[2024-01-24 14:39:01,520] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:39:01,521] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:39:01,522] [INFO] DQC Reference Directory: /var/lib/cwl/stgaef19020-fb28-4f11-abf2-dda0c709fa88/dqc_reference
[2024-01-24 14:39:04,243] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:39:04,244] [INFO] Task started: Prodigal
[2024-01-24 14:39:04,244] [INFO] Running command: gunzip -c /var/lib/cwl/stgafdce828-61a8-4060-ad25-bb5bdcef4a88/GCF_006494775.1_ASM649477v1_genomic.fna.gz | prodigal -d GCF_006494775.1_ASM649477v1_genomic.fna/cds.fna -a GCF_006494775.1_ASM649477v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:39:20,735] [INFO] Task succeeded: Prodigal
[2024-01-24 14:39:20,735] [INFO] Task started: HMMsearch
[2024-01-24 14:39:20,735] [INFO] Running command: hmmsearch --tblout GCF_006494775.1_ASM649477v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgaef19020-fb28-4f11-abf2-dda0c709fa88/dqc_reference/reference_markers.hmm GCF_006494775.1_ASM649477v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:39:21,088] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:39:21,089] [INFO] Found 6/6 markers.
[2024-01-24 14:39:21,190] [INFO] Query marker FASTA was written to GCF_006494775.1_ASM649477v1_genomic.fna/markers.fasta
[2024-01-24 14:39:21,190] [INFO] Task started: Blastn
[2024-01-24 14:39:21,191] [INFO] Running command: blastn -query GCF_006494775.1_ASM649477v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaef19020-fb28-4f11-abf2-dda0c709fa88/dqc_reference/reference_markers.fasta -out GCF_006494775.1_ASM649477v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:39:22,486] [INFO] Task succeeded: Blastn
[2024-01-24 14:39:22,489] [INFO] Selected 13 target genomes.
[2024-01-24 14:39:22,489] [INFO] Target genome list was writen to GCF_006494775.1_ASM649477v1_genomic.fna/target_genomes.txt
[2024-01-24 14:39:22,494] [INFO] Task started: fastANI
[2024-01-24 14:39:22,494] [INFO] Running command: fastANI --query /var/lib/cwl/stgafdce828-61a8-4060-ad25-bb5bdcef4a88/GCF_006494775.1_ASM649477v1_genomic.fna.gz --refList GCF_006494775.1_ASM649477v1_genomic.fna/target_genomes.txt --output GCF_006494775.1_ASM649477v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:39:41,827] [INFO] Task succeeded: fastANI
[2024-01-24 14:39:41,828] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgaef19020-fb28-4f11-abf2-dda0c709fa88/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:39:41,828] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgaef19020-fb28-4f11-abf2-dda0c709fa88/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:39:41,844] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:39:41,844] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:39:41,844] [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
Nocardioides humi	strain=DCY24	GCA_006494775.1	449461	449461	type	True	100.0	2072	2073	95	conclusive
Nocardioides daeguensis	strain=2C1-5	GCA_019192965.1	908359	908359	type	True	87.157	1132	2073	95	below_threshold
Nocardioides carbamazepini	strain=CBZ_1	GCA_024614185.1	2854259	2854259	type	True	87.064	1305	2073	95	below_threshold
Nocardioides kongjuensis	strain=DSM 19082	GCA_013409625.1	349522	349522	type	True	86.8414	1240	2073	95	below_threshold
Nocardioides nitrophenolicus	strain=DSM 15529	GCA_016907515.1	60489	60489	type	True	86.691	1324	2073	95	below_threshold
Nocardioides albidus	strain=CCTCC AB 2015297	GCA_006335005.1	1517589	1517589	type	True	86.2142	1077	2073	95	below_threshold
Pimelobacter simplex	strain=NBRC 12069	GCA_006538965.1	2045	2045	type	True	85.5903	1243	2073	95	below_threshold
Pimelobacter simplex	strain=ATCC 6946	GCA_900114845.1	2045	2045	type	True	85.5152	1256	2073	95	below_threshold
Nocardioides antri	strain=BN140041	GCA_008373765.1	2607659	2607659	type	True	81.6492	857	2073	95	below_threshold
Nocardioides sambongensis	strain=KUDC 5002	GCA_006494815.1	2589074	2589074	type	True	81.4025	877	2073	95	below_threshold
Nocardioides humilatus	strain=BN130099	GCA_008373755.1	2607660	2607660	type	True	81.1	846	2073	95	below_threshold
Nocardioides lacusdianchii	strain=JXJ CY 38	GCA_020102855.1	2783664	2783664	type	True	79.9977	749	2073	95	below_threshold
