[2024-01-24 15:01:14,724] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:01:14,731] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:01:14,731] [INFO] DQC Reference Directory: /var/lib/cwl/stg045f847d-633e-4512-9f54-a5aeb80e306f/dqc_reference
[2024-01-24 15:01:15,899] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:01:15,900] [INFO] Task started: Prodigal
[2024-01-24 15:01:15,900] [INFO] Running command: gunzip -c /var/lib/cwl/stgaee477ff-d5c9-45ad-ad06-43123806219f/GCF_004337475.1_ASM433747v1_genomic.fna.gz | prodigal -d GCF_004337475.1_ASM433747v1_genomic.fna/cds.fna -a GCF_004337475.1_ASM433747v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:01:24,770] [INFO] Task succeeded: Prodigal
[2024-01-24 15:01:24,770] [INFO] Task started: HMMsearch
[2024-01-24 15:01:24,771] [INFO] Running command: hmmsearch --tblout GCF_004337475.1_ASM433747v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg045f847d-633e-4512-9f54-a5aeb80e306f/dqc_reference/reference_markers.hmm GCF_004337475.1_ASM433747v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:01:24,996] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:01:24,998] [INFO] Found 6/6 markers.
[2024-01-24 15:01:25,026] [INFO] Query marker FASTA was written to GCF_004337475.1_ASM433747v1_genomic.fna/markers.fasta
[2024-01-24 15:01:25,027] [INFO] Task started: Blastn
[2024-01-24 15:01:25,027] [INFO] Running command: blastn -query GCF_004337475.1_ASM433747v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg045f847d-633e-4512-9f54-a5aeb80e306f/dqc_reference/reference_markers.fasta -out GCF_004337475.1_ASM433747v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:01:26,217] [INFO] Task succeeded: Blastn
[2024-01-24 15:01:26,228] [INFO] Selected 18 target genomes.
[2024-01-24 15:01:26,228] [INFO] Target genome list was writen to GCF_004337475.1_ASM433747v1_genomic.fna/target_genomes.txt
[2024-01-24 15:01:26,241] [INFO] Task started: fastANI
[2024-01-24 15:01:26,241] [INFO] Running command: fastANI --query /var/lib/cwl/stgaee477ff-d5c9-45ad-ad06-43123806219f/GCF_004337475.1_ASM433747v1_genomic.fna.gz --refList GCF_004337475.1_ASM433747v1_genomic.fna/target_genomes.txt --output GCF_004337475.1_ASM433747v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:01:41,195] [INFO] Task succeeded: fastANI
[2024-01-24 15:01:41,196] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg045f847d-633e-4512-9f54-a5aeb80e306f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:01:41,196] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg045f847d-633e-4512-9f54-a5aeb80e306f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:01:41,212] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:01:41,212] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:01:41,213] [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 jejuensis	strain=18JY15-6	GCA_004337475.1	2502782	2502782	type	True	100.0	1049	1054	95	conclusive
Nocardioides phosphati	strain=CGMCC 4.7371	GCA_014646375.1	1867775	1867775	type	True	86.3642	824	1054	95	below_threshold
Nocardioides cavernaquae	strain=K1W22B-1	GCA_003600895.1	2321396	2321396	type	True	82.9425	690	1054	95	below_threshold
Nocardioides nematodiphilus	strain=R-N-C8	GCA_020216525.1	2849669	2849669	type	True	80.3534	486	1054	95	below_threshold
Nocardioides guangzhouensis	strain=130	GCA_004519545.1	2497878	2497878	type	True	79.937	518	1054	95	below_threshold
Nocardioides lacusdianchii	strain=JXJ CY 38	GCA_020102855.1	2783664	2783664	type	True	79.9331	500	1054	95	below_threshold
Nocardioides jensenii	strain=NBRC 14755	GCA_001552535.1	1843	1843	type	True	79.9026	483	1054	95	below_threshold
Nocardioides ganghwensis	strain=9920	GCA_014779655.1	252230	252230	type	True	79.8898	491	1054	95	below_threshold
Nocardioides humilatus	strain=BN130099	GCA_008373755.1	2607660	2607660	type	True	79.8783	525	1054	95	below_threshold
Nocardioides glacieisoli	strain=HLT3-15	GCA_004137245.1	1168730	1168730	type	True	79.8158	487	1054	95	below_threshold
Nocardioides alpinus	strain=DSM 23325	GCA_002836395.1	748909	748909	type	True	79.8025	483	1054	95	below_threshold
Nocardioides alpinus	strain=CGMCC 1.10697	GCA_900112035.1	748909	748909	type	True	79.7892	478	1054	95	below_threshold
Nocardioides zhouii	strain=HLT2-9	GCA_004137345.1	1168729	1168729	type	True	79.7453	479	1054	95	below_threshold
Nocardioides carbamazepini	strain=CBZ_1	GCA_024614185.1	2854259	2854259	type	True	79.7238	518	1054	95	below_threshold
Nocardioides flavescens	strain=YIM 123512	GCA_009823805.1	2691959	2691959	type	True	79.6731	485	1054	95	below_threshold
