[2024-01-24 14:31:00,263] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:31:00,266] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:31:00,266] [INFO] DQC Reference Directory: /var/lib/cwl/stge3c4d045-1d7a-4a68-b189-61818dc265fe/dqc_reference
[2024-01-24 14:31:02,102] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:31:02,104] [INFO] Task started: Prodigal
[2024-01-24 14:31:02,105] [INFO] Running command: gunzip -c /var/lib/cwl/stg4d7b1288-d54a-499e-9e1a-2d0f73ed209a/GCF_009711445.1_ASM971144v1_genomic.fna.gz | prodigal -d GCF_009711445.1_ASM971144v1_genomic.fna/cds.fna -a GCF_009711445.1_ASM971144v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:31:09,368] [INFO] Task succeeded: Prodigal
[2024-01-24 14:31:09,369] [INFO] Task started: HMMsearch
[2024-01-24 14:31:09,369] [INFO] Running command: hmmsearch --tblout GCF_009711445.1_ASM971144v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge3c4d045-1d7a-4a68-b189-61818dc265fe/dqc_reference/reference_markers.hmm GCF_009711445.1_ASM971144v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:31:09,634] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:31:09,635] [INFO] Found 6/6 markers.
[2024-01-24 14:31:09,664] [INFO] Query marker FASTA was written to GCF_009711445.1_ASM971144v1_genomic.fna/markers.fasta
[2024-01-24 14:31:09,664] [INFO] Task started: Blastn
[2024-01-24 14:31:09,665] [INFO] Running command: blastn -query GCF_009711445.1_ASM971144v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge3c4d045-1d7a-4a68-b189-61818dc265fe/dqc_reference/reference_markers.fasta -out GCF_009711445.1_ASM971144v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:31:10,269] [INFO] Task succeeded: Blastn
[2024-01-24 14:31:10,272] [INFO] Selected 25 target genomes.
[2024-01-24 14:31:10,272] [INFO] Target genome list was writen to GCF_009711445.1_ASM971144v1_genomic.fna/target_genomes.txt
[2024-01-24 14:31:10,280] [INFO] Task started: fastANI
[2024-01-24 14:31:10,280] [INFO] Running command: fastANI --query /var/lib/cwl/stg4d7b1288-d54a-499e-9e1a-2d0f73ed209a/GCF_009711445.1_ASM971144v1_genomic.fna.gz --refList GCF_009711445.1_ASM971144v1_genomic.fna/target_genomes.txt --output GCF_009711445.1_ASM971144v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:31:26,401] [INFO] Task succeeded: fastANI
[2024-01-24 14:31:26,401] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge3c4d045-1d7a-4a68-b189-61818dc265fe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:31:26,401] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge3c4d045-1d7a-4a68-b189-61818dc265fe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:31:26,405] [INFO] Found 1 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:31:26,405] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:31:26,405] [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
Curvivirga aplysinae	strain=RKSG073	GCA_009711445.1	2529852	2529852	type	True	100.0	1079	1084	95	conclusive
--------------------------------------------------------------------------------
[2024-01-24 14:31:26,406] [INFO] DFAST Taxonomy check result was written to GCF_009711445.1_ASM971144v1_genomic.fna/tc_result.tsv
[2024-01-24 14:31:26,406] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:31:26,407] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:31:26,407] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge3c4d045-1d7a-4a68-b189-61818dc265fe/dqc_reference/checkm_data
[2024-01-24 14:31:26,407] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:31:26,443] [INFO] Task started: CheckM
[2024-01-24 14:31:26,443] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009711445.1_ASM971144v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009711445.1_ASM971144v1_genomic.fna/checkm_input GCF_009711445.1_ASM971144v1_genomic.fna/checkm_result
[2024-01-24 14:31:52,081] [INFO] Task succeeded: CheckM
[2024-01-24 14:31:52,082] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:31:52,098] [INFO] ===== Completeness check finished =====
[2024-01-24 14:31:52,098] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:31:52,099] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009711445.1_ASM971144v1_genomic.fna/markers.fasta)
[2024-01-24 14:31:52,099] [INFO] Task started: Blastn
[2024-01-24 14:31:52,099] [INFO] Running command: blastn -query GCF_009711445.1_ASM971144v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge3c4d045-1d7a-4a68-b189-61818dc265fe/dqc_reference/reference_markers_gtdb.fasta -out GCF_009711445.1_ASM971144v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:31:53,098] [INFO] Task succeeded: Blastn
[2024-01-24 14:31:53,100] [INFO] Selected 22 target genomes.
[2024-01-24 14:31:53,101] [INFO] Target genome list was writen to GCF_009711445.1_ASM971144v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:31:53,139] [INFO] Task started: fastANI
[2024-01-24 14:31:53,139] [INFO] Running command: fastANI --query /var/lib/cwl/stg4d7b1288-d54a-499e-9e1a-2d0f73ed209a/GCF_009711445.1_ASM971144v1_genomic.fna.gz --refList GCF_009711445.1_ASM971144v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009711445.1_ASM971144v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:32:05,009] [INFO] Task succeeded: fastANI
[2024-01-24 14:32:05,011] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:32:05,012] [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_009711445.1	s__Curvivirga aplysinae	100.0	1079	1084	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA8366;f__GCA-2696645;g__Curvivirga	95.0	N/A	N/A	N/A	N/A	1	conclusive
--------------------------------------------------------------------------------
[2024-01-24 14:32:05,013] [INFO] GTDB search result was written to GCF_009711445.1_ASM971144v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:32:05,013] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:32:05,015] [INFO] DFAST_QC result json was written to GCF_009711445.1_ASM971144v1_genomic.fna/dqc_result.json
[2024-01-24 14:32:05,015] [INFO] DFAST_QC completed!
[2024-01-24 14:32:05,015] [INFO] Total running time: 0h1m5s