[2024-01-24 12:31:58,531] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:31:58,533] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:31:58,533] [INFO] DQC Reference Directory: /var/lib/cwl/stg2f7aef32-b8a5-46af-88af-736c2dd9dbaa/dqc_reference
[2024-01-24 12:31:59,923] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:31:59,924] [INFO] Task started: Prodigal
[2024-01-24 12:31:59,924] [INFO] Running command: gunzip -c /var/lib/cwl/stg1bfbbe55-4ead-4998-aec5-366e5cd845c3/GCF_000308535.1_ASM30853v1_genomic.fna.gz | prodigal -d GCF_000308535.1_ASM30853v1_genomic.fna/cds.fna -a GCF_000308535.1_ASM30853v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:32:24,394] [INFO] Task succeeded: Prodigal
[2024-01-24 12:32:24,395] [INFO] Task started: HMMsearch
[2024-01-24 12:32:24,395] [INFO] Running command: hmmsearch --tblout GCF_000308535.1_ASM30853v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2f7aef32-b8a5-46af-88af-736c2dd9dbaa/dqc_reference/reference_markers.hmm GCF_000308535.1_ASM30853v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:32:24,806] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:32:24,807] [INFO] Found 6/6 markers.
[2024-01-24 12:32:24,874] [INFO] Query marker FASTA was written to GCF_000308535.1_ASM30853v1_genomic.fna/markers.fasta
[2024-01-24 12:32:24,875] [INFO] Task started: Blastn
[2024-01-24 12:32:24,875] [INFO] Running command: blastn -query GCF_000308535.1_ASM30853v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2f7aef32-b8a5-46af-88af-736c2dd9dbaa/dqc_reference/reference_markers.fasta -out GCF_000308535.1_ASM30853v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:32:26,125] [INFO] Task succeeded: Blastn
[2024-01-24 12:32:26,129] [INFO] Selected 8 target genomes.
[2024-01-24 12:32:26,129] [INFO] Target genome list was writen to GCF_000308535.1_ASM30853v1_genomic.fna/target_genomes.txt
[2024-01-24 12:32:26,147] [INFO] Task started: fastANI
[2024-01-24 12:32:26,148] [INFO] Running command: fastANI --query /var/lib/cwl/stg1bfbbe55-4ead-4998-aec5-366e5cd845c3/GCF_000308535.1_ASM30853v1_genomic.fna.gz --refList GCF_000308535.1_ASM30853v1_genomic.fna/target_genomes.txt --output GCF_000308535.1_ASM30853v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:32:43,340] [INFO] Task succeeded: fastANI
[2024-01-24 12:32:43,341] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2f7aef32-b8a5-46af-88af-736c2dd9dbaa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:32:43,341] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2f7aef32-b8a5-46af-88af-736c2dd9dbaa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:32:43,350] [INFO] Found 8 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:32:43,350] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 12:32:43,350] [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 cerradoensis	strain=NBRC 101014	GCA_000308535.1	85688	85688	type	True	100.0	2338	2354	95	inconclusive
Nocardia aobensis	strain=NBRC 100429	GCA_000308375.1	257277	257277	type	True	95.0126	1961	2354	95	inconclusive
Nocardia kruczakiae	strain=NBRC 101016	GCA_001612965.1	261477	261477	type	True	94.8413	1958	2354	95	below_threshold
Nocardia mikamii	strain=NBRC 108933	GCA_001613505.1	508464	508464	type	True	94.425	1984	2354	95	below_threshold
Nocardia africana	strain=NBRC 100379	GCA_001612635.1	134964	134964	type	True	92.4734	1916	2354	95	below_threshold
Nocardia africana	strain=FDAARGOS_1597	GCA_020731565.1	134964	134964	type	True	92.4452	1929	2354	95	below_threshold
Nocardia elegans	strain=NBRC 108235	GCA_001612845.1	300029	300029	type	True	92.3439	1852	2354	95	below_threshold
Nocardia nova	strain=NBRC 15556	GCA_001613005.1	37330	37330	type	True	92.2152	1889	2354	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:32:43,352] [INFO] DFAST Taxonomy check result was written to GCF_000308535.1_ASM30853v1_genomic.fna/tc_result.tsv
