[2024-01-24 12:53:56,857] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:53:56,859] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:53:56,859] [INFO] DQC Reference Directory: /var/lib/cwl/stg3fc42a7b-dcc8-419c-8ff1-26154f7a25e8/dqc_reference
[2024-01-24 12:53:58,242] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:53:58,254] [INFO] Task started: Prodigal
[2024-01-24 12:53:58,255] [INFO] Running command: gunzip -c /var/lib/cwl/stg95cd8832-177a-4f98-abd4-62abfb51f082/GCF_003047265.1_ASM304726v1_genomic.fna.gz | prodigal -d GCF_003047265.1_ASM304726v1_genomic.fna/cds.fna -a GCF_003047265.1_ASM304726v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:54:11,683] [INFO] Task succeeded: Prodigal
[2024-01-24 12:54:11,683] [INFO] Task started: HMMsearch
[2024-01-24 12:54:11,683] [INFO] Running command: hmmsearch --tblout GCF_003047265.1_ASM304726v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3fc42a7b-dcc8-419c-8ff1-26154f7a25e8/dqc_reference/reference_markers.hmm GCF_003047265.1_ASM304726v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:54:12,014] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:54:12,015] [INFO] Found 6/6 markers.
[2024-01-24 12:54:12,067] [INFO] Query marker FASTA was written to GCF_003047265.1_ASM304726v1_genomic.fna/markers.fasta
[2024-01-24 12:54:12,067] [INFO] Task started: Blastn
[2024-01-24 12:54:12,068] [INFO] Running command: blastn -query GCF_003047265.1_ASM304726v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3fc42a7b-dcc8-419c-8ff1-26154f7a25e8/dqc_reference/reference_markers.fasta -out GCF_003047265.1_ASM304726v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:54:13,376] [INFO] Task succeeded: Blastn
[2024-01-24 12:54:13,380] [INFO] Selected 27 target genomes.
[2024-01-24 12:54:13,380] [INFO] Target genome list was writen to GCF_003047265.1_ASM304726v1_genomic.fna/target_genomes.txt
[2024-01-24 12:54:13,405] [INFO] Task started: fastANI
[2024-01-24 12:54:13,405] [INFO] Running command: fastANI --query /var/lib/cwl/stg95cd8832-177a-4f98-abd4-62abfb51f082/GCF_003047265.1_ASM304726v1_genomic.fna.gz --refList GCF_003047265.1_ASM304726v1_genomic.fna/target_genomes.txt --output GCF_003047265.1_ASM304726v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:54:38,912] [INFO] Task succeeded: fastANI
[2024-01-24 12:54:38,913] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3fc42a7b-dcc8-419c-8ff1-26154f7a25e8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:54:38,913] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3fc42a7b-dcc8-419c-8ff1-26154f7a25e8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:54:38,932] [INFO] Found 23 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:54:38,932] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:54:38,932] [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 terrigena	strain=KCTC 19217	GCA_003047265.1	424797	424797	type	True	100.0	1564	1566	95	conclusive
Nocardioides sediminis	strain=KCTC 19271	GCA_003047295.1	433648	433648	type	True	86.946	1078	1566	95	below_threshold
Nocardioides currus	strain=IB-3	GCA_003057875.1	2133958	2133958	type	True	83.2271	939	1566	95	below_threshold
Nocardioides allogilvus	strain=KCTC 49020	GCA_003047285.1	2072017	2072017	type	True	83.1857	853	1566	95	below_threshold
Nocardioides lacusdianchii	strain=JXJ CY 38	GCA_020102855.1	2783664	2783664	type	True	82.5913	882	1566	95	below_threshold
Nocardioides exalbidus	strain=DSM 22017	GCA_900105585.1	402596	402596	type	True	82.4345	868	1566	95	below_threshold
Nocardioides okcheonensis	strain=MMS20-HV4-12	GCA_020991065.1	2894081	2894081	type	True	82.4067	896	1566	95	below_threshold
Nocardioides cavernae	strain=DSM 29950	GCA_016907475.1	1921566	1921566	type	True	82.389	903	1566	95	below_threshold
Nocardioides eburneiflavus	strain=MMS17-SY213	GCA_004785795.1	2518372	2518372	type	True	82.3877	903	1566	95	below_threshold
Nocardioides cavernae	strain=KCTC 39551	GCA_014779675.1	1921566	1921566	type	True	82.3805	895	1566	95	below_threshold
Nocardioides ganghwensis	strain=9920	GCA_014779655.1	252230	252230	type	True	82.3632	899	1566	95	below_threshold
Nocardioides baculatus	strain=G10	GCA_016735675.1	2801337	2801337	type	True	82.3525	880	1566	95	below_threshold
Nocardioides furvisabuli	strain=JCM 13813	GCA_021083185.1	375542	375542	type	True	82.3355	845	1566	95	below_threshold
Nocardioides zhouii	strain=HLT2-9	GCA_004137345.1	1168729	1168729	type	True	82.2204	871	1566	95	below_threshold
Nocardioides hwasunensis	strain=19197	GCA_014779665.1	397258	397258	type	True	82.1057	840	1566	95	below_threshold
Nocardioides ginsengisegetis	strain=DSM 21349	GCA_014138045.1	661491	661491	type	True	81.8232	778	1566	95	below_threshold
Nocardioides rubriscoriae	strain=DSM 23986	GCA_008087085.1	642762	642762	type	True	81.4422	762	1566	95	below_threshold
Nocardioides marinisabuli	strain=DSM 18965	GCA_013409965.1	419476	419476	type	True	81.429	769	1566	95	below_threshold
Nocardioides marinisabuli	strain=DSM 18965	GCA_013466785.1	419476	419476	type	True	81.4069	770	1566	95	below_threshold
Nocardioides salarius	strain=DSM 18239	GCA_015339545.1	374513	374513	type	True	81.0877	775	1566	95	below_threshold
Nocardioides marinus	strain=DSM 18248	GCA_013408145.1	374514	374514	type	True	80.9271	739	1566	95	below_threshold
