[2024-01-24 13:28:01,960] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:28:01,963] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:28:01,963] [INFO] DQC Reference Directory: /var/lib/cwl/stga63bcdd4-e590-4d09-a376-dab8103c88b4/dqc_reference
[2024-01-24 13:28:03,219] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:28:03,220] [INFO] Task started: Prodigal
[2024-01-24 13:28:03,220] [INFO] Running command: gunzip -c /var/lib/cwl/stgf7bad2de-fa90-48cb-983c-3088365398e3/GCF_020410765.1_ASM2041076v1_genomic.fna.gz | prodigal -d GCF_020410765.1_ASM2041076v1_genomic.fna/cds.fna -a GCF_020410765.1_ASM2041076v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:28:23,715] [INFO] Task succeeded: Prodigal
[2024-01-24 13:28:23,716] [INFO] Task started: HMMsearch
[2024-01-24 13:28:23,716] [INFO] Running command: hmmsearch --tblout GCF_020410765.1_ASM2041076v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga63bcdd4-e590-4d09-a376-dab8103c88b4/dqc_reference/reference_markers.hmm GCF_020410765.1_ASM2041076v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:28:24,026] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:28:24,027] [INFO] Found 6/6 markers.
[2024-01-24 13:28:24,082] [INFO] Query marker FASTA was written to GCF_020410765.1_ASM2041076v1_genomic.fna/markers.fasta
[2024-01-24 13:28:24,083] [INFO] Task started: Blastn
[2024-01-24 13:28:24,083] [INFO] Running command: blastn -query GCF_020410765.1_ASM2041076v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga63bcdd4-e590-4d09-a376-dab8103c88b4/dqc_reference/reference_markers.fasta -out GCF_020410765.1_ASM2041076v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:28:25,483] [INFO] Task succeeded: Blastn
[2024-01-24 13:28:25,487] [INFO] Selected 17 target genomes.
[2024-01-24 13:28:25,487] [INFO] Target genome list was writen to GCF_020410765.1_ASM2041076v1_genomic.fna/target_genomes.txt
[2024-01-24 13:28:25,500] [INFO] Task started: fastANI
[2024-01-24 13:28:25,500] [INFO] Running command: fastANI --query /var/lib/cwl/stgf7bad2de-fa90-48cb-983c-3088365398e3/GCF_020410765.1_ASM2041076v1_genomic.fna.gz --refList GCF_020410765.1_ASM2041076v1_genomic.fna/target_genomes.txt --output GCF_020410765.1_ASM2041076v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:28:55,006] [INFO] Task succeeded: fastANI
[2024-01-24 13:28:55,006] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga63bcdd4-e590-4d09-a376-dab8103c88b4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:28:55,006] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga63bcdd4-e590-4d09-a376-dab8103c88b4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:28:55,019] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:28:55,019] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:28:55,020] [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 marincola	strain=SCSIO 64649	GCA_020410765.1	2878388	2878388	type	True	100.0	2209	2209	95	conclusive
Streptomyces radicis	strain=DS1-2	GCA_003626575.1	1750517	1750517	type	True	82.5566	1378	2209	95	below_threshold
Streptomyces specialis	strain=type strain: GW41-1564	GCA_001493375.1	498367	498367	type	True	82.4788	1085	2209	95	below_threshold
Streptomyces hainanensis	strain=DSM 41900	GCA_004348415.1	402648	402648	type	True	81.5923	1129	2209	95	below_threshold
Streptomyces hoynatensis	strain=KCTC 29097	GCA_003626535.1	1141874	1141874	type	True	81.4357	1285	2209	95	below_threshold
Streptomyces triticirhizae	strain=NEAU-YY642	GCA_003696235.1	2483353	2483353	type	True	81.2879	1112	2209	95	below_threshold
Streptomyces mimosae	strain=3MP-10	GCA_006334995.2	2586635	2586635	type	True	81.1944	1247	2209	95	below_threshold
Streptomyces zhaozhouensis	strain=CGMCC 4.7095	GCA_900230195.1	1300267	1300267	type	True	81.1015	1176	2209	95	below_threshold
Streptomyces xiamenensis	strain=318	GCA_000993785.3	408015	408015	type	True	80.8098	1074	2209	95	below_threshold
Streptomyces buecherae	strain=AC541	GCA_014295035.1	2763006	2763006	type	True	78.9966	1057	2209	95	below_threshold
Streptomyces galbus	strain=DSM 40089	GCA_005280195.1	33898	33898	type	True	78.8612	991	2209	95	below_threshold
Streptomyces harenosi	strain=PRKS01-65	GCA_011008945.1	2697029	2697029	type	True	78.8484	963	2209	95	below_threshold
Streptomyces sennicomposti	strain=RCPT1-4	GCA_019890635.1	2873384	2873384	type	True	78.8431	936	2209	95	below_threshold
Streptomyces galbus	strain=JCM 4639	GCA_014650535.1	33898	33898	type	True	78.8424	990	2209	95	below_threshold
Streptomyces lichenis	strain=LCR6-01	GCA_023218175.1	2306967	2306967	type	True	78.8227	949	2209	95	below_threshold
