[2024-01-25 19:54:05,536] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:54:05,537] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:54:05,538] [INFO] DQC Reference Directory: /var/lib/cwl/stg08bcd352-d9d0-420f-a3a9-97fb6cbc9359/dqc_reference
[2024-01-25 19:54:06,750] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:54:06,751] [INFO] Task started: Prodigal
[2024-01-25 19:54:06,751] [INFO] Running command: gunzip -c /var/lib/cwl/stga98d2c82-39fa-4992-80a8-5830b36ecd69/GCF_003160695.1_ASM316069v1_genomic.fna.gz | prodigal -d GCF_003160695.1_ASM316069v1_genomic.fna/cds.fna -a GCF_003160695.1_ASM316069v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:54:17,519] [INFO] Task succeeded: Prodigal
[2024-01-25 19:54:17,519] [INFO] Task started: HMMsearch
[2024-01-25 19:54:17,519] [INFO] Running command: hmmsearch --tblout GCF_003160695.1_ASM316069v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg08bcd352-d9d0-420f-a3a9-97fb6cbc9359/dqc_reference/reference_markers.hmm GCF_003160695.1_ASM316069v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:54:17,745] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:54:17,746] [INFO] Found 6/6 markers.
[2024-01-25 19:54:17,783] [INFO] Query marker FASTA was written to GCF_003160695.1_ASM316069v1_genomic.fna/markers.fasta
[2024-01-25 19:54:17,783] [INFO] Task started: Blastn
[2024-01-25 19:54:17,784] [INFO] Running command: blastn -query GCF_003160695.1_ASM316069v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg08bcd352-d9d0-420f-a3a9-97fb6cbc9359/dqc_reference/reference_markers.fasta -out GCF_003160695.1_ASM316069v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:54:19,017] [INFO] Task succeeded: Blastn
[2024-01-25 19:54:19,019] [INFO] Selected 13 target genomes.
[2024-01-25 19:54:19,020] [INFO] Target genome list was writen to GCF_003160695.1_ASM316069v1_genomic.fna/target_genomes.txt
[2024-01-25 19:54:19,029] [INFO] Task started: fastANI
[2024-01-25 19:54:19,029] [INFO] Running command: fastANI --query /var/lib/cwl/stga98d2c82-39fa-4992-80a8-5830b36ecd69/GCF_003160695.1_ASM316069v1_genomic.fna.gz --refList GCF_003160695.1_ASM316069v1_genomic.fna/target_genomes.txt --output GCF_003160695.1_ASM316069v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:54:33,490] [INFO] Task succeeded: fastANI
[2024-01-25 19:54:33,490] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg08bcd352-d9d0-420f-a3a9-97fb6cbc9359/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:54:33,490] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg08bcd352-d9d0-420f-a3a9-97fb6cbc9359/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:54:33,500] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:54:33,500] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:54:33,500] [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 silvaticus	strain=CCTCC AB 2018079	GCA_003160695.1	2201891	2201891	type	True	100.0	1493	1494	95	conclusive
Nocardioides pelophilus	strain=CGMCC 4.7388	GCA_014180685.1	2172019	2172019	type	True	84.835	923	1494	95	below_threshold
Nocardioides immobilis	strain=CCTCC AB 2017083	GCA_003515065.1	2049295	2049295	type	True	84.566	1050	1494	95	below_threshold
Nocardioides antri	strain=BN140041	GCA_008373765.1	2607659	2607659	type	True	84.5532	977	1494	95	below_threshold
Nocardioides stalactiti	strain=1.0914	GCA_014180715.1	2755356	2755356	type	True	84.1748	912	1494	95	below_threshold
Nocardioides humilatus	strain=BN130099	GCA_008373755.1	2607660	2607660	type	True	83.6585	964	1494	95	below_threshold
Nocardioides thalensis	strain=DSM 103833	GCA_013410655.1	1914755	1914755	type	True	82.6513	926	1494	95	below_threshold
Nocardioides carbamazepini	strain=CBZ_1	GCA_024614185.1	2854259	2854259	type	True	81.3554	868	1494	95	below_threshold
Nocardioides sambongensis	strain=KUDC 5002	GCA_006494815.1	2589074	2589074	type	True	81.0028	762	1494	95	below_threshold
Nocardioides deserti	strain=CGMCC 4.7183	GCA_014646035.1	1588644	1588644	type	True	80.8908	725	1494	95	below_threshold
