[2024-01-24 13:49:00,084] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:49:00,085] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:49:00,086] [INFO] DQC Reference Directory: /var/lib/cwl/stg466fc784-90cb-4be5-afdb-c223d8368307/dqc_reference
[2024-01-24 13:49:01,408] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:01,409] [INFO] Task started: Prodigal
[2024-01-24 13:49:01,409] [INFO] Running command: gunzip -c /var/lib/cwl/stg93af10cc-0a83-446b-911c-1dffdf79aac4/GCF_000092185.1_ASM9218v1_genomic.fna.gz | prodigal -d GCF_000092185.1_ASM9218v1_genomic.fna/cds.fna -a GCF_000092185.1_ASM9218v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:49:04,375] [INFO] Task succeeded: Prodigal
[2024-01-24 13:49:04,376] [INFO] Task started: HMMsearch
[2024-01-24 13:49:04,376] [INFO] Running command: hmmsearch --tblout GCF_000092185.1_ASM9218v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg466fc784-90cb-4be5-afdb-c223d8368307/dqc_reference/reference_markers.hmm GCF_000092185.1_ASM9218v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:49:04,555] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:49:04,556] [WARNING] Found 2/6 markers. [/var/lib/cwl/stg93af10cc-0a83-446b-911c-1dffdf79aac4/GCF_000092185.1_ASM9218v1_genomic.fna.gz]
[2024-01-24 13:49:04,578] [INFO] Query marker FASTA was written to GCF_000092185.1_ASM9218v1_genomic.fna/markers.fasta
[2024-01-24 13:49:04,578] [INFO] Task started: Blastn
[2024-01-24 13:49:04,579] [INFO] Running command: blastn -query GCF_000092185.1_ASM9218v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg466fc784-90cb-4be5-afdb-c223d8368307/dqc_reference/reference_markers.fasta -out GCF_000092185.1_ASM9218v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:05,063] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:05,065] [INFO] Selected 1 target genomes.
[2024-01-24 13:49:05,066] [INFO] Target genome list was writen to GCF_000092185.1_ASM9218v1_genomic.fna/target_genomes.txt
[2024-01-24 13:49:05,067] [INFO] Task started: fastANI
[2024-01-24 13:49:05,067] [INFO] Running command: fastANI --query /var/lib/cwl/stg93af10cc-0a83-446b-911c-1dffdf79aac4/GCF_000092185.1_ASM9218v1_genomic.fna.gz --refList GCF_000092185.1_ASM9218v1_genomic.fna/target_genomes.txt --output GCF_000092185.1_ASM9218v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:49:05,497] [INFO] Task succeeded: fastANI
[2024-01-24 13:49:05,497] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg466fc784-90cb-4be5-afdb-c223d8368307/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:49:05,498] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg466fc784-90cb-4be5-afdb-c223d8368307/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:49:05,504] [INFO] Found 1 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:49:05,504] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:49:05,504] [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
Thermosphaera aggregans	strain=DSM 11486	GCA_000092185.1	54254	54254	type	True	100.0	438	438	95	conclusive
--------------------------------------------------------------------------------
[2024-01-24 13:49:05,505] [INFO] DFAST Taxonomy check result was written to GCF_000092185.1_ASM9218v1_genomic.fna/tc_result.tsv
[2024-01-24 13:49:05,506] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:49:05,506] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:49:05,506] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg466fc784-90cb-4be5-afdb-c223d8368307/dqc_reference/checkm_data
[2024-01-24 13:49:05,507] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:49:05,528] [INFO] Task started: CheckM
[2024-01-24 13:49:05,528] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000092185.1_ASM9218v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000092185.1_ASM9218v1_genomic.fna/checkm_input GCF_000092185.1_ASM9218v1_genomic.fna/checkm_result
[2024-01-24 13:49:22,082] [INFO] Task succeeded: CheckM
[2024-01-24 13:49:22,083] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:49:22,104] [INFO] ===== Completeness check finished =====
[2024-01-24 13:49:22,104] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:49:22,105] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000092185.1_ASM9218v1_genomic.fna/markers.fasta)
[2024-01-24 13:49:22,105] [INFO] Task started: Blastn
[2024-01-24 13:49:22,106] [INFO] Running command: blastn -query GCF_000092185.1_ASM9218v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg466fc784-90cb-4be5-afdb-c223d8368307/dqc_reference/reference_markers_gtdb.fasta -out GCF_000092185.1_ASM9218v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:22,620] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:22,624] [INFO] Selected 4 target genomes.
[2024-01-24 13:49:22,624] [INFO] Target genome list was writen to GCF_000092185.1_ASM9218v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:49:22,634] [INFO] Task started: fastANI
[2024-01-24 13:49:22,634] [INFO] Running command: fastANI --query /var/lib/cwl/stg93af10cc-0a83-446b-911c-1dffdf79aac4/GCF_000092185.1_ASM9218v1_genomic.fna.gz --refList GCF_000092185.1_ASM9218v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000092185.1_ASM9218v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:49:23,882] [INFO] Task succeeded: fastANI
[2024-01-24 13:49:23,887] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:49:23,888] [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_000092185.1	s__Thermosphaera aggregans	100.0	438	438	d__Archaea;p__Thermoproteota;c__Thermoproteia;o__Sulfolobales;f__Desulfurococcaceae;g__Thermosphaera	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014962245.1	s__Thermosphaera aggregans_B	83.3603	344	438	d__Archaea;p__Thermoproteota;c__Thermoproteia;o__Sulfolobales;f__Desulfurococcaceae;g__Thermosphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011053855.1	s__Thermosphaera aggregans_A	83.2111	315	438	d__Archaea;p__Thermoproteota;c__Thermoproteia;o__Sulfolobales;f__Desulfurococcaceae;g__Thermosphaera	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:49:23,889] [INFO] GTDB search result was written to GCF_000092185.1_ASM9218v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:49:23,890] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:49:23,893] [INFO] DFAST_QC result json was written to GCF_000092185.1_ASM9218v1_genomic.fna/dqc_result.json
[2024-01-24 13:49:23,893] [INFO] DFAST_QC completed!
[2024-01-24 13:49:23,893] [INFO] Total running time: 0h0m24s