[2024-01-24 12:07:06,586] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:07:06,588] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:07:06,588] [INFO] DQC Reference Directory: /var/lib/cwl/stgf0321644-eb0d-4801-9cbe-a6427231f91f/dqc_reference
[2024-01-24 12:07:07,862] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:07:07,863] [INFO] Task started: Prodigal
[2024-01-24 12:07:07,863] [INFO] Running command: gunzip -c /var/lib/cwl/stgf5b39ce4-1c60-40d7-8851-868208af4ded/GCF_024436055.1_ASM2443605v1_genomic.fna.gz | prodigal -d GCF_024436055.1_ASM2443605v1_genomic.fna/cds.fna -a GCF_024436055.1_ASM2443605v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:07:29,489] [INFO] Task succeeded: Prodigal
[2024-01-24 12:07:29,489] [INFO] Task started: HMMsearch
[2024-01-24 12:07:29,489] [INFO] Running command: hmmsearch --tblout GCF_024436055.1_ASM2443605v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf0321644-eb0d-4801-9cbe-a6427231f91f/dqc_reference/reference_markers.hmm GCF_024436055.1_ASM2443605v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:07:29,972] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:07:29,974] [INFO] Found 6/6 markers.
[2024-01-24 12:07:30,032] [INFO] Query marker FASTA was written to GCF_024436055.1_ASM2443605v1_genomic.fna/markers.fasta
[2024-01-24 12:07:30,032] [INFO] Task started: Blastn
[2024-01-24 12:07:30,032] [INFO] Running command: blastn -query GCF_024436055.1_ASM2443605v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf0321644-eb0d-4801-9cbe-a6427231f91f/dqc_reference/reference_markers.fasta -out GCF_024436055.1_ASM2443605v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:07:31,378] [INFO] Task succeeded: Blastn
[2024-01-24 12:07:31,381] [INFO] Selected 23 target genomes.
[2024-01-24 12:07:31,382] [INFO] Target genome list was writen to GCF_024436055.1_ASM2443605v1_genomic.fna/target_genomes.txt
[2024-01-24 12:07:31,392] [INFO] Task started: fastANI
[2024-01-24 12:07:31,393] [INFO] Running command: fastANI --query /var/lib/cwl/stgf5b39ce4-1c60-40d7-8851-868208af4ded/GCF_024436055.1_ASM2443605v1_genomic.fna.gz --refList GCF_024436055.1_ASM2443605v1_genomic.fna/target_genomes.txt --output GCF_024436055.1_ASM2443605v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:08:07,579] [INFO] Task succeeded: fastANI
[2024-01-24 12:08:07,580] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf0321644-eb0d-4801-9cbe-a6427231f91f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:08:07,580] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf0321644-eb0d-4801-9cbe-a6427231f91f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:08:07,602] [INFO] Found 23 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:08:07,602] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:08:07,602] [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 rubrisoli	strain=DSM 42083	GCA_024436055.1	1387313	1387313	type	True	100.0	2368	2373	95	conclusive
Streptomyces parmotrematis	strain=Ptm05	GCA_019890615.1	2873249	2873249	type	True	83.2793	1247	2373	95	below_threshold
Streptomyces palmae	strain=JCM 31289	GCA_004684805.1	1701085	1701085	type	True	81.3762	957	2373	95	below_threshold
Actinacidiphila glaucinigra	strain=CGMCC 4.1858	GCA_900188405.1	235986	235986	type	True	80.9361	1163	2373	95	below_threshold
Actinacidiphila bryophytorum	strain=DSM 42138	GCA_017164735.1	1436133	1436133	type	True	80.9279	900	2373	95	below_threshold
Streptomyces angustmyceticus	strain=NRRL B-2347	GCA_002154415.1	285578	285578	type	True	80.9168	933	2373	95	below_threshold
Actinacidiphila bryophytorum	strain=DSM 42138	GCA_016916835.1	1436133	1436133	type	True	80.8175	1018	2373	95	below_threshold
