[2024-01-24 12:15:04,156] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:15:04,157] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:15:04,158] [INFO] DQC Reference Directory: /var/lib/cwl/stg9321f313-1950-47a2-9d86-0fe4eda6100d/dqc_reference
[2024-01-24 12:15:05,387] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:15:05,388] [INFO] Task started: Prodigal
[2024-01-24 12:15:05,388] [INFO] Running command: gunzip -c /var/lib/cwl/stga6cb5078-6810-4b48-9079-003d1da2dfa4/GCF_006716745.1_ASM671674v1_genomic.fna.gz | prodigal -d GCF_006716745.1_ASM671674v1_genomic.fna/cds.fna -a GCF_006716745.1_ASM671674v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:15:39,477] [INFO] Task succeeded: Prodigal
[2024-01-24 12:15:39,478] [INFO] Task started: HMMsearch
[2024-01-24 12:15:39,478] [INFO] Running command: hmmsearch --tblout GCF_006716745.1_ASM671674v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9321f313-1950-47a2-9d86-0fe4eda6100d/dqc_reference/reference_markers.hmm GCF_006716745.1_ASM671674v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:15:39,992] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:15:39,994] [INFO] Found 6/6 markers.
[2024-01-24 12:15:40,072] [INFO] Query marker FASTA was written to GCF_006716745.1_ASM671674v1_genomic.fna/markers.fasta
[2024-01-24 12:15:40,072] [INFO] Task started: Blastn
[2024-01-24 12:15:40,073] [INFO] Running command: blastn -query GCF_006716745.1_ASM671674v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9321f313-1950-47a2-9d86-0fe4eda6100d/dqc_reference/reference_markers.fasta -out GCF_006716745.1_ASM671674v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:41,469] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:41,475] [INFO] Selected 13 target genomes.
[2024-01-24 12:15:41,476] [INFO] Target genome list was writen to GCF_006716745.1_ASM671674v1_genomic.fna/target_genomes.txt
[2024-01-24 12:15:41,482] [INFO] Task started: fastANI
[2024-01-24 12:15:41,483] [INFO] Running command: fastANI --query /var/lib/cwl/stga6cb5078-6810-4b48-9079-003d1da2dfa4/GCF_006716745.1_ASM671674v1_genomic.fna.gz --refList GCF_006716745.1_ASM671674v1_genomic.fna/target_genomes.txt --output GCF_006716745.1_ASM671674v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:16:15,831] [INFO] Task succeeded: fastANI
[2024-01-24 12:16:15,832] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9321f313-1950-47a2-9d86-0fe4eda6100d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:16:15,833] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9321f313-1950-47a2-9d86-0fe4eda6100d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:16:15,847] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:16:15,848] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:16:15,848] [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
Saccharothrix saharensis	strain=DSM 45456	GCA_006716745.1	571190	571190	type	True	100.0	2973	2974	95	conclusive
Saccharothrix carnea	strain=CGMCC 4.7097	GCA_003014735.1	1280637	1280637	type	True	90.592	2188	2974	95	below_threshold
Saccharothrix texasensis	strain=DSM 44231	GCA_003752005.1	103734	103734	type	True	90.2963	2288	2974	95	below_threshold
Saccharothrix deserti	strain=BMP B8144	GCA_009769385.1	2593674	2593674	type	True	87.8671	2067	2974	95	below_threshold
Saccharothrix ecbatanensis	strain=DSM 45486	GCA_014205015.1	1105145	1105145	type	True	87.1796	2068	2974	95	below_threshold
Saccharothrix syringae	strain=NRRL B-16468	GCA_009498035.1	103733	103733	type	True	85.2712	2091	2974	95	below_threshold
Saccharothrix syringae	strain=NRRL B-16468	GCA_000716755.1	103733	103733	type	True	85.1906	2072	2974	95	below_threshold
Saccharothrix australiensis	strain=DSM 43800	GCA_003634935.1	2072	2072	type	True	83.8601	1651	2974	95	below_threshold
Saccharothrix obliqua	strain=SC076	GCA_019375475.1	2861747	2861747	type	True	83.1416	1601	2974	95	below_threshold
Lentzea tibetensis	strain=FXJ1.1311	GCA_007845675.1	2591470	2591470	type	True	80.5404	1389	2974	95	below_threshold
Lentzea californiensis	strain=DSM 43393	GCA_024648825.1	438851	438851	type	True	80.1555	1393	2974	95	below_threshold
