[2024-01-24 13:18:46,231] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:18:46,234] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:18:46,234] [INFO] DQC Reference Directory: /var/lib/cwl/stg68ff1cc7-f0b6-4785-90d2-3dfa7c9839ef/dqc_reference
[2024-01-24 13:18:47,607] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:18:47,608] [INFO] Task started: Prodigal
[2024-01-24 13:18:47,608] [INFO] Running command: gunzip -c /var/lib/cwl/stg7a12f5a1-2e89-451e-9b54-e4619fae4b83/GCF_000422825.1_ASM42282v1_genomic.fna.gz | prodigal -d GCF_000422825.1_ASM42282v1_genomic.fna/cds.fna -a GCF_000422825.1_ASM42282v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:18:59,160] [INFO] Task succeeded: Prodigal
[2024-01-24 13:18:59,161] [INFO] Task started: HMMsearch
[2024-01-24 13:18:59,161] [INFO] Running command: hmmsearch --tblout GCF_000422825.1_ASM42282v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg68ff1cc7-f0b6-4785-90d2-3dfa7c9839ef/dqc_reference/reference_markers.hmm GCF_000422825.1_ASM42282v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:18:59,452] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:18:59,453] [INFO] Found 6/6 markers.
[2024-01-24 13:18:59,496] [INFO] Query marker FASTA was written to GCF_000422825.1_ASM42282v1_genomic.fna/markers.fasta
[2024-01-24 13:18:59,497] [INFO] Task started: Blastn
[2024-01-24 13:18:59,497] [INFO] Running command: blastn -query GCF_000422825.1_ASM42282v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg68ff1cc7-f0b6-4785-90d2-3dfa7c9839ef/dqc_reference/reference_markers.fasta -out GCF_000422825.1_ASM42282v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:00,754] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:00,758] [INFO] Selected 24 target genomes.
[2024-01-24 13:19:00,759] [INFO] Target genome list was writen to GCF_000422825.1_ASM42282v1_genomic.fna/target_genomes.txt
[2024-01-24 13:19:00,771] [INFO] Task started: fastANI
[2024-01-24 13:19:00,772] [INFO] Running command: fastANI --query /var/lib/cwl/stg7a12f5a1-2e89-451e-9b54-e4619fae4b83/GCF_000422825.1_ASM42282v1_genomic.fna.gz --refList GCF_000422825.1_ASM42282v1_genomic.fna/target_genomes.txt --output GCF_000422825.1_ASM42282v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:19:24,332] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:24,332] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg68ff1cc7-f0b6-4785-90d2-3dfa7c9839ef/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:19:24,332] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg68ff1cc7-f0b6-4785-90d2-3dfa7c9839ef/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:19:24,350] [INFO] Found 24 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:19:24,351] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:19:24,351] [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
Nocardioides insulae	strain=DSM 17944	GCA_000422825.1	394734	394734	type	True	100.0	1346	1346	95	conclusive
Nocardioides marinus	strain=DSM 18248	GCA_013408145.1	374514	374514	type	True	79.9314	540	1346	95	below_threshold
Nocardioides panaciterrulae	strain=DSM 21350	GCA_013409645.1	661492	661492	type	True	79.8501	562	1346	95	below_threshold
Nocardioides dongkuii	strain=S-713	GCA_014127485.1	2760089	2760089	type	True	79.7995	584	1346	95	below_threshold
Nocardioides deserti	strain=CGMCC 4.7183	GCA_014646035.1	1588644	1588644	type	True	79.7867	558	1346	95	below_threshold
Nocardioides ferulae	strain=SZ4R5S7	GCA_003660455.1	2340821	2340821	type	True	79.7589	572	1346	95	below_threshold
Nocardioides deserti	strain=SC8A-24	GCA_014266025.1	1588644	1588644	type	True	79.7447	553	1346	95	below_threshold
Nocardioides sambongensis	strain=KUDC 5002	GCA_006494815.1	2589074	2589074	type	True	79.6763	570	1346	95	below_threshold
Nocardioides szechwanensis	strain=CGMCC 1.11147	GCA_900103935.1	1005944	1005944	type	True	79.6129	527	1346	95	below_threshold
Nocardioides albertanoniae	strain=DSM 25218	GCA_006716315.1	1175486	1175486	type	True	79.5805	560	1346	95	below_threshold
Nocardioides soli	strain=DSM 105498	GCA_014191495.1	1036020	1036020	type	True	79.5677	617	1346	95	below_threshold
Nocardioides luteus	strain=JCM 3358	GCA_014648595.1	1844	1844	type	True	79.5675	583	1346	95	below_threshold
Nocardioides nematodiphilus	strain=R-N-C8	GCA_020216525.1	2849669	2849669	type	True	79.5532	515	1346	95	below_threshold
Nocardioides szechwanensis	strain=NBRC 108562	GCA_007992395.1	1005944	1005944	type	True	79.4997	533	1346	95	below_threshold
Nocardioides euryhalodurans	strain=MMS17-SY117	GCA_004564375.1	2518370	2518370	type	True	79.4547	501	1346	95	below_threshold
Nocardioides nitrophenolicus	strain=DSM 15529	GCA_016907515.1	60489	60489	type	True	79.4026	611	1346	95	below_threshold
Nocardioides lianchengensis	strain=CGMCC 4.6858	GCA_900101465.1	1045774	1045774	type	True	79.3569	639	1346	95	below_threshold
Nocardioides lacusdianchii	strain=JXJ CY 38	GCA_020102855.1	2783664	2783664	type	True	79.3408	502	1346	95	below_threshold
Nocardioides albus	strain=JCM 3185	GCA_014648255.1	1841	1841	type	True	79.3066	589	1346	95	below_threshold
Nocardioides lianchengensis	strain=CGMCC 4.6858	GCA_013409225.1	1045774	1045774	type	True	79.3012	635	1346	95	below_threshold
Nocardioides okcheonensis	strain=MMS20-HV4-12	GCA_020991065.1	2894081	2894081	type	True	79.1047	550	1346	95	below_threshold
Nocardioides guangzhouensis	strain=130	GCA_004519545.1	2497878	2497878	type	True	79.0669	556	1346	95	below_threshold
Nocardioides carbamazepini	strain=CBZ_1	GCA_024614185.1	2854259	2854259	type	True	79.0441	600	1346	95	below_threshold
