[2023-06-19 05:25:04,697] [INFO] DFAST_QC pipeline started.
[2023-06-19 05:25:04,710] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 05:25:04,711] [INFO] DQC Reference Directory: /var/lib/cwl/stgcd7e7932-2a98-4b22-be86-88ee2c73cac4/dqc_reference
[2023-06-19 05:25:05,908] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 05:25:05,909] [INFO] Task started: Prodigal
[2023-06-19 05:25:05,909] [INFO] Running command: gunzip -c /var/lib/cwl/stg4b70a269-968c-4eaf-9a43-983587b46ad7/GCA_018969265.1_ASM1896926v1_genomic.fna.gz | prodigal -d GCA_018969265.1_ASM1896926v1_genomic.fna/cds.fna -a GCA_018969265.1_ASM1896926v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 05:25:09,163] [INFO] Task succeeded: Prodigal
[2023-06-19 05:25:09,163] [INFO] Task started: HMMsearch
[2023-06-19 05:25:09,164] [INFO] Running command: hmmsearch --tblout GCA_018969265.1_ASM1896926v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcd7e7932-2a98-4b22-be86-88ee2c73cac4/dqc_reference/reference_markers.hmm GCA_018969265.1_ASM1896926v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 05:25:09,384] [INFO] Task succeeded: HMMsearch
[2023-06-19 05:25:09,385] [INFO] Found 6/6 markers.
[2023-06-19 05:25:09,409] [INFO] Query marker FASTA was written to GCA_018969265.1_ASM1896926v1_genomic.fna/markers.fasta
[2023-06-19 05:25:09,409] [INFO] Task started: Blastn
[2023-06-19 05:25:09,409] [INFO] Running command: blastn -query GCA_018969265.1_ASM1896926v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcd7e7932-2a98-4b22-be86-88ee2c73cac4/dqc_reference/reference_markers.fasta -out GCA_018969265.1_ASM1896926v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 05:25:10,014] [INFO] Task succeeded: Blastn
[2023-06-19 05:25:10,019] [INFO] Selected 22 target genomes.
[2023-06-19 05:25:10,020] [INFO] Target genome list was writen to GCA_018969265.1_ASM1896926v1_genomic.fna/target_genomes.txt
[2023-06-19 05:25:10,029] [INFO] Task started: fastANI
[2023-06-19 05:25:10,029] [INFO] Running command: fastANI --query /var/lib/cwl/stg4b70a269-968c-4eaf-9a43-983587b46ad7/GCA_018969265.1_ASM1896926v1_genomic.fna.gz --refList GCA_018969265.1_ASM1896926v1_genomic.fna/target_genomes.txt --output GCA_018969265.1_ASM1896926v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 05:25:22,766] [INFO] Task succeeded: fastANI
[2023-06-19 05:25:22,767] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcd7e7932-2a98-4b22-be86-88ee2c73cac4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 05:25:22,767] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcd7e7932-2a98-4b22-be86-88ee2c73cac4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 05:25:22,770] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 05:25:22,771] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-19 05:25:22,771] [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 05:25:22,800] [INFO] DFAST Taxonomy check result was written to GCA_018969265.1_ASM1896926v1_genomic.fna/tc_result.tsv
[2023-06-19 05:25:22,802] [INFO] ===== Taxonomy check completed =====
[2023-06-19 05:25:22,802] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 05:25:22,803] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcd7e7932-2a98-4b22-be86-88ee2c73cac4/dqc_reference/checkm_data
[2023-06-19 05:25:22,808] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 05:25:22,825] [INFO] Task started: CheckM
[2023-06-19 05:25:22,826] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018969265.1_ASM1896926v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018969265.1_ASM1896926v1_genomic.fna/checkm_input GCA_018969265.1_ASM1896926v1_genomic.fna/checkm_result
[2023-06-19 05:25:40,984] [INFO] Task succeeded: CheckM
[2023-06-19 05:25:40,985] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 84.26%
Contamintation: 10.42%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-19 05:25:41,015] [INFO] ===== Completeness check finished =====
[2023-06-19 05:25:41,015] [INFO] ===== Start GTDB Search =====
[2023-06-19 05:25:41,016] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018969265.1_ASM1896926v1_genomic.fna/markers.fasta)
[2023-06-19 05:25:41,016] [INFO] Task started: Blastn
[2023-06-19 05:25:41,016] [INFO] Running command: blastn -query GCA_018969265.1_ASM1896926v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcd7e7932-2a98-4b22-be86-88ee2c73cac4/dqc_reference/reference_markers_gtdb.fasta -out GCA_018969265.1_ASM1896926v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 05:25:41,808] [INFO] Task succeeded: Blastn
[2023-06-19 05:25:41,812] [INFO] Selected 31 target genomes.
[2023-06-19 05:25:41,812] [INFO] Target genome list was writen to GCA_018969265.1_ASM1896926v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 05:25:41,871] [INFO] Task started: fastANI
[2023-06-19 05:25:41,871] [INFO] Running command: fastANI --query /var/lib/cwl/stg4b70a269-968c-4eaf-9a43-983587b46ad7/GCA_018969265.1_ASM1896926v1_genomic.fna.gz --refList GCA_018969265.1_ASM1896926v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018969265.1_ASM1896926v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 05:25:54,467] [INFO] Task succeeded: fastANI
[2023-06-19 05:25:54,474] [INFO] Found 1 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-19 05:25:54,474] [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_009923495.1	s__UBA5976 sp009923495	79.0113	107	387	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__UBA5976;g__UBA5976	95.0	99.82	99.82	0.97	0.97	2	-
--------------------------------------------------------------------------------
[2023-06-19 05:25:54,478] [INFO] GTDB search result was written to GCA_018969265.1_ASM1896926v1_genomic.fna/result_gtdb.tsv
[2023-06-19 05:25:54,479] [INFO] ===== GTDB Search completed =====
[2023-06-19 05:25:54,482] [INFO] DFAST_QC result json was written to GCA_018969265.1_ASM1896926v1_genomic.fna/dqc_result.json
[2023-06-19 05:25:54,483] [INFO] DFAST_QC completed!
[2023-06-19 05:25:54,483] [INFO] Total running time: 0h0m50s