[2023-06-05 01:18:28,789] [INFO] DFAST_QC pipeline started.
[2023-06-05 01:18:28,792] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 01:18:28,793] [INFO] DQC Reference Directory: /var/lib/cwl/stg2f02ea8d-d25a-484c-87bf-4c92ea7c06d9/dqc_reference
[2023-06-05 01:18:30,396] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 01:18:30,397] [INFO] Task started: Prodigal
[2023-06-05 01:18:30,398] [INFO] Running command: gunzip -c /var/lib/cwl/stg5b58ce1b-bb6d-4c25-8b3c-948a3c3f9425/GCA_004144385.1_ASM414438v1_genomic.fna.gz | prodigal -d GCA_004144385.1_ASM414438v1_genomic.fna/cds.fna -a GCA_004144385.1_ASM414438v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 01:18:35,650] [INFO] Task succeeded: Prodigal
[2023-06-05 01:18:35,651] [INFO] Task started: HMMsearch
[2023-06-05 01:18:35,651] [INFO] Running command: hmmsearch --tblout GCA_004144385.1_ASM414438v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2f02ea8d-d25a-484c-87bf-4c92ea7c06d9/dqc_reference/reference_markers.hmm GCA_004144385.1_ASM414438v1_genomic.fna/protein.faa > /dev/null
[2023-06-05 01:18:35,871] [INFO] Task succeeded: HMMsearch
[2023-06-05 01:18:35,873] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg5b58ce1b-bb6d-4c25-8b3c-948a3c3f9425/GCA_004144385.1_ASM414438v1_genomic.fna.gz]
[2023-06-05 01:18:35,904] [INFO] Query marker FASTA was written to GCA_004144385.1_ASM414438v1_genomic.fna/markers.fasta
[2023-06-05 01:18:35,904] [INFO] Task started: Blastn
[2023-06-05 01:18:35,904] [INFO] Running command: blastn -query GCA_004144385.1_ASM414438v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2f02ea8d-d25a-484c-87bf-4c92ea7c06d9/dqc_reference/reference_markers.fasta -out GCA_004144385.1_ASM414438v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 01:18:36,720] [INFO] Task succeeded: Blastn
[2023-06-05 01:18:36,724] [INFO] Selected 28 target genomes.
[2023-06-05 01:18:36,725] [INFO] Target genome list was writen to GCA_004144385.1_ASM414438v1_genomic.fna/target_genomes.txt
[2023-06-05 01:18:36,732] [INFO] Task started: fastANI
[2023-06-05 01:18:36,732] [INFO] Running command: fastANI --query /var/lib/cwl/stg5b58ce1b-bb6d-4c25-8b3c-948a3c3f9425/GCA_004144385.1_ASM414438v1_genomic.fna.gz --refList GCA_004144385.1_ASM414438v1_genomic.fna/target_genomes.txt --output GCA_004144385.1_ASM414438v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 01:18:56,040] [INFO] Task succeeded: fastANI
[2023-06-05 01:18:56,041] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2f02ea8d-d25a-484c-87bf-4c92ea7c06d9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 01:18:56,042] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2f02ea8d-d25a-484c-87bf-4c92ea7c06d9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 01:18:56,049] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 01:18:56,049] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-05 01:18:56,049] [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
Devosia soli	strain=GH2-10	GCA_000970455.1	361041	361041	type	True	81.2912	51	124	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 01:18:56,051] [INFO] DFAST Taxonomy check result was written to GCA_004144385.1_ASM414438v1_genomic.fna/tc_result.tsv
[2023-06-05 01:18:56,052] [INFO] ===== Taxonomy check completed =====
[2023-06-05 01:18:56,052] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 01:18:56,052] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2f02ea8d-d25a-484c-87bf-4c92ea7c06d9/dqc_reference/checkm_data
[2023-06-05 01:18:56,053] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 01:18:56,083] [INFO] Task started: CheckM
[2023-06-05 01:18:56,084] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_004144385.1_ASM414438v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_004144385.1_ASM414438v1_genomic.fna/checkm_input GCA_004144385.1_ASM414438v1_genomic.fna/checkm_result
[2023-06-05 01:19:18,402] [INFO] Task succeeded: CheckM
[2023-06-05 01:19:18,404] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 60.17%
Contamintation: 18.52%
Strain heterogeneity: 20.00%
--------------------------------------------------------------------------------
[2023-06-05 01:19:18,430] [INFO] ===== Completeness check finished =====
[2023-06-05 01:19:18,430] [INFO] ===== Start GTDB Search =====
[2023-06-05 01:19:18,431] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_004144385.1_ASM414438v1_genomic.fna/markers.fasta)
[2023-06-05 01:19:18,431] [INFO] Task started: Blastn
[2023-06-05 01:19:18,431] [INFO] Running command: blastn -query GCA_004144385.1_ASM414438v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2f02ea8d-d25a-484c-87bf-4c92ea7c06d9/dqc_reference/reference_markers_gtdb.fasta -out GCA_004144385.1_ASM414438v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 01:19:19,803] [INFO] Task succeeded: Blastn
[2023-06-05 01:19:19,808] [INFO] Selected 27 target genomes.
[2023-06-05 01:19:19,808] [INFO] Target genome list was writen to GCA_004144385.1_ASM414438v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 01:19:19,957] [INFO] Task started: fastANI
[2023-06-05 01:19:19,958] [INFO] Running command: fastANI --query /var/lib/cwl/stg5b58ce1b-bb6d-4c25-8b3c-948a3c3f9425/GCA_004144385.1_ASM414438v1_genomic.fna.gz --refList GCA_004144385.1_ASM414438v1_genomic.fna/target_genomes_gtdb.txt --output GCA_004144385.1_ASM414438v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 01:19:36,017] [INFO] Task succeeded: fastANI
[2023-06-05 01:19:36,022] [INFO] Found 1 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-05 01:19:36,022] [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
GCF_000970455.1	s__Devosia soli	81.2912	51	124	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-05 01:19:36,025] [INFO] GTDB search result was written to GCA_004144385.1_ASM414438v1_genomic.fna/result_gtdb.tsv
[2023-06-05 01:19:36,025] [INFO] ===== GTDB Search completed =====
[2023-06-05 01:19:36,028] [INFO] DFAST_QC result json was written to GCA_004144385.1_ASM414438v1_genomic.fna/dqc_result.json
[2023-06-05 01:19:36,028] [INFO] DFAST_QC completed!
[2023-06-05 01:19:36,028] [INFO] Total running time: 0h1m7s