[2023-03-19 03:10:00,727] [INFO] DFAST_QC pipeline started.
[2023-03-19 03:10:00,727] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 03:10:00,727] [INFO] DQC Reference Directory: /var/lib/cwl/stg7d66ea52-bfad-428c-a2e8-96c228740c1c/dqc_reference
[2023-03-19 03:10:01,835] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 03:10:01,836] [INFO] Task started: Prodigal
[2023-03-19 03:10:01,836] [INFO] Running command: cat /var/lib/cwl/stg4a54a768-c05e-4bc5-afca-0174bb3938dd/OceanDNA-b13186.fa | prodigal -d OceanDNA-b13186/cds.fna -a OceanDNA-b13186/protein.faa -g 11 -q > /dev/null
[2023-03-19 03:10:14,616] [INFO] Task succeeded: Prodigal
[2023-03-19 03:10:14,616] [INFO] Task started: HMMsearch
[2023-03-19 03:10:14,616] [INFO] Running command: hmmsearch --tblout OceanDNA-b13186/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7d66ea52-bfad-428c-a2e8-96c228740c1c/dqc_reference/reference_markers.hmm OceanDNA-b13186/protein.faa > /dev/null
[2023-03-19 03:10:14,822] [INFO] Task succeeded: HMMsearch
[2023-03-19 03:10:14,823] [INFO] Found 6/6 markers.
[2023-03-19 03:10:14,843] [INFO] Query marker FASTA was written to OceanDNA-b13186/markers.fasta
[2023-03-19 03:10:14,843] [INFO] Task started: Blastn
[2023-03-19 03:10:14,843] [INFO] Running command: blastn -query OceanDNA-b13186/markers.fasta -db /var/lib/cwl/stg7d66ea52-bfad-428c-a2e8-96c228740c1c/dqc_reference/reference_markers.fasta -out OceanDNA-b13186/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 03:10:15,354] [INFO] Task succeeded: Blastn
[2023-03-19 03:10:15,354] [INFO] Selected 20 target genomes.
[2023-03-19 03:10:15,355] [INFO] Target genome list was writen to OceanDNA-b13186/target_genomes.txt
[2023-03-19 03:10:15,363] [INFO] Task started: fastANI
[2023-03-19 03:10:15,363] [INFO] Running command: fastANI --query /var/lib/cwl/stg4a54a768-c05e-4bc5-afca-0174bb3938dd/OceanDNA-b13186.fa --refList OceanDNA-b13186/target_genomes.txt --output OceanDNA-b13186/fastani_result.tsv --threads 1
[2023-03-19 03:10:27,369] [INFO] Task succeeded: fastANI
[2023-03-19 03:10:27,369] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7d66ea52-bfad-428c-a2e8-96c228740c1c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 03:10:27,369] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7d66ea52-bfad-428c-a2e8-96c228740c1c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 03:10:27,370] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 03:10:27,370] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-19 03:10:27,370] [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
--------------------------------------------------------------------------------
[2023-03-19 03:10:27,370] [INFO] DFAST Taxonomy check result was written to OceanDNA-b13186/tc_result.tsv
[2023-03-19 03:10:27,370] [INFO] ===== Taxonomy check completed =====
[2023-03-19 03:10:27,370] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 03:10:27,370] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7d66ea52-bfad-428c-a2e8-96c228740c1c/dqc_reference/checkm_data
[2023-03-19 03:10:27,373] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 03:10:27,378] [INFO] Task started: CheckM
[2023-03-19 03:10:27,378] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b13186/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b13186/checkm_input OceanDNA-b13186/checkm_result
[2023-03-19 03:11:03,430] [INFO] Task succeeded: CheckM
[2023-03-19 03:11:03,431] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.37%
Contamintation: 2.08%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 03:11:03,433] [INFO] ===== Completeness check finished =====
[2023-03-19 03:11:03,434] [INFO] ===== Start GTDB Search =====
[2023-03-19 03:11:03,434] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b13186/markers.fasta)
[2023-03-19 03:11:03,434] [INFO] Task started: Blastn
[2023-03-19 03:11:03,434] [INFO] Running command: blastn -query OceanDNA-b13186/markers.fasta -db /var/lib/cwl/stg7d66ea52-bfad-428c-a2e8-96c228740c1c/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b13186/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 03:11:04,128] [INFO] Task succeeded: Blastn
[2023-03-19 03:11:04,129] [INFO] Selected 16 target genomes.
[2023-03-19 03:11:04,129] [INFO] Target genome list was writen to OceanDNA-b13186/target_genomes_gtdb.txt
[2023-03-19 03:11:04,145] [INFO] Task started: fastANI
[2023-03-19 03:11:04,145] [INFO] Running command: fastANI --query /var/lib/cwl/stg4a54a768-c05e-4bc5-afca-0174bb3938dd/OceanDNA-b13186.fa --refList OceanDNA-b13186/target_genomes_gtdb.txt --output OceanDNA-b13186/fastani_result_gtdb.tsv --threads 1
[2023-03-19 03:11:12,392] [INFO] Task succeeded: fastANI
[2023-03-19 03:11:12,395] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-19 03:11:12,395] [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_002711995.1	s__UBA845 sp002711995	99.9435	739	743	d__Bacteria;p__Bdellovibrionota;c__Bacteriovoracia;o__Bacteriovoracales;f__Bacteriovoracaceae;g__UBA845	95.0	99.96	99.96	0.99	0.99	4	conclusive
GCA_002718735.1	s__UBA845 sp002718735	83.2434	216	743	d__Bacteria;p__Bdellovibrionota;c__Bacteriovoracia;o__Bacteriovoracales;f__Bacteriovoracaceae;g__UBA845	95.0	99.20	98.78	0.71	0.69	3	-
--------------------------------------------------------------------------------
[2023-03-19 03:11:12,395] [INFO] GTDB search result was written to OceanDNA-b13186/result_gtdb.tsv
[2023-03-19 03:11:12,395] [INFO] ===== GTDB Search completed =====
[2023-03-19 03:11:12,396] [INFO] DFAST_QC result json was written to OceanDNA-b13186/dqc_result.json
[2023-03-19 03:11:12,396] [INFO] DFAST_QC completed!
[2023-03-19 03:11:12,396] [INFO] Total running time: 0h1m12s