[2024-01-24 12:06:13,993] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:06:13,998] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:06:13,998] [INFO] DQC Reference Directory: /var/lib/cwl/stgeec99d44-c945-4c2d-8b44-2b7f89b75cd6/dqc_reference
[2024-01-24 12:06:15,444] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:06:15,444] [INFO] Task started: Prodigal
[2024-01-24 12:06:15,445] [INFO] Running command: gunzip -c /var/lib/cwl/stgf83976eb-757e-43df-bea6-6add7140ea76/GCF_003674095.1_ASM367409v1_genomic.fna.gz | prodigal -d GCF_003674095.1_ASM367409v1_genomic.fna/cds.fna -a GCF_003674095.1_ASM367409v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:06:25,544] [INFO] Task succeeded: Prodigal
[2024-01-24 12:06:25,545] [INFO] Task started: HMMsearch
[2024-01-24 12:06:25,545] [INFO] Running command: hmmsearch --tblout GCF_003674095.1_ASM367409v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgeec99d44-c945-4c2d-8b44-2b7f89b75cd6/dqc_reference/reference_markers.hmm GCF_003674095.1_ASM367409v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:06:25,856] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:06:25,857] [INFO] Found 6/6 markers.
[2024-01-24 12:06:25,896] [INFO] Query marker FASTA was written to GCF_003674095.1_ASM367409v1_genomic.fna/markers.fasta
[2024-01-24 12:06:25,896] [INFO] Task started: Blastn
[2024-01-24 12:06:25,896] [INFO] Running command: blastn -query GCF_003674095.1_ASM367409v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgeec99d44-c945-4c2d-8b44-2b7f89b75cd6/dqc_reference/reference_markers.fasta -out GCF_003674095.1_ASM367409v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:06:27,058] [INFO] Task succeeded: Blastn
[2024-01-24 12:06:27,061] [INFO] Selected 15 target genomes.
[2024-01-24 12:06:27,061] [INFO] Target genome list was writen to GCF_003674095.1_ASM367409v1_genomic.fna/target_genomes.txt
[2024-01-24 12:06:27,068] [INFO] Task started: fastANI
[2024-01-24 12:06:27,068] [INFO] Running command: fastANI --query /var/lib/cwl/stgf83976eb-757e-43df-bea6-6add7140ea76/GCF_003674095.1_ASM367409v1_genomic.fna.gz --refList GCF_003674095.1_ASM367409v1_genomic.fna/target_genomes.txt --output GCF_003674095.1_ASM367409v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:06:38,932] [INFO] Task succeeded: fastANI
[2024-01-24 12:06:38,933] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgeec99d44-c945-4c2d-8b44-2b7f89b75cd6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:06:38,933] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgeec99d44-c945-4c2d-8b44-2b7f89b75cd6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:06:38,946] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:06:38,946] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:06:38,947] [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
Aeromicrobium phragmitis	strain=9W16Y-2	GCA_003674095.1	2478914	2478914	type	True	100.0	1067	1068	95	conclusive
Aeromicrobium camelliae	strain=YS17T	GCA_003850045.1	1538144	1538144	type	True	87.6331	801	1068	95	below_threshold
Aeromicrobium piscarium	strain=Co35	GCA_007421815.1	2590901	2590901	type	True	80.8284	578	1068	95	below_threshold
Aeromicrobium tamlense	strain=DSM 19087	GCA_013408555.1	375541	375541	type	True	80.135	507	1068	95	below_threshold
Aeromicrobium choanae	strain=9H-4	GCA_900167475.1	1736691	1736691	type	True	80.0668	476	1068	95	below_threshold
Aeromicrobium phoceense	strain=Marseille-Q0843	GCA_013868155.1	2754045	2754045	type	True	80.0276	467	1068	95	below_threshold
Aeromicrobium tamlense	strain=SSW1-57	GCA_014672995.1	375541	375541	type	True	80.0159	517	1068	95	below_threshold
Aeromicrobium massiliense	strain=JC14	GCA_000312105.1	1464554	1464554	type	True	79.8961	468	1068	95	below_threshold
Aeromicrobium stalagmiti	strain=YC3-14	GCA_013283745.1	2738988	2738988	type	True	79.4224	464	1068	95	below_threshold
Nocardioides ganghwensis	strain=9920	GCA_014779655.1	252230	252230	type	True	78.2152	317	1068	95	below_threshold
Nocardioides lacusdianchii	strain=JXJ CY 38	GCA_020102855.1	2783664	2783664	type	True	78.1408	303	1068	95	below_threshold
Nocardioides baculatus	strain=G10	GCA_016735675.1	2801337	2801337	type	True	77.9018	299	1068	95	below_threshold
Nocardioides sambongensis	strain=KUDC 5002	GCA_006494815.1	2589074	2589074	type	True	77.6545	277	1068	95	below_threshold
Klenkia marina	strain=DSM 45722	GCA_900101025.1	1960309	1960309	type	True	77.1786	234	1068	95	below_threshold
Streptomyces ferrugineus	strain=CCTCC AA2014009	GCA_015160855.1	1413221	1413221	type	True	76.4557	263	1068	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:06:38,948] [INFO] DFAST Taxonomy check result was written to GCF_003674095.1_ASM367409v1_genomic.fna/tc_result.tsv
