[2024-01-24 15:10:22,935] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:10:22,942] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:10:22,942] [INFO] DQC Reference Directory: /var/lib/cwl/stgd3e9bf48-5da2-4601-b650-aa1339fdd85b/dqc_reference
[2024-01-24 15:10:24,583] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:10:24,584] [INFO] Task started: Prodigal
[2024-01-24 15:10:24,585] [INFO] Running command: gunzip -c /var/lib/cwl/stg01e9de47-9444-42aa-8e48-2c468f54ac6b/GCF_900156775.1_IMG-taxon_2681813555_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900156775.1_IMG-taxon_2681813555_annotated_assembly_genomic.fna/cds.fna -a GCF_900156775.1_IMG-taxon_2681813555_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:10:50,993] [INFO] Task succeeded: Prodigal
[2024-01-24 15:10:50,993] [INFO] Task started: HMMsearch
[2024-01-24 15:10:50,994] [INFO] Running command: hmmsearch --tblout GCF_900156775.1_IMG-taxon_2681813555_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd3e9bf48-5da2-4601-b650-aa1339fdd85b/dqc_reference/reference_markers.hmm GCF_900156775.1_IMG-taxon_2681813555_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:10:51,274] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:10:51,275] [INFO] Found 6/6 markers.
[2024-01-24 15:10:51,358] [INFO] Query marker FASTA was written to GCF_900156775.1_IMG-taxon_2681813555_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 15:10:51,358] [INFO] Task started: Blastn
[2024-01-24 15:10:51,359] [INFO] Running command: blastn -query GCF_900156775.1_IMG-taxon_2681813555_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgd3e9bf48-5da2-4601-b650-aa1339fdd85b/dqc_reference/reference_markers.fasta -out GCF_900156775.1_IMG-taxon_2681813555_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:10:52,682] [INFO] Task succeeded: Blastn
[2024-01-24 15:10:52,685] [INFO] Selected 7 target genomes.
[2024-01-24 15:10:52,686] [INFO] Target genome list was writen to GCF_900156775.1_IMG-taxon_2681813555_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 15:10:52,689] [INFO] Task started: fastANI
[2024-01-24 15:10:52,689] [INFO] Running command: fastANI --query /var/lib/cwl/stg01e9de47-9444-42aa-8e48-2c468f54ac6b/GCF_900156775.1_IMG-taxon_2681813555_annotated_assembly_genomic.fna.gz --refList GCF_900156775.1_IMG-taxon_2681813555_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900156775.1_IMG-taxon_2681813555_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:11:06,016] [INFO] Task succeeded: fastANI
[2024-01-24 15:11:06,017] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd3e9bf48-5da2-4601-b650-aa1339fdd85b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:11:06,017] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd3e9bf48-5da2-4601-b650-aa1339fdd85b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:11:06,025] [INFO] Found 7 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 15:11:06,025] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:11:06,025] [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
Nocardia farcinica	strain=DSM 43257	GCA_900156775.1	37329	37329	type	True	100.0	2113	2116	95	conclusive
Nocardia farcinica	strain=NCTC11134	GCA_001182745.2	37329	37329	type	True	99.9951	2113	2116	95	conclusive
Nocardia farcinica	strain=NBRC 15532	GCA_001612925.1	37329	37329	type	True	99.9444	2012	2116	95	conclusive
Nocardia higoensis	strain=NBRC 100133	GCA_000308595.1	228599	228599	type	True	84.7838	1278	2116	95	below_threshold
Nocardia shimofusensis	strain=NBRC 100134	GCA_001613125.1	228596	228596	type	True	84.6662	1317	2116	95	below_threshold
Nocardia bhagyanarayanae	strain=DSM 103495	GCA_006716565.1	1215925	1215925	type	True	83.5603	1337	2116	95	below_threshold
Nocardia lijiangensis	strain=NBRC 108240	GCA_001613045.1	299618	299618	type	True	83.4418	1250	2116	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:11:06,027] [INFO] DFAST Taxonomy check result was written to GCF_900156775.1_IMG-taxon_2681813555_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 15:11:06,028] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:11:06,028] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:11:06,028] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd3e9bf48-5da2-4601-b650-aa1339fdd85b/dqc_reference/checkm_data
