[2024-01-24 10:47:09,257] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:47:09,259] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:47:09,259] [INFO] DQC Reference Directory: /var/lib/cwl/stg3559c15c-9c60-4dcf-9e42-8fe5d680a263/dqc_reference
[2024-01-24 10:47:11,828] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:47:11,932] [INFO] Task started: Prodigal
[2024-01-24 10:47:11,933] [INFO] Running command: gunzip -c /var/lib/cwl/stgf26d596c-2d43-44cb-8b53-45049da133dd/GCF_014652455.1_ASM1465245v1_genomic.fna.gz | prodigal -d GCF_014652455.1_ASM1465245v1_genomic.fna/cds.fna -a GCF_014652455.1_ASM1465245v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:47:20,636] [INFO] Task succeeded: Prodigal
[2024-01-24 10:47:20,637] [INFO] Task started: HMMsearch
[2024-01-24 10:47:20,637] [INFO] Running command: hmmsearch --tblout GCF_014652455.1_ASM1465245v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3559c15c-9c60-4dcf-9e42-8fe5d680a263/dqc_reference/reference_markers.hmm GCF_014652455.1_ASM1465245v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:47:20,889] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:47:20,890] [INFO] Found 6/6 markers.
[2024-01-24 10:47:20,930] [INFO] Query marker FASTA was written to GCF_014652455.1_ASM1465245v1_genomic.fna/markers.fasta
[2024-01-24 10:47:20,930] [INFO] Task started: Blastn
[2024-01-24 10:47:20,931] [INFO] Running command: blastn -query GCF_014652455.1_ASM1465245v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3559c15c-9c60-4dcf-9e42-8fe5d680a263/dqc_reference/reference_markers.fasta -out GCF_014652455.1_ASM1465245v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:47:21,654] [INFO] Task succeeded: Blastn
[2024-01-24 10:47:21,658] [INFO] Selected 23 target genomes.
[2024-01-24 10:47:21,658] [INFO] Target genome list was writen to GCF_014652455.1_ASM1465245v1_genomic.fna/target_genomes.txt
[2024-01-24 10:47:22,510] [INFO] Task started: fastANI
[2024-01-24 10:47:22,511] [INFO] Running command: fastANI --query /var/lib/cwl/stgf26d596c-2d43-44cb-8b53-45049da133dd/GCF_014652455.1_ASM1465245v1_genomic.fna.gz --refList GCF_014652455.1_ASM1465245v1_genomic.fna/target_genomes.txt --output GCF_014652455.1_ASM1465245v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:47:38,101] [INFO] Task succeeded: fastANI
[2024-01-24 10:47:38,102] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3559c15c-9c60-4dcf-9e42-8fe5d680a263/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:47:38,102] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3559c15c-9c60-4dcf-9e42-8fe5d680a263/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:47:38,107] [INFO] Found 3 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 10:47:38,108] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:47:38,108] [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
Litorimonas cladophorae	strain=KCTC 23968	GCA_014652455.1	1220491	1220491	type	True	100.0	1004	1004	95	conclusive
Hellea balneolensis	strain=DSM 19091	GCA_000428525.1	287478	287478	type	True	77.0189	83	1004	95	below_threshold
Algimonas arctica	strain=KCTC 32513	GCA_014652695.1	1479486	1479486	type	True	76.381	84	1004	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:47:38,109] [INFO] DFAST Taxonomy check result was written to GCF_014652455.1_ASM1465245v1_genomic.fna/tc_result.tsv
[2024-01-24 10:47:38,110] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:47:38,110] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:47:38,110] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3559c15c-9c60-4dcf-9e42-8fe5d680a263/dqc_reference/checkm_data
[2024-01-24 10:47:38,111] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:47:38,150] [INFO] Task started: CheckM
[2024-01-24 10:47:38,150] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014652455.1_ASM1465245v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014652455.1_ASM1465245v1_genomic.fna/checkm_input GCF_014652455.1_ASM1465245v1_genomic.fna/checkm_result
[2024-01-24 10:48:09,183] [INFO] Task succeeded: CheckM
[2024-01-24 10:48:09,184] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:48:09,209] [INFO] ===== Completeness check finished =====
[2024-01-24 10:48:09,209] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:48:09,210] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014652455.1_ASM1465245v1_genomic.fna/markers.fasta)
[2024-01-24 10:48:09,210] [INFO] Task started: Blastn
[2024-01-24 10:48:09,211] [INFO] Running command: blastn -query GCF_014652455.1_ASM1465245v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3559c15c-9c60-4dcf-9e42-8fe5d680a263/dqc_reference/reference_markers_gtdb.fasta -out GCF_014652455.1_ASM1465245v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:48:10,387] [INFO] Task succeeded: Blastn
[2024-01-24 10:48:10,390] [INFO] Selected 21 target genomes.
[2024-01-24 10:48:10,390] [INFO] Target genome list was writen to GCF_014652455.1_ASM1465245v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:48:10,774] [INFO] Task started: fastANI
[2024-01-24 10:48:10,774] [INFO] Running command: fastANI --query /var/lib/cwl/stgf26d596c-2d43-44cb-8b53-45049da133dd/GCF_014652455.1_ASM1465245v1_genomic.fna.gz --refList GCF_014652455.1_ASM1465245v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014652455.1_ASM1465245v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:48:23,284] [INFO] Task succeeded: fastANI
[2024-01-24 10:48:23,288] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:48:23,288] [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_014652455.1	s__Litorimonas cladophorae	100.0	1004	1004	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Litorimonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000428525.1	s__Hellea balneolensis	77.0189	83	1004	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Hellea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014652695.1	s__Litorimonas arctica	76.381	84	1004	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Litorimonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 10:48:23,290] [INFO] GTDB search result was written to GCF_014652455.1_ASM1465245v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:48:23,290] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:48:23,293] [INFO] DFAST_QC result json was written to GCF_014652455.1_ASM1465245v1_genomic.fna/dqc_result.json
[2024-01-24 10:48:23,294] [INFO] DFAST_QC completed!
[2024-01-24 10:48:23,294] [INFO] Total running time: 0h1m14s