[2024-01-24 10:49:34,622] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:49:34,624] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:49:34,624] [INFO] DQC Reference Directory: /var/lib/cwl/stg9fd8555b-f11e-4ede-8c4c-b173552f25df/dqc_reference
[2024-01-24 10:49:35,847] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:49:35,848] [INFO] Task started: Prodigal
[2024-01-24 10:49:35,849] [INFO] Running command: gunzip -c /var/lib/cwl/stg52b7c9a0-ebda-46cb-b4d6-99a8897e894e/GCF_014645735.1_ASM1464573v1_genomic.fna.gz | prodigal -d GCF_014645735.1_ASM1464573v1_genomic.fna/cds.fna -a GCF_014645735.1_ASM1464573v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:50:19,038] [INFO] Task succeeded: Prodigal
[2024-01-24 10:50:19,039] [INFO] Task started: HMMsearch
[2024-01-24 10:50:19,039] [INFO] Running command: hmmsearch --tblout GCF_014645735.1_ASM1464573v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9fd8555b-f11e-4ede-8c4c-b173552f25df/dqc_reference/reference_markers.hmm GCF_014645735.1_ASM1464573v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:50:19,455] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:50:19,456] [INFO] Found 6/6 markers.
[2024-01-24 10:50:19,523] [INFO] Query marker FASTA was written to GCF_014645735.1_ASM1464573v1_genomic.fna/markers.fasta
[2024-01-24 10:50:19,523] [INFO] Task started: Blastn
[2024-01-24 10:50:19,523] [INFO] Running command: blastn -query GCF_014645735.1_ASM1464573v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9fd8555b-f11e-4ede-8c4c-b173552f25df/dqc_reference/reference_markers.fasta -out GCF_014645735.1_ASM1464573v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:50:20,569] [INFO] Task succeeded: Blastn
[2024-01-24 10:50:20,573] [INFO] Selected 9 target genomes.
[2024-01-24 10:50:20,573] [INFO] Target genome list was writen to GCF_014645735.1_ASM1464573v1_genomic.fna/target_genomes.txt
[2024-01-24 10:50:20,577] [INFO] Task started: fastANI
[2024-01-24 10:50:20,577] [INFO] Running command: fastANI --query /var/lib/cwl/stg52b7c9a0-ebda-46cb-b4d6-99a8897e894e/GCF_014645735.1_ASM1464573v1_genomic.fna.gz --refList GCF_014645735.1_ASM1464573v1_genomic.fna/target_genomes.txt --output GCF_014645735.1_ASM1464573v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:50:36,778] [INFO] Task succeeded: fastANI
[2024-01-24 10:50:36,779] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9fd8555b-f11e-4ede-8c4c-b173552f25df/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:50:36,779] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9fd8555b-f11e-4ede-8c4c-b173552f25df/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:50:36,788] [INFO] Found 9 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 10:50:36,788] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:50:36,788] [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 jinanensis	strain=CGMCC 4.3508	GCA_014645735.1	382504	382504	type	True	100.0	2623	2630	95	conclusive
Nocardia jinanensis	strain=NBRC 108249	GCA_001482675.1	382504	382504	type	True	99.9248	1619	2630	95	conclusive
Nocardia rhamnosiphila	strain=NRRL B-24637	GCA_000721005.1	426716	426716	type	True	87.1625	1859	2630	95	below_threshold
Nocardia rhamnosiphila	strain=NRRL B-24637	GCA_000720425.1	426716	426716	type	True	87.1619	1860	2630	95	below_threshold
Nocardia rhamnosiphila	strain=NBRC 108938	GCA_001613485.1	426716	426716	type	True	87.1362	1806	2630	95	below_threshold
Nocardia sienata	strain=NBRC 100364	GCA_001613205.1	248552	248552	type	True	86.8857	1689	2630	95	below_threshold
Nocardia testacea	strain=NBRC 100365	GCA_000308775.1	248551	248551	type	True	86.8407	1694	2630	95	below_threshold
Nocardia grenadensis	strain=NBRC 108939	GCA_001613445.1	931537	931537	type	True	86.7568	1626	2630	95	below_threshold
Nocardia flavorosea	strain=JCM 3332	GCA_012396035.1	53429	53429	type	True	82.7364	1425	2630	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:50:36,790] [INFO] DFAST Taxonomy check result was written to GCF_014645735.1_ASM1464573v1_genomic.fna/tc_result.tsv
[2024-01-24 10:50:36,791] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:50:36,791] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:50:36,791] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9fd8555b-f11e-4ede-8c4c-b173552f25df/dqc_reference/checkm_data
[2024-01-24 10:50:36,793] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:50:36,868] [INFO] Task started: CheckM
[2024-01-24 10:50:36,869] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014645735.1_ASM1464573v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014645735.1_ASM1464573v1_genomic.fna/checkm_input GCF_014645735.1_ASM1464573v1_genomic.fna/checkm_result
[2024-01-24 10:52:25,826] [INFO] Task succeeded: CheckM
[2024-01-24 10:52:25,828] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 2.78%
Strain heterogeneity: 28.57%
--------------------------------------------------------------------------------
[2024-01-24 10:52:25,858] [INFO] ===== Completeness check finished =====
[2024-01-24 10:52:25,858] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:52:25,858] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014645735.1_ASM1464573v1_genomic.fna/markers.fasta)
[2024-01-24 10:52:25,859] [INFO] Task started: Blastn
[2024-01-24 10:52:25,859] [INFO] Running command: blastn -query GCF_014645735.1_ASM1464573v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9fd8555b-f11e-4ede-8c4c-b173552f25df/dqc_reference/reference_markers_gtdb.fasta -out GCF_014645735.1_ASM1464573v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:52:27,365] [INFO] Task succeeded: Blastn
[2024-01-24 10:52:27,369] [INFO] Selected 8 target genomes.
[2024-01-24 10:52:27,369] [INFO] Target genome list was writen to GCF_014645735.1_ASM1464573v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:52:27,377] [INFO] Task started: fastANI
[2024-01-24 10:52:27,378] [INFO] Running command: fastANI --query /var/lib/cwl/stg52b7c9a0-ebda-46cb-b4d6-99a8897e894e/GCF_014645735.1_ASM1464573v1_genomic.fna.gz --refList GCF_014645735.1_ASM1464573v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014645735.1_ASM1464573v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:52:41,603] [INFO] Task succeeded: fastANI
[2024-01-24 10:52:41,614] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:52:41,614] [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_014645735.1	s__Nocardia jinanensis	100.0	2623	2630	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	99.99	99.97	1.00	1.00	3	conclusive
GCA_013361595.1	s__Nocardia sp013361595	88.0829	1110	2630	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001618425.1	s__Nocardia fusca	87.3551	1823	2630	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000720425.1	s__Nocardia rhamnosiphila	87.1453	1862	2630	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	99.99	99.99	0.99	0.99	3	-
GCF_001613205.1	s__Nocardia sienata	86.8897	1687	2630	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000308775.1	s__Nocardia testacea	86.8357	1695	2630	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001613445.1	s__Nocardia grenadensis	86.757	1626	2630	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000308515.1	s__Nocardia carnea	82.94	1439	2630	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	99.99	99.99	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 10:52:41,616] [INFO] GTDB search result was written to GCF_014645735.1_ASM1464573v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:52:41,617] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:52:41,620] [INFO] DFAST_QC result json was written to GCF_014645735.1_ASM1464573v1_genomic.fna/dqc_result.json
[2024-01-24 10:52:41,620] [INFO] DFAST_QC completed!
[2024-01-24 10:52:41,620] [INFO] Total running time: 0h3m7s