[2023-06-18 18:10:05,786] [INFO] DFAST_QC pipeline started.
[2023-06-18 18:10:05,797] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 18:10:05,797] [INFO] DQC Reference Directory: /var/lib/cwl/stg4d089224-a5a2-4b5d-bf51-3e5b36ade9d0/dqc_reference
[2023-06-18 18:10:07,233] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 18:10:07,234] [INFO] Task started: Prodigal
[2023-06-18 18:10:07,234] [INFO] Running command: gunzip -c /var/lib/cwl/stg7871e092-5b09-463d-aff7-487c073eb3a1/GCA_018655065.1_ASM1865506v1_genomic.fna.gz | prodigal -d GCA_018655065.1_ASM1865506v1_genomic.fna/cds.fna -a GCA_018655065.1_ASM1865506v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 18:10:18,500] [INFO] Task succeeded: Prodigal
[2023-06-18 18:10:18,500] [INFO] Task started: HMMsearch
[2023-06-18 18:10:18,500] [INFO] Running command: hmmsearch --tblout GCA_018655065.1_ASM1865506v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4d089224-a5a2-4b5d-bf51-3e5b36ade9d0/dqc_reference/reference_markers.hmm GCA_018655065.1_ASM1865506v1_genomic.fna/protein.faa > /dev/null
[2023-06-18 18:10:18,768] [INFO] Task succeeded: HMMsearch
[2023-06-18 18:10:18,769] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg7871e092-5b09-463d-aff7-487c073eb3a1/GCA_018655065.1_ASM1865506v1_genomic.fna.gz]
[2023-06-18 18:10:18,802] [INFO] Query marker FASTA was written to GCA_018655065.1_ASM1865506v1_genomic.fna/markers.fasta
[2023-06-18 18:10:18,802] [INFO] Task started: Blastn
[2023-06-18 18:10:18,803] [INFO] Running command: blastn -query GCA_018655065.1_ASM1865506v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4d089224-a5a2-4b5d-bf51-3e5b36ade9d0/dqc_reference/reference_markers.fasta -out GCA_018655065.1_ASM1865506v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 18:10:19,444] [INFO] Task succeeded: Blastn
[2023-06-18 18:10:19,448] [INFO] Selected 23 target genomes.
[2023-06-18 18:10:19,448] [INFO] Target genome list was writen to GCA_018655065.1_ASM1865506v1_genomic.fna/target_genomes.txt
[2023-06-18 18:10:19,450] [INFO] Task started: fastANI
[2023-06-18 18:10:19,450] [INFO] Running command: fastANI --query /var/lib/cwl/stg7871e092-5b09-463d-aff7-487c073eb3a1/GCA_018655065.1_ASM1865506v1_genomic.fna.gz --refList GCA_018655065.1_ASM1865506v1_genomic.fna/target_genomes.txt --output GCA_018655065.1_ASM1865506v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 18:10:33,180] [INFO] Task succeeded: fastANI
[2023-06-18 18:10:33,181] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4d089224-a5a2-4b5d-bf51-3e5b36ade9d0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 18:10:33,181] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4d089224-a5a2-4b5d-bf51-3e5b36ade9d0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 18:10:33,183] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-18 18:10:33,183] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-18 18:10:33,183] [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
--------------------------------------------------------------------------------
[2023-06-18 18:10:33,185] [INFO] DFAST Taxonomy check result was written to GCA_018655065.1_ASM1865506v1_genomic.fna/tc_result.tsv
[2023-06-18 18:10:33,186] [INFO] ===== Taxonomy check completed =====
[2023-06-18 18:10:33,186] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 18:10:33,186] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4d089224-a5a2-4b5d-bf51-3e5b36ade9d0/dqc_reference/checkm_data
[2023-06-18 18:10:33,189] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 18:10:33,212] [INFO] Task started: CheckM
[2023-06-18 18:10:33,212] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018655065.1_ASM1865506v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018655065.1_ASM1865506v1_genomic.fna/checkm_input GCA_018655065.1_ASM1865506v1_genomic.fna/checkm_result
[2023-06-18 18:11:11,250] [INFO] Task succeeded: CheckM
[2023-06-18 18:11:11,252] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-18 18:11:11,279] [INFO] ===== Completeness check finished =====
[2023-06-18 18:11:11,279] [INFO] ===== Start GTDB Search =====
[2023-06-18 18:11:11,279] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018655065.1_ASM1865506v1_genomic.fna/markers.fasta)
[2023-06-18 18:11:11,280] [INFO] Task started: Blastn
[2023-06-18 18:11:11,280] [INFO] Running command: blastn -query GCA_018655065.1_ASM1865506v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4d089224-a5a2-4b5d-bf51-3e5b36ade9d0/dqc_reference/reference_markers_gtdb.fasta -out GCA_018655065.1_ASM1865506v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 18:11:12,193] [INFO] Task succeeded: Blastn
[2023-06-18 18:11:12,199] [INFO] Selected 23 target genomes.
[2023-06-18 18:11:12,200] [INFO] Target genome list was writen to GCA_018655065.1_ASM1865506v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 18:11:12,203] [INFO] Task started: fastANI
[2023-06-18 18:11:12,204] [INFO] Running command: fastANI --query /var/lib/cwl/stg7871e092-5b09-463d-aff7-487c073eb3a1/GCA_018655065.1_ASM1865506v1_genomic.fna.gz --refList GCA_018655065.1_ASM1865506v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018655065.1_ASM1865506v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 18:11:23,934] [INFO] Task succeeded: fastANI
[2023-06-18 18:11:23,939] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-18 18:11:23,939] [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_002378565.1	s__UBA3442 sp002378565	99.2011	415	514	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__UBA3442	95.0	99.19	98.61	0.89	0.85	22	conclusive
--------------------------------------------------------------------------------
[2023-06-18 18:11:23,941] [INFO] GTDB search result was written to GCA_018655065.1_ASM1865506v1_genomic.fna/result_gtdb.tsv
[2023-06-18 18:11:23,942] [INFO] ===== GTDB Search completed =====
[2023-06-18 18:11:23,944] [INFO] DFAST_QC result json was written to GCA_018655065.1_ASM1865506v1_genomic.fna/dqc_result.json
[2023-06-18 18:11:23,944] [INFO] DFAST_QC completed!
[2023-06-18 18:11:23,945] [INFO] Total running time: 0h1m18s