[2024-01-24 15:11:06,029] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:11:06,086] [INFO] Task started: CheckM
[2024-01-24 15:11:06,086] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900156775.1_IMG-taxon_2681813555_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900156775.1_IMG-taxon_2681813555_annotated_assembly_genomic.fna/checkm_input GCF_900156775.1_IMG-taxon_2681813555_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 15:12:38,473] [INFO] Task succeeded: CheckM
[2024-01-24 15:12:38,475] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 2.78%
Strain heterogeneity: 57.14%
--------------------------------------------------------------------------------
[2024-01-24 15:12:38,494] [INFO] ===== Completeness check finished =====
[2024-01-24 15:12:38,495] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:12:38,496] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900156775.1_IMG-taxon_2681813555_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 15:12:38,496] [INFO] Task started: Blastn
[2024-01-24 15:12:38,496] [INFO] Running command: blastn -query GCF_900156775.1_IMG-taxon_2681813555_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgd3e9bf48-5da2-4601-b650-aa1339fdd85b/dqc_reference/reference_markers_gtdb.fasta -out GCF_900156775.1_IMG-taxon_2681813555_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:12:40,451] [INFO] Task succeeded: Blastn
[2024-01-24 15:12:40,455] [INFO] Selected 12 target genomes.
[2024-01-24 15:12:40,455] [INFO] Target genome list was writen to GCF_900156775.1_IMG-taxon_2681813555_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:12:40,462] [INFO] Task started: fastANI
[2024-01-24 15:12:40,463] [INFO] Running command: fastANI --query /var/lib/cwl/stg01e9de47-9444-42aa-8e48-2c468f54ac6b/GCF_900156775.1_IMG-taxon_2681813555_annotated_assembly_genomic.fna.gz --refList GCF_900156775.1_IMG-taxon_2681813555_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900156775.1_IMG-taxon_2681813555_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:13:01,541] [INFO] Task succeeded: fastANI
[2024-01-24 15:13:01,551] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:13:01,552] [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_001182745.1	s__Nocardia farcinica	99.9951	2113	2116	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	99.16	98.59	0.93	0.88	42	conclusive
GCF_000308595.1	s__Nocardia higoensis	84.7682	1280	2116	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001613125.1	s__Nocardia shimofusensis	84.6869	1315	2116	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015477835.1	s__Nocardia higoensis_A	84.4387	1336	2116	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001612615.1	s__Nocardia amikacinitolerans	83.5972	1297	2116	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	97.80	97.80	0.89	0.89	2	-
GCF_006716565.1	s__Nocardia bhagyanarayanae	83.5726	1336	2116	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001613045.1	s__Nocardia lijiangensis	83.4317	1252	2116	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001613365.1	s__Nocardia xishanensis	83.3783	1277	2116	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001612785.1	s__Nocardia beijingensis	82.3618	1207	2116	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	98.03	98.03	0.92	0.92	2	-
GCF_000308755.1	s__Nocardia pneumoniae	82.3233	1185	2116	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009829325.1	s__Nocardia sp009829325	82.0081	1212	2116	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	96.48	96.48	0.88	0.88	2	-
GCF_001613425.1	s__Nocardia vulneris	81.7004	1192	2116	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.8238	100.00	100.00	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-24 15:13:01,553] [INFO] GTDB search result was written to GCF_900156775.1_IMG-taxon_2681813555_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 15:13:01,554] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:13:01,556] [INFO] DFAST_QC result json was written to GCF_900156775.1_IMG-taxon_2681813555_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 15:13:01,556] [INFO] DFAST_QC completed!
[2024-01-24 15:13:01,557] [INFO] Total running time: 0h2m39s