Nocardioides alkalitolerans	strain=DSM 16699	GCA_000426525.1	281714	281714	type	True	80.0358	700	1566	95	below_threshold
Paenibacillus antri	strain=SYSU K30003	GCA_005765165.1	2582848	2582848	type	True	74.5587	60	1566	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:54:38,934] [INFO] DFAST Taxonomy check result was written to GCF_003047265.1_ASM304726v1_genomic.fna/tc_result.tsv
[2024-01-24 12:54:38,934] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:54:38,935] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:54:38,935] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3fc42a7b-dcc8-419c-8ff1-26154f7a25e8/dqc_reference/checkm_data
[2024-01-24 12:54:38,936] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:54:38,980] [INFO] Task started: CheckM
[2024-01-24 12:54:38,981] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003047265.1_ASM304726v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003047265.1_ASM304726v1_genomic.fna/checkm_input GCF_003047265.1_ASM304726v1_genomic.fna/checkm_result
[2024-01-24 12:55:44,862] [INFO] Task succeeded: CheckM
[2024-01-24 12:55:44,864] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:55:44,887] [INFO] ===== Completeness check finished =====
[2024-01-24 12:55:44,887] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:55:44,888] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003047265.1_ASM304726v1_genomic.fna/markers.fasta)
[2024-01-24 12:55:44,888] [INFO] Task started: Blastn
[2024-01-24 12:55:44,888] [INFO] Running command: blastn -query GCF_003047265.1_ASM304726v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3fc42a7b-dcc8-419c-8ff1-26154f7a25e8/dqc_reference/reference_markers_gtdb.fasta -out GCF_003047265.1_ASM304726v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:55:46,853] [INFO] Task succeeded: Blastn
[2024-01-24 12:55:46,857] [INFO] Selected 22 target genomes.
[2024-01-24 12:55:46,857] [INFO] Target genome list was writen to GCF_003047265.1_ASM304726v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:55:46,873] [INFO] Task started: fastANI
[2024-01-24 12:55:46,873] [INFO] Running command: fastANI --query /var/lib/cwl/stg95cd8832-177a-4f98-abd4-62abfb51f082/GCF_003047265.1_ASM304726v1_genomic.fna.gz --refList GCF_003047265.1_ASM304726v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003047265.1_ASM304726v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:56:07,803] [INFO] Task succeeded: fastANI
[2024-01-24 12:56:07,819] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:56:07,819] [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_003047265.1	s__Nocardioides terrigena	100.0	1564	1566	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	95.44	95.44	0.86	0.86	2	conclusive
GCF_001429625.1	s__Nocardioides sp001429625	88.0997	1136	1566	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003047295.1	s__Nocardioides sediminis	86.9463	1078	1566	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003057875.1	s__Nocardioides currus	83.2305	940	1566	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003047285.1	s__Nocardioides allogilvus	83.2064	851	1566	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	98.72	98.72	0.92	0.92	2	-
GCF_017310035.1	s__Nocardioides sp017310035	82.7674	891	1566	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009699265.1	s__Nocardioides sp009699265	82.4518	844	1566	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900105585.1	s__Nocardioides exalbidus	82.4355	868	1566	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014779655.1	s__Nocardioides ganghwensis	82.4336	890	1566	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004137255.1	s__Nocardioides oleivorans	82.4227	843	1566	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016907475.1	s__Nocardioides cavernae	82.3749	903	1566	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003076135.1	s__Nocardioides gansuensis	82.0425	803	1566	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014138045.1	s__Nocardioides ginsengisegetis	81.7762	783	1566	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	96.18	96.18	0.84	0.84	2	-
GCF_002117935.1	s__Nocardioides sp002117935	81.5203	752	1566	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.99	99.99	0.99	0.99	2	-
GCF_013466785.1	s__Nocardioides marinisabuli	81.4336	767	1566	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.99	99.99	1.00	1.00	2	-
GCA_009701885.1	s__Nocardioides sp009701885	81.1582	686	1566	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	80.9706	630	1566	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.38	96.50	0.91	0.88	12	-
GCA_016213595.1	s__Fen-668 sp016213595	77.4192	180	1566	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Fen-668	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005765165.1	s__Paenibacillus_AE antri	74.5599	59	1566	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__YIM-B00363;g__Paenibacillus_AE	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:56:07,821] [INFO] GTDB search result was written to GCF_003047265.1_ASM304726v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:56:07,821] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:56:07,825] [INFO] DFAST_QC result json was written to GCF_003047265.1_ASM304726v1_genomic.fna/dqc_result.json
[2024-01-24 12:56:07,826] [INFO] DFAST_QC completed!
[2024-01-24 12:56:07,826] [INFO] Total running time: 0h2m11s