[2024-01-24 13:58:10,772] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:58:10,773] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:58:10,773] [INFO] DQC Reference Directory: /var/lib/cwl/stgbe479a63-2780-447a-95f3-1d3b4160e0d1/dqc_reference
[2024-01-24 13:58:12,152] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:58:12,153] [INFO] Task started: Prodigal
[2024-01-24 13:58:12,153] [INFO] Running command: gunzip -c /var/lib/cwl/stgf8efb8b0-dc21-4cb3-abbc-9f7ec48d4033/GCF_014653095.1_ASM1465309v1_genomic.fna.gz | prodigal -d GCF_014653095.1_ASM1465309v1_genomic.fna/cds.fna -a GCF_014653095.1_ASM1465309v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:58:24,819] [INFO] Task succeeded: Prodigal
[2024-01-24 13:58:24,819] [INFO] Task started: HMMsearch
[2024-01-24 13:58:24,820] [INFO] Running command: hmmsearch --tblout GCF_014653095.1_ASM1465309v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbe479a63-2780-447a-95f3-1d3b4160e0d1/dqc_reference/reference_markers.hmm GCF_014653095.1_ASM1465309v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:58:25,098] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:58:25,100] [INFO] Found 6/6 markers.
[2024-01-24 13:58:25,147] [INFO] Query marker FASTA was written to GCF_014653095.1_ASM1465309v1_genomic.fna/markers.fasta
[2024-01-24 13:58:25,147] [INFO] Task started: Blastn
[2024-01-24 13:58:25,147] [INFO] Running command: blastn -query GCF_014653095.1_ASM1465309v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbe479a63-2780-447a-95f3-1d3b4160e0d1/dqc_reference/reference_markers.fasta -out GCF_014653095.1_ASM1465309v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:26,508] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:26,512] [INFO] Selected 6 target genomes.
[2024-01-24 13:58:26,513] [INFO] Target genome list was writen to GCF_014653095.1_ASM1465309v1_genomic.fna/target_genomes.txt
[2024-01-24 13:58:26,516] [INFO] Task started: fastANI
[2024-01-24 13:58:26,516] [INFO] Running command: fastANI --query /var/lib/cwl/stgf8efb8b0-dc21-4cb3-abbc-9f7ec48d4033/GCF_014653095.1_ASM1465309v1_genomic.fna.gz --refList GCF_014653095.1_ASM1465309v1_genomic.fna/target_genomes.txt --output GCF_014653095.1_ASM1465309v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:58:35,986] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:35,987] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbe479a63-2780-447a-95f3-1d3b4160e0d1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:58:35,988] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbe479a63-2780-447a-95f3-1d3b4160e0d1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:58:35,995] [INFO] Found 6 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:58:35,995] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:58:35,995] [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
Klenkia taihuensis	strain=CGMCC 1.12303	GCA_014653095.1	1225127	1225127	type	True	100.0	1431	1432	95	conclusive
Klenkia taihuensis	strain=DSM 45962	GCA_900112525.1	1225127	1225127	type	True	99.9994	1430	1432	95	conclusive
Klenkia brasiliensis	strain=DSM 44526	GCA_900100695.1	333142	333142	type	True	92.5327	1260	1432	95	below_threshold
Klenkia marina	strain=DSM 45722	GCA_900101025.1	1960309	1960309	type	True	88.2854	1168	1432	95	below_threshold
Klenkia soli	strain=DSM 45843	GCA_900103975.1	1052260	1052260	type	True	87.7618	1163	1432	95	below_threshold
Modestobacter versicolor	strain=DSM 16678	GCA_014195485.1	429133	429133	type	True	83.1328	950	1432	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:58:35,996] [INFO] DFAST Taxonomy check result was written to GCF_014653095.1_ASM1465309v1_genomic.fna/tc_result.tsv
[2024-01-24 13:58:35,997] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:58:35,997] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:58:35,997] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbe479a63-2780-447a-95f3-1d3b4160e0d1/dqc_reference/checkm_data
[2024-01-24 13:58:35,998] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:58:36,037] [INFO] Task started: CheckM
[2024-01-24 13:58:36,037] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014653095.1_ASM1465309v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014653095.1_ASM1465309v1_genomic.fna/checkm_input GCF_014653095.1_ASM1465309v1_genomic.fna/checkm_result
[2024-01-24 13:59:43,075] [INFO] Task succeeded: CheckM
[2024-01-24 13:59:43,076] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:59:43,098] [INFO] ===== Completeness check finished =====
[2024-01-24 13:59:43,098] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:59:43,099] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014653095.1_ASM1465309v1_genomic.fna/markers.fasta)
[2024-01-24 13:59:43,099] [INFO] Task started: Blastn
[2024-01-24 13:59:43,099] [INFO] Running command: blastn -query GCF_014653095.1_ASM1465309v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbe479a63-2780-447a-95f3-1d3b4160e0d1/dqc_reference/reference_markers_gtdb.fasta -out GCF_014653095.1_ASM1465309v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:59:45,114] [INFO] Task succeeded: Blastn
[2024-01-24 13:59:45,119] [INFO] Selected 8 target genomes.
[2024-01-24 13:59:45,119] [INFO] Target genome list was writen to GCF_014653095.1_ASM1465309v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:59:45,141] [INFO] Task started: fastANI
[2024-01-24 13:59:45,141] [INFO] Running command: fastANI --query /var/lib/cwl/stgf8efb8b0-dc21-4cb3-abbc-9f7ec48d4033/GCF_014653095.1_ASM1465309v1_genomic.fna.gz --refList GCF_014653095.1_ASM1465309v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014653095.1_ASM1465309v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:59:57,174] [INFO] Task succeeded: fastANI
[2024-01-24 13:59:57,184] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:59:57,185] [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_900112525.1	s__Klenkia taihuensis	99.9994	1430	1432	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Klenkia	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_900100695.1	s__Klenkia brasiliensis	92.5613	1258	1432	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Klenkia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900101025.1	s__Klenkia marina	88.3032	1166	1432	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Klenkia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900103975.1	s__Klenkia soli	87.7304	1166	1432	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Klenkia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001424485.1	s__Klenkia sp001424485	85.9611	1108	1432	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Klenkia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014218215.1	s__Klenkia sp001424455	85.7938	1108	1432	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Klenkia	95.0	98.10	98.10	0.94	0.94	2	-
GCF_014195485.1	s__Modestobacter versicolor	83.1801	946	1432	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Modestobacter	95.0	99.97	99.97	1.00	1.00	2	-
GCF_900110555.1	s__Geodermatophilus endophyticus	81.4766	871	1432	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Geodermatophilus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:59:57,188] [INFO] GTDB search result was written to GCF_014653095.1_ASM1465309v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:59:57,189] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:59:57,192] [INFO] DFAST_QC result json was written to GCF_014653095.1_ASM1465309v1_genomic.fna/dqc_result.json
[2024-01-24 13:59:57,193] [INFO] DFAST_QC completed!
[2024-01-24 13:59:57,193] [INFO] Total running time: 0h1m46s