Streptomyces fumigatiscleroticus	strain=JCM 3101	GCA_014647975.1	66371	66371	type	True	78.7637	1036	2209	95	below_threshold
Streptomyces barringtoniae	strain=JA03	GCA_020819595.1	2892029	2892029	type	True	78.7062	911	2209	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:28:55,022] [INFO] DFAST Taxonomy check result was written to GCF_020410765.1_ASM2041076v1_genomic.fna/tc_result.tsv
[2024-01-24 13:28:55,022] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:28:55,022] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:28:55,023] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga63bcdd4-e590-4d09-a376-dab8103c88b4/dqc_reference/checkm_data
[2024-01-24 13:28:55,024] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:28:55,083] [INFO] Task started: CheckM
[2024-01-24 13:28:55,084] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_020410765.1_ASM2041076v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_020410765.1_ASM2041076v1_genomic.fna/checkm_input GCF_020410765.1_ASM2041076v1_genomic.fna/checkm_result
[2024-01-24 13:30:31,950] [INFO] Task succeeded: CheckM
[2024-01-24 13:30:31,951] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 5.21%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:30:31,979] [INFO] ===== Completeness check finished =====
[2024-01-24 13:30:31,979] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:30:31,979] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_020410765.1_ASM2041076v1_genomic.fna/markers.fasta)
[2024-01-24 13:30:31,980] [INFO] Task started: Blastn
[2024-01-24 13:30:31,980] [INFO] Running command: blastn -query GCF_020410765.1_ASM2041076v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga63bcdd4-e590-4d09-a376-dab8103c88b4/dqc_reference/reference_markers_gtdb.fasta -out GCF_020410765.1_ASM2041076v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:30:34,399] [INFO] Task succeeded: Blastn
[2024-01-24 13:30:34,402] [INFO] Selected 14 target genomes.
[2024-01-24 13:30:34,402] [INFO] Target genome list was writen to GCF_020410765.1_ASM2041076v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:30:34,415] [INFO] Task started: fastANI
[2024-01-24 13:30:34,415] [INFO] Running command: fastANI --query /var/lib/cwl/stgf7bad2de-fa90-48cb-983c-3088365398e3/GCF_020410765.1_ASM2041076v1_genomic.fna.gz --refList GCF_020410765.1_ASM2041076v1_genomic.fna/target_genomes_gtdb.txt --output GCF_020410765.1_ASM2041076v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:30:58,700] [INFO] Task succeeded: fastANI
[2024-01-24 13:30:58,712] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:30:58,712] [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_002128305.1	s__Streptomyces sp002128305	96.8119	1943	2209	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_001984575.1	s__Streptomyces sp001984575	85.4472	1630	2209	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003626575.1	s__Streptomyces sp003626575	82.6354	1363	2209	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003311645.1	s__Streptomyces sp003311645	82.6266	1289	2209	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001083795.1	s__Streptomyces sp001083795	82.5723	1250	2209	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001493375.1	s__Streptomyces specialis	82.4451	1088	2209	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	81.8005	1141	2209	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004348415.1	s__Streptomyces hainanensis	81.5721	1131	2209	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003626535.1	s__Streptomyces hoynatensis	81.4233	1288	2209	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004193175.1	s__Streptomyces sp004193175	81.3007	1146	2209	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000719135.1	s__Streptomyces avicenniae	81.2592	1142	2209	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018114805.1	s__Streptomyces philanthi	78.9809	929	2209	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003248315.1	s__Streptomyces sp003248315	78.9285	1009	2209	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005280195.1	s__Streptomyces galbus	78.8269	1000	2209	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.26	98.53	0.96	0.94	3	-
--------------------------------------------------------------------------------
[2024-01-24 13:30:58,713] [INFO] GTDB search result was written to GCF_020410765.1_ASM2041076v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:30:58,714] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:30:58,718] [INFO] DFAST_QC result json was written to GCF_020410765.1_ASM2041076v1_genomic.fna/dqc_result.json
[2024-01-24 13:30:58,718] [INFO] DFAST_QC completed!
[2024-01-24 13:30:58,718] [INFO] Total running time: 0h2m57s