,832] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:30:48,832] [INFO] DQC Reference Directory: /var/lib/cwl/stg114781d3-13f8-4f3a-ae3e-cbe352fc7b4b/dqc_reference
[2024-01-24 12:30:50,053] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:30:50,054] [INFO] Task started: Prodigal
[2024-01-24 12:30:50,054] [INFO] Running command: gunzip -c /var/lib/cwl/stg8a60a1e7-c0df-4104-af87-d970658e44a7/GCF_022524345.1_ASM2252434v1_genomic.fna.gz | prodigal -d GCF_022524345.1_ASM2252434v1_genomic.fna/cds.fna -a GCF_022524345.1_ASM2252434v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:31:10,044] [INFO] Task succeeded: Prodigal
[2024-01-24 12:31:10,044] [INFO] Task started: HMMsearch
[2024-01-24 12:31:10,045] [INFO] Running command: hmmsearch --tblout GCF_022524345.1_ASM2252434v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg114781d3-13f8-4f3a-ae3e-cbe352fc7b4b/dqc_reference/reference_markers.hmm GCF_022524345.1_ASM2252434v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:31:10,364] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:31:10,366] [INFO] Found 6/6 markers.
[2024-01-24 12:31:10,418] [INFO] Query marker FASTA was written to GCF_022524345.1_ASM2252434v1_genomic.fna/markers.fasta
[2024-01-24 12:31:10,418] [INFO] Task started: Blastn
[2024-01-24 12:31:10,418] [INFO] Running command: blastn -query GCF_022524345.1_ASM2252434v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg114781d3-13f8-4f3a-ae3e-cbe352fc7b4b/dqc_reference/reference_markers.fasta -out GCF_022524345.1_ASM2252434v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:31:11,652] [INFO] Task succeeded: Blastn
[2024-01-24 12:31:11,656] [INFO] Selected 23 target genomes.
[2024-01-24 12:31:11,657] [INFO] Target genome list was writen to GCF_022524345.1_ASM2252434v1_genomic.fna/target_genomes.txt
[2024-01-24 12:31:11,685] [INFO] Task started: fastANI
[2024-01-24 12:31:11,685] [INFO] Running command: fastANI --query /var/lib/cwl/stg8a60a1e7-c0df-4104-af87-d970658e44a7/GCF_022524345.1_ASM2252434v1_genomic.fna.gz --refList GCF_022524345.1_ASM2252434v1_genomic.fna/target_genomes.txt --output GCF_022524345.1_ASM2252434v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:31:46,957] [INFO] Task succeeded: fastANI
[2024-01-24 12:31:46,958] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg114781d3-13f8-4f3a-ae3e-cbe352fc7b4b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:31:46,958] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg114781d3-13f8-4f3a-ae3e-cbe352fc7b4b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:31:46,976] [INFO] Found 23 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:31:46,976] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:31:46,976] [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	86.3503	1795	2230	95	below_threshold
Streptomyces albidus (ex Kaewkla and Franco 2021)	strain=CAP215	GCA_013870515.1	722709	722709	type	True	84.0155	1356	2230	95	below_threshold
Streptomyces daqingensis	strain=CGMCC 4.7178	GCA_014645895.1	1472640	1472640	type	True	83.4234	1539	2230	95	below_threshold
Streptomyces armeniacus	strain=ATCC 15676	GCA_003355155.1	83291	83291	type	True	80.8231	1209	2230	95	below_threshold
Streptomyces boncukensis	strain=SB3404	GCA_011045075.1	2711219	2711219	type	True	80.7653	944	2230	95	below_threshold
Streptomyces albus subsp. albus	strain=NRRL B-1811	GCA_000725885.1	67257	1888	suspected-type	True	80.6743	1047	2230	95	below_threshold
Streptomyces spirodelae	strain=DW4-2	GCA_017676385.1	2812904	2812904	type	True	80.6165	1084	2230	95	below_threshold
Streptomyces albus	strain=NBRC 13014	GCA_000813365.1	1888	1888	suspected-type	True	80.5722	1068	2230	95	below_threshold
Streptomyces radiopugnans	strain=CGMCC 4.3519	GCA_900110735.1	403935	403935	type	True	80.5393	1003	2230	95	below_threshold
Streptomyces pini	strain=PL19	GCA_900114215.1	1520580	1520580	type	True	80.4254	971	2230	95	below_threshold
Streptomyces verrucosisporus	strain=CPB1-1	GCA_017114865.1	1695161	1695161	type	True	80.4074	949	2230	95	below_threshold
Streptomyces sulphureus	strain=DSM 40104	GCA_000381025.1	47758	47758	type	True	80.1605	944	2230	95	below_threshold
Streptomyces pinistramenti	strain=SF28	GCA_020564935.1	2884812	2884812	type	True	79.9095	961	2230	95	below_threshold
Streptomyces buecherae	strain=AC541	GCA_014295035.1	2763006	2763006	type	True	79.8337	1000	2230	95	below_threshold
Streptomyces rapamycinicus	strain=NRRL 5491	GCA_024298965.1	1226757	1226757	type	True	79.6165	1089	2230	95	below_threshold
