[2024-01-24 13:22:00,155] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:22:00,157] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:22:00,157] [INFO] DQC Reference Directory: /var/lib/cwl/stg5f468d44-7ff0-4f84-bfd9-04a92a01689d/dqc_reference
[2024-01-24 13:22:01,476] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:22:01,477] [INFO] Task started: Prodigal
[2024-01-24 13:22:01,478] [INFO] Running command: gunzip -c /var/lib/cwl/stg5945e356-46c5-443e-a7b1-374b88b44fde/GCF_009362845.1_ASM936284v1_genomic.fna.gz | prodigal -d GCF_009362845.1_ASM936284v1_genomic.fna/cds.fna -a GCF_009362845.1_ASM936284v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:22:07,088] [INFO] Task succeeded: Prodigal
[2024-01-24 13:22:07,089] [INFO] Task started: HMMsearch
[2024-01-24 13:22:07,089] [INFO] Running command: hmmsearch --tblout GCF_009362845.1_ASM936284v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5f468d44-7ff0-4f84-bfd9-04a92a01689d/dqc_reference/reference_markers.hmm GCF_009362845.1_ASM936284v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:22:07,354] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:22:07,355] [INFO] Found 6/6 markers.
[2024-01-24 13:22:07,376] [INFO] Query marker FASTA was written to GCF_009362845.1_ASM936284v1_genomic.fna/markers.fasta
[2024-01-24 13:22:07,377] [INFO] Task started: Blastn
[2024-01-24 13:22:07,377] [INFO] Running command: blastn -query GCF_009362845.1_ASM936284v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5f468d44-7ff0-4f84-bfd9-04a92a01689d/dqc_reference/reference_markers.fasta -out GCF_009362845.1_ASM936284v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:22:08,110] [INFO] Task succeeded: Blastn
[2024-01-24 13:22:08,118] [INFO] Selected 30 target genomes.
[2024-01-24 13:22:08,119] [INFO] Target genome list was writen to GCF_009362845.1_ASM936284v1_genomic.fna/target_genomes.txt
[2024-01-24 13:22:08,132] [INFO] Task started: fastANI
[2024-01-24 13:22:08,133] [INFO] Running command: fastANI --query /var/lib/cwl/stg5945e356-46c5-443e-a7b1-374b88b44fde/GCF_009362845.1_ASM936284v1_genomic.fna.gz --refList GCF_009362845.1_ASM936284v1_genomic.fna/target_genomes.txt --output GCF_009362845.1_ASM936284v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:22:27,377] [INFO] Task succeeded: fastANI
[2024-01-24 13:22:27,377] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5f468d44-7ff0-4f84-bfd9-04a92a01689d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:22:27,378] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5f468d44-7ff0-4f84-bfd9-04a92a01689d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:22:27,381] [INFO] Found 1 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:22:27,381] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:22:27,381] [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
Ostreibacterium oceani	strain=ML27	GCA_009362845.1	2654998	2654998	type	True	100.0	710	711	95	conclusive
--------------------------------------------------------------------------------
[2024-01-24 13:22:27,383] [INFO] DFAST Taxonomy check result was written to GCF_009362845.1_ASM936284v1_genomic.fna/tc_result.tsv
[2024-01-24 13:22:27,384] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:22:27,384] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:22:27,384] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5f468d44-7ff0-4f84-bfd9-04a92a01689d/dqc_reference/checkm_data
[2024-01-24 13:22:27,385] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:22:27,412] [INFO] Task started: CheckM
[2024-01-24 13:22:27,412] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009362845.1_ASM936284v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009362845.1_ASM936284v1_genomic.fna/checkm_input GCF_009362845.1_ASM936284v1_genomic.fna/checkm_result
[2024-01-24 13:22:51,709] [INFO] Task succeeded: CheckM
[2024-01-24 13:22:51,711] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:22:51,731] [INFO] ===== Completeness check finished =====
[2024-01-24 13:22:51,731] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:22:51,732] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009362845.1_ASM936284v1_genomic.fna/markers.fasta)
[2024-01-24 13:22:51,732] [INFO] Task started: Blastn
[2024-01-24 13:22:51,733] [INFO] Running command: blastn -query GCF_009362845.1_ASM936284v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5f468d44-7ff0-4f84-bfd9-04a92a01689d/dqc_reference/reference_markers_gtdb.fasta -out GCF_009362845.1_ASM936284v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:22:52,764] [INFO] Task succeeded: Blastn
[2024-01-24 13:22:52,767] [INFO] Selected 29 target genomes.
[2024-01-24 13:22:52,768] [INFO] Target genome list was writen to GCF_009362845.1_ASM936284v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:22:52,833] [INFO] Task started: fastANI
[2024-01-24 13:22:52,833] [INFO] Running command: fastANI --query /var/lib/cwl/stg5945e356-46c5-443e-a7b1-374b88b44fde/GCF_009362845.1_ASM936284v1_genomic.fna.gz --refList GCF_009362845.1_ASM936284v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009362845.1_ASM936284v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:23:08,963] [INFO] Task succeeded: fastANI
[2024-01-24 13:23:08,968] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:23:08,969] [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_009362845.1	s__Ostreibacterium oceani	100.0	710	711	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Cardiobacteriales;f__Ostreibacteriaceae;g__Ostreibacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
--------------------------------------------------------------------------------
[2024-01-24 13:23:08,971] [INFO] GTDB search result was written to GCF_009362845.1_ASM936284v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:23:08,971] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:23:08,974] [INFO] DFAST_QC result json was written to GCF_009362845.1_ASM936284v1_genomic.fna/dqc_result.json
[2024-01-24 13:23:08,974] [INFO] DFAST_QC completed!
[2024-01-24 13:23:08,974] [INFO] Total running time: 0h1m9s