[2024-01-25 17:40:35,686] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:40:35,687] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:40:35,688] [INFO] DQC Reference Directory: /var/lib/cwl/stg56fd53b9-63a4-4ec9-9688-42f300fdf5d6/dqc_reference
[2024-01-25 17:40:36,812] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:40:36,812] [INFO] Task started: Prodigal
[2024-01-25 17:40:36,812] [INFO] Running command: gunzip -c /var/lib/cwl/stg1a54b5fa-7008-4e69-b0d2-402e4161c9c2/GCF_001613465.1_ASM161346v1_genomic.fna.gz | prodigal -d GCF_001613465.1_ASM161346v1_genomic.fna/cds.fna -a GCF_001613465.1_ASM161346v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:41:13,965] [INFO] Task succeeded: Prodigal
[2024-01-25 17:41:13,965] [INFO] Task started: HMMsearch
[2024-01-25 17:41:13,965] [INFO] Running command: hmmsearch --tblout GCF_001613465.1_ASM161346v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg56fd53b9-63a4-4ec9-9688-42f300fdf5d6/dqc_reference/reference_markers.hmm GCF_001613465.1_ASM161346v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:41:14,247] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:41:14,248] [INFO] Found 6/6 markers.
[2024-01-25 17:41:14,303] [INFO] Query marker FASTA was written to GCF_001613465.1_ASM161346v1_genomic.fna/markers.fasta
[2024-01-25 17:41:14,303] [INFO] Task started: Blastn
[2024-01-25 17:41:14,304] [INFO] Running command: blastn -query GCF_001613465.1_ASM161346v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg56fd53b9-63a4-4ec9-9688-42f300fdf5d6/dqc_reference/reference_markers.fasta -out GCF_001613465.1_ASM161346v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:41:15,482] [INFO] Task succeeded: Blastn
[2024-01-25 17:41:15,484] [INFO] Selected 11 target genomes.
[2024-01-25 17:41:15,485] [INFO] Target genome list was writen to GCF_001613465.1_ASM161346v1_genomic.fna/target_genomes.txt
[2024-01-25 17:41:15,487] [INFO] Task started: fastANI
[2024-01-25 17:41:15,487] [INFO] Running command: fastANI --query /var/lib/cwl/stg1a54b5fa-7008-4e69-b0d2-402e4161c9c2/GCF_001613465.1_ASM161346v1_genomic.fna.gz --refList GCF_001613465.1_ASM161346v1_genomic.fna/target_genomes.txt --output GCF_001613465.1_ASM161346v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:41:35,586] [INFO] Task succeeded: fastANI
[2024-01-25 17:41:35,586] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg56fd53b9-63a4-4ec9-9688-42f300fdf5d6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:41:35,587] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg56fd53b9-63a4-4ec9-9688-42f300fdf5d6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:41:35,595] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:41:35,595] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:41:35,595] [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 niwae	strain=NBRC 108934	GCA_001613465.1	626084	626084	type	True	100.0	2385	2389	95	conclusive
Nocardia gamkensis	strain=NBRC 108242	GCA_001612985.1	352869	352869	type	True	90.0138	1944	2389	95	below_threshold
Nocardia gamkensis	strain=NRRL B-24450	GCA_013181665.1	352869	352869	type	True	89.9978	1976	2389	95	below_threshold
Nocardia exalbida	strain=NBRC 100660	GCA_000308575.1	290231	290231	type	True	89.9917	1982	2389	95	below_threshold
Nocardia gamkensis	strain=DSM 44956	GCA_012396055.1	352869	352869	type	True	89.9873	1985	2389	95	below_threshold
Nocardia arthritidis	strain=NBRC 100137	GCA_001612765.1	228602	228602	type	True	89.8837	1942	2389	95	below_threshold
Nocardia araoensis	strain=NBRC 100135	GCA_000308435.1	228600	228600	type	True	89.6201	1855	2389	95	below_threshold
Nocardia beijingensis	strain=NBRC 16342	GCA_001612785.1	95162	95162	type	True	89.2765	1932	2389	95	below_threshold
Nocardia colli	strain=CICC 11023	GCA_008704205.1	2545717	2545717	type	True	82.5944	1431	2389	95	below_threshold
Nocardia farcinica	strain=NCTC11134	GCA_001182745.2	37329	37329	type	True	82.1604	1201	2389	95	below_threshold
