[2024-01-24 14:31:14,692] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:31:14,694] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:31:14,694] [INFO] DQC Reference Directory: /var/lib/cwl/stgb674ea2f-5c9d-4d15-a440-ac293919ec2e/dqc_reference
[2024-01-24 14:31:16,079] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:31:16,080] [INFO] Task started: Prodigal
[2024-01-24 14:31:16,080] [INFO] Running command: gunzip -c /var/lib/cwl/stg42e3d3c3-aece-4d69-8924-b3b3d30ad296/GCF_030852425.1_ASM3085242v1_genomic.fna.gz | prodigal -d GCF_030852425.1_ASM3085242v1_genomic.fna/cds.fna -a GCF_030852425.1_ASM3085242v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:31:56,997] [INFO] Task succeeded: Prodigal
[2024-01-24 14:31:56,998] [INFO] Task started: HMMsearch
[2024-01-24 14:31:56,998] [INFO] Running command: hmmsearch --tblout GCF_030852425.1_ASM3085242v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb674ea2f-5c9d-4d15-a440-ac293919ec2e/dqc_reference/reference_markers.hmm GCF_030852425.1_ASM3085242v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:31:57,406] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:31:57,408] [INFO] Found 6/6 markers.
[2024-01-24 14:31:57,482] [INFO] Query marker FASTA was written to GCF_030852425.1_ASM3085242v1_genomic.fna/markers.fasta
[2024-01-24 14:31:57,482] [INFO] Task started: Blastn
[2024-01-24 14:31:57,483] [INFO] Running command: blastn -query GCF_030852425.1_ASM3085242v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb674ea2f-5c9d-4d15-a440-ac293919ec2e/dqc_reference/reference_markers.fasta -out GCF_030852425.1_ASM3085242v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:31:58,953] [INFO] Task succeeded: Blastn
[2024-01-24 14:31:58,956] [INFO] Selected 16 target genomes.
[2024-01-24 14:31:58,957] [INFO] Target genome list was writen to GCF_030852425.1_ASM3085242v1_genomic.fna/target_genomes.txt
[2024-01-24 14:31:59,061] [INFO] Task started: fastANI
[2024-01-24 14:31:59,062] [INFO] Running command: fastANI --query /var/lib/cwl/stg42e3d3c3-aece-4d69-8924-b3b3d30ad296/GCF_030852425.1_ASM3085242v1_genomic.fna.gz --refList GCF_030852425.1_ASM3085242v1_genomic.fna/target_genomes.txt --output GCF_030852425.1_ASM3085242v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:32:41,219] [INFO] Task succeeded: fastANI
[2024-01-24 14:32:41,220] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb674ea2f-5c9d-4d15-a440-ac293919ec2e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:32:41,221] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb674ea2f-5c9d-4d15-a440-ac293919ec2e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:32:41,238] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:32:41,238] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:32:41,238] [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 carnea	strain=CGMCC 4.7097	GCA_003014735.1	1280637	1280637	type	True	85.7427	1812	2735	95	below_threshold
Saccharothrix texasensis	strain=DSM 44231	GCA_003752005.1	103734	103734	type	True	85.7215	1925	2735	95	below_threshold
Saccharothrix syringae	strain=NRRL B-16468	GCA_009498035.1	103733	103733	type	True	85.666	1995	2735	95	below_threshold
Saccharothrix saharensis	strain=DSM 45456	GCA_006716745.1	571190	571190	type	True	85.6601	1885	2735	95	below_threshold
Saccharothrix syringae	strain=NRRL B-16468	GCA_000716755.1	103733	103733	type	True	85.6125	1974	2735	95	below_threshold
Saccharothrix deserti	strain=BMP B8144	GCA_009769385.1	2593674	2593674	type	True	85.3463	1816	2735	95	below_threshold
Saccharothrix ecbatanensis	strain=DSM 45486	GCA_014205015.1	1105145	1105145	type	True	84.8924	1759	2735	95	below_threshold
Saccharothrix coeruleofusca	strain=DSM 43679	GCA_017876325.1	33919	33919	type	True	83.8191	1603	2735	95	below_threshold
Saccharothrix coeruleofusca	strain=JCM 3313	GCA_014648515.1	33919	33919	type	True	83.7813	1613	2735	95	below_threshold
Saccharothrix australiensis	strain=DSM 43800	GCA_003634935.1	2072	2072	type	True	83.6764	1576	2735	95	below_threshold
Saccharothrix espanaensis	strain=type strain: DSM 44229	GCA_000328705.1	103731	103731	type	True	83.5222	1652	2735	95	below_threshold
Saccharothrix obliqua	strain=SC076	GCA_019375475.1	2861747	2861747	type	True	83.0646	1508	2735	95	below_threshold
Lentzea tibetensis	strain=FXJ1.1311	GCA_007845675.1	2591470	2591470	type	True	80.5658	1293	2735	95	below_threshold