Streptomyces morookaense	strain=JCM 4793	GCA_014656115.1	1970	1970	type	True	80.8128	1098	2373	95	below_threshold
Streptomyces morookaense	strain=DSM 40503	GCA_013030945.1	1970	1970	type	True	80.7934	1032	2373	95	below_threshold
Streptomyces angustmyceticus	strain=JCM 4053	GCA_019933235.1	285578	285578	type	True	80.7652	1127	2373	95	below_threshold
Streptomyces mobaraensis	strain=DSM 40847	GCA_000342125.1	35621	35621	type	True	80.7241	1013	2373	95	below_threshold
Streptomyces mashuensis	strain=JCM 4059	GCA_014654785.1	33904	33904	type	True	80.7218	1049	2373	95	below_threshold
Streptomyces angustmyceticus	strain=NBRC 3934	GCA_009176265.1	285578	285578	type	True	80.7165	1130	2373	95	below_threshold
Streptomyces orinoci	strain=NRRL B-3379	GCA_003121295.1	67339	67339	type	True	80.6288	1091	2373	95	below_threshold
Streptomyces mobaraensis	strain=DSM 40847	GCA_017916255.1	35621	35621	type	True	80.6288	1056	2373	95	below_threshold
Streptomyces caniferus	strain=NBRC 15389	GCA_009811555.1	285557	285557	type	True	80.5762	1127	2373	95	below_threshold
Streptomyces thermodiastaticus	strain=DSM 40573	GCA_021394575.1	44061	44061	type	True	80.5455	948	2373	95	below_threshold
Actinacidiphila paucisporea	strain=CGMCC 4.2025	GCA_900142575.1	310782	310782	type	True	80.5364	1039	2373	95	below_threshold
Streptomyces albireticuli	strain=NRRL B1670	GCA_021228125.1	1940	1940	type	True	80.45	1073	2373	95	below_threshold
Streptomyces sudanensis	strain=SD 504	GCA_023614315.1	436397	436397	type	True	80.3891	818	2373	95	below_threshold
Streptomyces griseicoloratus	strain=TRM S81-3	GCA_014534645.1	2752516	2752516	type	True	80.3041	1058	2373	95	below_threshold
Streptomyces fuscichromogenes	strain=CGMCC 4.7110	GCA_014645815.1	1324013	1324013	type	True	80.0229	1096	2373	95	below_threshold
Streptomyces dysideae	strain=RV15	GCA_001514305.1	909626	909626	type	True	79.7617	1007	2373	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:08:07,604] [INFO] DFAST Taxonomy check result was written to GCF_024436055.1_ASM2443605v1_genomic.fna/tc_result.tsv
[2024-01-24 12:08:07,604] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:08:07,604] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:08:07,605] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf0321644-eb0d-4801-9cbe-a6427231f91f/dqc_reference/checkm_data
[2024-01-24 12:08:07,606] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:08:07,678] [INFO] Task started: CheckM
[2024-01-24 12:08:07,679] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024436055.1_ASM2443605v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024436055.1_ASM2443605v1_genomic.fna/checkm_input GCF_024436055.1_ASM2443605v1_genomic.fna/checkm_result
[2024-01-24 12:09:16,246] [INFO] Task succeeded: CheckM
[2024-01-24 12:09:16,248] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2024-01-24 12:09:16,274] [INFO] ===== Completeness check finished =====
[2024-01-24 12:09:16,275] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:09:16,275] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024436055.1_ASM2443605v1_genomic.fna/markers.fasta)
[2024-01-24 12:09:16,276] [INFO] Task started: Blastn
[2024-01-24 12:09:16,276] [INFO] Running command: blastn -query GCF_024436055.1_ASM2443605v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf0321644-eb0d-4801-9cbe-a6427231f91f/dqc_reference/reference_markers_gtdb.fasta -out GCF_024436055.1_ASM2443605v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:09:18,364] [INFO] Task succeeded: Blastn
[2024-01-24 12:09:18,371] [INFO] Selected 25 target genomes.
