[2023-06-17 16:43:07,147] [INFO] DFAST_QC pipeline started.
[2023-06-17 16:43:07,149] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 16:43:07,149] [INFO] DQC Reference Directory: /var/lib/cwl/stg07eafac9-38cb-48e0-a492-da7516842ee7/dqc_reference
[2023-06-17 16:43:08,386] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 16:43:08,386] [INFO] Task started: Prodigal
[2023-06-17 16:43:08,387] [INFO] Running command: gunzip -c /var/lib/cwl/stg66a0955b-84e6-4fa6-a99a-cd30bf84f8c1/GCA_003644565.1_ASM364456v1_genomic.fna.gz | prodigal -d GCA_003644565.1_ASM364456v1_genomic.fna/cds.fna -a GCA_003644565.1_ASM364456v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 16:43:11,653] [INFO] Task succeeded: Prodigal
[2023-06-17 16:43:11,654] [INFO] Task started: HMMsearch
[2023-06-17 16:43:11,654] [INFO] Running command: hmmsearch --tblout GCA_003644565.1_ASM364456v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg07eafac9-38cb-48e0-a492-da7516842ee7/dqc_reference/reference_markers.hmm GCA_003644565.1_ASM364456v1_genomic.fna/protein.faa > /dev/null
[2023-06-17 16:43:11,893] [INFO] Task succeeded: HMMsearch
[2023-06-17 16:43:11,895] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg66a0955b-84e6-4fa6-a99a-cd30bf84f8c1/GCA_003644565.1_ASM364456v1_genomic.fna.gz]
[2023-06-17 16:43:11,923] [INFO] Query marker FASTA was written to GCA_003644565.1_ASM364456v1_genomic.fna/markers.fasta
[2023-06-17 16:43:11,923] [INFO] Task started: Blastn
[2023-06-17 16:43:11,923] [INFO] Running command: blastn -query GCA_003644565.1_ASM364456v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg07eafac9-38cb-48e0-a492-da7516842ee7/dqc_reference/reference_markers.fasta -out GCA_003644565.1_ASM364456v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 16:43:12,398] [INFO] Task succeeded: Blastn
[2023-06-17 16:43:12,404] [INFO] Selected 5 target genomes.
[2023-06-17 16:43:12,404] [INFO] Target genome list was writen to GCA_003644565.1_ASM364456v1_genomic.fna/target_genomes.txt
[2023-06-17 16:43:12,406] [INFO] Task started: fastANI
[2023-06-17 16:43:12,407] [INFO] Running command: fastANI --query /var/lib/cwl/stg66a0955b-84e6-4fa6-a99a-cd30bf84f8c1/GCA_003644565.1_ASM364456v1_genomic.fna.gz --refList GCA_003644565.1_ASM364456v1_genomic.fna/target_genomes.txt --output GCA_003644565.1_ASM364456v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 16:43:14,749] [INFO] Task succeeded: fastANI
[2023-06-17 16:43:14,750] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg07eafac9-38cb-48e0-a492-da7516842ee7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 16:43:14,750] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg07eafac9-38cb-48e0-a492-da7516842ee7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 16:43:14,752] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-17 16:43:14,752] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-17 16:43:14,752] [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
--------------------------------------------------------------------------------
[2023-06-17 16:43:14,754] [INFO] DFAST Taxonomy check result was written to GCA_003644565.1_ASM364456v1_genomic.fna/tc_result.tsv
[2023-06-17 16:43:14,755] [INFO] ===== Taxonomy check completed =====
[2023-06-17 16:43:14,756] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 16:43:14,756] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg07eafac9-38cb-48e0-a492-da7516842ee7/dqc_reference/checkm_data
[2023-06-17 16:43:14,760] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 16:43:14,788] [INFO] Task started: CheckM
[2023-06-17 16:43:14,788] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_003644565.1_ASM364456v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_003644565.1_ASM364456v1_genomic.fna/checkm_input GCA_003644565.1_ASM364456v1_genomic.fna/checkm_result
[2023-06-17 16:43:32,362] [INFO] Task succeeded: CheckM
[2023-06-17 16:43:32,363] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.25%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-17 16:43:32,391] [INFO] ===== Completeness check finished =====
[2023-06-17 16:43:32,392] [INFO] ===== Start GTDB Search =====
[2023-06-17 16:43:32,392] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_003644565.1_ASM364456v1_genomic.fna/markers.fasta)
[2023-06-17 16:43:32,393] [INFO] Task started: Blastn
[2023-06-17 16:43:32,393] [INFO] Running command: blastn -query GCA_003644565.1_ASM364456v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg07eafac9-38cb-48e0-a492-da7516842ee7/dqc_reference/reference_markers_gtdb.fasta -out GCA_003644565.1_ASM364456v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 16:43:32,849] [INFO] Task succeeded: Blastn
[2023-06-17 16:43:32,854] [INFO] Selected 12 target genomes.
[2023-06-17 16:43:32,854] [INFO] Target genome list was writen to GCA_003644565.1_ASM364456v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 16:43:32,870] [INFO] Task started: fastANI
[2023-06-17 16:43:32,871] [INFO] Running command: fastANI --query /var/lib/cwl/stg66a0955b-84e6-4fa6-a99a-cd30bf84f8c1/GCA_003644565.1_ASM364456v1_genomic.fna.gz --refList GCA_003644565.1_ASM364456v1_genomic.fna/target_genomes_gtdb.txt --output GCA_003644565.1_ASM364456v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 16:43:37,611] [INFO] Task succeeded: fastANI
[2023-06-17 16:43:37,615] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-17 16:43:37,615] [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_003645825.1	s__B5-G15 sp003645825	96.9679	330	451	d__Bacteria;p__Marinisomatota;c__UBA2242;o__UBA2242;f__B5-G15;g__B5-G15	95.0	98.19	97.10	0.84	0.73	3	conclusive
--------------------------------------------------------------------------------
[2023-06-17 16:43:37,618] [INFO] GTDB search result was written to GCA_003644565.1_ASM364456v1_genomic.fna/result_gtdb.tsv
[2023-06-17 16:43:37,619] [INFO] ===== GTDB Search completed =====
[2023-06-17 16:43:37,623] [INFO] DFAST_QC result json was written to GCA_003644565.1_ASM364456v1_genomic.fna/dqc_result.json
[2023-06-17 16:43:37,624] [INFO] DFAST_QC completed!
[2023-06-17 16:43:37,624] [INFO] Total running time: 0h0m30s