[2024-01-24 11:34:41,274] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:34:41,276] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:34:41,277] [INFO] DQC Reference Directory: /var/lib/cwl/stg206ed33e-f243-4c0a-b783-6aee6b4c5890/dqc_reference
[2024-01-24 11:34:42,680] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:34:42,681] [INFO] Task started: Prodigal
[2024-01-24 11:34:42,681] [INFO] Running command: gunzip -c /var/lib/cwl/stg75c62d46-3283-4217-bff3-68b94d760f30/GCF_003987655.1_ASM398765v1_genomic.fna.gz | prodigal -d GCF_003987655.1_ASM398765v1_genomic.fna/cds.fna -a GCF_003987655.1_ASM398765v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:34:49,971] [INFO] Task succeeded: Prodigal
[2024-01-24 11:34:49,971] [INFO] Task started: HMMsearch
[2024-01-24 11:34:49,971] [INFO] Running command: hmmsearch --tblout GCF_003987655.1_ASM398765v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg206ed33e-f243-4c0a-b783-6aee6b4c5890/dqc_reference/reference_markers.hmm GCF_003987655.1_ASM398765v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:34:50,215] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:34:50,216] [INFO] Found 6/6 markers.
[2024-01-24 11:34:50,252] [INFO] Query marker FASTA was written to GCF_003987655.1_ASM398765v1_genomic.fna/markers.fasta
[2024-01-24 11:34:50,252] [INFO] Task started: Blastn
[2024-01-24 11:34:50,252] [INFO] Running command: blastn -query GCF_003987655.1_ASM398765v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg206ed33e-f243-4c0a-b783-6aee6b4c5890/dqc_reference/reference_markers.fasta -out GCF_003987655.1_ASM398765v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:34:50,849] [INFO] Task succeeded: Blastn
[2024-01-24 11:34:50,852] [INFO] Selected 25 target genomes.
[2024-01-24 11:34:50,853] [INFO] Target genome list was writen to GCF_003987655.1_ASM398765v1_genomic.fna/target_genomes.txt
[2024-01-24 11:34:50,867] [INFO] Task started: fastANI
[2024-01-24 11:34:50,868] [INFO] Running command: fastANI --query /var/lib/cwl/stg75c62d46-3283-4217-bff3-68b94d760f30/GCF_003987655.1_ASM398765v1_genomic.fna.gz --refList GCF_003987655.1_ASM398765v1_genomic.fna/target_genomes.txt --output GCF_003987655.1_ASM398765v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:35:03,783] [INFO] Task succeeded: fastANI
[2024-01-24 11:35:03,783] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg206ed33e-f243-4c0a-b783-6aee6b4c5890/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:35:03,783] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg206ed33e-f243-4c0a-b783-6aee6b4c5890/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:35:03,787] [INFO] Found 2 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:35:03,787] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:35:03,788] [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
Vagococcus acidifermentans	strain=LMG 24798	GCA_003987655.1	564710	564710	type	True	100.0	936	937	95	conclusive
Vagococcus carniphilus	strain=ATCC BAA-640	GCA_014397115.1	218144	218144	type	True	77.6736	59	937	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:35:03,789] [INFO] DFAST Taxonomy check result was written to GCF_003987655.1_ASM398765v1_genomic.fna/tc_result.tsv
[2024-01-24 11:35:03,790] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:35:03,790] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:35:03,790] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg206ed33e-f243-4c0a-b783-6aee6b4c5890/dqc_reference/checkm_data
[2024-01-24 11:35:03,791] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:35:03,819] [INFO] Task started: CheckM
[2024-01-24 11:35:03,820] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003987655.1_ASM398765v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003987655.1_ASM398765v1_genomic.fna/checkm_input GCF_003987655.1_ASM398765v1_genomic.fna/checkm_result
[2024-01-24 11:35:32,373] [INFO] Task succeeded: CheckM
[2024-01-24 11:35:32,374] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:35:32,389] [INFO] ===== Completeness check finished =====
[2024-01-24 11:35:32,389] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:35:32,390] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003987655.1_ASM398765v1_genomic.fna/markers.fasta)
[2024-01-24 11:35:32,390] [INFO] Task started: Blastn
[2024-01-24 11:35:32,390] [INFO] Running command: blastn -query GCF_003987655.1_ASM398765v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg206ed33e-f243-4c0a-b783-6aee6b4c5890/dqc_reference/reference_markers_gtdb.fasta -out GCF_003987655.1_ASM398765v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:35:33,153] [INFO] Task succeeded: Blastn
[2024-01-24 11:35:33,157] [INFO] Selected 28 target genomes.
[2024-01-24 11:35:33,157] [INFO] Target genome list was writen to GCF_003987655.1_ASM398765v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:35:33,175] [INFO] Task started: fastANI
[2024-01-24 11:35:33,176] [INFO] Running command: fastANI --query /var/lib/cwl/stg75c62d46-3283-4217-bff3-68b94d760f30/GCF_003987655.1_ASM398765v1_genomic.fna.gz --refList GCF_003987655.1_ASM398765v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003987655.1_ASM398765v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:35:46,328] [INFO] Task succeeded: fastANI
[2024-01-24 11:35:46,332] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:35:46,333] [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_003987655.1	s__Vagococcus_B acidifermentans	100.0	936	937	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Vagococcaceae;g__Vagococcus_B	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014397115.1	s__Vagococcus carniphilus	77.6593	60	937	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Vagococcaceae;g__Vagococcus	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 11:35:46,334] [INFO] GTDB search result was written to GCF_003987655.1_ASM398765v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:35:46,335] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:35:46,337] [INFO] DFAST_QC result json was written to GCF_003987655.1_ASM398765v1_genomic.fna/dqc_result.json
[2024-01-24 11:35:46,337] [INFO] DFAST_QC completed!
[2024-01-24 11:35:46,338] [INFO] Total running time: 0h1m5s