[2023-03-16 10:20:34,619] [INFO] DFAST_QC pipeline started.
[2023-03-16 10:20:34,619] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 10:20:34,619] [INFO] DQC Reference Directory: /var/lib/cwl/stg2d79c415-34b7-4451-889e-6110452a812a/dqc_reference
[2023-03-16 10:20:35,842] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 10:20:35,843] [INFO] Task started: Prodigal
[2023-03-16 10:20:35,843] [INFO] Running command: cat /var/lib/cwl/stg9fb80587-ba6b-4e0b-8c80-3d3e39e63f40/OceanDNA-b13295.fa | prodigal -d OceanDNA-b13295/cds.fna -a OceanDNA-b13295/protein.faa -g 11 -q > /dev/null
[2023-03-16 10:20:52,042] [INFO] Task succeeded: Prodigal
[2023-03-16 10:20:52,042] [INFO] Task started: HMMsearch
[2023-03-16 10:20:52,042] [INFO] Running command: hmmsearch --tblout OceanDNA-b13295/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2d79c415-34b7-4451-889e-6110452a812a/dqc_reference/reference_markers.hmm OceanDNA-b13295/protein.faa > /dev/null
[2023-03-16 10:20:52,325] [INFO] Task succeeded: HMMsearch
[2023-03-16 10:20:52,325] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg9fb80587-ba6b-4e0b-8c80-3d3e39e63f40/OceanDNA-b13295.fa]
[2023-03-16 10:20:52,351] [INFO] Query marker FASTA was written to OceanDNA-b13295/markers.fasta
[2023-03-16 10:20:52,352] [INFO] Task started: Blastn
[2023-03-16 10:20:52,352] [INFO] Running command: blastn -query OceanDNA-b13295/markers.fasta -db /var/lib/cwl/stg2d79c415-34b7-4451-889e-6110452a812a/dqc_reference/reference_markers.fasta -out OceanDNA-b13295/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 10:20:52,821] [INFO] Task succeeded: Blastn
[2023-03-16 10:20:52,823] [INFO] Selected 16 target genomes.
[2023-03-16 10:20:52,823] [INFO] Target genome list was writen to OceanDNA-b13295/target_genomes.txt
[2023-03-16 10:20:52,834] [INFO] Task started: fastANI
[2023-03-16 10:20:52,835] [INFO] Running command: fastANI --query /var/lib/cwl/stg9fb80587-ba6b-4e0b-8c80-3d3e39e63f40/OceanDNA-b13295.fa --refList OceanDNA-b13295/target_genomes.txt --output OceanDNA-b13295/fastani_result.tsv --threads 1
[2023-03-16 10:21:04,361] [INFO] Task succeeded: fastANI
[2023-03-16 10:21:04,361] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2d79c415-34b7-4451-889e-6110452a812a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 10:21:04,361] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2d79c415-34b7-4451-889e-6110452a812a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 10:21:04,362] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 10:21:04,362] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 10:21:04,362] [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
--------------------------------------------------------------------------------
[2023-03-16 10:21:04,362] [INFO] DFAST Taxonomy check result was written to OceanDNA-b13295/tc_result.tsv
[2023-03-16 10:21:04,362] [INFO] ===== Taxonomy check completed =====
[2023-03-16 10:21:04,363] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 10:21:04,363] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2d79c415-34b7-4451-889e-6110452a812a/dqc_reference/checkm_data
[2023-03-16 10:21:04,365] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 10:21:04,370] [INFO] Task started: CheckM
[2023-03-16 10:21:04,370] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b13295/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b13295/checkm_input OceanDNA-b13295/checkm_result
[2023-03-16 10:21:48,163] [INFO] Task succeeded: CheckM
[2023-03-16 10:21:48,163] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 66.15%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 10:21:48,166] [INFO] ===== Completeness check finished =====
[2023-03-16 10:21:48,166] [INFO] ===== Start GTDB Search =====
[2023-03-16 10:21:48,166] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b13295/markers.fasta)
[2023-03-16 10:21:48,168] [INFO] Task started: Blastn
[2023-03-16 10:21:48,168] [INFO] Running command: blastn -query OceanDNA-b13295/markers.fasta -db /var/lib/cwl/stg2d79c415-34b7-4451-889e-6110452a812a/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b13295/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 10:21:48,623] [INFO] Task succeeded: Blastn
[2023-03-16 10:21:48,624] [INFO] Selected 16 target genomes.
[2023-03-16 10:21:48,624] [INFO] Target genome list was writen to OceanDNA-b13295/target_genomes_gtdb.txt
[2023-03-16 10:21:48,666] [INFO] Task started: fastANI
[2023-03-16 10:21:48,667] [INFO] Running command: fastANI --query /var/lib/cwl/stg9fb80587-ba6b-4e0b-8c80-3d3e39e63f40/OceanDNA-b13295.fa --refList OceanDNA-b13295/target_genomes_gtdb.txt --output OceanDNA-b13295/fastani_result_gtdb.tsv --threads 1
[2023-03-16 10:21:59,063] [INFO] Task succeeded: fastANI
[2023-03-16 10:21:59,065] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 10:21:59,065] [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_003447545.1	s__UBA12015 sp003447545	99.3803	632	873	d__Bacteria;p__Desulfobacterota_B;c__Binatia;o__UBA12015;f__UBA12015;g__UBA12015	95.0	N/A	N/A	N/A	N/A	1	conclusive
--------------------------------------------------------------------------------
[2023-03-16 10:21:59,065] [INFO] GTDB search result was written to OceanDNA-b13295/result_gtdb.tsv
[2023-03-16 10:21:59,065] [INFO] ===== GTDB Search completed =====
[2023-03-16 10:21:59,066] [INFO] DFAST_QC result json was written to OceanDNA-b13295/dqc_result.json
[2023-03-16 10:21:59,066] [INFO] DFAST_QC completed!
[2023-03-16 10:21:59,066] [INFO] Total running time: 0h1m24s