[2024-01-24 11:12:57,726] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:12:57,729] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:12:57,729] [INFO] DQC Reference Directory: /var/lib/cwl/stgb4365a1a-a9e0-4d7e-9b08-55e78957e6f1/dqc_reference
[2024-01-24 11:12:59,101] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:12:59,102] [INFO] Task started: Prodigal
[2024-01-24 11:12:59,102] [INFO] Running command: gunzip -c /var/lib/cwl/stg91f25486-8a53-4ec5-93ec-d709ffdadd43/GCF_012034385.1_ASM1203438v1_genomic.fna.gz | prodigal -d GCF_012034385.1_ASM1203438v1_genomic.fna/cds.fna -a GCF_012034385.1_ASM1203438v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:13:13,563] [INFO] Task succeeded: Prodigal
[2024-01-24 11:13:13,563] [INFO] Task started: HMMsearch
[2024-01-24 11:13:13,563] [INFO] Running command: hmmsearch --tblout GCF_012034385.1_ASM1203438v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb4365a1a-a9e0-4d7e-9b08-55e78957e6f1/dqc_reference/reference_markers.hmm GCF_012034385.1_ASM1203438v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:13:13,916] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:13:13,917] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg91f25486-8a53-4ec5-93ec-d709ffdadd43/GCF_012034385.1_ASM1203438v1_genomic.fna.gz]
[2024-01-24 11:13:13,965] [INFO] Query marker FASTA was written to GCF_012034385.1_ASM1203438v1_genomic.fna/markers.fasta
[2024-01-24 11:13:13,965] [INFO] Task started: Blastn
[2024-01-24 11:13:13,965] [INFO] Running command: blastn -query GCF_012034385.1_ASM1203438v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb4365a1a-a9e0-4d7e-9b08-55e78957e6f1/dqc_reference/reference_markers.fasta -out GCF_012034385.1_ASM1203438v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:13:15,400] [INFO] Task succeeded: Blastn
[2024-01-24 11:13:15,403] [INFO] Selected 17 target genomes.
[2024-01-24 11:13:15,404] [INFO] Target genome list was writen to GCF_012034385.1_ASM1203438v1_genomic.fna/target_genomes.txt
[2024-01-24 11:13:15,415] [INFO] Task started: fastANI
[2024-01-24 11:13:15,416] [INFO] Running command: fastANI --query /var/lib/cwl/stg91f25486-8a53-4ec5-93ec-d709ffdadd43/GCF_012034385.1_ASM1203438v1_genomic.fna.gz --refList GCF_012034385.1_ASM1203438v1_genomic.fna/target_genomes.txt --output GCF_012034385.1_ASM1203438v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:13:39,466] [INFO] Task succeeded: fastANI
[2024-01-24 11:13:39,467] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb4365a1a-a9e0-4d7e-9b08-55e78957e6f1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:13:39,468] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb4365a1a-a9e0-4d7e-9b08-55e78957e6f1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:13:39,487] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:13:39,487] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:13:39,487] [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	90.1955	1320	1666	95	below_threshold
Streptomyces bohaiensis	strain=11A07	GCA_012033785.1	1431344	1431344	type	True	89.5467	1199	1666	95	below_threshold
Streptomyces otsuchiensis	strain=OTB305	GCA_004305975.1	2681388	2681388	type	True	83.8411	1067	1666	95	below_threshold
Streptomyces alkaliterrae	strain=OF1	GCA_007097205.2	2213162	2213162	type	True	79.8614	644	1666	95	below_threshold
Streptomyces tardus	strain=P38-E01	GCA_018101125.2	2780544	2780544	type	True	79.8529	727	1666	95	below_threshold
Streptomyces durbertensis	strain=DSM 104538	GCA_014156695.1	2448886	2448886	type	True	79.7942	631	1666	95	below_threshold
Streptomyces megasporus	strain=NRRL B-16372	GCA_000718985.1	44060	44060	type	True	79.783	724	1666	95	below_threshold
Streptomyces chumphonensis	strain=KK1-2	GCA_014779715.1	1214925	1214925	type	True	79.7399	692	1666	95	below_threshold
Streptomyces hainanensis	strain=DSM 41900	GCA_004348415.1	402648	402648	type	True	79.3647	788	1666	95	below_threshold
Streptomyces gobiensis	strain=1_25	GCA_021216675.1	2875706	2875706	type	True	79.2893	551	1666	95	below_threshold
Streptomyces harenosi	strain=PRKS01-65	GCA_011008945.1	2697029	2697029	type	True	79.2235	705	1666	95	below_threshold
Streptomyces marincola	strain=SCSIO 64649	GCA_020410765.1	2878388	2878388	type	True	79.2045	796	1666	95	below_threshold
Streptomyces thermodiastaticus	strain=DSM 40573	GCA_021394575.1	44061	44061	type	True	79.1661	692	1666	95	below_threshold