[2024-01-24 12:09:18,371] [INFO] Target genome list was writen to GCF_024436055.1_ASM2443605v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:09:18,424] [INFO] Task started: fastANI
[2024-01-24 12:09:18,424] [INFO] Running command: fastANI --query /var/lib/cwl/stgf5b39ce4-1c60-40d7-8851-868208af4ded/GCF_024436055.1_ASM2443605v1_genomic.fna.gz --refList GCF_024436055.1_ASM2443605v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024436055.1_ASM2443605v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:09:58,711] [INFO] Task succeeded: fastANI
[2024-01-24 12:09:58,735] [INFO] Found 25 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:09:58,735] [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_003144095.1	s__Streptomyces sp003144095	83.4203	1242	2373	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000240165.1	s__Streptomyces cattleya	83.0639	1281	2373	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.99	99.99	1.00	1.00	3	-
GCF_007595705.1	s__Streptomyces sp007595705	81.1716	1121	2373	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001704635.1	s__Streptomyces sparsogenes	80.9785	1094	2373	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.81	99.81	0.87	0.87	2	-
GCF_900188405.1	s__Streptomyces glauciniger	80.9062	1164	2373	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.09	95.09	0.86	0.86	3	-
GCF_016916835.1	s__Streptomyces bryophytorum	80.794	1022	2373	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.96	99.96	0.99	0.99	2	-
GCF_013030945.1	s__Streptomyces morookaense	80.7862	1032	2373	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	100.00	100.00	0.99	0.99	2	-
GCF_014654785.1	s__Streptomyces mashuensis	80.748	1046	2373	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009176265.1	s__Streptomyces angustmyceticus	80.7402	1125	2373	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.96	99.96	1.00	1.00	2	-
GCF_003999195.1	s__Streptomyces sp003999195	80.7058	1062	2373	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000701325.1	s__Streptomyces sp000701325	80.7057	1015	2373	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017916255.1	s__Streptomyces mobaraensis	80.6505	1053	2373	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.59	99.19	0.96	0.92	3	-
GCF_003121295.1	s__Streptomyces orinoci	80.634	1088	2373	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003389455.1	s__Streptomyces inhibens	80.6333	1055	2373	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009811555.1	s__Streptomyces caniferus	80.598	1123	2373	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142575.1	s__Streptomyces paucisporeus	80.5759	1033	2373	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001270575.1	s__Streptomyces decoyicus	80.5501	1049	2373	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.25	96.25	0.87	0.87	2	-
GCF_014253015.1	s__Streptomyces sp014253015	80.5102	1045	2373	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004784465.1	s__Streptomyces griseoluteus	80.4313	981	2373	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.3953	97.39	95.67	0.90	0.82	4	-
GCF_008704855.1	s__Streptomyces platensis	80.4243	1121	2373	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.55	95.21	0.91	0.87	7	-
GCF_008042045.1	s__Streptomyces sp008042045	80.3341	996	2373	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014649855.1	s__Streptomyces roseolus	80.1477	961	2373	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000719555.1	s__Streptomyces sp000719555	80.0691	991	2373	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014596915.1	s__Streptomyces sp014596915	80.0357	1019	2373	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004342105.1	s__Streptomyces sp004342105	80.0288	1097	2373	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 12:09:58,737] [INFO] GTDB search result was written to GCF_024436055.1_ASM2443605v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:09:58,737] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:09:58,742] [INFO] DFAST_QC result json was written to GCF_024436055.1_ASM2443605v1_genomic.fna/dqc_result.json
[2024-01-24 12:09:58,742] [INFO] DFAST_QC completed!
[2024-01-24 12:09:58,742] [INFO] Total running time: 0h2m52s