[2024-01-24 13:25:47,045] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:25:47,047] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:25:47,047] [INFO] DQC Reference Directory: /var/lib/cwl/stg67e23f7f-4853-4384-b634-e1070452b624/dqc_reference
[2024-01-24 13:25:48,482] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:25:48,483] [INFO] Task started: Prodigal
[2024-01-24 13:25:48,483] [INFO] Running command: gunzip -c /var/lib/cwl/stge35fb386-613f-4f6a-a0bf-6cbccde319ce/GCF_021216675.1_ASM2121667v1_genomic.fna.gz | prodigal -d GCF_021216675.1_ASM2121667v1_genomic.fna/cds.fna -a GCF_021216675.1_ASM2121667v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:26:05,663] [INFO] Task succeeded: Prodigal
[2024-01-24 13:26:05,664] [INFO] Task started: HMMsearch
[2024-01-24 13:26:05,664] [INFO] Running command: hmmsearch --tblout GCF_021216675.1_ASM2121667v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg67e23f7f-4853-4384-b634-e1070452b624/dqc_reference/reference_markers.hmm GCF_021216675.1_ASM2121667v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:26:05,996] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:26:05,998] [INFO] Found 6/6 markers.
[2024-01-24 13:26:06,047] [INFO] Query marker FASTA was written to GCF_021216675.1_ASM2121667v1_genomic.fna/markers.fasta
[2024-01-24 13:26:06,048] [INFO] Task started: Blastn
[2024-01-24 13:26:06,048] [INFO] Running command: blastn -query GCF_021216675.1_ASM2121667v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg67e23f7f-4853-4384-b634-e1070452b624/dqc_reference/reference_markers.fasta -out GCF_021216675.1_ASM2121667v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:26:07,257] [INFO] Task succeeded: Blastn
[2024-01-24 13:26:07,261] [INFO] Selected 24 target genomes.
[2024-01-24 13:26:07,261] [INFO] Target genome list was writen to GCF_021216675.1_ASM2121667v1_genomic.fna/target_genomes.txt
[2024-01-24 13:26:07,269] [INFO] Task started: fastANI
[2024-01-24 13:26:07,270] [INFO] Running command: fastANI --query /var/lib/cwl/stge35fb386-613f-4f6a-a0bf-6cbccde319ce/GCF_021216675.1_ASM2121667v1_genomic.fna.gz --refList GCF_021216675.1_ASM2121667v1_genomic.fna/target_genomes.txt --output GCF_021216675.1_ASM2121667v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:26:46,110] [INFO] Task succeeded: fastANI
[2024-01-24 13:26:46,111] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg67e23f7f-4853-4384-b634-e1070452b624/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:26:46,111] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg67e23f7f-4853-4384-b634-e1070452b624/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:26:46,129] [INFO] Found 24 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:26:46,129] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:26:46,129] [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 gobiensis	strain=1_25	GCA_021216675.1	2875706	2875706	type	True	100.0	1895	1897	95	conclusive
Streptomyces radiopugnans	strain=CGMCC 4.3519	GCA_900110735.1	403935	403935	type	True	81.4345	957	1897	95	below_threshold
Streptomyces pini	strain=PL19	GCA_900114215.1	1520580	1520580	type	True	81.3701	955	1897	95	below_threshold
Streptomyces barkulensis	strain=RC 1831	GCA_002811705.2	1257026	1257026	type	True	81.3233	940	1897	95	below_threshold
Streptomyces barkulensis	strain=RC 1831	GCA_002843305.1	1257026	1257026	type	True	81.3113	963	1897	95	below_threshold
Streptomyces durbertensis	strain=DSM 104538	GCA_014156695.1	2448886	2448886	type	True	81.2559	809	1897	95	below_threshold
Streptomyces alkaliterrae	strain=OF1	GCA_007097205.2	2213162	2213162	type	True	81.2092	846	1897	95	below_threshold
Streptomyces carminius	strain=TRM SA0054	GCA_002794255.1	2665496	2665496	type	True	81.1901	926	1897	95	below_threshold
Streptomyces taklimakanensis	strain=TRM43335	GCA_009709575.1	2569853	2569853	type	True	81.1232	906	1897	95	below_threshold
Streptomyces megasporus	strain=NRRL B-16372	GCA_000718985.1	44060	44060	type	True	81.1016	897	1897	95	below_threshold
Streptomyces tardus	strain=P38-E01	GCA_018101125.2	2780544	2780544	type	True	80.8363	895	1897	95	below_threshold
Streptomyces platensis	strain=DSM 40041	GCA_002119195.1	58346	58346	type	True	80.7013	973	1897	95	below_threshold
Streptomyces platensis	strain=ATCC 23948	GCA_008704855.1	58346	58346	type	True	80.6845	990	1897	95	below_threshold
Streptomyces angustmyceticus	strain=JCM 4053	GCA_019933235.1	285578	285578	type	True	80.6636	1008	1897	95	below_threshold
Streptomyces palmae	strain=JCM 31289	GCA_004684805.1	1701085	1701085	type	True	80.6409	826	1897	95	below_threshold
Streptomyces rapamycinicus	strain=NRRL 5491	GCA_024298965.1	1226757	1226757	type	True	80.5917	1024	1897	95	below_threshold
Streptomyces lichenis	strain=LCR6-01	GCA_023218175.1	2306967	2306967	type	True	80.4013	922	1897	95	below_threshold
Streptomyces albireticuli	strain=NRRL B1670	GCA_021228125.1	1940	1940	type	True	80.3718	952	1897	95	below_threshold
Streptomyces monomycini	strain=NRRL B-24309	GCA_022271435.1	371720	371720	type	True	80.3596	974	1897	95	below_threshold
Streptomyces otsuchiensis	strain=OTB305	GCA_004305975.1	2681388	2681388	type	True	79.8425	649	1897	95	below_threshold
Streptomyces phaeolivaceus	strain=GY16	GCA_009184865.1	2653200	2653200	type	True	79.776	897	1897	95	below_threshold
Streptomyces tailanensis	strain=TRM68348	GCA_008386495.1	2569858	2569858	type	True	79.7642	848	1897	95	below_threshold
Streptomyces dysideae	strain=RV15	GCA_001514305.1	909626	909626	type	True	79.7598	925	1897	95	below_threshold