Nocardioides litoris	strain=DSM 103718	GCA_006346315.1	1926648	1926648	type	True	80.2845	755	1494	95	below_threshold
Nocardioides zhouii	strain=HLT2-9	GCA_004137345.1	1168729	1168729	type	True	79.9867	648	1494	95	below_threshold
Nocardioides donggukensis	strain=MJB4	GCA_014842875.1	2774019	2774019	type	True	79.8152	587	1494	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:54:33,509] [INFO] DFAST Taxonomy check result was written to GCF_003160695.1_ASM316069v1_genomic.fna/tc_result.tsv
[2024-01-25 19:54:33,510] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:54:33,510] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:54:33,510] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg08bcd352-d9d0-420f-a3a9-97fb6cbc9359/dqc_reference/checkm_data
[2024-01-25 19:54:33,511] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:54:33,557] [INFO] Task started: CheckM
[2024-01-25 19:54:33,558] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003160695.1_ASM316069v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003160695.1_ASM316069v1_genomic.fna/checkm_input GCF_003160695.1_ASM316069v1_genomic.fna/checkm_result
[2024-01-25 19:55:24,840] [INFO] Task succeeded: CheckM
[2024-01-25 19:55:24,841] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:55:24,856] [INFO] ===== Completeness check finished =====
[2024-01-25 19:55:24,856] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:55:24,857] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003160695.1_ASM316069v1_genomic.fna/markers.fasta)
[2024-01-25 19:55:24,857] [INFO] Task started: Blastn
[2024-01-25 19:55:24,857] [INFO] Running command: blastn -query GCF_003160695.1_ASM316069v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg08bcd352-d9d0-420f-a3a9-97fb6cbc9359/dqc_reference/reference_markers_gtdb.fasta -out GCF_003160695.1_ASM316069v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:55:26,912] [INFO] Task succeeded: Blastn
[2024-01-25 19:55:26,915] [INFO] Selected 10 target genomes.
[2024-01-25 19:55:26,915] [INFO] Target genome list was writen to GCF_003160695.1_ASM316069v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:55:26,928] [INFO] Task started: fastANI
[2024-01-25 19:55:26,929] [INFO] Running command: fastANI --query /var/lib/cwl/stga98d2c82-39fa-4992-80a8-5830b36ecd69/GCF_003160695.1_ASM316069v1_genomic.fna.gz --refList GCF_003160695.1_ASM316069v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003160695.1_ASM316069v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:55:39,131] [INFO] Task succeeded: fastANI
[2024-01-25 19:55:39,139] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:55:39,139] [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_003160695.1	s__Nocardioides silvaticus	100.0	1493	1494	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_014180685.1	s__Nocardioides pelophilus	84.7985	927	1494	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003515065.1	s__Nocardioides immobilis	84.5645	1049	1494	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	84.5181	980	1494	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014180715.1	s__Nocardioides stalactiti	84.1245	917	1494	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	83.611	969	1494	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013410655.1	s__Nocardioides thalensis	82.6739	924	1494	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006494775.1	s__Nocardioides humi	81.9258	895	1494	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	81.804	866	1494	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011250565.1	s__Nocardioides sp011250565	81.162	725	1494	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:55:39,140] [INFO] GTDB search result was written to GCF_003160695.1_ASM316069v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:55:39,141] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:55:39,143] [INFO] DFAST_QC result json was written to GCF_003160695.1_ASM316069v1_genomic.fna/dqc_result.json
[2024-01-25 19:55:39,144] [INFO] DFAST_QC completed!
[2024-01-25 19:55:39,144] [INFO] Total running time: 0h1m34s