[2024-01-24 13:31:30,084] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:31:30,086] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:31:30,087] [INFO] DQC Reference Directory: /var/lib/cwl/stgc727c01f-b6ea-4ea7-8b81-7ab43799859b/dqc_reference
[2024-01-24 13:31:31,362] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:31:31,363] [INFO] Task started: Prodigal
[2024-01-24 13:31:31,363] [INFO] Running command: gunzip -c /var/lib/cwl/stgff1c8d1a-ad71-4742-8548-d9f9c93f6190/GCF_007992415.1_ASM799241v1_genomic.fna.gz | prodigal -d GCF_007992415.1_ASM799241v1_genomic.fna/cds.fna -a GCF_007992415.1_ASM799241v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:31:43,984] [INFO] Task succeeded: Prodigal
[2024-01-24 13:31:43,984] [INFO] Task started: HMMsearch
[2024-01-24 13:31:43,985] [INFO] Running command: hmmsearch --tblout GCF_007992415.1_ASM799241v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc727c01f-b6ea-4ea7-8b81-7ab43799859b/dqc_reference/reference_markers.hmm GCF_007992415.1_ASM799241v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:31:44,286] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:31:44,289] [INFO] Found 6/6 markers.
[2024-01-24 13:31:44,341] [INFO] Query marker FASTA was written to GCF_007992415.1_ASM799241v1_genomic.fna/markers.fasta
[2024-01-24 13:31:44,342] [INFO] Task started: Blastn
[2024-01-24 13:31:44,342] [INFO] Running command: blastn -query GCF_007992415.1_ASM799241v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc727c01f-b6ea-4ea7-8b81-7ab43799859b/dqc_reference/reference_markers.fasta -out GCF_007992415.1_ASM799241v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:31:45,647] [INFO] Task succeeded: Blastn
[2024-01-24 13:31:45,651] [INFO] Selected 12 target genomes.
[2024-01-24 13:31:45,652] [INFO] Target genome list was writen to GCF_007992415.1_ASM799241v1_genomic.fna/target_genomes.txt
[2024-01-24 13:31:45,657] [INFO] Task started: fastANI
[2024-01-24 13:31:45,657] [INFO] Running command: fastANI --query /var/lib/cwl/stgff1c8d1a-ad71-4742-8548-d9f9c93f6190/GCF_007992415.1_ASM799241v1_genomic.fna.gz --refList GCF_007992415.1_ASM799241v1_genomic.fna/target_genomes.txt --output GCF_007992415.1_ASM799241v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:31:58,017] [INFO] Task succeeded: fastANI
[2024-01-24 13:31:58,017] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc727c01f-b6ea-4ea7-8b81-7ab43799859b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:31:58,018] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc727c01f-b6ea-4ea7-8b81-7ab43799859b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:31:58,028] [INFO] Found 12 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:31:58,029] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:31:58,029] [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 psychrotolerans	strain=NBRC 108563	GCA_007992415.1	1005945	1005945	type	True	100.0	1461	1463	95	conclusive
Nocardioides psychrotolerans	strain=CGMCC 1.11156	GCA_900113685.1	1005945	1005945	type	True	99.9949	1463	1463	95	conclusive
Nocardioides szechwanensis	strain=NBRC 108562	GCA_007992395.1	1005944	1005944	type	True	84.0286	981	1463	95	below_threshold
Nocardioides szechwanensis	strain=CGMCC 1.11147	GCA_900103935.1	1005944	1005944	type	True	83.9493	988	1463	95	below_threshold
Nocardioides lijunqiniae	strain=S-531	GCA_015024225.1	2760832	2760832	type	True	83.8193	919	1463	95	below_threshold
Nocardioides dongkuii	strain=S-713	GCA_014127485.1	2760089	2760089	type	True	81.7801	790	1463	95	below_threshold
Nocardioides rubriscoriae	strain=DSM 23986	GCA_008087085.1	642762	642762	type	True	81.6822	868	1463	95	below_threshold
Nocardioides lacusdianchii	strain=JXJ CY 38	GCA_020102855.1	2783664	2783664	type	True	80.8486	708	1463	95	below_threshold
Nocardioides ganghwensis	strain=9920	GCA_014779655.1	252230	252230	type	True	80.824	697	1463	95	below_threshold
Nocardioides furvisabuli	strain=JCM 13813	GCA_021083185.1	375542	375542	type	True	80.6196	705	1463	95	below_threshold
Nocardioides humilatus	strain=BN130099	GCA_008373755.1	2607660	2607660	type	True	80.2376	691	1463	95	below_threshold
Nocardioides sambongensis	strain=KUDC 5002	GCA_006494815.1	2589074	2589074	type	True	79.6829	632	1463	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:31:58,031] [INFO] DFAST Taxonomy check result was written to GCF_007992415.1_ASM799241v1_genomic.fna/tc_result.tsv