Lentzea californiensis	strain=DSM 43393	GCA_024648825.1	438851	438851	type	True	80.277	1352	2735	95	below_threshold
Amycolatopsis acidiphila	strain=KCTC 39523	GCA_021391495.1	715473	715473	type	True	78.2053	928	2735	95	below_threshold
Prauserella aidingensis	strain=DSM 45266	GCA_024171865.1	387890	387890	type	True	77.7955	723	2735	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:32:41,240] [INFO] DFAST Taxonomy check result was written to GCF_030852425.1_ASM3085242v1_genomic.fna/tc_result.tsv
[2024-01-24 14:32:41,241] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:32:41,241] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:32:41,241] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb674ea2f-5c9d-4d15-a440-ac293919ec2e/dqc_reference/checkm_data
[2024-01-24 14:32:41,242] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:32:41,316] [INFO] Task started: CheckM
[2024-01-24 14:32:41,316] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030852425.1_ASM3085242v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030852425.1_ASM3085242v1_genomic.fna/checkm_input GCF_030852425.1_ASM3085242v1_genomic.fna/checkm_result
[2024-01-24 14:35:39,312] [INFO] Task succeeded: CheckM
[2024-01-24 14:35:39,314] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:35:39,342] [INFO] ===== Completeness check finished =====
[2024-01-24 14:35:39,343] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:35:39,343] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030852425.1_ASM3085242v1_genomic.fna/markers.fasta)
[2024-01-24 14:35:39,344] [INFO] Task started: Blastn
[2024-01-24 14:35:39,344] [INFO] Running command: blastn -query GCF_030852425.1_ASM3085242v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb674ea2f-5c9d-4d15-a440-ac293919ec2e/dqc_reference/reference_markers_gtdb.fasta -out GCF_030852425.1_ASM3085242v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:35:41,465] [INFO] Task succeeded: Blastn
[2024-01-24 14:35:41,469] [INFO] Selected 12 target genomes.
[2024-01-24 14:35:41,469] [INFO] Target genome list was writen to GCF_030852425.1_ASM3085242v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:35:41,487] [INFO] Task started: fastANI
[2024-01-24 14:35:41,488] [INFO] Running command: fastANI --query /var/lib/cwl/stg42e3d3c3-aece-4d69-8924-b3b3d30ad296/GCF_030852425.1_ASM3085242v1_genomic.fna.gz --refList GCF_030852425.1_ASM3085242v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030852425.1_ASM3085242v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:36:14,407] [INFO] Task succeeded: fastANI
[2024-01-24 14:36:14,423] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 14:36:14,423] [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_003752005.1	s__Actinosynnema texasense	85.7717	1916	2735	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	85.6749	1882	2735	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	85.6597	1827	2735	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	95.10	95.10	0.83	0.83	2	-
GCF_009498035.1	s__Actinosynnema syringae	85.6535	1996	2735	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	99.98	99.98	1.00	1.00	2	-
GCF_001280085.1	s__Actinosynnema sp001280085	85.4441	1907	2735	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	85.3316	1821	2735	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	85.1052	1776	2735	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	84.979	1818	2735	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016907655.1	s__Actinosynnema algeriensis	83.9014	1531	2735	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	83.8357	1603	2735	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	99.37	99.37	0.97	0.97	2	-
GCF_003634935.1	s__Actinosynnema australiense	83.6179	1588	2735	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	83.522	1651	2735	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 14:36:14,425] [INFO] GTDB search result was written to GCF_030852425.1_ASM3085242v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:36:14,425] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:36:14,433] [INFO] DFAST_QC result json was written to GCF_030852425.1_ASM3085242v1_genomic.fna/dqc_result.json
[2024-01-24 14:36:14,433] [INFO] DFAST_QC completed!
[2024-01-24 14:36:14,433] [INFO] Total running time: 0h4m60s