Streptomyces sennicomposti	strain=RCPT1-4	GCA_019890635.1	2873384	2873384	type	True	79.0062	730	1666	95	below_threshold
Streptomyces diacarni	strain=LHW51701	GCA_003323715.1	2800381	2800381	type	True	78.9994	718	1666	95	below_threshold
Streptomyces alfalfae	strain=XY25	GCA_004212445.1	1642299	1642299	type	True	78.9324	684	1666	95	below_threshold
Streptomyces sabulosicollis	strain=PRKS01-29	GCA_016103465.1	2715963	2715963	type	True	78.8425	720	1666	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:13:39,489] [INFO] DFAST Taxonomy check result was written to GCF_012034385.1_ASM1203438v1_genomic.fna/tc_result.tsv
[2024-01-24 11:13:39,490] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:13:39,490] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:13:39,490] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb4365a1a-a9e0-4d7e-9b08-55e78957e6f1/dqc_reference/checkm_data
[2024-01-24 11:13:39,491] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:13:39,548] [INFO] Task started: CheckM
[2024-01-24 11:13:39,548] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_012034385.1_ASM1203438v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_012034385.1_ASM1203438v1_genomic.fna/checkm_input GCF_012034385.1_ASM1203438v1_genomic.fna/checkm_result
[2024-01-24 11:14:28,656] [INFO] Task succeeded: CheckM
[2024-01-24 11:14:28,658] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:14:28,675] [INFO] ===== Completeness check finished =====
[2024-01-24 11:14:28,675] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:14:28,676] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_012034385.1_ASM1203438v1_genomic.fna/markers.fasta)
[2024-01-24 11:14:28,676] [INFO] Task started: Blastn
[2024-01-24 11:14:28,676] [INFO] Running command: blastn -query GCF_012034385.1_ASM1203438v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb4365a1a-a9e0-4d7e-9b08-55e78957e6f1/dqc_reference/reference_markers_gtdb.fasta -out GCF_012034385.1_ASM1203438v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:14:30,932] [INFO] Task succeeded: Blastn
[2024-01-24 11:14:30,935] [INFO] Selected 10 target genomes.
[2024-01-24 11:14:30,935] [INFO] Target genome list was writen to GCF_012034385.1_ASM1203438v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:14:30,954] [INFO] Task started: fastANI
[2024-01-24 11:14:30,955] [INFO] Running command: fastANI --query /var/lib/cwl/stg91f25486-8a53-4ec5-93ec-d709ffdadd43/GCF_012034385.1_ASM1203438v1_genomic.fna.gz --refList GCF_012034385.1_ASM1203438v1_genomic.fna/target_genomes_gtdb.txt --output GCF_012034385.1_ASM1203438v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:14:45,441] [INFO] Task succeeded: fastANI
[2024-01-24 11:14:45,454] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:14:45,455] [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_012034385.1	s__Streptomyces sp012034385	100.0	1641	1666	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_012033735.1	s__Streptomyces lonarensis	90.2203	1318	1666	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012033785.1	s__Streptomyces bohaiensis	89.5854	1195	1666	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	83.823	1070	1666	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.30	98.24	0.80	0.78	3	-
GCF_018101125.2	s__Streptomyces sp018101125	79.9051	721	1666	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	79.9008	637	1666	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.63	99.32	0.91	0.86	3	-
GCF_000718985.1	s__Streptomyces megasporus	79.7761	725	1666	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002794255.1	s__Streptomyces carminius	79.6375	755	1666	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004348315.1	s__Streptomyces sp004348315	79.4916	734	1666	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005405945.1	s__Streptomyces violaceusniger	78.9144	755	1666	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.67	97.67	0.85	0.85	2	-
--------------------------------------------------------------------------------
[2024-01-24 11:14:45,456] [INFO] GTDB search result was written to GCF_012034385.1_ASM1203438v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:14:45,457] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:14:45,461] [INFO] DFAST_QC result json was written to GCF_012034385.1_ASM1203438v1_genomic.fna/dqc_result.json
[2024-01-24 11:14:45,461] [INFO] DFAST_QC completed!
[2024-01-24 11:14:45,462] [INFO] Total running time: 0h1m48s