[2023-03-17 15:09:40,789] [INFO] DFAST_QC pipeline started.
[2023-03-17 15:09:40,789] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 15:09:40,789] [INFO] DQC Reference Directory: /var/lib/cwl/stgeeab88d5-4169-4642-94b9-4c28752802ea/dqc_reference
[2023-03-17 15:09:42,013] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 15:09:42,038] [INFO] Task started: Prodigal
[2023-03-17 15:09:42,038] [INFO] Running command: cat /var/lib/cwl/stg679e1172-23f6-458c-8fff-4b91505ac42f/OceanDNA-b32695.fa | prodigal -d OceanDNA-b32695/cds.fna -a OceanDNA-b32695/protein.faa -g 11 -q > /dev/null
[2023-03-17 15:10:02,569] [INFO] Task succeeded: Prodigal
[2023-03-17 15:10:02,570] [INFO] Task started: HMMsearch
[2023-03-17 15:10:02,570] [INFO] Running command: hmmsearch --tblout OceanDNA-b32695/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgeeab88d5-4169-4642-94b9-4c28752802ea/dqc_reference/reference_markers.hmm OceanDNA-b32695/protein.faa > /dev/null
[2023-03-17 15:10:02,756] [INFO] Task succeeded: HMMsearch
[2023-03-17 15:10:02,756] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg679e1172-23f6-458c-8fff-4b91505ac42f/OceanDNA-b32695.fa]
[2023-03-17 15:10:02,774] [INFO] Query marker FASTA was written to OceanDNA-b32695/markers.fasta
[2023-03-17 15:10:02,774] [INFO] Task started: Blastn
[2023-03-17 15:10:02,774] [INFO] Running command: blastn -query OceanDNA-b32695/markers.fasta -db /var/lib/cwl/stgeeab88d5-4169-4642-94b9-4c28752802ea/dqc_reference/reference_markers.fasta -out OceanDNA-b32695/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 15:10:03,291] [INFO] Task succeeded: Blastn
[2023-03-17 15:10:03,292] [INFO] Selected 19 target genomes.
[2023-03-17 15:10:03,292] [INFO] Target genome list was writen to OceanDNA-b32695/target_genomes.txt
[2023-03-17 15:10:03,322] [INFO] Task started: fastANI
[2023-03-17 15:10:03,322] [INFO] Running command: fastANI --query /var/lib/cwl/stg679e1172-23f6-458c-8fff-4b91505ac42f/OceanDNA-b32695.fa --refList OceanDNA-b32695/target_genomes.txt --output OceanDNA-b32695/fastani_result.tsv --threads 1
[2023-03-17 15:10:14,231] [INFO] Task succeeded: fastANI
[2023-03-17 15:10:14,232] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgeeab88d5-4169-4642-94b9-4c28752802ea/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 15:10:14,232] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgeeab88d5-4169-4642-94b9-4c28752802ea/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 15:10:14,232] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 15:10:14,232] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 15:10:14,232] [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
--------------------------------------------------------------------------------
[2023-03-17 15:10:14,232] [INFO] DFAST Taxonomy check result was written to OceanDNA-b32695/tc_result.tsv
[2023-03-17 15:10:14,232] [INFO] ===== Taxonomy check completed =====
[2023-03-17 15:10:14,232] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 15:10:14,233] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgeeab88d5-4169-4642-94b9-4c28752802ea/dqc_reference/checkm_data
[2023-03-17 15:10:14,235] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 15:10:14,239] [INFO] Task started: CheckM
[2023-03-17 15:10:14,240] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b32695/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b32695/checkm_input OceanDNA-b32695/checkm_result
[2023-03-17 15:11:09,883] [INFO] Task succeeded: CheckM
[2023-03-17 15:11:09,884] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 86.27%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 15:11:09,886] [INFO] ===== Completeness check finished =====
[2023-03-17 15:11:09,886] [INFO] ===== Start GTDB Search =====
[2023-03-17 15:11:09,886] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b32695/markers.fasta)
[2023-03-17 15:11:09,887] [INFO] Task started: Blastn
[2023-03-17 15:11:09,888] [INFO] Running command: blastn -query OceanDNA-b32695/markers.fasta -db /var/lib/cwl/stgeeab88d5-4169-4642-94b9-4c28752802ea/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b32695/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 15:11:10,711] [INFO] Task succeeded: Blastn
[2023-03-17 15:11:10,712] [INFO] Selected 32 target genomes.
[2023-03-17 15:11:10,712] [INFO] Target genome list was writen to OceanDNA-b32695/target_genomes_gtdb.txt
[2023-03-17 15:11:11,399] [INFO] Task started: fastANI
[2023-03-17 15:11:11,399] [INFO] Running command: fastANI --query /var/lib/cwl/stg679e1172-23f6-458c-8fff-4b91505ac42f/OceanDNA-b32695.fa --refList OceanDNA-b32695/target_genomes_gtdb.txt --output OceanDNA-b32695/fastani_result_gtdb.tsv --threads 1
[2023-03-17 15:11:37,529] [INFO] Task succeeded: fastANI
[2023-03-17 15:11:37,531] [INFO] Found 1 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 15:11:37,531] [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_002348365.1	s__UBA2966 sp002348365	77.6154	324	903	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA2966;f__UBA2966;g__UBA2966	95.0	98.52	97.79	0.84	0.83	3	-
--------------------------------------------------------------------------------
[2023-03-17 15:11:37,531] [INFO] GTDB search result was written to OceanDNA-b32695/result_gtdb.tsv
[2023-03-17 15:11:37,531] [INFO] ===== GTDB Search completed =====
[2023-03-17 15:11:37,532] [INFO] DFAST_QC result json was written to OceanDNA-b32695/dqc_result.json
[2023-03-17 15:11:37,532] [INFO] DFAST_QC completed!
[2023-03-17 15:11:37,532] [INFO] Total running time: 0h1m57s