[2024-01-25 18:53:50,862] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:53:50,863] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:53:50,863] [INFO] DQC Reference Directory: /var/lib/cwl/stgbea61941-d5ad-4334-be89-36f7fcf548d2/dqc_reference
[2024-01-25 18:53:51,980] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:53:51,980] [INFO] Task started: Prodigal
[2024-01-25 18:53:51,981] [INFO] Running command: gunzip -c /var/lib/cwl/stg16c7b842-1680-42eb-8afe-924a201c5ba1/GCF_014202105.1_ASM1420210v1_genomic.fna.gz | prodigal -d GCF_014202105.1_ASM1420210v1_genomic.fna/cds.fna -a GCF_014202105.1_ASM1420210v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:53:57,721] [INFO] Task succeeded: Prodigal
[2024-01-25 18:53:57,721] [INFO] Task started: HMMsearch
[2024-01-25 18:53:57,721] [INFO] Running command: hmmsearch --tblout GCF_014202105.1_ASM1420210v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbea61941-d5ad-4334-be89-36f7fcf548d2/dqc_reference/reference_markers.hmm GCF_014202105.1_ASM1420210v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:53:57,899] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:53:57,901] [WARNING] Found 1/6 markers. [/var/lib/cwl/stg16c7b842-1680-42eb-8afe-924a201c5ba1/GCF_014202105.1_ASM1420210v1_genomic.fna.gz]
[2024-01-25 18:53:57,926] [INFO] Query marker FASTA was written to GCF_014202105.1_ASM1420210v1_genomic.fna/markers.fasta
[2024-01-25 18:53:57,927] [INFO] Task started: Blastn
[2024-01-25 18:53:57,927] [INFO] Running command: blastn -query GCF_014202105.1_ASM1420210v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbea61941-d5ad-4334-be89-36f7fcf548d2/dqc_reference/reference_markers.fasta -out GCF_014202105.1_ASM1420210v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:53:58,351] [INFO] Task succeeded: Blastn
[2024-01-25 18:53:58,354] [INFO] Selected 3 target genomes.
[2024-01-25 18:53:58,354] [INFO] Target genome list was writen to GCF_014202105.1_ASM1420210v1_genomic.fna/target_genomes.txt
[2024-01-25 18:53:58,356] [INFO] Task started: fastANI
[2024-01-25 18:53:58,356] [INFO] Running command: fastANI --query /var/lib/cwl/stg16c7b842-1680-42eb-8afe-924a201c5ba1/GCF_014202105.1_ASM1420210v1_genomic.fna.gz --refList GCF_014202105.1_ASM1420210v1_genomic.fna/target_genomes.txt --output GCF_014202105.1_ASM1420210v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:54:01,198] [INFO] Task succeeded: fastANI
[2024-01-25 18:54:01,198] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbea61941-d5ad-4334-be89-36f7fcf548d2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:54:01,198] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbea61941-d5ad-4334-be89-36f7fcf548d2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:54:01,203] [INFO] Found 3 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 18:54:01,203] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:54:01,203] [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
Sulfurisphaera ohwakuensis	strain=DSM 12421	GCA_014202105.1	69656	69656	type	True	100.0	866	874	95	conclusive
Sulfurisphaera ohwakuensis	strain=TA-1	GCA_009729055.1	69656	69656	type	True	99.998	873	874	95	conclusive
Sulfurisphaera tokodaii	strain=7	GCA_000011205.1	111955	111955	type	True	94.9535	753	874	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:54:01,204] [INFO] DFAST Taxonomy check result was written to GCF_014202105.1_ASM1420210v1_genomic.fna/tc_result.tsv
[2024-01-25 18:54:01,205] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:54:01,205] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:54:01,205] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbea61941-d5ad-4334-be89-36f7fcf548d2/dqc_reference/checkm_data
[2024-01-25 18:54:01,206] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:54:01,238] [INFO] Task started: CheckM
[2024-01-25 18:54:01,238] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014202105.1_ASM1420210v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014202105.1_ASM1420210v1_genomic.fna/checkm_input GCF_014202105.1_ASM1420210v1_genomic.fna/checkm_result
[2024-01-25 18:54:23,321] [INFO] Task succeeded: CheckM
[2024-01-25 18:54:23,322] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:54:23,344] [INFO] ===== Completeness check finished =====
[2024-01-25 18:54:23,344] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:54:23,344] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014202105.1_ASM1420210v1_genomic.fna/markers.fasta)
[2024-01-25 18:54:23,345] [INFO] Task started: Blastn
[2024-01-25 18:54:23,345] [INFO] Running command: blastn -query GCF_014202105.1_ASM1420210v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbea61941-d5ad-4334-be89-36f7fcf548d2/dqc_reference/reference_markers_gtdb.fasta -out GCF_014202105.1_ASM1420210v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:54:23,758] [INFO] Task succeeded: Blastn
[2024-01-25 18:54:23,760] [INFO] Selected 3 target genomes.
[2024-01-25 18:54:23,761] [INFO] Target genome list was writen to GCF_014202105.1_ASM1420210v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:54:23,765] [INFO] Task started: fastANI
[2024-01-25 18:54:23,766] [INFO] Running command: fastANI --query /var/lib/cwl/stg16c7b842-1680-42eb-8afe-924a201c5ba1/GCF_014202105.1_ASM1420210v1_genomic.fna.gz --refList GCF_014202105.1_ASM1420210v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014202105.1_ASM1420210v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:54:26,592] [INFO] Task succeeded: fastANI
[2024-01-25 18:54:26,596] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:54:26,596] [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_009729055.1	s__Sulfurisphaera ohwakuensis	99.998	873	874	d__Archaea;p__Thermoproteota;c__Thermoproteia;o__Sulfolobales;f__Sulfolobaceae;g__Sulfurisphaera	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_000011205.1	s__Sulfurisphaera tokodaii	94.9535	753	874	d__Archaea;p__Thermoproteota;c__Thermoproteia;o__Sulfolobales;f__Sulfolobaceae;g__Sulfurisphaera	95.0	100.00	100.00	1.00	1.00	2	-
GCF_012222305.1	s__Sulfurisphaera sp012222305	91.1225	738	874	d__Archaea;p__Thermoproteota;c__Thermoproteia;o__Sulfolobales;f__Sulfolobaceae;g__Sulfurisphaera	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:54:26,598] [INFO] GTDB search result was written to GCF_014202105.1_ASM1420210v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:54:26,599] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:54:26,602] [INFO] DFAST_QC result json was written to GCF_014202105.1_ASM1420210v1_genomic.fna/dqc_result.json
[2024-01-25 18:54:26,602] [INFO] DFAST_QC completed!
[2024-01-25 18:54:26,602] [INFO] Total running time: 0h0m36s