Nocardioides coralli	strain=SCSIO 67246	GCA_019880385.1	2872154	2872154	type	True	78.9876	483	1346	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:19:24,353] [INFO] DFAST Taxonomy check result was written to GCF_000422825.1_ASM42282v1_genomic.fna/tc_result.tsv
[2024-01-24 13:19:24,353] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:19:24,354] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:19:24,354] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg68ff1cc7-f0b6-4785-90d2-3dfa7c9839ef/dqc_reference/checkm_data
[2024-01-24 13:19:24,356] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:19:24,402] [INFO] Task started: CheckM
[2024-01-24 13:19:24,402] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000422825.1_ASM42282v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000422825.1_ASM42282v1_genomic.fna/checkm_input GCF_000422825.1_ASM42282v1_genomic.fna/checkm_result
[2024-01-24 13:20:22,581] [INFO] Task succeeded: CheckM
[2024-01-24 13:20:22,583] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:20:22,601] [INFO] ===== Completeness check finished =====
[2024-01-24 13:20:22,602] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:20:22,602] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000422825.1_ASM42282v1_genomic.fna/markers.fasta)
[2024-01-24 13:20:22,602] [INFO] Task started: Blastn
[2024-01-24 13:20:22,602] [INFO] Running command: blastn -query GCF_000422825.1_ASM42282v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg68ff1cc7-f0b6-4785-90d2-3dfa7c9839ef/dqc_reference/reference_markers_gtdb.fasta -out GCF_000422825.1_ASM42282v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:20:24,352] [INFO] Task succeeded: Blastn
[2024-01-24 13:20:24,362] [INFO] Selected 23 target genomes.
[2024-01-24 13:20:24,362] [INFO] Target genome list was writen to GCF_000422825.1_ASM42282v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:20:24,414] [INFO] Task started: fastANI
[2024-01-24 13:20:24,415] [INFO] Running command: fastANI --query /var/lib/cwl/stg7a12f5a1-2e89-451e-9b54-e4619fae4b83/GCF_000422825.1_ASM42282v1_genomic.fna.gz --refList GCF_000422825.1_ASM42282v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000422825.1_ASM42282v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:20:44,680] [INFO] Task succeeded: fastANI
[2024-01-24 13:20:44,698] [INFO] Found 23 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:20:44,698] [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_000422825.1	s__Nocardioides insulae	100.0	1346	1346	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_009557055.1	s__Nocardioides sp009557055	80.167	551	1346	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	1.00	1.00	2	-
GCF_011420305.2	s__Nocardioides sp011420305	80.106	559	1346	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.38	99.38	0.96	0.96	2	-
GCF_013408145.1	s__Nocardioides marinus	79.9409	539	1346	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	96.85	95.82	0.82	0.73	3	-
GCF_013177455.1	s__Nocardioides sp013177455	79.9145	578	1346	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.28	98.92	0.97	0.95	4	-
GCF_003710085.1	s__Nocardioides sp003710085	79.8432	573	1346	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.05	99.05	0.97	0.97	2	-
GCF_016907435.1	s__Nocardioides salarius	79.8279	583	1346	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	1.00	1.00	3	-
GCF_013409645.1	s__Nocardioides panaciterrulae	79.8211	565	1346	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014127485.1	s__Nocardioides sp014127485	79.8083	583	1346	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.37	99.37	0.97	0.97	2	-
GCF_014873835.1	s__Nocardioides sp014873835	79.8019	578	1346	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001627335.1	s__Nocardioides sp001627335	79.793	479	1346	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.38	96.50	0.91	0.88	12	-
GCF_013778305.1	s__Nocardioides sp013778305	79.7757	567	1346	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	1.00	1.00	2	-
GCF_011250565.1	s__Nocardioides sp011250565	79.7231	566	1346	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000364605.1	s__Nocardioides sp000364605	79.6528	529	1346	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900103935.1	s__Nocardioides szechwanensis	79.5952	529	1346	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.99	99.99	1.00	1.00	2	-
GCF_014191495.1	s__Nocardioides soli	79.5947	614	1346	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	98.71	98.71	0.90	0.90	2	-
GCF_014648595.1	s__Nocardioides luteus	79.5735	583	1346	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001425175.1	s__Nocardioides sp001425175	79.4837	602	1346	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004564375.1	s__Nocardioides euryhalodurans	79.4493	501	1346	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000519005.1	s__Nocardioides sp000519005	79.4044	554	1346	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	98.89	98.89	0.90	0.90	2	-
GCF_900101465.1	s__Nocardioides lianchengensis	79.3646	638	1346	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014873635.1	s__Nocardioides sp014873635	79.2882	564	1346	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004519545.1	s__Nocardioides guangzhouensis	79.0724	555	1346	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:20:44,700] [INFO] GTDB search result was written to GCF_000422825.1_ASM42282v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:20:44,701] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:20:44,706] [INFO] DFAST_QC result json was written to GCF_000422825.1_ASM42282v1_genomic.fna/dqc_result.json
[2024-01-24 13:20:44,706] [INFO] DFAST_QC completed!
[2024-01-24 13:20:44,707] [INFO] Total running time: 0h1m58s