Nocardioides jishulii	strain=dk3136	GCA_006007965.1	2575440	2575440	type	True	79.6687	434	1054	95	below_threshold
Nocardioides alkalitolerans	strain=DSM 16699	GCA_000426525.1	281714	281714	type	True	79.664	475	1054	95	below_threshold
Nocardioides panaciterrulae	strain=DSM 21350	GCA_013409645.1	661492	661492	type	True	79.5587	484	1054	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:01:41,215] [INFO] DFAST Taxonomy check result was written to GCF_004337475.1_ASM433747v1_genomic.fna/tc_result.tsv
[2024-01-24 15:01:41,215] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:01:41,215] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:01:41,215] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg045f847d-633e-4512-9f54-a5aeb80e306f/dqc_reference/checkm_data
[2024-01-24 15:01:41,216] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:01:41,255] [INFO] Task started: CheckM
[2024-01-24 15:01:41,256] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004337475.1_ASM433747v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004337475.1_ASM433747v1_genomic.fna/checkm_input GCF_004337475.1_ASM433747v1_genomic.fna/checkm_result
[2024-01-24 15:02:27,314] [INFO] Task succeeded: CheckM
[2024-01-24 15:02:27,316] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:02:27,337] [INFO] ===== Completeness check finished =====
[2024-01-24 15:02:27,338] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:02:27,338] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004337475.1_ASM433747v1_genomic.fna/markers.fasta)
[2024-01-24 15:02:27,339] [INFO] Task started: Blastn
[2024-01-24 15:02:27,339] [INFO] Running command: blastn -query GCF_004337475.1_ASM433747v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg045f847d-633e-4512-9f54-a5aeb80e306f/dqc_reference/reference_markers_gtdb.fasta -out GCF_004337475.1_ASM433747v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:02:29,233] [INFO] Task succeeded: Blastn
[2024-01-24 15:02:29,236] [INFO] Selected 13 target genomes.
[2024-01-24 15:02:29,236] [INFO] Target genome list was writen to GCF_004337475.1_ASM433747v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:02:29,251] [INFO] Task started: fastANI
[2024-01-24 15:02:29,251] [INFO] Running command: fastANI --query /var/lib/cwl/stgaee477ff-d5c9-45ad-ad06-43123806219f/GCF_004337475.1_ASM433747v1_genomic.fna.gz --refList GCF_004337475.1_ASM433747v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004337475.1_ASM433747v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:02:40,441] [INFO] Task succeeded: fastANI
[2024-01-24 15:02:40,457] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:02:40,457] [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_004337475.1	s__Nocardioides jejuensis	100.0	1049	1054	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_014646375.1	s__Nocardioides phosphati	86.4182	820	1054	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003053885.1	s__Nocardioides sp003053885	85.7065	794	1054	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003600895.1	s__Nocardioides sp003600895	82.9505	690	1054	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013778305.1	s__Nocardioides sp013778305	80.0207	511	1054	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004519545.1	s__Nocardioides guangzhouensis	79.9481	517	1054	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001426745.1	s__Nocardioides sp001426745	79.93	533	1054	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	98.99	98.75	0.96	0.95	3	-
GCF_013177455.1	s__Nocardioides sp013177455	79.8419	507	1054	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.28	98.92	0.97	0.95	4	-
GCF_900112035.1	s__Nocardioides alpinus	79.8106	476	1054	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.99	99.99	1.00	1.00	2	-
GCF_011250565.1	s__Nocardioides sp011250565	79.7813	510	1054	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	79.7586	443	1054	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.38	96.50	0.91	0.88	12	-
GCF_015070375.1	s__Nocardioides kribbensis	79.5948	487	1054	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	97.79	97.79	0.94	0.92	3	-
GCF_013409645.1	s__Nocardioides panaciterrulae	79.5383	486	1054	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 15:02:40,459] [INFO] GTDB search result was written to GCF_004337475.1_ASM433747v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:02:40,459] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:02:40,463] [INFO] DFAST_QC result json was written to GCF_004337475.1_ASM433747v1_genomic.fna/dqc_result.json
[2024-01-24 15:02:40,463] [INFO] DFAST_QC completed!
[2024-01-24 15:02:40,463] [INFO] Total running time: 0h1m26s