[2024-01-24 13:18:41,425] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:18:41,426] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:18:41,427] [INFO] DQC Reference Directory: /var/lib/cwl/stg07dc384d-d55d-49a1-aaa7-353a04cfb9b2/dqc_reference
[2024-01-24 13:18:42,621] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:18:42,622] [INFO] Task started: Prodigal
[2024-01-24 13:18:42,622] [INFO] Running command: gunzip -c /var/lib/cwl/stgdc149dac-45d3-4623-80a1-9b0661598187/GCF_008326425.1_SulIC006_1.0_genomic.fna.gz | prodigal -d GCF_008326425.1_SulIC006_1.0_genomic.fna/cds.fna -a GCF_008326425.1_SulIC006_1.0_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:18:52,395] [INFO] Task succeeded: Prodigal
[2024-01-24 13:18:52,395] [INFO] Task started: HMMsearch
[2024-01-24 13:18:52,395] [INFO] Running command: hmmsearch --tblout GCF_008326425.1_SulIC006_1.0_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg07dc384d-d55d-49a1-aaa7-353a04cfb9b2/dqc_reference/reference_markers.hmm GCF_008326425.1_SulIC006_1.0_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:18:52,608] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:18:52,610] [WARNING] Found 1/6 markers. [/var/lib/cwl/stgdc149dac-45d3-4623-80a1-9b0661598187/GCF_008326425.1_SulIC006_1.0_genomic.fna.gz]
[2024-01-24 13:18:52,640] [INFO] Query marker FASTA was written to GCF_008326425.1_SulIC006_1.0_genomic.fna/markers.fasta
[2024-01-24 13:18:52,640] [INFO] Task started: Blastn
[2024-01-24 13:18:52,640] [INFO] Running command: blastn -query GCF_008326425.1_SulIC006_1.0_genomic.fna/markers.fasta -db /var/lib/cwl/stg07dc384d-d55d-49a1-aaa7-353a04cfb9b2/dqc_reference/reference_markers.fasta -out GCF_008326425.1_SulIC006_1.0_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:18:53,117] [INFO] Task succeeded: Blastn
[2024-01-24 13:18:53,121] [INFO] Selected 2 target genomes.
[2024-01-24 13:18:53,121] [INFO] Target genome list was writen to GCF_008326425.1_SulIC006_1.0_genomic.fna/target_genomes.txt
[2024-01-24 13:18:53,124] [INFO] Task started: fastANI
[2024-01-24 13:18:53,124] [INFO] Running command: fastANI --query /var/lib/cwl/stgdc149dac-45d3-4623-80a1-9b0661598187/GCF_008326425.1_SulIC006_1.0_genomic.fna.gz --refList GCF_008326425.1_SulIC006_1.0_genomic.fna/target_genomes.txt --output GCF_008326425.1_SulIC006_1.0_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:18:54,700] [INFO] Task succeeded: fastANI
[2024-01-24 13:18:54,701] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg07dc384d-d55d-49a1-aaa7-353a04cfb9b2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:18:54,701] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg07dc384d-d55d-49a1-aaa7-353a04cfb9b2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:18:54,709] [INFO] Found 2 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:18:54,709] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:18:54,709] [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
Sulfuracidifex tepidarius	strain=IC-006	GCA_008326425.1	1294262	1294262	type	True	100.0	853	853	95	conclusive
Sulfuracidifex tepidarius	strain=JCM 16833	GCA_001316085.1	1294262	1294262	type	True	99.8769	808	853	95	conclusive
--------------------------------------------------------------------------------
[2024-01-24 13:18:54,711] [INFO] DFAST Taxonomy check result was written to GCF_008326425.1_SulIC006_1.0_genomic.fna/tc_result.tsv
[2024-01-24 13:18:54,712] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:18:54,712] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:18:54,712] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg07dc384d-d55d-49a1-aaa7-353a04cfb9b2/dqc_reference/checkm_data
[2024-01-24 13:18:54,713] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:18:54,744] [INFO] Task started: CheckM
[2024-01-24 13:18:54,744] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008326425.1_SulIC006_1.0_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008326425.1_SulIC006_1.0_genomic.fna/checkm_input GCF_008326425.1_SulIC006_1.0_genomic.fna/checkm_result
[2024-01-24 13:19:27,436] [INFO] Task succeeded: CheckM
[2024-01-24 13:19:27,438] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:19:27,466] [INFO] ===== Completeness check finished =====
[2024-01-24 13:19:27,466] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:19:27,467] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008326425.1_SulIC006_1.0_genomic.fna/markers.fasta)
[2024-01-24 13:19:27,467] [INFO] Task started: Blastn
[2024-01-24 13:19:27,467] [INFO] Running command: blastn -query GCF_008326425.1_SulIC006_1.0_genomic.fna/markers.fasta -db /var/lib/cwl/stg07dc384d-d55d-49a1-aaa7-353a04cfb9b2/dqc_reference/reference_markers_gtdb.fasta -out GCF_008326425.1_SulIC006_1.0_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:27,902] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:27,907] [INFO] Selected 2 target genomes.
[2024-01-24 13:19:27,907] [INFO] Target genome list was writen to GCF_008326425.1_SulIC006_1.0_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:19:27,910] [INFO] Task started: fastANI
[2024-01-24 13:19:27,910] [INFO] Running command: fastANI --query /var/lib/cwl/stgdc149dac-45d3-4623-80a1-9b0661598187/GCF_008326425.1_SulIC006_1.0_genomic.fna.gz --refList GCF_008326425.1_SulIC006_1.0_genomic.fna/target_genomes_gtdb.txt --output GCF_008326425.1_SulIC006_1.0_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:19:29,268] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:29,272] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:19:29,273] [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_008326425.1	s__Sulfuracidifex tepidarius	100.0	853	853	d__Archaea;p__Thermoproteota;c__Thermoproteia;o__Sulfolobales;f__Sulfolobaceae;g__Sulfuracidifex	95.0	99.84	99.74	0.98	0.97	3	conclusive
--------------------------------------------------------------------------------
[2024-01-24 13:19:29,274] [INFO] GTDB search result was written to GCF_008326425.1_SulIC006_1.0_genomic.fna/result_gtdb.tsv
[2024-01-24 13:19:29,275] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:19:29,277] [INFO] DFAST_QC result json was written to GCF_008326425.1_SulIC006_1.0_genomic.fna/dqc_result.json
[2024-01-24 13:19:29,278] [INFO] DFAST_QC completed!
[2024-01-24 13:19:29,278] [INFO] Total running time: 0h0m48s