[2023-03-15 04:38:20,727] [INFO] DFAST_QC pipeline started.
[2023-03-15 04:38:20,728] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 04:38:20,728] [INFO] DQC Reference Directory: /var/lib/cwl/stg5d35ed3b-b36a-4047-89bd-8bf7acdbb573/dqc_reference
[2023-03-15 04:38:22,317] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 04:38:22,318] [INFO] Task started: Prodigal
[2023-03-15 04:38:22,318] [INFO] Running command: cat /var/lib/cwl/stg206c1a38-28e2-405e-b9e2-902c6cb70d7a/OceanDNA-b35813.fa | prodigal -d OceanDNA-b35813/cds.fna -a OceanDNA-b35813/protein.faa -g 11 -q > /dev/null
[2023-03-15 04:38:38,027] [INFO] Task succeeded: Prodigal
[2023-03-15 04:38:38,028] [INFO] Task started: HMMsearch
[2023-03-15 04:38:38,028] [INFO] Running command: hmmsearch --tblout OceanDNA-b35813/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5d35ed3b-b36a-4047-89bd-8bf7acdbb573/dqc_reference/reference_markers.hmm OceanDNA-b35813/protein.faa > /dev/null
[2023-03-15 04:38:38,217] [INFO] Task succeeded: HMMsearch
[2023-03-15 04:38:38,217] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg206c1a38-28e2-405e-b9e2-902c6cb70d7a/OceanDNA-b35813.fa]
[2023-03-15 04:38:38,239] [INFO] Query marker FASTA was written to OceanDNA-b35813/markers.fasta
[2023-03-15 04:38:38,241] [INFO] Task started: Blastn
[2023-03-15 04:38:38,241] [INFO] Running command: blastn -query OceanDNA-b35813/markers.fasta -db /var/lib/cwl/stg5d35ed3b-b36a-4047-89bd-8bf7acdbb573/dqc_reference/reference_markers.fasta -out OceanDNA-b35813/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 04:38:38,778] [INFO] Task succeeded: Blastn
[2023-03-15 04:38:38,779] [INFO] Selected 25 target genomes.
[2023-03-15 04:38:38,779] [INFO] Target genome list was writen to OceanDNA-b35813/target_genomes.txt
[2023-03-15 04:38:38,794] [INFO] Task started: fastANI
[2023-03-15 04:38:38,794] [INFO] Running command: fastANI --query /var/lib/cwl/stg206c1a38-28e2-405e-b9e2-902c6cb70d7a/OceanDNA-b35813.fa --refList OceanDNA-b35813/target_genomes.txt --output OceanDNA-b35813/fastani_result.tsv --threads 1
[2023-03-15 04:38:53,101] [INFO] Task succeeded: fastANI
[2023-03-15 04:38:53,101] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5d35ed3b-b36a-4047-89bd-8bf7acdbb573/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 04:38:53,102] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5d35ed3b-b36a-4047-89bd-8bf7acdbb573/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 04:38:53,102] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 04:38:53,102] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 04:38:53,102] [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
--------------------------------------------------------------------------------
[2023-03-15 04:38:53,102] [INFO] DFAST Taxonomy check result was written to OceanDNA-b35813/tc_result.tsv
[2023-03-15 04:38:53,102] [INFO] ===== Taxonomy check completed =====
[2023-03-15 04:38:53,102] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 04:38:53,102] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5d35ed3b-b36a-4047-89bd-8bf7acdbb573/dqc_reference/checkm_data
[2023-03-15 04:38:53,105] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 04:38:53,419] [INFO] Task started: CheckM
[2023-03-15 04:38:53,419] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b35813/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b35813/checkm_input OceanDNA-b35813/checkm_result
[2023-03-15 04:39:34,603] [INFO] Task succeeded: CheckM
[2023-03-15 04:39:34,603] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.69%
Contamintation: 0.46%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 04:39:34,606] [INFO] ===== Completeness check finished =====
[2023-03-15 04:39:34,606] [INFO] ===== Start GTDB Search =====
[2023-03-15 04:39:34,606] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b35813/markers.fasta)
[2023-03-15 04:39:34,607] [INFO] Task started: Blastn
[2023-03-15 04:39:34,607] [INFO] Running command: blastn -query OceanDNA-b35813/markers.fasta -db /var/lib/cwl/stg5d35ed3b-b36a-4047-89bd-8bf7acdbb573/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b35813/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 04:39:35,415] [INFO] Task succeeded: Blastn
[2023-03-15 04:39:35,415] [INFO] Selected 16 target genomes.
[2023-03-15 04:39:35,415] [INFO] Target genome list was writen to OceanDNA-b35813/target_genomes_gtdb.txt
[2023-03-15 04:39:35,426] [INFO] Task started: fastANI
[2023-03-15 04:39:35,426] [INFO] Running command: fastANI --query /var/lib/cwl/stg206c1a38-28e2-405e-b9e2-902c6cb70d7a/OceanDNA-b35813.fa --refList OceanDNA-b35813/target_genomes_gtdb.txt --output OceanDNA-b35813/fastani_result_gtdb.tsv --threads 1
[2023-03-15 04:39:45,795] [INFO] Task succeeded: fastANI
[2023-03-15 04:39:45,799] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 04:39:45,799] [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_903866355.1	s__Ga0077536 sp903866355	93.6684	527	771	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ga0077536;f__Ga0077536;g__Ga0077536	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009692365.1	s__Ga0077536 sp009692365	83.7209	541	771	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ga0077536;f__Ga0077536;g__Ga0077536	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016874535.1	s__CAIKBL01 sp016874535	75.9675	53	771	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ga0077536;f__Ga0077536;g__CAIKBL01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001464935.1	s__Ga0077536 sp001464935	75.8219	100	771	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ga0077536;f__Ga0077536;g__Ga0077536	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016719885.1	s__JADJYF01 sp016719885	75.6867	72	771	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ga0077536;f__Ga0077536;g__JADJYF01	95.0	97.68	97.68	0.89	0.89	2	-
--------------------------------------------------------------------------------
[2023-03-15 04:39:45,800] [INFO] GTDB search result was written to OceanDNA-b35813/result_gtdb.tsv
[2023-03-15 04:39:45,800] [INFO] ===== GTDB Search completed =====
[2023-03-15 04:39:45,800] [INFO] DFAST_QC result json was written to OceanDNA-b35813/dqc_result.json
[2023-03-15 04:39:45,800] [INFO] DFAST_QC completed!
[2023-03-15 04:39:45,800] [INFO] Total running time: 0h1m25s