[2023-03-16 17:03:59,024] [INFO] DFAST_QC pipeline started.
[2023-03-16 17:03:59,024] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 17:03:59,024] [INFO] DQC Reference Directory: /var/lib/cwl/stga82711cc-68c0-4b7b-bf97-f77f418e8794/dqc_reference
[2023-03-16 17:04:00,140] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 17:04:00,140] [INFO] Task started: Prodigal
[2023-03-16 17:04:00,140] [INFO] Running command: cat /var/lib/cwl/stgefc18643-f508-4b86-a8d1-674cf8096c02/OceanDNA-b4531.fa | prodigal -d OceanDNA-b4531/cds.fna -a OceanDNA-b4531/protein.faa -g 11 -q > /dev/null
[2023-03-16 17:04:11,644] [INFO] Task succeeded: Prodigal
[2023-03-16 17:04:11,644] [INFO] Task started: HMMsearch
[2023-03-16 17:04:11,644] [INFO] Running command: hmmsearch --tblout OceanDNA-b4531/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga82711cc-68c0-4b7b-bf97-f77f418e8794/dqc_reference/reference_markers.hmm OceanDNA-b4531/protein.faa > /dev/null
[2023-03-16 17:04:11,810] [INFO] Task succeeded: HMMsearch
[2023-03-16 17:04:11,811] [INFO] Found 6/6 markers.
[2023-03-16 17:04:11,825] [INFO] Query marker FASTA was written to OceanDNA-b4531/markers.fasta
[2023-03-16 17:04:11,826] [INFO] Task started: Blastn
[2023-03-16 17:04:11,826] [INFO] Running command: blastn -query OceanDNA-b4531/markers.fasta -db /var/lib/cwl/stga82711cc-68c0-4b7b-bf97-f77f418e8794/dqc_reference/reference_markers.fasta -out OceanDNA-b4531/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 17:04:12,352] [INFO] Task succeeded: Blastn
[2023-03-16 17:04:12,352] [INFO] Selected 22 target genomes.
[2023-03-16 17:04:12,353] [INFO] Target genome list was writen to OceanDNA-b4531/target_genomes.txt
[2023-03-16 17:04:12,422] [INFO] Task started: fastANI
[2023-03-16 17:04:12,422] [INFO] Running command: fastANI --query /var/lib/cwl/stgefc18643-f508-4b86-a8d1-674cf8096c02/OceanDNA-b4531.fa --refList OceanDNA-b4531/target_genomes.txt --output OceanDNA-b4531/fastani_result.tsv --threads 1
[2023-03-16 17:04:24,406] [INFO] Task succeeded: fastANI
[2023-03-16 17:04:24,406] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga82711cc-68c0-4b7b-bf97-f77f418e8794/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 17:04:24,406] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga82711cc-68c0-4b7b-bf97-f77f418e8794/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 17:04:24,406] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 17:04:24,407] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 17:04:24,407] [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 17:04:24,407] [INFO] DFAST Taxonomy check result was written to OceanDNA-b4531/tc_result.tsv
[2023-03-16 17:04:24,407] [INFO] ===== Taxonomy check completed =====
[2023-03-16 17:04:24,407] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 17:04:24,407] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga82711cc-68c0-4b7b-bf97-f77f418e8794/dqc_reference/checkm_data
[2023-03-16 17:04:24,410] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 17:04:24,461] [INFO] Task started: CheckM
[2023-03-16 17:04:24,461] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b4531/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b4531/checkm_input OceanDNA-b4531/checkm_result
[2023-03-16 17:05:09,350] [INFO] Task succeeded: CheckM
[2023-03-16 17:05:09,351] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 64.58%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 17:05:09,354] [INFO] ===== Completeness check finished =====
[2023-03-16 17:05:09,354] [INFO] ===== Start GTDB Search =====
[2023-03-16 17:05:09,354] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b4531/markers.fasta)
[2023-03-16 17:05:09,356] [INFO] Task started: Blastn
[2023-03-16 17:05:09,356] [INFO] Running command: blastn -query OceanDNA-b4531/markers.fasta -db /var/lib/cwl/stga82711cc-68c0-4b7b-bf97-f77f418e8794/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b4531/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 17:05:10,169] [INFO] Task succeeded: Blastn
[2023-03-16 17:05:10,170] [INFO] Selected 25 target genomes.
[2023-03-16 17:05:10,170] [INFO] Target genome list was writen to OceanDNA-b4531/target_genomes_gtdb.txt
[2023-03-16 17:05:10,360] [INFO] Task started: fastANI
[2023-03-16 17:05:10,360] [INFO] Running command: fastANI --query /var/lib/cwl/stgefc18643-f508-4b86-a8d1-674cf8096c02/OceanDNA-b4531.fa --refList OceanDNA-b4531/target_genomes_gtdb.txt --output OceanDNA-b4531/fastani_result_gtdb.tsv --threads 1
[2023-03-16 17:05:26,833] [INFO] Task succeeded: fastANI
[2023-03-16 17:05:26,835] [INFO] Found 1 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 17:05:26,835] [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_002336485.1	s__SHAN690 sp002336485	76.8613	57	491	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Salibacteraceae;g__SHAN690	95.0	99.81	99.70	0.91	0.80	7	-
--------------------------------------------------------------------------------
[2023-03-16 17:05:26,835] [INFO] GTDB search result was written to OceanDNA-b4531/result_gtdb.tsv
[2023-03-16 17:05:26,835] [INFO] ===== GTDB Search completed =====
[2023-03-16 17:05:26,836] [INFO] DFAST_QC result json was written to OceanDNA-b4531/dqc_result.json
[2023-03-16 17:05:26,836] [INFO] DFAST_QC completed!
[2023-03-16 17:05:26,836] [INFO] Total running time: 0h1m28s