[2024-01-24 13:57:32,218] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:57:32,220] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:57:32,220] [INFO] DQC Reference Directory: /var/lib/cwl/stg544d1e90-7033-4652-bd3c-9789c442f497/dqc_reference
[2024-01-24 13:57:33,636] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:57:33,637] [INFO] Task started: Prodigal
[2024-01-24 13:57:33,638] [INFO] Running command: gunzip -c /var/lib/cwl/stgc9cca045-9bdc-4fa4-a7a2-b27f9d048f06/GCF_004305975.1_ASM430597v1_genomic.fna.gz | prodigal -d GCF_004305975.1_ASM430597v1_genomic.fna/cds.fna -a GCF_004305975.1_ASM430597v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:57:49,023] [INFO] Task succeeded: Prodigal
[2024-01-24 13:57:49,023] [INFO] Task started: HMMsearch
[2024-01-24 13:57:49,023] [INFO] Running command: hmmsearch --tblout GCF_004305975.1_ASM430597v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg544d1e90-7033-4652-bd3c-9789c442f497/dqc_reference/reference_markers.hmm GCF_004305975.1_ASM430597v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:57:49,343] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:57:49,344] [INFO] Found 6/6 markers.
[2024-01-24 13:57:49,400] [INFO] Query marker FASTA was written to GCF_004305975.1_ASM430597v1_genomic.fna/markers.fasta
[2024-01-24 13:57:49,401] [INFO] Task started: Blastn
[2024-01-24 13:57:49,401] [INFO] Running command: blastn -query GCF_004305975.1_ASM430597v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg544d1e90-7033-4652-bd3c-9789c442f497/dqc_reference/reference_markers.fasta -out GCF_004305975.1_ASM430597v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:57:50,752] [INFO] Task succeeded: Blastn
[2024-01-24 13:57:50,756] [INFO] Selected 19 target genomes.
[2024-01-24 13:57:50,757] [INFO] Target genome list was writen to GCF_004305975.1_ASM430597v1_genomic.fna/target_genomes.txt
[2024-01-24 13:57:50,763] [INFO] Task started: fastANI
[2024-01-24 13:57:50,763] [INFO] Running command: fastANI --query /var/lib/cwl/stgc9cca045-9bdc-4fa4-a7a2-b27f9d048f06/GCF_004305975.1_ASM430597v1_genomic.fna.gz --refList GCF_004305975.1_ASM430597v1_genomic.fna/target_genomes.txt --output GCF_004305975.1_ASM430597v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:58:17,932] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:17,932] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg544d1e90-7033-4652-bd3c-9789c442f497/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:58:17,933] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg544d1e90-7033-4652-bd3c-9789c442f497/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:58:17,948] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:58:17,948] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:58:17,949] [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 otsuchiensis	strain=OTB305	GCA_004305975.1	2681388	2681388	type	True	100.0	1731	1746	95	conclusive
Streptomyces bohaiensis	strain=11A07	GCA_012033785.1	1431344	1431344	type	True	84.0307	1034	1746	95	below_threshold
Streptomyces lonarensis	strain=NCL716	GCA_012033735.1	700599	700599	type	True	83.8924	1079	1746	95	below_threshold
Streptomyces calidiresistens	strain=DSM 42108	GCA_014141525.1	1485586	1485586	type	True	80.855	633	1746	95	below_threshold
Streptomyces megasporus	strain=NRRL B-16372	GCA_000718985.1	44060	44060	type	True	80.3039	774	1746	95	below_threshold
Streptomyces durbertensis	strain=DSM 104538	GCA_014156695.1	2448886	2448886	type	True	80.2974	686	1746	95	below_threshold
Streptomyces alkaliterrae	strain=OF1	GCA_007097205.2	2213162	2213162	type	True	80.2491	693	1746	95	below_threshold
Streptomyces zhaozhouensis	strain=CGMCC 4.7095	GCA_900230195.1	1300267	1300267	type	True	80.0352	885	1746	95	below_threshold
Streptomyces benahoarensis	strain=MZ03-37	GCA_007280575.1	2595054	2595054	type	True	79.8599	709	1746	95	below_threshold
Streptomyces tardus	strain=P38-E01	GCA_018101125.2	2780544	2780544	type	True	79.8013	798	1746	95	below_threshold
Streptomyces lichenis	strain=LCR6-01	GCA_023218175.1	2306967	2306967	type	True	79.7789	834	1746	95	below_threshold
Streptomyces marincola	strain=SCSIO 64649	GCA_020410765.1	2878388	2878388	type	True	79.6618	860	1746	95	below_threshold
Streptomyces pactum	strain=ATCC 27456	GCA_016031615.1	68249	68249	type	True	79.5494	903	1746	95	below_threshold
Streptomyces hoynatensis	strain=KCTC 29097	GCA_003626535.1	1141874	1141874	type	True	79.4883	880	1746	95	below_threshold
Streptomyces rubrisoli	strain=DSM 42083	GCA_024436055.1	1387313	1387313	type	True	79.4444	693	1746	95	below_threshold
