[2024-01-24 13:32:13,299] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:32:13,301] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:32:13,301] [INFO] DQC Reference Directory: /var/lib/cwl/stgb0902fff-83fd-41e7-ac7e-f92bcb416b66/dqc_reference
[2024-01-24 13:32:14,522] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:32:14,523] [INFO] Task started: Prodigal
[2024-01-24 13:32:14,523] [INFO] Running command: gunzip -c /var/lib/cwl/stg3eb8c435-4f8f-45bf-8a51-7b8d8541eead/GCF_001485475.2_ASM148547v2_genomic.fna.gz | prodigal -d GCF_001485475.2_ASM148547v2_genomic.fna/cds.fna -a GCF_001485475.2_ASM148547v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:32:19,561] [INFO] Task succeeded: Prodigal
[2024-01-24 13:32:19,561] [INFO] Task started: HMMsearch
[2024-01-24 13:32:19,561] [INFO] Running command: hmmsearch --tblout GCF_001485475.2_ASM148547v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb0902fff-83fd-41e7-ac7e-f92bcb416b66/dqc_reference/reference_markers.hmm GCF_001485475.2_ASM148547v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:32:19,790] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:32:19,792] [INFO] Found 6/6 markers.
[2024-01-24 13:32:19,817] [INFO] Query marker FASTA was written to GCF_001485475.2_ASM148547v2_genomic.fna/markers.fasta
[2024-01-24 13:32:19,817] [INFO] Task started: Blastn
[2024-01-24 13:32:19,818] [INFO] Running command: blastn -query GCF_001485475.2_ASM148547v2_genomic.fna/markers.fasta -db /var/lib/cwl/stgb0902fff-83fd-41e7-ac7e-f92bcb416b66/dqc_reference/reference_markers.fasta -out GCF_001485475.2_ASM148547v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:20,392] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:20,396] [INFO] Selected 12 target genomes.
[2024-01-24 13:32:20,397] [INFO] Target genome list was writen to GCF_001485475.2_ASM148547v2_genomic.fna/target_genomes.txt
[2024-01-24 13:32:20,435] [INFO] Task started: fastANI
[2024-01-24 13:32:20,435] [INFO] Running command: fastANI --query /var/lib/cwl/stg3eb8c435-4f8f-45bf-8a51-7b8d8541eead/GCF_001485475.2_ASM148547v2_genomic.fna.gz --refList GCF_001485475.2_ASM148547v2_genomic.fna/target_genomes.txt --output GCF_001485475.2_ASM148547v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:32:26,108] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:26,109] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb0902fff-83fd-41e7-ac7e-f92bcb416b66/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:32:26,109] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb0902fff-83fd-41e7-ac7e-f92bcb416b66/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:32:26,114] [INFO] Found 1 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:32:26,114] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:32:26,114] [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
Tepidanaerobacter syntrophicus	strain=JL	GCA_001485475.2	224999	224999	type	True	100.0	803	804	95	conclusive
--------------------------------------------------------------------------------
[2024-01-24 13:32:26,116] [INFO] DFAST Taxonomy check result was written to GCF_001485475.2_ASM148547v2_genomic.fna/tc_result.tsv
[2024-01-24 13:32:26,117] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:32:26,117] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:32:26,117] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb0902fff-83fd-41e7-ac7e-f92bcb416b66/dqc_reference/checkm_data
[2024-01-24 13:32:26,118] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:32:26,148] [INFO] Task started: CheckM
[2024-01-24 13:32:26,148] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001485475.2_ASM148547v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001485475.2_ASM148547v2_genomic.fna/checkm_input GCF_001485475.2_ASM148547v2_genomic.fna/checkm_result
[2024-01-24 13:32:48,055] [INFO] Task succeeded: CheckM
[2024-01-24 13:32:48,056] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:32:48,082] [INFO] ===== Completeness check finished =====
[2024-01-24 13:32:48,082] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:32:48,083] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001485475.2_ASM148547v2_genomic.fna/markers.fasta)
[2024-01-24 13:32:48,083] [INFO] Task started: Blastn
[2024-01-24 13:32:48,083] [INFO] Running command: blastn -query GCF_001485475.2_ASM148547v2_genomic.fna/markers.fasta -db /var/lib/cwl/stgb0902fff-83fd-41e7-ac7e-f92bcb416b66/dqc_reference/reference_markers_gtdb.fasta -out GCF_001485475.2_ASM148547v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:48,958] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:48,961] [INFO] Selected 19 target genomes.
[2024-01-24 13:32:48,961] [INFO] Target genome list was writen to GCF_001485475.2_ASM148547v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:32:48,993] [INFO] Task started: fastANI
[2024-01-24 13:32:48,994] [INFO] Running command: fastANI --query /var/lib/cwl/stg3eb8c435-4f8f-45bf-8a51-7b8d8541eead/GCF_001485475.2_ASM148547v2_genomic.fna.gz --refList GCF_001485475.2_ASM148547v2_genomic.fna/target_genomes_gtdb.txt --output GCF_001485475.2_ASM148547v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:33:00,040] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:00,046] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:33:00,046] [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_001485475.2	s__Tepidanaerobacter syntrophicus	100.0	803	804	d__Bacteria;p__Firmicutes_A;c__Thermosediminibacteria;o__Thermosediminibacterales;f__Tepidanaerobacteraceae;g__Tepidanaerobacter	95.0	98.53	98.38	0.86	0.82	5	conclusive
GCA_012842445.1	s__DTU063 sp012842445	77.0594	54	804	d__Bacteria;p__Firmicutes_A;c__Thermosediminibacteria;o__Thermosediminibacterales;f__Tepidanaerobacteraceae;g__DTU063	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:33:00,048] [INFO] GTDB search result was written to GCF_001485475.2_ASM148547v2_genomic.fna/result_gtdb.tsv
[2024-01-24 13:33:00,048] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:33:00,050] [INFO] DFAST_QC result json was written to GCF_001485475.2_ASM148547v2_genomic.fna/dqc_result.json
[2024-01-24 13:33:00,050] [INFO] DFAST_QC completed!
[2024-01-24 13:33:00,050] [INFO] Total running time: 0h0m47s