[2024-01-24 12:06:38,949] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:06:38,949] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:06:38,950] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgeec99d44-c945-4c2d-8b44-2b7f89b75cd6/dqc_reference/checkm_data
[2024-01-24 12:06:38,951] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:06:38,987] [INFO] Task started: CheckM
[2024-01-24 12:06:38,987] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003674095.1_ASM367409v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003674095.1_ASM367409v1_genomic.fna/checkm_input GCF_003674095.1_ASM367409v1_genomic.fna/checkm_result
[2024-01-24 12:07:15,160] [INFO] Task succeeded: CheckM
[2024-01-24 12:07:15,161] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:07:15,192] [INFO] ===== Completeness check finished =====
[2024-01-24 12:07:15,192] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:07:15,193] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003674095.1_ASM367409v1_genomic.fna/markers.fasta)
[2024-01-24 12:07:15,193] [INFO] Task started: Blastn
[2024-01-24 12:07:15,193] [INFO] Running command: blastn -query GCF_003674095.1_ASM367409v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgeec99d44-c945-4c2d-8b44-2b7f89b75cd6/dqc_reference/reference_markers_gtdb.fasta -out GCF_003674095.1_ASM367409v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:07:16,972] [INFO] Task succeeded: Blastn
[2024-01-24 12:07:16,981] [INFO] Selected 11 target genomes.
[2024-01-24 12:07:16,981] [INFO] Target genome list was writen to GCF_003674095.1_ASM367409v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:07:16,991] [INFO] Task started: fastANI
[2024-01-24 12:07:16,992] [INFO] Running command: fastANI --query /var/lib/cwl/stgf83976eb-757e-43df-bea6-6add7140ea76/GCF_003674095.1_ASM367409v1_genomic.fna.gz --refList GCF_003674095.1_ASM367409v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003674095.1_ASM367409v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:07:25,391] [INFO] Task succeeded: fastANI
[2024-01-24 12:07:25,405] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:07:25,406] [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_003674095.1	s__Aeromicrobium phragmitis	100.0	1067	1068	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Aeromicrobium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003850045.1	s__Aeromicrobium camelliae	87.6621	800	1068	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Aeromicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007421815.1	s__Aeromicrobium piscarium	80.8281	578	1068	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Aeromicrobium	95.0	97.34	97.34	0.85	0.85	2	-
GCF_002174305.1	s__Aeromicrobium sp002174305	80.6248	559	1068	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Aeromicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007992115.1	s__Aeromicrobium flavum	80.3107	463	1068	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Aeromicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014334735.1	s__Aeromicrobium sp014334735	80.1908	442	1068	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Aeromicrobium	95.0	99.41	98.82	0.96	0.93	3	-
GCF_013408555.1	s__Aeromicrobium tamlense	80.1017	510	1068	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Aeromicrobium	95.0	100.00	100.00	0.99	0.99	2	-
GCF_900167475.1	s__Aeromicrobium choanae	80.0601	477	1068	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Aeromicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013868155.1	s__Aeromicrobium phoceense	80.0208	467	1068	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Aeromicrobium	95.0	97.64	97.64	0.92	0.92	2	-
GCA_000471045.1	s__Aeromicrobium sp000471045	80.0008	413	1068	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Aeromicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004336805.1	s__Aeromicrobium sp004336805	79.7918	464	1068	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Aeromicrobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:07:25,408] [INFO] GTDB search result was written to GCF_003674095.1_ASM367409v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:07:25,410] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:07:25,414] [INFO] DFAST_QC result json was written to GCF_003674095.1_ASM367409v1_genomic.fna/dqc_result.json
[2024-01-24 12:07:25,415] [INFO] DFAST_QC completed!
[2024-01-24 12:07:25,415] [INFO] Total running time: 0h1m11s