[2024-01-24 13:27:45,489] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:27:45,491] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:27:45,492] [INFO] DQC Reference Directory: /var/lib/cwl/stg14d5d251-9b13-42d2-9129-b884b78a8c59/dqc_reference
[2024-01-24 13:27:46,908] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:27:46,909] [INFO] Task started: Prodigal
[2024-01-24 13:27:46,909] [INFO] Running command: gunzip -c /var/lib/cwl/stga0aa2938-869d-4d3c-a9f0-bd4d8ea96169/GCF_013343295.1_ASM1334329v1_genomic.fna.gz | prodigal -d GCF_013343295.1_ASM1334329v1_genomic.fna/cds.fna -a GCF_013343295.1_ASM1334329v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:27:55,668] [INFO] Task succeeded: Prodigal
[2024-01-24 13:27:55,668] [INFO] Task started: HMMsearch
[2024-01-24 13:27:55,668] [INFO] Running command: hmmsearch --tblout GCF_013343295.1_ASM1334329v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg14d5d251-9b13-42d2-9129-b884b78a8c59/dqc_reference/reference_markers.hmm GCF_013343295.1_ASM1334329v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:27:55,895] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:27:55,896] [WARNING] Found 1/6 markers. [/var/lib/cwl/stga0aa2938-869d-4d3c-a9f0-bd4d8ea96169/GCF_013343295.1_ASM1334329v1_genomic.fna.gz]
[2024-01-24 13:27:55,919] [INFO] Query marker FASTA was written to GCF_013343295.1_ASM1334329v1_genomic.fna/markers.fasta
[2024-01-24 13:27:55,919] [INFO] Task started: Blastn
[2024-01-24 13:27:55,919] [INFO] Running command: blastn -query GCF_013343295.1_ASM1334329v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg14d5d251-9b13-42d2-9129-b884b78a8c59/dqc_reference/reference_markers.fasta -out GCF_013343295.1_ASM1334329v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:27:56,431] [INFO] Task succeeded: Blastn
[2024-01-24 13:27:56,434] [INFO] Selected 1 target genomes.
[2024-01-24 13:27:56,435] [INFO] Target genome list was writen to GCF_013343295.1_ASM1334329v1_genomic.fna/target_genomes.txt
[2024-01-24 13:27:56,437] [INFO] Task started: fastANI
[2024-01-24 13:27:56,437] [INFO] Running command: fastANI --query /var/lib/cwl/stga0aa2938-869d-4d3c-a9f0-bd4d8ea96169/GCF_013343295.1_ASM1334329v1_genomic.fna.gz --refList GCF_013343295.1_ASM1334329v1_genomic.fna/target_genomes.txt --output GCF_013343295.1_ASM1334329v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:27:57,328] [INFO] Task succeeded: fastANI
[2024-01-24 13:27:57,328] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg14d5d251-9b13-42d2-9129-b884b78a8c59/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:27:57,329] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg14d5d251-9b13-42d2-9129-b884b78a8c59/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:27:57,332] [INFO] Found 1 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:27:57,332] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:27:57,333] [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
Metallosphaera tengchongensis	strain=Ric-A	GCA_013343295.1	1532350	1532350	type	True	100.0	725	725	95	conclusive
--------------------------------------------------------------------------------
[2024-01-24 13:27:57,334] [INFO] DFAST Taxonomy check result was written to GCF_013343295.1_ASM1334329v1_genomic.fna/tc_result.tsv
[2024-01-24 13:27:57,335] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:27:57,335] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:27:57,335] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg14d5d251-9b13-42d2-9129-b884b78a8c59/dqc_reference/checkm_data
[2024-01-24 13:27:57,336] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:27:57,358] [INFO] Task started: CheckM
[2024-01-24 13:27:57,359] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013343295.1_ASM1334329v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013343295.1_ASM1334329v1_genomic.fna/checkm_input GCF_013343295.1_ASM1334329v1_genomic.fna/checkm_result
[2024-01-24 13:28:28,245] [INFO] Task succeeded: CheckM
[2024-01-24 13:28:28,246] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:28:28,287] [INFO] ===== Completeness check finished =====
[2024-01-24 13:28:28,288] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:28:28,288] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013343295.1_ASM1334329v1_genomic.fna/markers.fasta)
[2024-01-24 13:28:28,289] [INFO] Task started: Blastn
[2024-01-24 13:28:28,289] [INFO] Running command: blastn -query GCF_013343295.1_ASM1334329v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg14d5d251-9b13-42d2-9129-b884b78a8c59/dqc_reference/reference_markers_gtdb.fasta -out GCF_013343295.1_ASM1334329v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:28:28,751] [INFO] Task succeeded: Blastn
[2024-01-24 13:28:28,754] [INFO] Selected 2 target genomes.
[2024-01-24 13:28:28,754] [INFO] Target genome list was writen to GCF_013343295.1_ASM1334329v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:28:28,757] [INFO] Task started: fastANI
[2024-01-24 13:28:28,757] [INFO] Running command: fastANI --query /var/lib/cwl/stga0aa2938-869d-4d3c-a9f0-bd4d8ea96169/GCF_013343295.1_ASM1334329v1_genomic.fna.gz --refList GCF_013343295.1_ASM1334329v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013343295.1_ASM1334329v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:28:29,796] [INFO] Task succeeded: fastANI
[2024-01-24 13:28:29,799] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:28:29,799] [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_013343295.1	s__Metallosphaera tengchongensis	100.0	725	725	d__Archaea;p__Thermoproteota;c__Thermoproteia;o__Sulfolobales;f__Sulfolobaceae;g__Metallosphaera	95.0	N/A	N/A	N/A	N/A	1	conclusive
--------------------------------------------------------------------------------
[2024-01-24 13:28:29,800] [INFO] GTDB search result was written to GCF_013343295.1_ASM1334329v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:28:29,801] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:28:29,802] [INFO] DFAST_QC result json was written to GCF_013343295.1_ASM1334329v1_genomic.fna/dqc_result.json
[2024-01-24 13:28:29,803] [INFO] DFAST_QC completed!
[2024-01-24 13:28:29,803] [INFO] Total running time: 0h0m44s