Streptomyces sennicomposti	strain=RCPT1-4	GCA_019890635.1	2873384	2873384	type	True	79.3896	805	1746	95	below_threshold
Streptomyces rapamycinicus	strain=NRRL 5491	GCA_024298965.1	1226757	1226757	type	True	79.355	877	1746	95	below_threshold
Streptomyces orinoci	strain=NRRL B-3379	GCA_003121295.1	67339	67339	type	True	79.3033	744	1746	95	below_threshold
Streptomyces panaciradicis	strain=NBRC 109811	GCA_023516615.1	1470261	1470261	type	True	79.1274	803	1746	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:58:17,950] [INFO] DFAST Taxonomy check result was written to GCF_004305975.1_ASM430597v1_genomic.fna/tc_result.tsv
[2024-01-24 13:58:17,951] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:58:17,951] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:58:17,951] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg544d1e90-7033-4652-bd3c-9789c442f497/dqc_reference/checkm_data
[2024-01-24 13:58:17,953] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:58:18,012] [INFO] Task started: CheckM
[2024-01-24 13:58:18,012] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004305975.1_ASM430597v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004305975.1_ASM430597v1_genomic.fna/checkm_input GCF_004305975.1_ASM430597v1_genomic.fna/checkm_result
[2024-01-24 13:59:08,862] [INFO] Task succeeded: CheckM
[2024-01-24 13:59:08,863] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:59:08,882] [INFO] ===== Completeness check finished =====
[2024-01-24 13:59:08,883] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:59:08,883] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004305975.1_ASM430597v1_genomic.fna/markers.fasta)
[2024-01-24 13:59:08,883] [INFO] Task started: Blastn
[2024-01-24 13:59:08,883] [INFO] Running command: blastn -query GCF_004305975.1_ASM430597v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg544d1e90-7033-4652-bd3c-9789c442f497/dqc_reference/reference_markers_gtdb.fasta -out GCF_004305975.1_ASM430597v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:59:10,961] [INFO] Task succeeded: Blastn
[2024-01-24 13:59:10,971] [INFO] Selected 13 target genomes.
[2024-01-24 13:59:10,972] [INFO] Target genome list was writen to GCF_004305975.1_ASM430597v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:59:11,003] [INFO] Task started: fastANI
[2024-01-24 13:59:11,004] [INFO] Running command: fastANI --query /var/lib/cwl/stgc9cca045-9bdc-4fa4-a7a2-b27f9d048f06/GCF_004305975.1_ASM430597v1_genomic.fna.gz --refList GCF_004305975.1_ASM430597v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004305975.1_ASM430597v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:59:28,962] [INFO] Task succeeded: fastANI
[2024-01-24 13:59:28,976] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:59:28,976] [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_004305975.1	s__Streptomyces otsuchiensis	100.0	1731	1746	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.30	98.24	0.80	0.78	3	conclusive
GCF_012033785.1	s__Streptomyces bohaiensis	84.0317	1035	1746	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012033735.1	s__Streptomyces lonarensis	83.8853	1080	1746	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	83.861	1056	1746	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900116145.1	s__Streptomyces harbinensis	80.6581	912	1746	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.20	99.18	0.96	0.96	3	-
GCF_000718985.1	s__Streptomyces megasporus	80.3425	769	1746	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007097205.2	s__Streptomyces alkaliterrae	80.2297	695	1746	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	79.9124	805	1746	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007280575.1	s__Streptomyces sp007280575	79.8781	708	1746	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	79.8719	748	1746	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	79.7951	798	1746	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001509485.1	s__Streptomyces sp001509485	79.7447	815	1746	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001653515.1	s__Streptomyces sp001653515	79.2824	706	1746	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 13:59:28,978] [INFO] GTDB search result was written to GCF_004305975.1_ASM430597v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:59:28,979] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:59:28,984] [INFO] DFAST_QC result json was written to GCF_004305975.1_ASM430597v1_genomic.fna/dqc_result.json
[2024-01-24 13:59:28,984] [INFO] DFAST_QC completed!
[2024-01-24 13:59:28,984] [INFO] Total running time: 0h1m57s