[2024-01-24 12:44:53,756] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:44:53,761] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:44:53,761] [INFO] DQC Reference Directory: /var/lib/cwl/stg5721dc8d-aa68-4c80-8159-23bf36dd94e4/dqc_reference
[2024-01-24 12:44:55,198] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:44:55,200] [INFO] Task started: Prodigal
[2024-01-24 12:44:55,200] [INFO] Running command: gunzip -c /var/lib/cwl/stgff8f0776-0bd8-4621-99ca-623b24d8645e/GCF_014648235.1_ASM1464823v1_genomic.fna.gz | prodigal -d GCF_014648235.1_ASM1464823v1_genomic.fna/cds.fna -a GCF_014648235.1_ASM1464823v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:45:05,872] [INFO] Task succeeded: Prodigal
[2024-01-24 12:45:05,873] [INFO] Task started: HMMsearch
[2024-01-24 12:45:05,873] [INFO] Running command: hmmsearch --tblout GCF_014648235.1_ASM1464823v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5721dc8d-aa68-4c80-8159-23bf36dd94e4/dqc_reference/reference_markers.hmm GCF_014648235.1_ASM1464823v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:45:06,094] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:45:06,095] [WARNING] Found 1/6 markers. [/var/lib/cwl/stgff8f0776-0bd8-4621-99ca-623b24d8645e/GCF_014648235.1_ASM1464823v1_genomic.fna.gz]
[2024-01-24 12:45:06,132] [INFO] Query marker FASTA was written to GCF_014648235.1_ASM1464823v1_genomic.fna/markers.fasta
[2024-01-24 12:45:06,133] [INFO] Task started: Blastn
[2024-01-24 12:45:06,133] [INFO] Running command: blastn -query GCF_014648235.1_ASM1464823v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5721dc8d-aa68-4c80-8159-23bf36dd94e4/dqc_reference/reference_markers.fasta -out GCF_014648235.1_ASM1464823v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:45:06,646] [INFO] Task succeeded: Blastn
[2024-01-24 12:45:06,650] [INFO] Selected 2 target genomes.
[2024-01-24 12:45:06,650] [INFO] Target genome list was writen to GCF_014648235.1_ASM1464823v1_genomic.fna/target_genomes.txt
[2024-01-24 12:45:06,654] [INFO] Task started: fastANI
[2024-01-24 12:45:06,654] [INFO] Running command: fastANI --query /var/lib/cwl/stgff8f0776-0bd8-4621-99ca-623b24d8645e/GCF_014648235.1_ASM1464823v1_genomic.fna.gz --refList GCF_014648235.1_ASM1464823v1_genomic.fna/target_genomes.txt --output GCF_014648235.1_ASM1464823v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:45:09,218] [INFO] Task succeeded: fastANI
[2024-01-24 12:45:09,218] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5721dc8d-aa68-4c80-8159-23bf36dd94e4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:45:09,219] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5721dc8d-aa68-4c80-8159-23bf36dd94e4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:45:09,223] [INFO] Found 2 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:45:09,223] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:45:09,223] [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
Sulfodiicoccus acidiphilus	strain=JCM 31740	GCA_014648235.1	1670455	1670455	type	True	100.0	759	760	95	conclusive
Sulfodiicoccus acidiphilus	strain=HS-1	GCA_003967175.1	1670455	1670455	type	True	99.9853	758	760	95	conclusive
--------------------------------------------------------------------------------
[2024-01-24 12:45:09,225] [INFO] DFAST Taxonomy check result was written to GCF_014648235.1_ASM1464823v1_genomic.fna/tc_result.tsv
[2024-01-24 12:45:09,226] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:45:09,227] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:45:09,227] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5721dc8d-aa68-4c80-8159-23bf36dd94e4/dqc_reference/checkm_data
[2024-01-24 12:45:09,228] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:45:09,262] [INFO] Task started: CheckM
[2024-01-24 12:45:09,263] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014648235.1_ASM1464823v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014648235.1_ASM1464823v1_genomic.fna/checkm_input GCF_014648235.1_ASM1464823v1_genomic.fna/checkm_result
[2024-01-24 12:45:42,440] [INFO] Task succeeded: CheckM
[2024-01-24 12:45:42,441] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:45:42,467] [INFO] ===== Completeness check finished =====
[2024-01-24 12:45:42,467] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:45:42,468] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014648235.1_ASM1464823v1_genomic.fna/markers.fasta)
[2024-01-24 12:45:42,468] [INFO] Task started: Blastn
[2024-01-24 12:45:42,468] [INFO] Running command: blastn -query GCF_014648235.1_ASM1464823v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5721dc8d-aa68-4c80-8159-23bf36dd94e4/dqc_reference/reference_markers_gtdb.fasta -out GCF_014648235.1_ASM1464823v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:45:42,887] [INFO] Task succeeded: Blastn
[2024-01-24 12:45:42,891] [INFO] Selected 1 target genomes.
[2024-01-24 12:45:42,891] [INFO] Target genome list was writen to GCF_014648235.1_ASM1464823v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:45:42,892] [INFO] Task started: fastANI
[2024-01-24 12:45:42,893] [INFO] Running command: fastANI --query /var/lib/cwl/stgff8f0776-0bd8-4621-99ca-623b24d8645e/GCF_014648235.1_ASM1464823v1_genomic.fna.gz --refList GCF_014648235.1_ASM1464823v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014648235.1_ASM1464823v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:45:44,331] [INFO] Task succeeded: fastANI
[2024-01-24 12:45:44,335] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:45:44,335] [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_003967175.1	s__Sulfodiicoccus acidiphilus	99.9853	758	760	d__Archaea;p__Thermoproteota;c__Thermoproteia;o__Sulfolobales;f__Sulfolobaceae;g__Sulfodiicoccus	95.0	99.99	99.99	1.00	1.00	2	conclusive
--------------------------------------------------------------------------------
[2024-01-24 12:45:44,338] [INFO] GTDB search result was written to GCF_014648235.1_ASM1464823v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:45:44,339] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:45:44,343] [INFO] DFAST_QC result json was written to GCF_014648235.1_ASM1464823v1_genomic.fna/dqc_result.json
[2024-01-24 12:45:44,343] [INFO] DFAST_QC completed!
[2024-01-24 12:45:44,343] [INFO] Total running time: 0h0m51s