Nocardia farcinica	strain=DSM 43257	GCA_900156775.1	37329	37329	type	True	82.1009	1193	2389	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:41:35,597] [INFO] DFAST Taxonomy check result was written to GCF_001613465.1_ASM161346v1_genomic.fna/tc_result.tsv
[2024-01-25 17:41:35,597] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:41:35,597] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:41:35,597] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg56fd53b9-63a4-4ec9-9688-42f300fdf5d6/dqc_reference/checkm_data
[2024-01-25 17:41:35,598] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:41:35,666] [INFO] Task started: CheckM
[2024-01-25 17:41:35,666] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001613465.1_ASM161346v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001613465.1_ASM161346v1_genomic.fna/checkm_input GCF_001613465.1_ASM161346v1_genomic.fna/checkm_result
[2024-01-25 17:43:16,202] [INFO] Task succeeded: CheckM
[2024-01-25 17:43:16,203] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.85%
Strain heterogeneity: 25.00%
--------------------------------------------------------------------------------
[2024-01-25 17:43:16,228] [INFO] ===== Completeness check finished =====
[2024-01-25 17:43:16,229] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:43:16,230] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001613465.1_ASM161346v1_genomic.fna/markers.fasta)
[2024-01-25 17:43:16,230] [INFO] Task started: Blastn
[2024-01-25 17:43:16,230] [INFO] Running command: blastn -query GCF_001613465.1_ASM161346v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg56fd53b9-63a4-4ec9-9688-42f300fdf5d6/dqc_reference/reference_markers_gtdb.fasta -out GCF_001613465.1_ASM161346v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:43:18,047] [INFO] Task succeeded: Blastn
[2024-01-25 17:43:18,051] [INFO] Selected 9 target genomes.
[2024-01-25 17:43:18,051] [INFO] Target genome list was writen to GCF_001613465.1_ASM161346v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:43:18,053] [INFO] Task started: fastANI
[2024-01-25 17:43:18,053] [INFO] Running command: fastANI --query /var/lib/cwl/stg1a54b5fa-7008-4e69-b0d2-402e4161c9c2/GCF_001613465.1_ASM161346v1_genomic.fna.gz --refList GCF_001613465.1_ASM161346v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001613465.1_ASM161346v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:43:36,198] [INFO] Task succeeded: fastANI
[2024-01-25 17:43:36,205] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:43:36,205] [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_001613465.1	s__Nocardia niwae	100.0	2385	2389	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_009829325.1	s__Nocardia sp009829325	92.2661	2040	2389	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	96.48	96.48	0.88	0.88	2	-
GCF_001612985.1	s__Nocardia gamkensis	90.0058	1945	2389	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	96.7192	100.00	100.00	1.00	0.99	3	-
GCF_000308575.1	s__Nocardia exalbida	89.9832	1983	2389	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	89.8808	1942	2389	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.103	N/A	N/A	N/A	N/A	1	-
GCF_000308435.1	s__Nocardia araoensis	89.627	1855	2389	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	89.2828	1931	2389	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	98.03	98.03	0.92	0.92	2	-
GCF_015477775.1	s__Nocardia abscessus_A	88.9766	1989	2389	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001182745.1	s__Nocardia farcinica	82.1491	1203	2389	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	99.16	98.59	0.93	0.88	42	-
--------------------------------------------------------------------------------
[2024-01-25 17:43:36,206] [INFO] GTDB search result was written to GCF_001613465.1_ASM161346v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:43:36,207] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:43:36,209] [INFO] DFAST_QC result json was written to GCF_001613465.1_ASM161346v1_genomic.fna/dqc_result.json
[2024-01-25 17:43:36,210] [INFO] DFAST_QC completed!
[2024-01-25 17:43:36,210] [INFO] Total running time: 0h3m1s