[2023-06-19 04:44:27,080] [INFO] DFAST_QC pipeline started.
[2023-06-19 04:44:27,084] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 04:44:27,084] [INFO] DQC Reference Directory: /var/lib/cwl/stg71f6edf2-e9ab-4b87-8ced-d9fcb02810e1/dqc_reference
[2023-06-19 04:44:28,699] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 04:44:28,701] [INFO] Task started: Prodigal
[2023-06-19 04:44:28,702] [INFO] Running command: gunzip -c /var/lib/cwl/stg2badabc0-657b-45a2-ab56-40756b33251a/GCA_018644705.1_ASM1864470v1_genomic.fna.gz | prodigal -d GCA_018644705.1_ASM1864470v1_genomic.fna/cds.fna -a GCA_018644705.1_ASM1864470v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 04:44:35,034] [INFO] Task succeeded: Prodigal
[2023-06-19 04:44:35,035] [INFO] Task started: HMMsearch
[2023-06-19 04:44:35,035] [INFO] Running command: hmmsearch --tblout GCA_018644705.1_ASM1864470v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg71f6edf2-e9ab-4b87-8ced-d9fcb02810e1/dqc_reference/reference_markers.hmm GCA_018644705.1_ASM1864470v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 04:44:35,293] [INFO] Task succeeded: HMMsearch
[2023-06-19 04:44:35,294] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg2badabc0-657b-45a2-ab56-40756b33251a/GCA_018644705.1_ASM1864470v1_genomic.fna.gz]
[2023-06-19 04:44:35,356] [INFO] Query marker FASTA was written to GCA_018644705.1_ASM1864470v1_genomic.fna/markers.fasta
[2023-06-19 04:44:35,357] [INFO] Task started: Blastn
[2023-06-19 04:44:35,357] [INFO] Running command: blastn -query GCA_018644705.1_ASM1864470v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg71f6edf2-e9ab-4b87-8ced-d9fcb02810e1/dqc_reference/reference_markers.fasta -out GCA_018644705.1_ASM1864470v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 04:44:35,940] [INFO] Task succeeded: Blastn
[2023-06-19 04:44:35,943] [INFO] Selected 16 target genomes.
[2023-06-19 04:44:35,944] [INFO] Target genome list was writen to GCA_018644705.1_ASM1864470v1_genomic.fna/target_genomes.txt
[2023-06-19 04:44:35,950] [INFO] Task started: fastANI
[2023-06-19 04:44:35,950] [INFO] Running command: fastANI --query /var/lib/cwl/stg2badabc0-657b-45a2-ab56-40756b33251a/GCA_018644705.1_ASM1864470v1_genomic.fna.gz --refList GCA_018644705.1_ASM1864470v1_genomic.fna/target_genomes.txt --output GCA_018644705.1_ASM1864470v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 04:44:43,883] [INFO] Task succeeded: fastANI
[2023-06-19 04:44:43,884] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg71f6edf2-e9ab-4b87-8ced-d9fcb02810e1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 04:44:43,884] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg71f6edf2-e9ab-4b87-8ced-d9fcb02810e1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 04:44:43,887] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 04:44:43,887] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-19 04:44:43,887] [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 04:44:43,889] [INFO] DFAST Taxonomy check result was written to GCA_018644705.1_ASM1864470v1_genomic.fna/tc_result.tsv
[2023-06-19 04:44:43,890] [INFO] ===== Taxonomy check completed =====
[2023-06-19 04:44:43,890] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 04:44:43,890] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg71f6edf2-e9ab-4b87-8ced-d9fcb02810e1/dqc_reference/checkm_data
[2023-06-19 04:44:43,893] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 04:44:43,935] [INFO] Task started: CheckM
[2023-06-19 04:44:43,935] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018644705.1_ASM1864470v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018644705.1_ASM1864470v1_genomic.fna/checkm_input GCA_018644705.1_ASM1864470v1_genomic.fna/checkm_result
[2023-06-19 04:45:10,360] [INFO] Task succeeded: CheckM
[2023-06-19 04:45:10,362] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 62.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 04:45:10,389] [INFO] ===== Completeness check finished =====
[2023-06-19 04:45:10,390] [INFO] ===== Start GTDB Search =====
[2023-06-19 04:45:10,390] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018644705.1_ASM1864470v1_genomic.fna/markers.fasta)
[2023-06-19 04:45:10,390] [INFO] Task started: Blastn
[2023-06-19 04:45:10,391] [INFO] Running command: blastn -query GCA_018644705.1_ASM1864470v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg71f6edf2-e9ab-4b87-8ced-d9fcb02810e1/dqc_reference/reference_markers_gtdb.fasta -out GCA_018644705.1_ASM1864470v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 04:45:10,831] [INFO] Task succeeded: Blastn
[2023-06-19 04:45:10,843] [INFO] Selected 19 target genomes.
[2023-06-19 04:45:10,844] [INFO] Target genome list was writen to GCA_018644705.1_ASM1864470v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 04:45:10,858] [INFO] Task started: fastANI
[2023-06-19 04:45:10,858] [INFO] Running command: fastANI --query /var/lib/cwl/stg2badabc0-657b-45a2-ab56-40756b33251a/GCA_018644705.1_ASM1864470v1_genomic.fna.gz --refList GCA_018644705.1_ASM1864470v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018644705.1_ASM1864470v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 04:45:19,628] [INFO] Task succeeded: fastANI
[2023-06-19 04:45:19,633] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 04:45:19,634] [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_018657495.1	s__JABHXA01 sp018657495	99.9492	874	899	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__SCGC-AAA003-L08;f__JACNLC01;g__JABHXA01	95.0	99.97	99.94	0.97	0.96	15	conclusive
--------------------------------------------------------------------------------
[2023-06-19 04:45:19,636] [INFO] GTDB search result was written to GCA_018644705.1_ASM1864470v1_genomic.fna/result_gtdb.tsv
[2023-06-19 04:45:19,636] [INFO] ===== GTDB Search completed =====
[2023-06-19 04:45:19,638] [INFO] DFAST_QC result json was written to GCA_018644705.1_ASM1864470v1_genomic.fna/dqc_result.json
[2023-06-19 04:45:19,638] [INFO] DFAST_QC completed!
[2023-06-19 04:45:19,639] [INFO] Total running time: 0h0m53s