[2023-03-15 17:39:54,921] [INFO] DFAST_QC pipeline started.
[2023-03-15 17:39:54,921] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 17:39:54,921] [INFO] DQC Reference Directory: /var/lib/cwl/stgf72e2a51-16ba-444d-b212-95de81727556/dqc_reference
[2023-03-15 17:39:57,554] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 17:39:57,554] [INFO] Task started: Prodigal
[2023-03-15 17:39:57,554] [INFO] Running command: cat /var/lib/cwl/stgf6125efc-bc5d-4388-b28e-6b99e2da36cf/OceanDNA-b32385.fa | prodigal -d OceanDNA-b32385/cds.fna -a OceanDNA-b32385/protein.faa -g 11 -q > /dev/null
[2023-03-15 17:40:03,727] [INFO] Task succeeded: Prodigal
[2023-03-15 17:40:03,727] [INFO] Task started: HMMsearch
[2023-03-15 17:40:03,727] [INFO] Running command: hmmsearch --tblout OceanDNA-b32385/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf72e2a51-16ba-444d-b212-95de81727556/dqc_reference/reference_markers.hmm OceanDNA-b32385/protein.faa > /dev/null
[2023-03-15 17:40:03,966] [INFO] Task succeeded: HMMsearch
[2023-03-15 17:40:03,967] [INFO] Found 6/6 markers.
[2023-03-15 17:40:03,978] [INFO] Query marker FASTA was written to OceanDNA-b32385/markers.fasta
[2023-03-15 17:40:03,979] [INFO] Task started: Blastn
[2023-03-15 17:40:03,979] [INFO] Running command: blastn -query OceanDNA-b32385/markers.fasta -db /var/lib/cwl/stgf72e2a51-16ba-444d-b212-95de81727556/dqc_reference/reference_markers.fasta -out OceanDNA-b32385/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 17:40:07,650] [INFO] Task succeeded: Blastn
[2023-03-15 17:40:07,651] [INFO] Selected 20 target genomes.
[2023-03-15 17:40:07,651] [INFO] Target genome list was writen to OceanDNA-b32385/target_genomes.txt
[2023-03-15 17:40:07,694] [INFO] Task started: fastANI
[2023-03-15 17:40:07,694] [INFO] Running command: fastANI --query /var/lib/cwl/stgf6125efc-bc5d-4388-b28e-6b99e2da36cf/OceanDNA-b32385.fa --refList OceanDNA-b32385/target_genomes.txt --output OceanDNA-b32385/fastani_result.tsv --threads 1
[2023-03-15 17:40:15,638] [INFO] Task succeeded: fastANI
[2023-03-15 17:40:15,639] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf72e2a51-16ba-444d-b212-95de81727556/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 17:40:15,639] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf72e2a51-16ba-444d-b212-95de81727556/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 17:40:15,639] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 17:40:15,639] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 17:40:15,639] [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 17:40:15,639] [INFO] DFAST Taxonomy check result was written to OceanDNA-b32385/tc_result.tsv
[2023-03-15 17:40:15,640] [INFO] ===== Taxonomy check completed =====
[2023-03-15 17:40:15,640] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 17:40:15,640] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf72e2a51-16ba-444d-b212-95de81727556/dqc_reference/checkm_data
[2023-03-15 17:40:15,651] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 17:40:15,656] [INFO] Task started: CheckM
[2023-03-15 17:40:15,657] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b32385/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b32385/checkm_input OceanDNA-b32385/checkm_result
[2023-03-15 17:40:39,658] [INFO] Task succeeded: CheckM
[2023-03-15 17:40:39,659] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 5.53%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-15 17:40:39,660] [INFO] ===== Completeness check finished =====
[2023-03-15 17:40:39,660] [INFO] ===== Start GTDB Search =====
[2023-03-15 17:40:39,661] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b32385/markers.fasta)
[2023-03-15 17:40:39,662] [INFO] Task started: Blastn
[2023-03-15 17:40:39,662] [INFO] Running command: blastn -query OceanDNA-b32385/markers.fasta -db /var/lib/cwl/stgf72e2a51-16ba-444d-b212-95de81727556/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b32385/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 17:40:40,713] [INFO] Task succeeded: Blastn
[2023-03-15 17:40:40,714] [INFO] Selected 22 target genomes.
[2023-03-15 17:40:40,714] [INFO] Target genome list was writen to OceanDNA-b32385/target_genomes_gtdb.txt
[2023-03-15 17:40:41,134] [INFO] Task started: fastANI
[2023-03-15 17:40:41,134] [INFO] Running command: fastANI --query /var/lib/cwl/stgf6125efc-bc5d-4388-b28e-6b99e2da36cf/OceanDNA-b32385.fa --refList OceanDNA-b32385/target_genomes_gtdb.txt --output OceanDNA-b32385/fastani_result_gtdb.tsv --threads 1
[2023-03-15 17:40:46,590] [INFO] Task succeeded: fastANI
[2023-03-15 17:40:46,593] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 17:40:46,593] [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_002937675.1	s__MarineAlpha9-Bin2 sp002937675	98.9654	350	416	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__TMED109;f__TMED109;g__MarineAlpha9-Bin2	95.0	99.26	99.26	0.85	0.85	2	conclusive
GCA_002714055.1	s__GCA-2714055 sp002714055	80.6777	105	416	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__TMED109;f__TMED109;g__GCA-2714055	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002720535.1	s__TMED109 sp002720535	75.5865	56	416	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__TMED109;f__TMED109;g__TMED109	95.0	95.89	95.27	0.82	0.81	3	-
--------------------------------------------------------------------------------
[2023-03-15 17:40:46,593] [INFO] GTDB search result was written to OceanDNA-b32385/result_gtdb.tsv
[2023-03-15 17:40:46,593] [INFO] ===== GTDB Search completed =====
[2023-03-15 17:40:46,594] [INFO] DFAST_QC result json was written to OceanDNA-b32385/dqc_result.json
[2023-03-15 17:40:46,594] [INFO] DFAST_QC completed!
[2023-03-15 17:40:46,594] [INFO] Total running time: 0h0m52s