[2024-01-24 11:30:49,393] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:30:49,395] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:30:49,395] [INFO] DQC Reference Directory: /var/lib/cwl/stg56b20d62-dc15-4c86-9e0d-14fab9234d50/dqc_reference
[2024-01-24 11:30:50,607] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:30:50,608] [INFO] Task started: Prodigal
[2024-01-24 11:30:50,608] [INFO] Running command: gunzip -c /var/lib/cwl/stg32b0570d-969c-43db-8392-cf14bffe8862/GCF_019704315.1_ASM1970431v1_genomic.fna.gz | prodigal -d GCF_019704315.1_ASM1970431v1_genomic.fna/cds.fna -a GCF_019704315.1_ASM1970431v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:30:59,581] [INFO] Task succeeded: Prodigal
[2024-01-24 11:30:59,582] [INFO] Task started: HMMsearch
[2024-01-24 11:30:59,582] [INFO] Running command: hmmsearch --tblout GCF_019704315.1_ASM1970431v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg56b20d62-dc15-4c86-9e0d-14fab9234d50/dqc_reference/reference_markers.hmm GCF_019704315.1_ASM1970431v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:30:59,822] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:30:59,824] [WARNING] Found 1/6 markers. [/var/lib/cwl/stg32b0570d-969c-43db-8392-cf14bffe8862/GCF_019704315.1_ASM1970431v1_genomic.fna.gz]
[2024-01-24 11:30:59,855] [INFO] Query marker FASTA was written to GCF_019704315.1_ASM1970431v1_genomic.fna/markers.fasta
[2024-01-24 11:30:59,856] [INFO] Task started: Blastn
[2024-01-24 11:30:59,856] [INFO] Running command: blastn -query GCF_019704315.1_ASM1970431v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg56b20d62-dc15-4c86-9e0d-14fab9234d50/dqc_reference/reference_markers.fasta -out GCF_019704315.1_ASM1970431v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:31:00,373] [INFO] Task succeeded: Blastn
[2024-01-24 11:31:00,377] [INFO] Selected 1 target genomes.
[2024-01-24 11:31:00,377] [INFO] Target genome list was writen to GCF_019704315.1_ASM1970431v1_genomic.fna/target_genomes.txt
[2024-01-24 11:31:00,379] [INFO] Task started: fastANI
[2024-01-24 11:31:00,379] [INFO] Running command: fastANI --query /var/lib/cwl/stg32b0570d-969c-43db-8392-cf14bffe8862/GCF_019704315.1_ASM1970431v1_genomic.fna.gz --refList GCF_019704315.1_ASM1970431v1_genomic.fna/target_genomes.txt --output GCF_019704315.1_ASM1970431v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:31:01,478] [INFO] Task succeeded: fastANI
[2024-01-24 11:31:01,479] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg56b20d62-dc15-4c86-9e0d-14fab9234d50/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:31:01,480] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg56b20d62-dc15-4c86-9e0d-14fab9234d50/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:31:01,486] [INFO] Found 1 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:31:01,486] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:31:01,487] [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
Stygiolobus caldivivus	strain=KN-1	GCA_019704315.1	2824673	2824673	type	True	100.0	986	986	95	conclusive
--------------------------------------------------------------------------------
[2024-01-24 11:31:01,489] [INFO] DFAST Taxonomy check result was written to GCF_019704315.1_ASM1970431v1_genomic.fna/tc_result.tsv
[2024-01-24 11:31:01,489] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:31:01,489] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:31:01,490] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg56b20d62-dc15-4c86-9e0d-14fab9234d50/dqc_reference/checkm_data
[2024-01-24 11:31:01,491] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:31:01,522] [INFO] Task started: CheckM
[2024-01-24 11:31:01,522] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019704315.1_ASM1970431v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019704315.1_ASM1970431v1_genomic.fna/checkm_input GCF_019704315.1_ASM1970431v1_genomic.fna/checkm_result
[2024-01-24 11:31:35,718] [INFO] Task succeeded: CheckM
[2024-01-24 11:31:35,720] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:31:35,736] [INFO] ===== Completeness check finished =====
[2024-01-24 11:31:35,736] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:31:35,736] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019704315.1_ASM1970431v1_genomic.fna/markers.fasta)
[2024-01-24 11:31:35,737] [INFO] Task started: Blastn
[2024-01-24 11:31:35,737] [INFO] Running command: blastn -query GCF_019704315.1_ASM1970431v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg56b20d62-dc15-4c86-9e0d-14fab9234d50/dqc_reference/reference_markers_gtdb.fasta -out GCF_019704315.1_ASM1970431v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:31:36,169] [INFO] Task succeeded: Blastn
[2024-01-24 11:31:36,173] [INFO] Selected 1 target genomes.
[2024-01-24 11:31:36,173] [INFO] Target genome list was writen to GCF_019704315.1_ASM1970431v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:31:36,175] [INFO] Task started: fastANI
[2024-01-24 11:31:36,175] [INFO] Running command: fastANI --query /var/lib/cwl/stg32b0570d-969c-43db-8392-cf14bffe8862/GCF_019704315.1_ASM1970431v1_genomic.fna.gz --refList GCF_019704315.1_ASM1970431v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019704315.1_ASM1970431v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:31:36,705] [INFO] Task succeeded: fastANI
[2024-01-24 11:31:36,707] [INFO] Found 0 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 11:31:36,707] [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
--------------------------------------------------------------------------------
[2024-01-24 11:31:36,709] [INFO] GTDB search result was written to GCF_019704315.1_ASM1970431v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:31:36,710] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:31:36,712] [INFO] DFAST_QC result json was written to GCF_019704315.1_ASM1970431v1_genomic.fna/dqc_result.json
[2024-01-24 11:31:36,713] [INFO] DFAST_QC completed!
[2024-01-24 11:31:36,713] [INFO] Total running time: 0h0m47s