[2024-01-24 12:32:43,353] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:32:43,353] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:32:43,354] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2f7aef32-b8a5-46af-88af-736c2dd9dbaa/dqc_reference/checkm_data
[2024-01-24 12:32:43,355] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:32:43,431] [INFO] Task started: CheckM
[2024-01-24 12:32:43,431] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000308535.1_ASM30853v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000308535.1_ASM30853v1_genomic.fna/checkm_input GCF_000308535.1_ASM30853v1_genomic.fna/checkm_result
[2024-01-24 12:33:54,618] [INFO] Task succeeded: CheckM
[2024-01-24 12:33:54,619] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 2.31%
Strain heterogeneity: 40.00%
--------------------------------------------------------------------------------
[2024-01-24 12:33:54,652] [INFO] ===== Completeness check finished =====
[2024-01-24 12:33:54,652] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:33:54,653] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000308535.1_ASM30853v1_genomic.fna/markers.fasta)
[2024-01-24 12:33:54,653] [INFO] Task started: Blastn
[2024-01-24 12:33:54,653] [INFO] Running command: blastn -query GCF_000308535.1_ASM30853v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2f7aef32-b8a5-46af-88af-736c2dd9dbaa/dqc_reference/reference_markers_gtdb.fasta -out GCF_000308535.1_ASM30853v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:33:56,364] [INFO] Task succeeded: Blastn
[2024-01-24 12:33:56,368] [INFO] Selected 8 target genomes.
[2024-01-24 12:33:56,368] [INFO] Target genome list was writen to GCF_000308535.1_ASM30853v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:33:56,379] [INFO] Task started: fastANI
[2024-01-24 12:33:56,379] [INFO] Running command: fastANI --query /var/lib/cwl/stg1bfbbe55-4ead-4998-aec5-366e5cd845c3/GCF_000308535.1_ASM30853v1_genomic.fna.gz --refList GCF_000308535.1_ASM30853v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000308535.1_ASM30853v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:34:11,742] [INFO] Task succeeded: fastANI
[2024-01-24 12:34:11,753] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:34:11,754] [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_000308535.1	s__Nocardia cerradoensis	100.0	2338	2354	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0231	99.71	99.43	1.00	0.99	3	conclusive
GCF_000308375.1	s__Nocardia aobensis	95.0126	1961	2354	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.6988	98.11	97.03	0.89	0.86	3	-
GCF_015354405.1	s__Nocardia sp015354405	94.9011	1942	2354	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001612965.1	s__Nocardia kruczakiae	94.8553	1956	2354	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.6988	N/A	N/A	N/A	N/A	1	-
GCF_001613505.1	s__Nocardia mikamii	94.4165	1985	2354	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001612635.1	s__Nocardia africana	92.4732	1916	2354	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	99.93	99.93	0.99	0.99	2	-
GCF_001612845.1	s__Nocardia elegans	92.3247	1854	2354	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	96.9334	99.79	99.59	0.97	0.94	3	-
GCF_001613005.1	s__Nocardia nova	92.2013	1891	2354	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	96.9334	98.75	97.55	0.88	0.84	13	-
--------------------------------------------------------------------------------
[2024-01-24 12:34:11,755] [INFO] GTDB search result was written to GCF_000308535.1_ASM30853v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:34:11,756] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:34:11,759] [INFO] DFAST_QC result json was written to GCF_000308535.1_ASM30853v1_genomic.fna/dqc_result.json
[2024-01-24 12:34:11,759] [INFO] DFAST_QC completed!
[2024-01-24 12:34:11,759] [INFO] Total running time: 0h2m13s