[2024-01-24 14:31:30,086] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:31:30,087] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:31:30,087] [INFO] DQC Reference Directory: /var/lib/cwl/stg4b1e5a6a-8af1-479c-9b41-965fe8fc382f/dqc_reference
[2024-01-24 14:31:31,424] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:31:31,425] [INFO] Task started: Prodigal
[2024-01-24 14:31:31,425] [INFO] Running command: gunzip -c /var/lib/cwl/stg3f1e745f-0d9b-4a40-ac23-cf11739d8af1/GCF_014641495.1_ASM1464149v1_genomic.fna.gz | prodigal -d GCF_014641495.1_ASM1464149v1_genomic.fna/cds.fna -a GCF_014641495.1_ASM1464149v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:31:43,294] [INFO] Task succeeded: Prodigal
[2024-01-24 14:31:43,295] [INFO] Task started: HMMsearch
[2024-01-24 14:31:43,295] [INFO] Running command: hmmsearch --tblout GCF_014641495.1_ASM1464149v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4b1e5a6a-8af1-479c-9b41-965fe8fc382f/dqc_reference/reference_markers.hmm GCF_014641495.1_ASM1464149v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:31:43,594] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:31:43,595] [INFO] Found 6/6 markers.
[2024-01-24 14:31:43,629] [INFO] Query marker FASTA was written to GCF_014641495.1_ASM1464149v1_genomic.fna/markers.fasta
[2024-01-24 14:31:43,630] [INFO] Task started: Blastn
[2024-01-24 14:31:43,630] [INFO] Running command: blastn -query GCF_014641495.1_ASM1464149v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4b1e5a6a-8af1-479c-9b41-965fe8fc382f/dqc_reference/reference_markers.fasta -out GCF_014641495.1_ASM1464149v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:31:44,375] [INFO] Task succeeded: Blastn
[2024-01-24 14:31:44,381] [INFO] Selected 24 target genomes.
[2024-01-24 14:31:44,381] [INFO] Target genome list was writen to GCF_014641495.1_ASM1464149v1_genomic.fna/target_genomes.txt
[2024-01-24 14:31:44,441] [INFO] Task started: fastANI
[2024-01-24 14:31:44,442] [INFO] Running command: fastANI --query /var/lib/cwl/stg3f1e745f-0d9b-4a40-ac23-cf11739d8af1/GCF_014641495.1_ASM1464149v1_genomic.fna.gz --refList GCF_014641495.1_ASM1464149v1_genomic.fna/target_genomes.txt --output GCF_014641495.1_ASM1464149v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:31:58,995] [INFO] Task succeeded: fastANI
[2024-01-24 14:31:58,996] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4b1e5a6a-8af1-479c-9b41-965fe8fc382f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:31:58,996] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4b1e5a6a-8af1-479c-9b41-965fe8fc382f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:31:59,000] [INFO] Found 2 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:31:59,000] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:31:59,001] [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
Terasakiella brassicae	strain=CGMCC 1.15254	GCA_014641495.1	1634917	1634917	type	True	100.0	1165	1171	95	conclusive
Terasakiella pusilla	strain=DSM 6293	GCA_000688235.1	64973	64973	type	True	78.9021	359	1171	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:31:59,003] [INFO] DFAST Taxonomy check result was written to GCF_014641495.1_ASM1464149v1_genomic.fna/tc_result.tsv
[2024-01-24 14:31:59,004] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:31:59,009] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:31:59,010] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4b1e5a6a-8af1-479c-9b41-965fe8fc382f/dqc_reference/checkm_data
[2024-01-24 14:31:59,011] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:31:59,053] [INFO] Task started: CheckM
[2024-01-24 14:31:59,053] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014641495.1_ASM1464149v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014641495.1_ASM1464149v1_genomic.fna/checkm_input GCF_014641495.1_ASM1464149v1_genomic.fna/checkm_result
[2024-01-24 14:32:37,610] [INFO] Task succeeded: CheckM
[2024-01-24 14:32:37,611] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:32:37,637] [INFO] ===== Completeness check finished =====
[2024-01-24 14:32:37,638] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:32:37,638] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014641495.1_ASM1464149v1_genomic.fna/markers.fasta)
[2024-01-24 14:32:37,639] [INFO] Task started: Blastn
[2024-01-24 14:32:37,639] [INFO] Running command: blastn -query GCF_014641495.1_ASM1464149v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4b1e5a6a-8af1-479c-9b41-965fe8fc382f/dqc_reference/reference_markers_gtdb.fasta -out GCF_014641495.1_ASM1464149v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:32:38,731] [INFO] Task succeeded: Blastn
[2024-01-24 14:32:38,734] [INFO] Selected 16 target genomes.
[2024-01-24 14:32:38,735] [INFO] Target genome list was writen to GCF_014641495.1_ASM1464149v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:32:38,747] [INFO] Task started: fastANI
[2024-01-24 14:32:38,747] [INFO] Running command: fastANI --query /var/lib/cwl/stg3f1e745f-0d9b-4a40-ac23-cf11739d8af1/GCF_014641495.1_ASM1464149v1_genomic.fna.gz --refList GCF_014641495.1_ASM1464149v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014641495.1_ASM1464149v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:32:50,323] [INFO] Task succeeded: fastANI
[2024-01-24 14:32:50,331] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:32:50,331] [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_014641495.1	s__Terasakiella brassicae	100.0	1165	1171	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Terasakiellaceae;g__Terasakiella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000688235.1	s__Terasakiella pusilla	78.8964	360	1171	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Terasakiellaceae;g__Terasakiella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013373205.1	s__Terasakiella sp013373205	78.6518	365	1171	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Terasakiellaceae;g__Terasakiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004564135.1	s__Terasakiella sp004564135	78.4977	406	1171	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Terasakiellaceae;g__Terasakiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900093605.1	s__Terasakiella magnetica_A	78.3924	386	1171	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Terasakiellaceae;g__Terasakiella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013373265.1	s__Terasakiella sp013373265	77.9906	313	1171	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Terasakiellaceae;g__Terasakiella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:32:50,333] [INFO] GTDB search result was written to GCF_014641495.1_ASM1464149v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:32:50,334] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:32:50,336] [INFO] DFAST_QC result json was written to GCF_014641495.1_ASM1464149v1_genomic.fna/dqc_result.json
[2024-01-24 14:32:50,337] [INFO] DFAST_QC completed!
[2024-01-24 14:32:50,337] [INFO] Total running time: 0h1m20s