[2024-01-25 17:45:20,498] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:45:20,499] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:45:20,499] [INFO] DQC Reference Directory: /var/lib/cwl/stg928837b7-f692-4e84-a749-73085932b968/dqc_reference
[2024-01-25 17:45:21,675] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:45:21,675] [INFO] Task started: Prodigal
[2024-01-25 17:45:21,676] [INFO] Running command: gunzip -c /var/lib/cwl/stg2238ff2c-e0c5-4909-82e3-5cab9b03d02b/GCF_012396555.1_ASM1239655v1_genomic.fna.gz | prodigal -d GCF_012396555.1_ASM1239655v1_genomic.fna/cds.fna -a GCF_012396555.1_ASM1239655v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:45:24,962] [INFO] Task succeeded: Prodigal
[2024-01-25 17:45:24,962] [INFO] Task started: HMMsearch
[2024-01-25 17:45:24,962] [INFO] Running command: hmmsearch --tblout GCF_012396555.1_ASM1239655v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg928837b7-f692-4e84-a749-73085932b968/dqc_reference/reference_markers.hmm GCF_012396555.1_ASM1239655v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:45:25,188] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:45:25,189] [INFO] Found 6/6 markers.
[2024-01-25 17:45:25,211] [INFO] Query marker FASTA was written to GCF_012396555.1_ASM1239655v1_genomic.fna/markers.fasta
[2024-01-25 17:45:25,211] [INFO] Task started: Blastn
[2024-01-25 17:45:25,211] [INFO] Running command: blastn -query GCF_012396555.1_ASM1239655v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg928837b7-f692-4e84-a749-73085932b968/dqc_reference/reference_markers.fasta -out GCF_012396555.1_ASM1239655v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:45:25,753] [INFO] Task succeeded: Blastn
[2024-01-25 17:45:25,756] [INFO] Selected 28 target genomes.
[2024-01-25 17:45:25,757] [INFO] Target genome list was writen to GCF_012396555.1_ASM1239655v1_genomic.fna/target_genomes.txt
[2024-01-25 17:45:25,824] [INFO] Task started: fastANI
[2024-01-25 17:45:25,824] [INFO] Running command: fastANI --query /var/lib/cwl/stg2238ff2c-e0c5-4909-82e3-5cab9b03d02b/GCF_012396555.1_ASM1239655v1_genomic.fna.gz --refList GCF_012396555.1_ASM1239655v1_genomic.fna/target_genomes.txt --output GCF_012396555.1_ASM1239655v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:45:38,897] [INFO] Task succeeded: fastANI
[2024-01-25 17:45:38,897] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg928837b7-f692-4e84-a749-73085932b968/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:45:38,898] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg928837b7-f692-4e84-a749-73085932b968/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:45:38,902] [INFO] Found 2 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:45:38,902] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:45:38,902] [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
Facklamia miroungae	strain=CCUG 42728	GCA_012396555.1	120956	120956	type	True	100.0	664	665	95	conclusive
Facklamia lactis	strain=DSM 111018	GCA_015863205.1	2749967	2749967	type	True	78.2125	85	665	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:45:38,903] [INFO] DFAST Taxonomy check result was written to GCF_012396555.1_ASM1239655v1_genomic.fna/tc_result.tsv
[2024-01-25 17:45:38,904] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:45:38,904] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:45:38,904] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg928837b7-f692-4e84-a749-73085932b968/dqc_reference/checkm_data
[2024-01-25 17:45:38,905] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:45:38,929] [INFO] Task started: CheckM
[2024-01-25 17:45:38,929] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_012396555.1_ASM1239655v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_012396555.1_ASM1239655v1_genomic.fna/checkm_input GCF_012396555.1_ASM1239655v1_genomic.fna/checkm_result
[2024-01-25 17:45:54,938] [INFO] Task succeeded: CheckM
[2024-01-25 17:45:54,939] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:45:54,970] [INFO] ===== Completeness check finished =====
[2024-01-25 17:45:54,970] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:45:54,970] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_012396555.1_ASM1239655v1_genomic.fna/markers.fasta)
[2024-01-25 17:45:54,971] [INFO] Task started: Blastn
[2024-01-25 17:45:54,971] [INFO] Running command: blastn -query GCF_012396555.1_ASM1239655v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg928837b7-f692-4e84-a749-73085932b968/dqc_reference/reference_markers_gtdb.fasta -out GCF_012396555.1_ASM1239655v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:45:55,787] [INFO] Task succeeded: Blastn
[2024-01-25 17:45:55,790] [INFO] Selected 28 target genomes.
[2024-01-25 17:45:55,791] [INFO] Target genome list was writen to GCF_012396555.1_ASM1239655v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:45:55,823] [INFO] Task started: fastANI
[2024-01-25 17:45:55,823] [INFO] Running command: fastANI --query /var/lib/cwl/stg2238ff2c-e0c5-4909-82e3-5cab9b03d02b/GCF_012396555.1_ASM1239655v1_genomic.fna.gz --refList GCF_012396555.1_ASM1239655v1_genomic.fna/target_genomes_gtdb.txt --output GCF_012396555.1_ASM1239655v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:46:07,000] [INFO] Task succeeded: fastANI
[2024-01-25 17:46:07,005] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:46:07,006] [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_012396555.1	s__Facklamia miroungae	100.0	664	665	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Aerococcaceae;g__Facklamia	95.0	100.00	100.00	0.99	0.99	2	conclusive
GCF_015863265.1	s__Facklamia sp015863265	77.9649	89	665	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Aerococcaceae;g__Facklamia	95.0	99.29	99.29	0.96	0.96	2	-
--------------------------------------------------------------------------------
[2024-01-25 17:46:07,012] [INFO] GTDB search result was written to GCF_012396555.1_ASM1239655v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:46:07,012] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:46:07,014] [INFO] DFAST_QC result json was written to GCF_012396555.1_ASM1239655v1_genomic.fna/dqc_result.json
[2024-01-25 17:46:07,014] [INFO] DFAST_QC completed!
[2024-01-25 17:46:07,014] [INFO] Total running time: 0h0m47s