Streptomyces adelaidensis	strain=CAP261	GCA_016598475.1	2796465	2796465	type	True	79.4957	859	1897	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:26:46,131] [INFO] DFAST Taxonomy check result was written to GCF_021216675.1_ASM2121667v1_genomic.fna/tc_result.tsv
[2024-01-24 13:26:46,131] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:26:46,132] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:26:46,132] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg67e23f7f-4853-4384-b634-e1070452b624/dqc_reference/checkm_data
[2024-01-24 13:26:46,133] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:26:46,190] [INFO] Task started: CheckM
[2024-01-24 13:26:46,190] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_021216675.1_ASM2121667v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_021216675.1_ASM2121667v1_genomic.fna/checkm_input GCF_021216675.1_ASM2121667v1_genomic.fna/checkm_result
[2024-01-24 13:27:39,028] [INFO] Task succeeded: CheckM
[2024-01-24 13:27:39,030] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:27:39,052] [INFO] ===== Completeness check finished =====
[2024-01-24 13:27:39,053] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:27:39,053] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_021216675.1_ASM2121667v1_genomic.fna/markers.fasta)
[2024-01-24 13:27:39,054] [INFO] Task started: Blastn
[2024-01-24 13:27:39,054] [INFO] Running command: blastn -query GCF_021216675.1_ASM2121667v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg67e23f7f-4853-4384-b634-e1070452b624/dqc_reference/reference_markers_gtdb.fasta -out GCF_021216675.1_ASM2121667v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:27:40,865] [INFO] Task succeeded: Blastn
[2024-01-24 13:27:40,869] [INFO] Selected 24 target genomes.
[2024-01-24 13:27:40,869] [INFO] Target genome list was writen to GCF_021216675.1_ASM2121667v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:27:40,932] [INFO] Task started: fastANI
[2024-01-24 13:27:40,933] [INFO] Running command: fastANI --query /var/lib/cwl/stge35fb386-613f-4f6a-a0bf-6cbccde319ce/GCF_021216675.1_ASM2121667v1_genomic.fna.gz --refList GCF_021216675.1_ASM2121667v1_genomic.fna/target_genomes_gtdb.txt --output GCF_021216675.1_ASM2121667v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:28:13,232] [INFO] Task succeeded: fastANI
[2024-01-24 13:28:13,256] [INFO] Found 24 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:28:13,256] [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_900110735.1	s__Streptomyces radiopugnans	81.4531	954	1897	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114215.1	s__Streptomyces pini	81.3694	957	1897	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	96.765	N/A	N/A	N/A	N/A	1	-
GCF_002843305.1	s__Streptomyces barkulensis	81.3262	961	1897	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	96.765	99.92	99.92	0.99	0.99	2	-
GCF_017114865.1	s__Streptomyces verrucosisporus	81.3134	934	1897	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.1585	N/A	N/A	N/A	N/A	1	-
GCF_007097205.2	s__Streptomyces alkaliterrae	81.2144	846	1897	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.63	99.32	0.91	0.86	3	-
GCF_002794255.1	s__Streptomyces carminius	81.2126	924	1897	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	81.1091	906	1897	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000424845.1	s__Streptomyces sp000424845	81.0902	919	1897	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	81.0898	899	1897	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018101125.2	s__Streptomyces sp018101125	80.8239	890	1897	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008704855.1	s__Streptomyces platensis	80.7208	988	1897	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.55	95.21	0.91	0.87	7	-
GCF_004684805.1	s__Streptomyces palmae	80.6886	820	1897	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	80.61	986	1897	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.96	99.96	1.00	1.00	2	-
GCF_000424825.1	s__Streptomyces sp000424825	80.5599	916	1897	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017676365.1	s__Streptomyces oryzae	80.4717	875	1897	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002224125.1	s__Streptomyces sp002224125	80.4098	993	1897	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001590865.1	s__Streptomyces sp001590865	80.4009	936	1897	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000716335.1	s__Streptomyces sp000716335	80.2159	902	1897	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004305975.1	s__Streptomyces otsuchiensis	79.8295	651	1897	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.30	98.24	0.80	0.78	3	-
GCF_001514305.1	s__Streptomyces dysideae	79.7685	923	1897	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009184865.1	s__Streptomyces phaeolivaceus	79.7626	902	1897	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008386495.1	s__Streptomyces tailanensis	79.7525	849	1897	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016598475.1	s__Streptomyces adelaidensis	79.5058	858	1897	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013698395.1	s__JACCUZ01 sp013698395	76.7676	149	1897	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__JACCUZ01;f__JACCUZ01;g__JACCUZ01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:28:13,258] [INFO] GTDB search result was written to GCF_021216675.1_ASM2121667v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:28:13,259] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:28:13,264] [INFO] DFAST_QC result json was written to GCF_021216675.1_ASM2121667v1_genomic.fna/dqc_result.json
[2024-01-24 13:28:13,264] [INFO] DFAST_QC completed!
[2024-01-24 13:28:13,264] [INFO] Total running time: 0h2m26s