[2024-01-24 12:39:38,091] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:39:38,093] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:39:38,093] [INFO] DQC Reference Directory: /var/lib/cwl/stg809215d0-d236-43c2-8372-9d619436528b/dqc_reference
[2024-01-24 12:39:39,329] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:39:39,330] [INFO] Task started: Prodigal
[2024-01-24 12:39:39,330] [INFO] Running command: gunzip -c /var/lib/cwl/stg50183e45-7e31-4f48-9311-7899bf397052/GCF_009498035.1_ASM949803v1_genomic.fna.gz | prodigal -d GCF_009498035.1_ASM949803v1_genomic.fna/cds.fna -a GCF_009498035.1_ASM949803v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:40:43,625] [INFO] Task succeeded: Prodigal
[2024-01-24 12:40:43,626] [INFO] Task started: HMMsearch
[2024-01-24 12:40:43,626] [INFO] Running command: hmmsearch --tblout GCF_009498035.1_ASM949803v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg809215d0-d236-43c2-8372-9d619436528b/dqc_reference/reference_markers.hmm GCF_009498035.1_ASM949803v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:40:44,064] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:40:44,065] [INFO] Found 6/6 markers.
[2024-01-24 12:40:44,143] [INFO] Query marker FASTA was written to GCF_009498035.1_ASM949803v1_genomic.fna/markers.fasta
[2024-01-24 12:40:44,144] [INFO] Task started: Blastn
[2024-01-24 12:40:44,144] [INFO] Running command: blastn -query GCF_009498035.1_ASM949803v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg809215d0-d236-43c2-8372-9d619436528b/dqc_reference/reference_markers.fasta -out GCF_009498035.1_ASM949803v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:40:45,557] [INFO] Task succeeded: Blastn
[2024-01-24 12:40:45,561] [INFO] Selected 16 target genomes.
[2024-01-24 12:40:45,561] [INFO] Target genome list was writen to GCF_009498035.1_ASM949803v1_genomic.fna/target_genomes.txt
[2024-01-24 12:40:45,568] [INFO] Task started: fastANI
[2024-01-24 12:40:45,568] [INFO] Running command: fastANI --query /var/lib/cwl/stg50183e45-7e31-4f48-9311-7899bf397052/GCF_009498035.1_ASM949803v1_genomic.fna.gz --refList GCF_009498035.1_ASM949803v1_genomic.fna/target_genomes.txt --output GCF_009498035.1_ASM949803v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:41:31,388] [INFO] Task succeeded: fastANI
[2024-01-24 12:41:31,389] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg809215d0-d236-43c2-8372-9d619436528b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:41:31,389] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg809215d0-d236-43c2-8372-9d619436528b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:41:31,407] [INFO] Found 16 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:41:31,407] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:41:31,408] [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 syringae	strain=NRRL B-16468	GCA_009498035.1	103733	103733	type	True	100.0	3643	3643	95	conclusive
Saccharothrix syringae	strain=NRRL B-16468	GCA_000716755.1	103733	103733	type	True	99.9672	3546	3643	95	conclusive
Saccharothrix texasensis	strain=DSM 44231	GCA_003752005.1	103734	103734	type	True	85.3116	2138	3643	95	below_threshold
Saccharothrix saharensis	strain=DSM 45456	GCA_006716745.1	571190	571190	type	True	85.094	2117	3643	95	below_threshold
Saccharothrix carnea	strain=CGMCC 4.7097	GCA_003014735.1	1280637	1280637	type	True	85.0634	2063	3643	95	below_threshold
Saccharothrix deserti	strain=BMP B8144	GCA_009769385.1	2593674	2593674	type	True	84.6032	2025	3643	95	below_threshold
Saccharothrix coeruleofusca	strain=DSM 43679	GCA_017876325.1	33919	33919	type	True	84.1597	1812	3643	95	below_threshold
Saccharothrix coeruleofusca	strain=JCM 3313	GCA_014648515.1	33919	33919	type	True	84.1512	1786	3643	95	below_threshold
Saccharothrix algeriensis	strain=DSM 44581	GCA_016907655.1	173560	173560	type	True	83.7012	1652	3643	95	below_threshold
Saccharothrix australiensis	strain=DSM 43800	GCA_003634935.1	2072	2072	type	True	83.2734	1772	3643	95	below_threshold
Saccharothrix tamanrassetensis	strain=CECT 8640	GCA_014203665.1	1051531	1051531	type	True	83.258	1725	3643	95	below_threshold
Saccharothrix obliqua	strain=SC076	GCA_019375475.1	2861747	2861747	type	True	82.603	1686	3643	95	below_threshold
Lentzea tibetensis	strain=FXJ1.1311	GCA_007845675.1	2591470	2591470	type	True	79.9582	1476	3643	95	below_threshold
Lentzea californiensis	strain=DSM 43393	GCA_024648825.1	438851	438851	type	True	79.6873	1516	3643	95	below_threshold
