[2023-06-19 14:15:54,829] [INFO] DFAST_QC pipeline started.
[2023-06-19 14:15:54,833] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 14:15:54,833] [INFO] DQC Reference Directory: /var/lib/cwl/stgd05e04a9-33e0-4b6c-80b8-439883776fd6/dqc_reference
[2023-06-19 14:15:56,285] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 14:15:56,287] [INFO] Task started: Prodigal
[2023-06-19 14:15:56,287] [INFO] Running command: gunzip -c /var/lib/cwl/stg4b7b1826-6974-45ba-80c4-8f74177173b2/GCA_018692455.1_ASM1869245v1_genomic.fna.gz | prodigal -d GCA_018692455.1_ASM1869245v1_genomic.fna/cds.fna -a GCA_018692455.1_ASM1869245v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 14:15:58,490] [INFO] Task succeeded: Prodigal
[2023-06-19 14:15:58,491] [INFO] Task started: HMMsearch
[2023-06-19 14:15:58,491] [INFO] Running command: hmmsearch --tblout GCA_018692455.1_ASM1869245v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd05e04a9-33e0-4b6c-80b8-439883776fd6/dqc_reference/reference_markers.hmm GCA_018692455.1_ASM1869245v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 14:15:58,713] [INFO] Task succeeded: HMMsearch
[2023-06-19 14:15:58,715] [WARNING] Found 2/6 markers. [/var/lib/cwl/stg4b7b1826-6974-45ba-80c4-8f74177173b2/GCA_018692455.1_ASM1869245v1_genomic.fna.gz]
[2023-06-19 14:15:58,742] [INFO] Query marker FASTA was written to GCA_018692455.1_ASM1869245v1_genomic.fna/markers.fasta
[2023-06-19 14:15:58,743] [INFO] Task started: Blastn
[2023-06-19 14:15:58,743] [INFO] Running command: blastn -query GCA_018692455.1_ASM1869245v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd05e04a9-33e0-4b6c-80b8-439883776fd6/dqc_reference/reference_markers.fasta -out GCA_018692455.1_ASM1869245v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 14:15:59,306] [INFO] Task succeeded: Blastn
[2023-06-19 14:15:59,310] [INFO] Selected 5 target genomes.
[2023-06-19 14:15:59,311] [INFO] Target genome list was writen to GCA_018692455.1_ASM1869245v1_genomic.fna/target_genomes.txt
[2023-06-19 14:15:59,315] [INFO] Task started: fastANI
[2023-06-19 14:15:59,315] [INFO] Running command: fastANI --query /var/lib/cwl/stg4b7b1826-6974-45ba-80c4-8f74177173b2/GCA_018692455.1_ASM1869245v1_genomic.fna.gz --refList GCA_018692455.1_ASM1869245v1_genomic.fna/target_genomes.txt --output GCA_018692455.1_ASM1869245v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 14:16:01,982] [INFO] Task succeeded: fastANI
[2023-06-19 14:16:01,982] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd05e04a9-33e0-4b6c-80b8-439883776fd6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 14:16:01,983] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd05e04a9-33e0-4b6c-80b8-439883776fd6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 14:16:01,984] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 14:16:01,984] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-19 14:16:01,985] [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
--------------------------------------------------------------------------------
[2023-06-19 14:16:01,987] [INFO] DFAST Taxonomy check result was written to GCA_018692455.1_ASM1869245v1_genomic.fna/tc_result.tsv
[2023-06-19 14:16:01,988] [INFO] ===== Taxonomy check completed =====
[2023-06-19 14:16:01,988] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 14:16:01,988] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd05e04a9-33e0-4b6c-80b8-439883776fd6/dqc_reference/checkm_data
[2023-06-19 14:16:01,991] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 14:16:02,012] [INFO] Task started: CheckM
[2023-06-19 14:16:02,012] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018692455.1_ASM1869245v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018692455.1_ASM1869245v1_genomic.fna/checkm_input GCA_018692455.1_ASM1869245v1_genomic.fna/checkm_result
[2023-06-19 14:16:17,886] [INFO] Task succeeded: CheckM
[2023-06-19 14:16:17,887] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.12%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 14:16:17,910] [INFO] ===== Completeness check finished =====
[2023-06-19 14:16:17,910] [INFO] ===== Start GTDB Search =====
[2023-06-19 14:16:17,910] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018692455.1_ASM1869245v1_genomic.fna/markers.fasta)
[2023-06-19 14:16:17,911] [INFO] Task started: Blastn
[2023-06-19 14:16:17,911] [INFO] Running command: blastn -query GCA_018692455.1_ASM1869245v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd05e04a9-33e0-4b6c-80b8-439883776fd6/dqc_reference/reference_markers_gtdb.fasta -out GCA_018692455.1_ASM1869245v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 14:16:18,397] [INFO] Task succeeded: Blastn
[2023-06-19 14:16:18,402] [INFO] Selected 7 target genomes.
[2023-06-19 14:16:18,402] [INFO] Target genome list was writen to GCA_018692455.1_ASM1869245v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 14:16:18,407] [INFO] Task started: fastANI
[2023-06-19 14:16:18,407] [INFO] Running command: fastANI --query /var/lib/cwl/stg4b7b1826-6974-45ba-80c4-8f74177173b2/GCA_018692455.1_ASM1869245v1_genomic.fna.gz --refList GCA_018692455.1_ASM1869245v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018692455.1_ASM1869245v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 14:16:21,058] [INFO] Task succeeded: fastANI
[2023-06-19 14:16:21,062] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 14:16:21,062] [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
GCA_018653365.1	s__JABIAG01 sp018653365	99.9964	358	365	d__Archaea;p__Nanoarchaeota;c__Nanoarchaeia;o__Woesearchaeales;f__JABIAG01;g__JABIAG01	95.0	100.00	99.99	0.99	0.99	7	conclusive
--------------------------------------------------------------------------------
[2023-06-19 14:16:21,065] [INFO] GTDB search result was written to GCA_018692455.1_ASM1869245v1_genomic.fna/result_gtdb.tsv
[2023-06-19 14:16:21,065] [INFO] ===== GTDB Search completed =====
[2023-06-19 14:16:21,068] [INFO] DFAST_QC result json was written to GCA_018692455.1_ASM1869245v1_genomic.fna/dqc_result.json
[2023-06-19 14:16:21,068] [INFO] DFAST_QC completed!
[2023-06-19 14:16:21,068] [INFO] Total running time: 0h0m26s