[2024-01-24 14:53:50,179] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:53:50,181] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:53:50,181] [INFO] DQC Reference Directory: /var/lib/cwl/stg4d39661b-7e1d-4ca3-83bd-f718a8df7f47/dqc_reference
[2024-01-24 14:53:51,358] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:53:51,359] [INFO] Task started: Prodigal
[2024-01-24 14:53:51,359] [INFO] Running command: gunzip -c /var/lib/cwl/stg8c97fdf1-c634-458a-9183-4abe0b235aeb/GCF_012033735.1_ASM1203373v1_genomic.fna.gz | prodigal -d GCF_012033735.1_ASM1203373v1_genomic.fna/cds.fna -a GCF_012033735.1_ASM1203373v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:54:06,004] [INFO] Task succeeded: Prodigal
[2024-01-24 14:54:06,005] [INFO] Task started: HMMsearch
[2024-01-24 14:54:06,005] [INFO] Running command: hmmsearch --tblout GCF_012033735.1_ASM1203373v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4d39661b-7e1d-4ca3-83bd-f718a8df7f47/dqc_reference/reference_markers.hmm GCF_012033735.1_ASM1203373v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:54:06,300] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:54:06,302] [INFO] Found 6/6 markers.
[2024-01-24 14:54:06,359] [INFO] Query marker FASTA was written to GCF_012033735.1_ASM1203373v1_genomic.fna/markers.fasta
[2024-01-24 14:54:06,360] [INFO] Task started: Blastn
[2024-01-24 14:54:06,360] [INFO] Running command: blastn -query GCF_012033735.1_ASM1203373v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4d39661b-7e1d-4ca3-83bd-f718a8df7f47/dqc_reference/reference_markers.fasta -out GCF_012033735.1_ASM1203373v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:54:07,689] [INFO] Task succeeded: Blastn
[2024-01-24 14:54:07,692] [INFO] Selected 20 target genomes.
[2024-01-24 14:54:07,693] [INFO] Target genome list was writen to GCF_012033735.1_ASM1203373v1_genomic.fna/target_genomes.txt
[2024-01-24 14:54:07,720] [INFO] Task started: fastANI
[2024-01-24 14:54:07,720] [INFO] Running command: fastANI --query /var/lib/cwl/stg8c97fdf1-c634-458a-9183-4abe0b235aeb/GCF_012033735.1_ASM1203373v1_genomic.fna.gz --refList GCF_012033735.1_ASM1203373v1_genomic.fna/target_genomes.txt --output GCF_012033735.1_ASM1203373v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:54:35,776] [INFO] Task succeeded: fastANI
[2024-01-24 14:54:35,777] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4d39661b-7e1d-4ca3-83bd-f718a8df7f47/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:54:35,778] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4d39661b-7e1d-4ca3-83bd-f718a8df7f47/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:54:35,795] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:54:35,795] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:54:35,795] [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 lonarensis	strain=NCL716	GCA_012033735.1	700599	700599	type	True	100.0	1722	1743	95	conclusive
Streptomyces bohaiensis	strain=11A07	GCA_012033785.1	1431344	1431344	type	True	90.8161	1231	1743	95	below_threshold
Streptomyces otsuchiensis	strain=OTB305	GCA_004305975.1	2681388	2681388	type	True	83.7472	1078	1743	95	below_threshold
Streptomyces calidiresistens	strain=DSM 42108	GCA_014141525.1	1485586	1485586	type	True	80.6277	591	1743	95	below_threshold
Streptomyces durbertensis	strain=DSM 104538	GCA_014156695.1	2448886	2448886	type	True	80.1265	647	1743	95	below_threshold
Streptomyces alkaliterrae	strain=OF1	GCA_007097205.2	2213162	2213162	type	True	80.0292	673	1743	95	below_threshold
Streptomyces megasporus	strain=NRRL B-16372	GCA_000718985.1	44060	44060	type	True	79.9158	752	1743	95	below_threshold
Streptomyces hainanensis	strain=DSM 41900	GCA_004348415.1	402648	402648	type	True	79.7451	778	1743	95	below_threshold
Streptomyces carminius	strain=TRM SA0054	GCA_002794255.1	2665496	2665496	type	True	79.6272	805	1743	95	below_threshold
Streptomyces zhaozhouensis	strain=CGMCC 4.7095	GCA_900230195.1	1300267	1300267	type	True	79.5299	872	1743	95	below_threshold
Streptomyces griseocarneus	strain=JCM 4580	GCA_014655595.1	51201	51201	type	True	79.4829	733	1743	95	below_threshold
Streptomyces gobiensis	strain=1_25	GCA_021216675.1	2875706	2875706	type	True	79.4087	582	1743	95	below_threshold
Streptomyces marincola	strain=SCSIO 64649	GCA_020410765.1	2878388	2878388	type	True	79.3643	850	1743	95	below_threshold
Streptomyces diacarni	strain=LHW51701	GCA_003323715.1	2800381	2800381	type	True	79.2193	734	1743	95	below_threshold
Streptomyces rubrisoli	strain=DSM 42083	GCA_024436055.1	1387313	1387313	type	True	79.1928	657	1743	95	below_threshold
Streptomyces albireticuli	strain=NRRL B1670	GCA_021228125.1	1940	1940	type	True	79.1754	788	1743	95	below_threshold