Amycolatopsis acidiphila	strain=KCTC 39523	GCA_021391495.1	715473	715473	type	True	77.8803	1096	3643	95	below_threshold
Prauserella aidingensis	strain=DSM 45266	GCA_024171865.1	387890	387890	type	True	77.6496	783	3643	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:41:31,410] [INFO] DFAST Taxonomy check result was written to GCF_009498035.1_ASM949803v1_genomic.fna/tc_result.tsv
[2024-01-24 12:41:31,410] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:41:31,411] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:41:31,411] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg809215d0-d236-43c2-8372-9d619436528b/dqc_reference/checkm_data
[2024-01-24 12:41:31,412] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:41:31,515] [INFO] Task started: CheckM
[2024-01-24 12:41:31,515] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009498035.1_ASM949803v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009498035.1_ASM949803v1_genomic.fna/checkm_input GCF_009498035.1_ASM949803v1_genomic.fna/checkm_result
[2024-01-24 12:48:17,155] [INFO] Task succeeded: CheckM
[2024-01-24 12:48:17,157] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:48:17,184] [INFO] ===== Completeness check finished =====
[2024-01-24 12:48:17,185] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:48:17,186] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009498035.1_ASM949803v1_genomic.fna/markers.fasta)
[2024-01-24 12:48:17,186] [INFO] Task started: Blastn
[2024-01-24 12:48:17,186] [INFO] Running command: blastn -query GCF_009498035.1_ASM949803v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg809215d0-d236-43c2-8372-9d619436528b/dqc_reference/reference_markers_gtdb.fasta -out GCF_009498035.1_ASM949803v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:48:19,515] [INFO] Task succeeded: Blastn
[2024-01-24 12:48:19,518] [INFO] Selected 13 target genomes.
[2024-01-24 12:48:19,518] [INFO] Target genome list was writen to GCF_009498035.1_ASM949803v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:48:19,528] [INFO] Task started: fastANI
[2024-01-24 12:48:19,528] [INFO] Running command: fastANI --query /var/lib/cwl/stg50183e45-7e31-4f48-9311-7899bf397052/GCF_009498035.1_ASM949803v1_genomic.fna.gz --refList GCF_009498035.1_ASM949803v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009498035.1_ASM949803v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:49:00,980] [INFO] Task succeeded: fastANI
[2024-01-24 12:49:00,994] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:49:00,995] [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_009498035.1	s__Actinosynnema syringae	100.0	3643	3643	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	99.98	99.98	1.00	1.00	2	conclusive
GCF_003752005.1	s__Actinosynnema texasense	85.2926	2138	3643	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	98.51	98.51	0.92	0.92	2	-
GCF_006716745.1	s__Actinosynnema saharense	85.0931	2118	3643	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003014735.1	s__Actinosynnema carneum	85.0661	2060	3643	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	95.10	95.10	0.83	0.83	2	-
GCF_001280085.1	s__Actinosynnema sp001280085	84.9061	2189	3643	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	84.5563	2030	3643	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	84.5466	1995	3643	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	84.4088	1946	3643	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014648515.1	s__Actinosynnema coeruleofuscum	84.171	1784	3643	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	99.37	99.37	0.97	0.97	2	-
GCF_016907655.1	s__Actinosynnema algeriensis	83.6163	1667	3643	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003634995.1	s__Actinosynnema variisporeum	83.337	1920	3643	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003634935.1	s__Actinosynnema australiense	83.2798	1771	3643	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	82.8766	1895	3643	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 12:49:00,996] [INFO] GTDB search result was written to GCF_009498035.1_ASM949803v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:49:00,997] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:49:01,000] [INFO] DFAST_QC result json was written to GCF_009498035.1_ASM949803v1_genomic.fna/dqc_result.json
[2024-01-24 12:49:01,000] [INFO] DFAST_QC completed!
[2024-01-24 12:49:01,000] [INFO] Total running time: 0h9m23s