[2024-01-24 11:13:04,484] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:13:04,486] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:13:04,486] [INFO] DQC Reference Directory: /var/lib/cwl/stg59378e10-a9ea-46f6-bcf1-fa33485f3b69/dqc_reference
[2024-01-24 11:13:05,743] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:13:05,761] [INFO] Task started: Prodigal
[2024-01-24 11:13:05,762] [INFO] Running command: gunzip -c /var/lib/cwl/stg54ef9888-c053-4671-9d31-dc4a7e911871/GCF_014646535.1_ASM1464653v1_genomic.fna.gz | prodigal -d GCF_014646535.1_ASM1464653v1_genomic.fna/cds.fna -a GCF_014646535.1_ASM1464653v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:13:16,723] [INFO] Task succeeded: Prodigal
[2024-01-24 11:13:16,723] [INFO] Task started: HMMsearch
[2024-01-24 11:13:16,724] [INFO] Running command: hmmsearch --tblout GCF_014646535.1_ASM1464653v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg59378e10-a9ea-46f6-bcf1-fa33485f3b69/dqc_reference/reference_markers.hmm GCF_014646535.1_ASM1464653v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:13:16,963] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:13:16,965] [WARNING] Found 2/6 markers. [/var/lib/cwl/stg54ef9888-c053-4671-9d31-dc4a7e911871/GCF_014646535.1_ASM1464653v1_genomic.fna.gz]
[2024-01-24 11:13:16,988] [INFO] Query marker FASTA was written to GCF_014646535.1_ASM1464653v1_genomic.fna/markers.fasta
[2024-01-24 11:13:16,988] [INFO] Task started: Blastn
[2024-01-24 11:13:16,988] [INFO] Running command: blastn -query GCF_014646535.1_ASM1464653v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg59378e10-a9ea-46f6-bcf1-fa33485f3b69/dqc_reference/reference_markers.fasta -out GCF_014646535.1_ASM1464653v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:13:17,482] [INFO] Task succeeded: Blastn
[2024-01-24 11:13:17,487] [INFO] Selected 4 target genomes.
[2024-01-24 11:13:17,488] [INFO] Target genome list was writen to GCF_014646535.1_ASM1464653v1_genomic.fna/target_genomes.txt
[2024-01-24 11:13:17,502] [INFO] Task started: fastANI
[2024-01-24 11:13:17,502] [INFO] Running command: fastANI --query /var/lib/cwl/stg54ef9888-c053-4671-9d31-dc4a7e911871/GCF_014646535.1_ASM1464653v1_genomic.fna.gz --refList GCF_014646535.1_ASM1464653v1_genomic.fna/target_genomes.txt --output GCF_014646535.1_ASM1464653v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:13:18,712] [INFO] Task succeeded: fastANI
[2024-01-24 11:13:18,713] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg59378e10-a9ea-46f6-bcf1-fa33485f3b69/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:13:18,713] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg59378e10-a9ea-46f6-bcf1-fa33485f3b69/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:13:18,717] [INFO] Found 1 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:13:18,717] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:13:18,717] [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
Thermocladium modestius	strain=JCM 10088	GCA_014646535.1	62609	62609	type	True	100.0	630	632	95	conclusive
--------------------------------------------------------------------------------
[2024-01-24 11:13:18,719] [INFO] DFAST Taxonomy check result was written to GCF_014646535.1_ASM1464653v1_genomic.fna/tc_result.tsv
[2024-01-24 11:13:18,720] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:13:18,720] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:13:18,720] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg59378e10-a9ea-46f6-bcf1-fa33485f3b69/dqc_reference/checkm_data
[2024-01-24 11:13:18,721] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:13:18,742] [INFO] Task started: CheckM
[2024-01-24 11:13:18,743] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014646535.1_ASM1464653v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014646535.1_ASM1464653v1_genomic.fna/checkm_input GCF_014646535.1_ASM1464653v1_genomic.fna/checkm_result
[2024-01-24 11:13:53,566] [INFO] Task succeeded: CheckM
[2024-01-24 11:13:53,568] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 85.73%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:13:53,592] [INFO] ===== Completeness check finished =====
[2024-01-24 11:13:53,592] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:13:53,592] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014646535.1_ASM1464653v1_genomic.fna/markers.fasta)
[2024-01-24 11:13:53,593] [INFO] Task started: Blastn
[2024-01-24 11:13:53,593] [INFO] Running command: blastn -query GCF_014646535.1_ASM1464653v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg59378e10-a9ea-46f6-bcf1-fa33485f3b69/dqc_reference/reference_markers_gtdb.fasta -out GCF_014646535.1_ASM1464653v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:13:54,124] [INFO] Task succeeded: Blastn
[2024-01-24 11:13:54,128] [INFO] Selected 5 target genomes.
[2024-01-24 11:13:54,128] [INFO] Target genome list was writen to GCF_014646535.1_ASM1464653v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:13:54,134] [INFO] Task started: fastANI
[2024-01-24 11:13:54,134] [INFO] Running command: fastANI --query /var/lib/cwl/stg54ef9888-c053-4671-9d31-dc4a7e911871/GCF_014646535.1_ASM1464653v1_genomic.fna.gz --refList GCF_014646535.1_ASM1464653v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014646535.1_ASM1464653v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:13:55,748] [INFO] Task succeeded: fastANI
[2024-01-24 11:13:55,755] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:13:55,756] [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
GCA_001315925.1	s__Thermocladium modestius	99.1662	569	632	d__Archaea;p__Thermoproteota;c__Thermoproteia;o__Thermoproteales;f__Thermocladiaceae;g__Thermocladium	95.0	99.26	99.26	0.99	0.99	2	conclusive
GCA_002508315.1	s__Thermocladium sp002508315	88.749	391	632	d__Archaea;p__Thermoproteota;c__Thermoproteia;o__Thermoproteales;f__Thermocladiaceae;g__Thermocladium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:13:55,758] [INFO] GTDB search result was written to GCF_014646535.1_ASM1464653v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:13:55,759] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:13:55,761] [INFO] DFAST_QC result json was written to GCF_014646535.1_ASM1464653v1_genomic.fna/dqc_result.json
[2024-01-24 11:13:55,761] [INFO] DFAST_QC completed!
[2024-01-24 11:13:55,761] [INFO] Total running time: 0h0m51s