Streptomyces oceani	strain=SCSIO 02100	GCA_001751245.1	1075402	1075402	type	True	79.5566	848	2230	95	below_threshold
Streptomyces genisteinicus	strain=CRPJ-33	GCA_014489615.1	2768068	2768068	type	True	79.5438	1021	2230	95	below_threshold
Streptomyces violaceochromogenes	strain=JCM 4530	GCA_014650235.1	67377	67377	type	True	79.3666	1002	2230	95	below_threshold
Streptomyces gossypiisoli	strain=TRM 44567	GCA_013433285.1	2748864	2748864	type	True	79.3535	996	2230	95	below_threshold
Streptomyces apocyni	strain=TRM 66233	GCA_009739465.1	2654677	2654677	type	True	79.3196	879	2230	95	below_threshold
Streptomyces smaragdinus	strain=RB5	GCA_009604385.1	2585196	2585196	type	True	79.2465	858	2230	95	below_threshold
Streptomyces populi	strain=A249	GCA_002911015.1	2058924	2058924	type	True	79.2164	964	2230	95	below_threshold
Streptomyces canus	strain=DSM 40017	GCA_001514145.1	58343	58343	suspected-type	True	78.9879	990	2230	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:31:46,979] [INFO] DFAST Taxonomy check result was written to GCF_022524345.1_ASM2252434v1_genomic.fna/tc_result.tsv
[2024-01-24 12:31:46,979] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:31:46,979] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:31:46,980] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg114781d3-13f8-4f3a-ae3e-cbe352fc7b4b/dqc_reference/checkm_data
[2024-01-24 12:31:46,981] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:31:47,044] [INFO] Task started: CheckM
[2024-01-24 12:31:47,044] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_022524345.1_ASM2252434v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_022524345.1_ASM2252434v1_genomic.fna/checkm_input GCF_022524345.1_ASM2252434v1_genomic.fna/checkm_result
[2024-01-24 12:32:54,992] [INFO] Task succeeded: CheckM
[2024-01-24 12:32:54,994] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:32:55,024] [INFO] ===== Completeness check finished =====
[2024-01-24 12:32:55,025] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:32:55,025] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_022524345.1_ASM2252434v1_genomic.fna/markers.fasta)
[2024-01-24 12:32:55,026] [INFO] Task started: Blastn
[2024-01-24 12:32:55,026] [INFO] Running command: blastn -query GCF_022524345.1_ASM2252434v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg114781d3-13f8-4f3a-ae3e-cbe352fc7b4b/dqc_reference/reference_markers_gtdb.fasta -out GCF_022524345.1_ASM2252434v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:32:56,967] [INFO] Task succeeded: Blastn
[2024-01-24 12:32:56,971] [INFO] Selected 8 target genomes.
[2024-01-24 12:32:56,972] [INFO] Target genome list was writen to GCF_022524345.1_ASM2252434v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:32:56,978] [INFO] Task started: fastANI
[2024-01-24 12:32:56,979] [INFO] Running command: fastANI --query /var/lib/cwl/stg8a60a1e7-c0df-4104-af87-d970658e44a7/GCF_022524345.1_ASM2252434v1_genomic.fna.gz --refList GCF_022524345.1_ASM2252434v1_genomic.fna/target_genomes_gtdb.txt --output GCF_022524345.1_ASM2252434v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:33:10,879] [INFO] Task succeeded: fastANI
[2024-01-24 12:33:10,891] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:33:10,892] [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_012726265.1	s__Streptomyces sp012726265	88.5977	1800	2230	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014204855.1	s__Streptomyces haliclonae	86.6395	1711	2230	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	86.6218	1490	2230	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.85	97.85	0.86	0.86	2	-
GCF_001751365.1	s__Streptomyces abyssalis	86.5756	1709	2230	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.91	99.91	0.99	0.99	2	-
GCF_015910445.1	s__Streptomyces bathyalis	86.3579	1793	2230	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000426165.1	s__Streptomyces sp000426165	86.0658	1725	2230	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	85.758	1662	2230	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.71	95.43	0.94	0.89	3	-
GCF_001751245.1	s__Streptomyces oceani	79.5591	848	2230	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 12:33:10,893] [INFO] GTDB search result was written to GCF_022524345.1_ASM2252434v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:33:10,894] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:33:10,898] [INFO] DFAST_QC result json was written to GCF_022524345.1_ASM2252434v1_genomic.fna/dqc_result.json
[2024-01-24 12:33:10,898] [INFO] DFAST_QC completed!
[2024-01-24 12:33:10,898] [INFO] Total running time: 0h2m22s