[2023-06-29 21:45:04,702] [INFO] DFAST_QC pipeline started.
[2023-06-29 21:45:04,705] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 21:45:04,705] [INFO] DQC Reference Directory: /var/lib/cwl/stg475116fa-4430-4de0-baa3-0c5e8a4a3fbe/dqc_reference
[2023-06-29 21:45:05,887] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 21:45:05,887] [INFO] Task started: Prodigal
[2023-06-29 21:45:05,888] [INFO] Running command: gunzip -c /var/lib/cwl/stgf2862236-57f5-4975-927b-3e72eaa7c947/GCA_024403175.1_ASM2440317v1_genomic.fna.gz | prodigal -d GCA_024403175.1_ASM2440317v1_genomic.fna/cds.fna -a GCA_024403175.1_ASM2440317v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 21:45:08,198] [INFO] Task succeeded: Prodigal
[2023-06-29 21:45:08,199] [INFO] Task started: HMMsearch
[2023-06-29 21:45:08,199] [INFO] Running command: hmmsearch --tblout GCA_024403175.1_ASM2440317v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg475116fa-4430-4de0-baa3-0c5e8a4a3fbe/dqc_reference/reference_markers.hmm GCA_024403175.1_ASM2440317v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 21:45:08,401] [INFO] Task succeeded: HMMsearch
[2023-06-29 21:45:08,402] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgf2862236-57f5-4975-927b-3e72eaa7c947/GCA_024403175.1_ASM2440317v1_genomic.fna.gz]
[2023-06-29 21:45:08,426] [INFO] Query marker FASTA was written to GCA_024403175.1_ASM2440317v1_genomic.fna/markers.fasta
[2023-06-29 21:45:08,427] [INFO] Task started: Blastn
[2023-06-29 21:45:08,427] [INFO] Running command: blastn -query GCA_024403175.1_ASM2440317v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg475116fa-4430-4de0-baa3-0c5e8a4a3fbe/dqc_reference/reference_markers.fasta -out GCA_024403175.1_ASM2440317v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 21:45:08,976] [INFO] Task succeeded: Blastn
[2023-06-29 21:45:08,981] [INFO] Selected 15 target genomes.
[2023-06-29 21:45:08,982] [INFO] Target genome list was writen to GCA_024403175.1_ASM2440317v1_genomic.fna/target_genomes.txt
[2023-06-29 21:45:08,985] [INFO] Task started: fastANI
[2023-06-29 21:45:08,985] [INFO] Running command: fastANI --query /var/lib/cwl/stgf2862236-57f5-4975-927b-3e72eaa7c947/GCA_024403175.1_ASM2440317v1_genomic.fna.gz --refList GCA_024403175.1_ASM2440317v1_genomic.fna/target_genomes.txt --output GCA_024403175.1_ASM2440317v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 21:45:13,956] [INFO] Task succeeded: fastANI
[2023-06-29 21:45:13,957] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg475116fa-4430-4de0-baa3-0c5e8a4a3fbe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 21:45:13,958] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg475116fa-4430-4de0-baa3-0c5e8a4a3fbe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 21:45:13,959] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 21:45:13,960] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-29 21:45:13,960] [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
--------------------------------------------------------------------------------
[2023-06-29 21:45:13,962] [INFO] DFAST Taxonomy check result was written to GCA_024403175.1_ASM2440317v1_genomic.fna/tc_result.tsv
[2023-06-29 21:45:13,963] [INFO] ===== Taxonomy check completed =====
[2023-06-29 21:45:13,963] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 21:45:13,963] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg475116fa-4430-4de0-baa3-0c5e8a4a3fbe/dqc_reference/checkm_data
[2023-06-29 21:45:13,967] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 21:45:13,985] [INFO] Task started: CheckM
[2023-06-29 21:45:13,985] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_024403175.1_ASM2440317v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_024403175.1_ASM2440317v1_genomic.fna/checkm_input GCA_024403175.1_ASM2440317v1_genomic.fna/checkm_result
[2023-06-29 21:45:29,425] [INFO] Task succeeded: CheckM
[2023-06-29 21:45:29,426] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 67.39%
Contamintation: 11.74%
Strain heterogeneity: 18.75%
--------------------------------------------------------------------------------
[2023-06-29 21:45:29,451] [INFO] ===== Completeness check finished =====
[2023-06-29 21:45:29,451] [INFO] ===== Start GTDB Search =====
[2023-06-29 21:45:29,452] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_024403175.1_ASM2440317v1_genomic.fna/markers.fasta)
[2023-06-29 21:45:29,452] [INFO] Task started: Blastn
[2023-06-29 21:45:29,452] [INFO] Running command: blastn -query GCA_024403175.1_ASM2440317v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg475116fa-4430-4de0-baa3-0c5e8a4a3fbe/dqc_reference/reference_markers_gtdb.fasta -out GCA_024403175.1_ASM2440317v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 21:45:30,425] [INFO] Task succeeded: Blastn
[2023-06-29 21:45:30,430] [INFO] Selected 23 target genomes.
[2023-06-29 21:45:30,430] [INFO] Target genome list was writen to GCA_024403175.1_ASM2440317v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 21:45:30,478] [INFO] Task started: fastANI
[2023-06-29 21:45:30,478] [INFO] Running command: fastANI --query /var/lib/cwl/stgf2862236-57f5-4975-927b-3e72eaa7c947/GCA_024403175.1_ASM2440317v1_genomic.fna.gz --refList GCA_024403175.1_ASM2440317v1_genomic.fna/target_genomes_gtdb.txt --output GCA_024403175.1_ASM2440317v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 21:45:37,190] [INFO] Task succeeded: fastANI
[2023-06-29 21:45:37,192] [INFO] Found 0 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 21:45:37,192] [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
--------------------------------------------------------------------------------
[2023-06-29 21:45:37,196] [INFO] GTDB search result was written to GCA_024403175.1_ASM2440317v1_genomic.fna/result_gtdb.tsv
[2023-06-29 21:45:37,196] [INFO] ===== GTDB Search completed =====
[2023-06-29 21:45:37,199] [INFO] DFAST_QC result json was written to GCA_024403175.1_ASM2440317v1_genomic.fna/dqc_result.json
[2023-06-29 21:45:37,199] [INFO] DFAST_QC completed!
[2023-06-29 21:45:37,199] [INFO] Total running time: 0h0m32s