[2024-01-24 13:31:58,031] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:31:58,032] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:31:58,032] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc727c01f-b6ea-4ea7-8b81-7ab43799859b/dqc_reference/checkm_data
[2024-01-24 13:31:58,034] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:31:58,085] [INFO] Task started: CheckM
[2024-01-24 13:31:58,085] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007992415.1_ASM799241v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007992415.1_ASM799241v1_genomic.fna/checkm_input GCF_007992415.1_ASM799241v1_genomic.fna/checkm_result
[2024-01-24 13:33:00,221] [INFO] Task succeeded: CheckM
[2024-01-24 13:33:00,222] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:33:00,244] [INFO] ===== Completeness check finished =====
[2024-01-24 13:33:00,244] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:33:00,245] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007992415.1_ASM799241v1_genomic.fna/markers.fasta)
[2024-01-24 13:33:00,245] [INFO] Task started: Blastn
[2024-01-24 13:33:00,245] [INFO] Running command: blastn -query GCF_007992415.1_ASM799241v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc727c01f-b6ea-4ea7-8b81-7ab43799859b/dqc_reference/reference_markers_gtdb.fasta -out GCF_007992415.1_ASM799241v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:33:02,367] [INFO] Task succeeded: Blastn
[2024-01-24 13:33:02,370] [INFO] Selected 13 target genomes.
[2024-01-24 13:33:02,370] [INFO] Target genome list was writen to GCF_007992415.1_ASM799241v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:33:02,382] [INFO] Task started: fastANI
[2024-01-24 13:33:02,383] [INFO] Running command: fastANI --query /var/lib/cwl/stgff1c8d1a-ad71-4742-8548-d9f9c93f6190/GCF_007992415.1_ASM799241v1_genomic.fna.gz --refList GCF_007992415.1_ASM799241v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007992415.1_ASM799241v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:33:17,828] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:17,842] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:33:17,842] [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_900113685.1	s__Nocardioides psychrotolerans	99.9949	1463	1463	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.99	99.99	1.00	1.00	2	conclusive
GCF_900103935.1	s__Nocardioides szechwanensis	83.949	988	1463	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.99	99.99	1.00	1.00	2	-
GCF_004522095.1	s__Nocardioides sp004522095	83.8664	914	1463	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015024225.1	s__Nocardioides sp015024225	83.8276	920	1463	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	97.48	97.48	0.91	0.91	2	-
GCF_014212315.1	s__Nocardioides luti	82.1726	836	1463	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	81.7812	790	1463	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.37	99.37	0.97	0.97	2	-
GCF_015070375.1	s__Nocardioides kribbensis	81.7409	805	1463	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	97.79	97.79	0.94	0.92	3	-
GCF_013466785.1	s__Nocardioides marinisabuli	81.7096	800	1463	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.99	99.99	1.00	1.00	2	-
GCF_008087085.1	s__Nocardioides rubriscoriae	81.6786	868	1463	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002117935.1	s__Nocardioides sp002117935	81.6488	833	1463	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.99	99.99	0.99	0.99	2	-
GCF_005954645.2	s__Nocardioides dongxiaopingii	81.4477	782	1463	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	98.98	98.98	0.96	0.96	2	-
GCF_004522105.1	s__Nocardioides sp004522105	81.3693	794	1463	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002698575.1	s__Nocardioides sp002698575	80.8854	679	1463	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 13:33:17,844] [INFO] GTDB search result was written to GCF_007992415.1_ASM799241v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:33:17,845] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:33:17,849] [INFO] DFAST_QC result json was written to GCF_007992415.1_ASM799241v1_genomic.fna/dqc_result.json
[2024-01-24 13:33:17,849] [INFO] DFAST_QC completed!
[2024-01-24 13:33:17,849] [INFO] Total running time: 0h1m48s