Amycolatopsis acidiphila	strain=KCTC 39523	GCA_021391495.1	715473	715473	type	True	78.1281	952	2974	95	below_threshold
Amycolatopsis camponoti	strain=A23	GCA_902497555.1	2606593	2606593	type	True	77.9189	1236	2974	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:16:15,850] [INFO] DFAST Taxonomy check result was written to GCF_006716745.1_ASM671674v1_genomic.fna/tc_result.tsv
[2024-01-24 12:16:15,850] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:16:15,850] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:16:15,850] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9321f313-1950-47a2-9d86-0fe4eda6100d/dqc_reference/checkm_data
[2024-01-24 12:16:15,851] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:16:15,929] [INFO] Task started: CheckM
[2024-01-24 12:16:15,930] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_006716745.1_ASM671674v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_006716745.1_ASM671674v1_genomic.fna/checkm_input GCF_006716745.1_ASM671674v1_genomic.fna/checkm_result
[2024-01-24 12:20:00,282] [INFO] Task succeeded: CheckM
[2024-01-24 12:20:00,283] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:20:00,312] [INFO] ===== Completeness check finished =====
[2024-01-24 12:20:00,312] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:20:00,313] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_006716745.1_ASM671674v1_genomic.fna/markers.fasta)
[2024-01-24 12:20:00,313] [INFO] Task started: Blastn
[2024-01-24 12:20:00,313] [INFO] Running command: blastn -query GCF_006716745.1_ASM671674v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9321f313-1950-47a2-9d86-0fe4eda6100d/dqc_reference/reference_markers_gtdb.fasta -out GCF_006716745.1_ASM671674v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:20:02,478] [INFO] Task succeeded: Blastn
[2024-01-24 12:20:02,485] [INFO] Selected 10 target genomes.
[2024-01-24 12:20:02,485] [INFO] Target genome list was writen to GCF_006716745.1_ASM671674v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:20:02,608] [INFO] Task started: fastANI
[2024-01-24 12:20:02,609] [INFO] Running command: fastANI --query /var/lib/cwl/stga6cb5078-6810-4b48-9079-003d1da2dfa4/GCF_006716745.1_ASM671674v1_genomic.fna.gz --refList GCF_006716745.1_ASM671674v1_genomic.fna/target_genomes_gtdb.txt --output GCF_006716745.1_ASM671674v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:20:31,318] [INFO] Task succeeded: fastANI
[2024-01-24 12:20:31,343] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:20:31,344] [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_006716745.1	s__Actinosynnema saharense	100.0	2974	2974	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003014735.1	s__Actinosynnema carneum	90.5846	2189	2974	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	95.10	95.10	0.83	0.83	2	-
GCF_003752005.1	s__Actinosynnema texasense	90.2845	2291	2974	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	98.51	98.51	0.92	0.92	2	-
GCF_001280085.1	s__Actinosynnema sp001280085	90.1755	2331	2974	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009769385.1	s__Actinosynnema deserti	87.9315	2057	2974	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001984175.1	s__Actinosynnema sp001984175	87.6066	1995	2974	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000716595.1	s__Actinosynnema sp000716595	87.4897	2035	2974	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009498035.1	s__Actinosynnema syringae	85.2455	2095	2974	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	99.98	99.98	1.00	1.00	2	-
GCF_014203665.1	s__Actinosynnema tamanrassetense	84.0858	1664	2974	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000328705.1	s__Actinosynnema espanaense	83.6832	1740	2974	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:20:31,349] [INFO] GTDB search result was written to GCF_006716745.1_ASM671674v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:20:31,350] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:20:31,355] [INFO] DFAST_QC result json was written to GCF_006716745.1_ASM671674v1_genomic.fna/dqc_result.json
[2024-01-24 12:20:31,356] [INFO] DFAST_QC completed!
[2024-01-24 12:20:31,356] [INFO] Total running time: 0h5m27s