[2024-01-24 14:06:00,263] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:06:00,267] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:06:00,267] [INFO] DQC Reference Directory: /var/lib/cwl/stgc19f9566-1321-47af-8ba2-fba2d523ca22/dqc_reference
[2024-01-24 14:06:01,502] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:06:01,503] [INFO] Task started: Prodigal
[2024-01-24 14:06:01,503] [INFO] Running command: gunzip -c /var/lib/cwl/stg9bee516f-8885-4199-b204-e1b93332e20f/GCF_001612985.1_ASM161298v1_genomic.fna.gz | prodigal -d GCF_001612985.1_ASM161298v1_genomic.fna/cds.fna -a GCF_001612985.1_ASM161298v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:06:31,243] [INFO] Task succeeded: Prodigal
[2024-01-24 14:06:31,243] [INFO] Task started: HMMsearch
[2024-01-24 14:06:31,243] [INFO] Running command: hmmsearch --tblout GCF_001612985.1_ASM161298v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc19f9566-1321-47af-8ba2-fba2d523ca22/dqc_reference/reference_markers.hmm GCF_001612985.1_ASM161298v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:06:31,602] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:06:31,603] [INFO] Found 6/6 markers.
[2024-01-24 14:06:31,677] [INFO] Query marker FASTA was written to GCF_001612985.1_ASM161298v1_genomic.fna/markers.fasta
[2024-01-24 14:06:31,678] [INFO] Task started: Blastn
[2024-01-24 14:06:31,678] [INFO] Running command: blastn -query GCF_001612985.1_ASM161298v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc19f9566-1321-47af-8ba2-fba2d523ca22/dqc_reference/reference_markers.fasta -out GCF_001612985.1_ASM161298v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:32,854] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:32,858] [INFO] Selected 6 target genomes.
[2024-01-24 14:06:32,858] [INFO] Target genome list was writen to GCF_001612985.1_ASM161298v1_genomic.fna/target_genomes.txt
[2024-01-24 14:06:32,862] [INFO] Task started: fastANI
[2024-01-24 14:06:32,862] [INFO] Running command: fastANI --query /var/lib/cwl/stg9bee516f-8885-4199-b204-e1b93332e20f/GCF_001612985.1_ASM161298v1_genomic.fna.gz --refList GCF_001612985.1_ASM161298v1_genomic.fna/target_genomes.txt --output GCF_001612985.1_ASM161298v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:06:45,557] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:45,557] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc19f9566-1321-47af-8ba2-fba2d523ca22/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:06:45,558] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc19f9566-1321-47af-8ba2-fba2d523ca22/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:06:45,568] [INFO] Found 6 fastANI hits (5 hits with ANI > threshold)
[2024-01-24 14:06:45,568] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 14:06:45,568] [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 gamkensis	strain=NBRC 108242	GCA_001612985.1	352869	352869	type	True	100.0	2511	2515	95	inconclusive
Nocardia gamkensis	strain=DSM 44956	GCA_012396055.1	352869	352869	type	True	99.9982	2509	2515	95	inconclusive
Nocardia gamkensis	strain=NRRL B-24450	GCA_013181665.1	352869	352869	type	True	99.995	2499	2515	95	inconclusive
Nocardia exalbida	strain=NBRC 100660	GCA_000308575.1	290231	290231	type	True	96.6838	2099	2515	95	inconclusive
Nocardia arthritidis	strain=NBRC 100137	GCA_001612765.1	228602	228602	type	True	95.0562	1978	2515	95	inconclusive
Nocardia gipuzkoensis	strain=234509	GCA_013839485.1	2749991	2749991	type	True	89.4543	1977	2515	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:06:45,570] [INFO] DFAST Taxonomy check result was written to GCF_001612985.1_ASM161298v1_genomic.fna/tc_result.tsv
[2024-01-24 14:06:45,570] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:06:45,570] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:06:45,571] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc19f9566-1321-47af-8ba2-fba2d523ca22/dqc_reference/checkm_data
[2024-01-24 14:06:45,572] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:06:45,721] [INFO] Task started: CheckM
[2024-01-24 14:06:45,722] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001612985.1_ASM161298v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001612985.1_ASM161298v1_genomic.fna/checkm_input GCF_001612985.1_ASM161298v1_genomic.fna/checkm_result
[2024-01-24 14:08:06,875] [INFO] Task succeeded: CheckM
[2024-01-24 14:08:06,876] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.39%
Strain heterogeneity: 33.33%
--------------------------------------------------------------------------------
[2024-01-24 14:08:06,899] [INFO] ===== Completeness check finished =====
[2024-01-24 14:08:06,899] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:08:06,900] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001612985.1_ASM161298v1_genomic.fna/markers.fasta)
[2024-01-24 14:08:06,900] [INFO] Task started: Blastn
[2024-01-24 14:08:06,900] [INFO] Running command: blastn -query GCF_001612985.1_ASM161298v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc19f9566-1321-47af-8ba2-fba2d523ca22/dqc_reference/reference_markers_gtdb.fasta -out GCF_001612985.1_ASM161298v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:08:08,896] [INFO] Task succeeded: Blastn
[2024-01-24 14:08:08,905] [INFO] Selected 11 target genomes.
[2024-01-24 14:08:08,905] [INFO] Target genome list was writen to GCF_001612985.1_ASM161298v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:08:08,915] [INFO] Task started: fastANI
[2024-01-24 14:08:08,915] [INFO] Running command: fastANI --query /var/lib/cwl/stg9bee516f-8885-4199-b204-e1b93332e20f/GCF_001612985.1_ASM161298v1_genomic.fna.gz --refList GCF_001612985.1_ASM161298v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001612985.1_ASM161298v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:08:31,287] [INFO] Task succeeded: fastANI
[2024-01-24 14:08:31,301] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:08:31,302] [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_001612985.1	s__Nocardia gamkensis	100.0	2511	2515	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	96.7192	100.00	100.00	1.00	0.99	3	conclusive
GCF_000308575.1	s__Nocardia exalbida	96.6838	2099	2515	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	96.7192	N/A	N/A	N/A	N/A	1	-
GCF_001612765.1	s__Nocardia arthritidis	95.0607	1978	2515	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.103	N/A	N/A	N/A	N/A	1	-
GCF_001613465.1	s__Nocardia niwae	89.9585	1946	2515	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	89.7008	1962	2515	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	96.48	96.48	0.88	0.88	2	-
GCF_000308435.1	s__Nocardia araoensis	89.57	1839	2515	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015477775.1	s__Nocardia abscessus_A	89.4488	2049	2515	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000308455.1	s__Nocardia abscessus	89.3417	1994	2515	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	96.07	95.78	0.84	0.83	5	-
GCF_013315795.1	s__Nocardia barduliensis	89.1688	1927	2515	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009829295.1	s__Nocardia sp009829295	88.9167	1884	2515	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	99.64	99.39	0.96	0.94	4	-
GCF_000308415.1	s__Nocardia asiatica	88.8721	1784	2515	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:08:31,303] [INFO] GTDB search result was written to GCF_001612985.1_ASM161298v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:08:31,304] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:08:31,310] [INFO] DFAST_QC result json was written to GCF_001612985.1_ASM161298v1_genomic.fna/dqc_result.json
[2024-01-24 14:08:31,310] [INFO] DFAST_QC completed!
[2024-01-24 14:08:31,310] [INFO] Total running time: 0h2m31s