Actinacidiphila glaucinigra	strain=CGMCC 4.1858	GCA_900188405.1	235986	235986	type	True	79.1089	832	1743	95	below_threshold
Streptomyces orinoci	strain=NRRL B-3379	GCA_003121295.1	67339	67339	type	True	79.0598	691	1743	95	below_threshold
Streptomyces olivaceoviridis	strain=JCM 4499	GCA_014650115.1	1921	1921	type	True	78.8831	799	1743	95	below_threshold
Streptomyces panaciradicis	strain=NBRC 109811	GCA_023516615.1	1470261	1470261	type	True	78.769	771	1743	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:54:35,797] [INFO] DFAST Taxonomy check result was written to GCF_012033735.1_ASM1203373v1_genomic.fna/tc_result.tsv
[2024-01-24 14:54:35,797] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:54:35,797] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:54:35,798] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4d39661b-7e1d-4ca3-83bd-f718a8df7f47/dqc_reference/checkm_data
[2024-01-24 14:54:35,799] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:54:35,858] [INFO] Task started: CheckM
[2024-01-24 14:54:35,858] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_012033735.1_ASM1203373v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_012033735.1_ASM1203373v1_genomic.fna/checkm_input GCF_012033735.1_ASM1203373v1_genomic.fna/checkm_result
[2024-01-24 14:55:30,135] [INFO] Task succeeded: CheckM
[2024-01-24 14:55:30,137] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:55:30,159] [INFO] ===== Completeness check finished =====
[2024-01-24 14:55:30,159] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:55:30,160] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_012033735.1_ASM1203373v1_genomic.fna/markers.fasta)
[2024-01-24 14:55:30,160] [INFO] Task started: Blastn
[2024-01-24 14:55:30,160] [INFO] Running command: blastn -query GCF_012033735.1_ASM1203373v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4d39661b-7e1d-4ca3-83bd-f718a8df7f47/dqc_reference/reference_markers_gtdb.fasta -out GCF_012033735.1_ASM1203373v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:55:32,221] [INFO] Task succeeded: Blastn
[2024-01-24 14:55:32,225] [INFO] Selected 12 target genomes.
[2024-01-24 14:55:32,225] [INFO] Target genome list was writen to GCF_012033735.1_ASM1203373v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:55:32,242] [INFO] Task started: fastANI
[2024-01-24 14:55:32,242] [INFO] Running command: fastANI --query /var/lib/cwl/stg8c97fdf1-c634-458a-9183-4abe0b235aeb/GCF_012033735.1_ASM1203373v1_genomic.fna.gz --refList GCF_012033735.1_ASM1203373v1_genomic.fna/target_genomes_gtdb.txt --output GCF_012033735.1_ASM1203373v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:55:53,793] [INFO] Task succeeded: fastANI
[2024-01-24 14:55:53,808] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:55:53,808] [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_012033735.1	s__Streptomyces lonarensis	100.0	1722	1743	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_012033785.1	s__Streptomyces bohaiensis	90.8021	1232	1743	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012034385.1	s__Streptomyces sp012034385	90.2824	1307	1743	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	83.7492	1078	1743	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.30	98.24	0.80	0.78	3	-
GCF_007097205.2	s__Streptomyces alkaliterrae	80.103	663	1743	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.63	99.32	0.91	0.86	3	-
GCF_004348315.1	s__Streptomyces sp004348315	79.7217	767	1743	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900230195.1	s__Streptomyces zhaozhouensis	79.5888	863	1743	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007595705.1	s__Streptomyces sp007595705	79.3182	806	1743	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003665095.1	s__Streptomyces sp003665095	79.2877	790	1743	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900188405.1	s__Streptomyces glauciniger	79.1587	820	1743	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.09	95.09	0.86	0.86	3	-
GCF_000968685.2	s__Streptomyces antioxidans	78.8495	775	1743	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016741935.1	s__Streptomyces sp016741935	78.5605	861	1743	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0488	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:55:53,810] [INFO] GTDB search result was written to GCF_012033735.1_ASM1203373v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:55:53,810] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:55:53,814] [INFO] DFAST_QC result json was written to GCF_012033735.1_ASM1203373v1_genomic.fna/dqc_result.json
[2024-01-24 14:55:53,814] [INFO] DFAST_QC completed!
[2024-01-24 14:55:53,814] [INFO] Total running time: 0h2m4s