Nocardioides furvisabuli	strain=JCM 13813	GCA_021083185.1	375542	375542	type	True	79.8386	706	2073	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:39:41,846] [INFO] DFAST Taxonomy check result was written to GCF_006494775.1_ASM649477v1_genomic.fna/tc_result.tsv
[2024-01-24 14:39:41,847] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:39:41,847] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:39:41,847] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgaef19020-fb28-4f11-abf2-dda0c709fa88/dqc_reference/checkm_data
[2024-01-24 14:39:41,848] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:39:41,982] [INFO] Task started: CheckM
[2024-01-24 14:39:41,982] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_006494775.1_ASM649477v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_006494775.1_ASM649477v1_genomic.fna/checkm_input GCF_006494775.1_ASM649477v1_genomic.fna/checkm_result
[2024-01-24 14:41:17,753] [INFO] Task succeeded: CheckM
[2024-01-24 14:41:17,754] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:41:17,773] [INFO] ===== Completeness check finished =====
[2024-01-24 14:41:17,773] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:41:17,774] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_006494775.1_ASM649477v1_genomic.fna/markers.fasta)
[2024-01-24 14:41:17,774] [INFO] Task started: Blastn
[2024-01-24 14:41:17,774] [INFO] Running command: blastn -query GCF_006494775.1_ASM649477v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaef19020-fb28-4f11-abf2-dda0c709fa88/dqc_reference/reference_markers_gtdb.fasta -out GCF_006494775.1_ASM649477v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:41:19,788] [INFO] Task succeeded: Blastn
[2024-01-24 14:41:19,791] [INFO] Selected 13 target genomes.
[2024-01-24 14:41:19,791] [INFO] Target genome list was writen to GCF_006494775.1_ASM649477v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:41:19,799] [INFO] Task started: fastANI
[2024-01-24 14:41:19,800] [INFO] Running command: fastANI --query /var/lib/cwl/stgafdce828-61a8-4060-ad25-bb5bdcef4a88/GCF_006494775.1_ASM649477v1_genomic.fna.gz --refList GCF_006494775.1_ASM649477v1_genomic.fna/target_genomes_gtdb.txt --output GCF_006494775.1_ASM649477v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:41:38,490] [INFO] Task succeeded: fastANI
[2024-01-24 14:41:38,503] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:41:38,503] [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_006494775.1	s__Nocardioides humi	100.0	2073	2073	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_016803235.1	s__Nocardioides simplex_A	87.1638	1206	2073	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019192965.1	s__Nocardioides daeguensis	87.1449	1132	2073	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013409625.1	s__Nocardioides kongjuensis	86.8407	1241	2073	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006715725.1	s__Nocardioides sp006715725	86.7904	1278	2073	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016907515.1	s__Nocardioides nitrophenolicus	86.7198	1322	2073	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006335005.1	s__Nocardioides albidus	86.2356	1074	2073	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018831735.1	s__Nocardioides sp018831735	85.595	1239	2073	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003054165.1	s__Nocardioides sp003054165	84.5469	1116	2073	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001428565.1	s__Nocardioides sp001428565	83.2349	1074	2073	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014108865.1	s__Nocardioides sp014108865	82.3854	998	2073	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008373765.1	s__Nocardioides antri	81.66	857	2073	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008373755.1	s__Nocardioides sp008373755	81.1004	846	2073	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:41:38,505] [INFO] GTDB search result was written to GCF_006494775.1_ASM649477v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:41:38,506] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:41:38,512] [INFO] DFAST_QC result json was written to GCF_006494775.1_ASM649477v1_genomic.fna/dqc_result.json
[2024-01-24 14:41:38,513] [INFO] DFAST_QC completed!
[2024-01-24 14:41:38,513] [INFO] Total running time: 0h2m37s